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In Oblivion, all objects (a book, a race, a spawn point, a spawned npc) are identified by formids. Formids are eight digit hexadecimal numbers (e.g. 0A012C43), where the first two digits represent the source mod and the following six digits are the object index.
While playing, you can usually find the formid of any visible object by opening the console and clicking the object. The object's formid will display at the top of the screen.
Note that there is a difference between the object definition and a placed instance of that object. For example the definition ("base object") of the NPC Palonirya (proprietress of "Divine Elegance" in the IC Market District) is 00015ea8, while her placed instance ("reference") is . When you click on an object in the game, what you'll see is the formid of the placed instance (e.g.
for Palonirya).
In the construction set (CS), you'll find the formid in the second column of the grid display of most windows. Note that this column is usually collapsed -- i.e. you'll need to widen the column to actually see the formid. For placed references, the easiest way to find the formid is to double click the reference in the cell view window -- the resulting dialog will list both the reference formid and the base object formid.
Note that the modindex may vary between CS and game. In both cases, the modindex represents the order of the source mod in the current context. E.g. the Boots of the Crusader from Knights of the Nine is 01000ecf in the Construction Set, but in game might be it 0A000ecf, if KOTN is the 10th mod loaded after Oblivion.esm.
Note too that objects that specifically belong to the savegame and not to any mod are given the modindex FF. You'll actually find these quite commonly: all spawned npcs and creatures, plus all items initially acquired out of inventories and containers, plus all items created in game (spells, potions, enchanted armor and weapons) will all have modindex FF.
If you know the CS formid and need to know the in-game formid, then you need to replace the CS modindex with the in-game modindex. In other words, you just need to find the modindex of the source mod (e.g. Knights.esp), while you're playing. Here's how:
Find an object that you know was placed by the source mod. E.g. for KOTN, both the prophet and the Priory of the Nine are placed by the mod, so if you console-click on either of them, then the first two digits of their formid is the modindex.
If you're running Oblivion Mod Manager, the modindex will be shown when you mouse-over the mod in the main mod listing. (Mistakenly labeled as "formid" in the popup info box.)
If you're running Wrye Bash, the modindex for all active mods is listed in the second column of the Mods tab.
Oblivion.esm is always first (has modindex 00) in both the CS and in-game. No conversion is necessary.
If a mod has multiple masters (e.g. Oblivion.esm, Cobl Main.esm), then objects coming from the mod itself will have their modindex shifted upwards in the CS, however the techniques above will still work with no change. (This complexity is something that only toolmakers and advanced modders need to worry about.)
can be used to determine in-game FormID for items, object, NPCs.
For folks who don't know what a hexadecimal number is... Okay, decimal numbers go like this: 0 1 2 3 4 5 6 7 8 9 10 11..., while hexadecimal numbers go like this: 0 1 2 3 4 5 6 7 8 9 A B C D E F 10 11 .. 19 1A 1B ... etc. Hex 'A' equals decimal 10, hex 'B' equals decimal 11, ... hex 'F' equals decimal 15. Since hexadecimal is base 16 ('hex' = six +'deci' = ten), they "roll over" at 'F' (= 15 decimal), the same way that decimal numbers roll over at 9.
This section is intended for modders only. It provides a bit more detail than the players section and addresses some other advanced topics.
Formids have two components: the first two digits are the modindex, and the following six digits are the objectindex. The objectindex for any data object in your mod is unique and fixed within the mod -- i.e., once it's assigned to the object, it will not change no matter what you do to the object.
The modindex represents the load position of the source mod for the data object, and it will change depending on context. Typically in CS4 the modindex for any data object that you create will be '01', since your mod is typically the second to load (after Oblivion.esm, which has modindex '00' because it loads first).
In-game, the modindex will reflect the load position of your mod. E.g., if your mod loads fifth, then the modindex will be '04'. (Oblivion.esm loads first, and the modindex numbering is zero based (0, 1, 2,...), so Oblivion's modindex will remain '00'.)
Note: The modindex of a data object in CS4 is the native modindex. The modindex of that same data object in-game is the in-game modindex.
CS4: If, while editing your mod, you change one of Oblivion's data objects rather than creating a new one, then no new formid will be created. Instead, the formid recorded in your mod file will be the same as Oblivion.esm's formid. This is how the game knows that your data object is replacing the data object from Oblivion.
In-Game: If you pick up an already existing object while in-game, that picked up object will retain its original formid. And if you later drop it and click on it, you'll continue to see the original formid.
If a new object is created in game, then it will be assigned modindex FF (i.e., 255, i.e. the last 'slot' available). New objects are created if you buy an item from a merchant or pull an item out a container.
EditorIds are the plain text ids of data objects (e.g., 'BearPelt01'). While these are what you'll usually think of and be concerned with while editing, they're really just aliases (nicknames) for formIds, which are the true identifiers of data objects.
For example, if you change the 'BearPelt01' to 'BearPeltO1x' (without creating a new formid), you're just changing the alias -- and only so far as your mod is concerned -- as far as other mods are concerned, the alias is still 'BearPelt01'.
Note that although you can change the editor id of a data object, you cannot change the formid. And changing the EditorId has very little effect on the mod, since internally, references to data objects are stored as formids. Again, note that changing the editor id in your mod, does not effect the editor id in other mods.
Scripts provide a nice illustration of EditorId vs. formid: If a script says something like "player.additem BearPelt01 1", then the compiled script will actually add item '' which is the formid corresponding to 'BearPelt01'. (In fact, you can write the script using the formid directly instead of the editorid.) In game, script commands will generally not accept EditorIds -- instead you must enter the formid itself.
For objects placed into the game world there are two formids: the reference formid or RefID (associated with that particular placed object), and the base formid or BaseID (used for all versions of that same object).
The BaseID provides the information that is common to all instances of that object. For example, every copy of the book
has the same BaseID (0002457E); that BaseID record contains information such as the weight, value, appearance, and text of the book. The specific type of record used for the BaseID depends upon the type of item. For example , , , and
are all records used exclusively for BaseIDs. In the Construction Set, all of the formids listed in the "Object Window" are BaseIDs. Most formids provided on this site are BaseIDs.
The RefID provides access to information such as the object's location. There are only three types of records used for RefIDs; the specific type of record depends upon the object:
For NPCs, a
record is used.
For creatures, a
record is used.
For all items, a
record is used.
In game, when you console-click on a placed object, the formid that you will see is the RefID, not the BaseID. In the CS, when you look at objects in the "Cell View", the IDs are all RefIDs; if you edit the object, the BaseID is provided under "Base Object" (and "Edit Base" allows you to edit it). When RefIDs are provided on this site, they are explicitly identified as RefIDs.
Formids were introduced for several reasons, but a main reason was to do away with the mod conflicts that plagued the Morrowind community -- mods conflict has been removed by almost completely isolating mods from each other.
Unfortunately, this isolation makes it difficult to intentionally make mods interact with each other. In fact, using CS by itself, it's impossible to make an esp directly reference (use) anything in any other esp! Fortunately, several tricks have been developed to deal with this. For more info, see .
Note that CS4 does allow you to load non-master mods, but it does not allow your mod to become dependent on them. Again, see
for more info. Despite this, the modindex of the formids belonging to your mod will not be '01', but rather will reflect the load position of your mod -- which is always last. E.g., if you load Oblivion plus 4 esps, then the modindex that you'll see in the formids for your data objects will be '04' (since your mod would be fifth in order and the order numbering starts at '00').
While you might suspect that this would cause problems if your mod is loaded later into CS4 without those other esps, or when it's loaded into the game, CS4 and the game engine seem to adjust for it. (However, any changes that you made to non-esm mods may raise errors.)
The fact that the modindex is represented by a byte (two hex digits) indicates that the maximum number of mods that can be used at once is 255. (One byte allows 256 different 'slots', and one of those ('FF') is used by the save game itself. Of course, we're counting Oblivion.esm as a 'mod', so it will use up one of the remaining 255 slots.)
Modindex zero ('00') is special, since the game engine itself defines certain default objects with modindex zero. You'll see these if you start the construction set without any mods (including Oblivion.esm) loaded. This suggests that Oblivion.esm should always be the first mod to load -- i.e. it should always be dated earlier than any other esm files.
Modindex zero is also used in a plugin (ESP) to indicate that the object is defined in one of the mod's masters (ESM files) and not in the plugin. This is needed because the plugin cannot predict in advance what the modindex will be for each of its masters. For example, if MyMod.esp has masters Oblivion.esm and MyMod.esm, and the player has also installed Foo.esm and Bar.esm, then MyMod.esm could be at index 01, 02, or 03 depending on where it is compared to Foo.esm and Bar.esm.
For details on exactly how to load and merge multiple mods see the
Suppose that you delete an object. Can the formid that was assigned to it be assigned to a newly created object?
Yes. Base formids can be recycled, as long as there are never two objects with the same formid in a mod. In game, temporary formids (those starting with FF) are incremented by the game engine for each object created. When the counter reaches FFFFFFFF it is reset to FF000000, and formids which are no longer in use are recycled. (There were problems with this recycling not working correctly before patch 1.2.0416 - most notably the counter was incorrectly reset to
instead of FF000000.)
What's up with GMSTs?
Many GMSTs have formids == 0, yet it's possible to change the EditorId. If you try to change the value of a GMST that has formid == 0, a new formid will be assigned. I suspect that GMSTs are an exception -- i.e., that unlike every other data object, their formids are not used.
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卡伦在伊特鱼利亚(Etruria)这个地方，以「冥界船夫」的身分为人所熟知。死者要前往应去的国度时，必然会经过这条河。这条河的名字是阿谢隆河，它意味着「悲伤之河」或「无喜悦之河」。卡伦的职责就是这条河的摆渡人，负责接运死者的灵魂，因此也被视为「灵魂的导引者」。他的外貌有着如马喙般大大的鹰钩鼻、零乱的胡髭和头发，以及长耳、尖牙、歪唇等，给人一种野兽般的印象，而且全身散发一股令人不而栗的恐怖气息。 在时代，人们有着在下葬的死者口中或眼睑上放置钱币的习俗。这钱币当然是支付给卡伦的渡河费用。音乐作品外文名Charon地&&&&区伊特鱼利亚所属国家芬兰
在&&的&地狱篇&中，也曾描写过卡伦(Charon /亡灵摆渡人)。但丁为了拜访地狱，和其它Charon的死者一起来到河边，这时出现一条载着白发老人的小船(但丁描写的卡伦并非冥界而是地狱的船老大)，卡伦对着死者们如此喊道。
你们这些如害般的卑贱灵魂啊，
别希望能再重见天日了，
让我将你们载到彼岸，
到那永远的黑暗、炎热和冰冷里，
来吧，让我载你们去吧！
这时，但丁被发现了。
「那位生者啊，请你离开死者们！」
但是，因为但丁不想离开，所以又被忠告。
「你得走其它的路，你和他们是不一样的渡口。你的渡口不在这里，你应该乘坐更轻的船。」轻的船大概是指到天国的船吧，或是只有死者不能坐的船，文中并没有明确说明。引导但丁的人向卡伦说明后，卡伦才勉强答应让他参观。之后，卡伦聚集死者让他们上船，可是，即使有些死者只迟到一点，卡伦都会眼冒怒火，以船桨毫不留情地痛殴他们。
当然，卡伦不单是个摆渡人而已，在但丁的记述中，他还负责监视没有死的人，或是不该去地狱的死者，防止他们蒙混上船。因为如果发生这种事情，一定会造成地狱的混乱。总之，卡伦是死者的引领者，同时也是刑吏。因为卡伦非常熟悉该如何处理下地狱的死者，所以一般人认为，和卡伦碰面的地点，就是地狱的起点。
附带一提的是，卡伦的父亲名叫亚勒伯斯(Erebus，黑暗)，母亲是尼克斯(Nyx，夜晚)。他们原是兄妹关系，而他们共同的母亲是混沌(Chaos，空洞或混沌)。关于亚勒伯斯没有什么特别的数据，但是尼克斯所生的孩子中，除了卡伦以外，有不少是会令人毛骨悚然的神，例如桑纳托斯(Thanatos，死亡)、摩洛斯(Moros，命运)、卡尔(Ker，破坏)、莫墨斯(Momus，不满)、涅墨西斯(Nemesis，报复)、厄里斯(Eris，纷争)等。芬兰charon乐队国家：
成军时间：1992年
风格：，死亡金属
唱片厂牌：SPINEFARM
主唱 - Juha-Pekka Leppaluoto
吉他手 - Pasi Sipila
贝司手 - Teemu Hautamaki
鼓手 - Antti Karihtala
吉他手 - Lauri Tuohimaa1992年成军时，Charon还是支原始传统并稍带有死金色彩的乐队。三年后，形势越来越明显，Charon自己也发觉是时候做些改变了。从年，乐队逐渐转为更具旋律性的氛围多层次金属风格。
1997年，Charon的一张小样和录像带引起了总部在丹麦的唱片公司Emanzipation Productions的注意。该唱片公司与他们签下一纸合约。从97年十月到98年一月，Charon为处女专辑Sorrowburn录制了十首歌曲。这十首精挑细选的金属作品散发着孤寂，渴望，感性和情色。这些歌受到了Diehard Music的注意，他们取得许可并在1998年夏天发行。新闻界的反响十分积极，而且Sorrowburn进驻芬兰官方歌曲榜，超过了Celine Dion, Massive Attack, Cradle of Filth, 和Rancid这些卓越的艺人。评论家们赞赏Charon横跨歌特，厄运和古典金属的潜力，并虏获了各方歌迷的心。Sorrowburn把Charon的名字写在了欧洲歌特金属的大旗上。
近两年时间过去了，Charon完成了苦心经营另他们满脸泪痕的专辑Tearstained（泪痕）。乐队再次来到了录制Sorrowburn的位与芬兰首都赫尔辛基的Brr录音室。经过两个月的辛苦工作，10首全新的作品出炉，之后在Finnvox录音室（Amorphis, HIM, Sentenced）混音。为了开拓新的音乐疆土并扩张音乐领域，Charon请来了大提琴演奏家Jarmo Paloniemi和女歌剧演唱家Jenny Heinonens献艺。Charon的J.P.说，大提琴演奏的加入和Jenny Heinonens美妙歌喉带领乐队经历了一场音乐的另类之旅。
“Jenny的歌声有震慑人心的魅力。我认为她给我们的音乐带来了戏剧化的紧凑感。”
Tearstained的歌词写作对主唱J.P.来说成了很个人化甚至有些痛苦的经历。
“与单纯的凭空编造相比，写到与我相关的歌词内容时，我感觉轻松得多。这次，我深深的开掘自己，却发现自己的生活处在一个新的低谷里。作曲过程帮我重新找回了自己。这就是为什么我说作词对我来说是很私人化的事。”
Charon再次向人们证明他们是支极具创新精神的乐队，不断寻找新的音乐挑战。在时间上，Tearstained在乐队的音乐生涯上留下了重要的一笔。11首歌曲美丽，气氛感很强，并有宽广的情感深度。
显示方式：专辑列表 | 专辑详情
专辑名称 发行时间 语言 试听专辑 详情
Downhearted
At the End of Our Day
Bitter Joy
Come Tonight
Desire You
Little Angel
Sister Misery
Sorrowsong
Tearstained
Christina Bleeds
Deepest Scar
Sorrowbringer
Your Christ
Sorrowburn
Neverbirth
November's eve
To serve you
冥王星外一颗矮行星:Charon ( KAIR en ),即。发现时间:1978年
发现者:Jim Christy
冥卫一是在1978年被Jim Christy发现的。在此之前由于冥卫一与冥王星被模糊地看成一体，所以冥王星被看作的比实际的大许多。
命名：Charon（或－－译注）是以神话中的人物命名的，他专门摆渡死者通过River Styx冥河来到冥界。（虽然学术界以这个神秘人物来命名，但的发现者Jim Christy这样命名也是为了纪念他的妻子Charlene。正如所知道的，他们英语发音的第一音节是相同的，就象“shard&（&SHAHR en&）一样。）
轨道: 离19,640 千米
直径: 1172 千米
质量: 1.90×10^21 千克
卡戎在冥王星赤道上空约1.9余万公里（地月距离的1/20）的圆形轨道上运转。其运行周期与冥王星自转周期相等。观测表明，卡戎自身的引力大到足以使它呈球形，而冥王星和卡戎的共同重心位于外部空间里，并不位于冥王星内部，“卡戎”其实与冥王星构成了双行星系统，同步围绕太阳旋转（248个地球年）它与太阳的距离也与冥王星基本相同，平均约59亿公里。在很长时间里，卡戎一直被视作冥王星的卫星，中文称为冥卫一。但自发现之日起，人们就注意到它有许多特殊之处，与其他行星的卫星迥然不同。卡戎本身并不很大，直径约为1200公里，质量约为月球的1/45。但以卫星与其行星的大小之比而论，它却是太阳系里最大的卫星。冥王星的质量大约只是卡戎的10倍，而地球的质量是月球的81倍，木星比它最大的卫星大上千倍。
卡戎很不寻常是因为在太阳系中相对于各自主星来比较，它是最大的一颗卫星。（一个与月球的区别）。一些人认为冥王星与冥卫一系统是一个双行星系统而不是行星与卫星的系统。
卡戎的半径也不是知道得很清楚，JPL认为586千米的数据存在±15的误差，大于2%。它的质量和密度也不是知道得很确切。
冥王星与卡戎是独一无二的，因为他们自转是同步的。它们俩保持同一面相对（这使得在冥王星上看见的冥卫一的位相十分有趣）。
卡戎的组成还不知道，但它的低密度（大约2克/立方厘米）表示它可能很像土星的冰质卫星（如土卫五）。它的表面可能覆盖着冰水。
不像冥王星那样，卡戎没有很大反照率，虽然还未断定它的是不是已经更小了。
有人认为卡戎是经过一次巨大的撞击形成的，就好像形成月球那样。
人们还怀疑卡戎拥有一个值得注意的大气层。
由于距离非常遥远，人们对卡戎的认识还很少，现今最强大的天文望远镜也只能拍到模糊的照片。美国宇航局的探测器“新地平线”已于2006年1月出发，预计将在2015年到达冥王星附近，对冥王星和卡戎进行探测。《辐射3》中的人物Charon名称：Charon
种族：Ghoul
职业：保镖
位置：Underworld
阵营：随意
BaseID:15616Charon是一个从小就被洗脑过的保镖。会对他的合约持有者无条件的服从。玩家一开始可以在underworld的酒吧里找到他。此时的他正为酒吧老板服务。与酒吧老板对话，有2种要领从老板弄到他的合约，购买，或者提老板做一件事。假如购买的话须要 2000瓶盖，或者1000，假如玩家口才高的话。至于做事，则是应老板要求去杀隔壁旅馆的GRETA。拿到合约后与charon交谈，他会冲过去把老板爆头。理由是他以前对他太坏。。。
charon运用的来复枪比通常的来复枪拥有更广的射击范围（大约一倍以上）和更高的精确度。理论上是游戏里最强的（可惜无法扒下来自己用）。另外他对玩家的KARMA没有任何要求。是泛用性特别强的伙伴。
新手上路我有疑问投诉建议参考资料 查看structureViz: Linking Cytoscape and Chimera
outreach & training
visitors center
structureViz: Linking Cytoscape and Chimera
structureViz in action.
In this screenshot, the PFAM
family PTE (phosphotriesterase) has been opened in Cytoscape.
Three of the available structures have been
opened in UCSF Chimera and spatially aligned.
Parts of one structure (pdb: 1EZ2) are selected, as indicated with green
outlines in the Chimera window.
Click on the image to enlarge it.
UCSF structureViz is a Cytoscape plugin that links
visualization of biological networks in
with visualization and analysis of molecular structures in
It is part of a broader effort
to develop and apply tools for the .
Networks have nodes and edges. For structureViz,
molecular structures are associated with nodes using the node attributes.
Macromolecular structures are specified by Protein Data Bank identifiers
() and small molecule structures by
Homology-modeled protein structures can also be associated,
as detailed .
As an alternative to interacting with Chimera directly,
structureViz provides a simplified, tree-based interface to structures
called the Cytoscape Molecular Structure Navigator.
This interface allows selecting models, chains, and residues
and adjusting their display.
Basic interfaces are also provided
for spatially aligning macromolecular structures and
for analyzing steric clashes and hydrogen bonds.
If you haven't already done so,
and install UCSF Chimera.
Install structureViz from the Cytoscape Plugin Manager (see the
Manage Plugins
option in the Plugins
structureViz is listed under the
Analysis Plugins category).
Restart Cytoscape.
Now structureViz actions should be available in the Cytoscape
Plugins menu and node context menus.
Annotating a network with structures entails
creating new node attributes and populating those attributes
with structure identifiers.
The type of each attribute can be String (if multiple identifiers,
a comma-separated list) or List (with each identifier given as a single string).
Macromolecular structure (PDB) identifiers.
One or more
codes can be associated with a node as
an attribute named
Structure, structure,
pdb, pdbFileName,
or biopax.xref.PDB.
Small molecule (SMILES) identifiers.
One or more
can be associated with a node as an attribute named
Smiles, smiles, or
This mainly provides a convenient way
to load small molecule structures into Chimera.
For more traditional cheminformatics applications, see the
Cytoscape plugin.
Residue identifiers.
An attribute named FunctionalResidues or
ResidueList can be used to specify
residues of interest.
In general, a residue specification is of the form
pdbID#residueID.chainID.
The pdbID is the 4-character
of the structure.
A chainID is a character used in the structure file to
group residues by chain. A residueID
may be a single-letter code and residue number
such as H263, a three-letter code and number such as His263,
or simply a residue number, such as 263.
Like the other types of identifiers, residue specifications
can be given individually or as a comma-separated list:
His236,Lys238, Met240.
A range of residues can also be specified: 236-250.
To handle cases in which a node is associated with multiple structures
and the residues of interest differ between those structures,
PDB identifiers can be included:
2uz9#His82,2uz9#Thr102.
If no PDB identifier is given,
the residue specification is assumed to apply
to all of the structures annotated to the node.
In addition, homology-modeled structures can be fetched from
if the node ID is a ModBase-searchable type of sequence identifier
and models are available for that sequence
structureViz provides two similar sets of menus, one under the
Plugins&Sequence/Structure Tools top-level menu
and the other as part of
the node context menus under Structure Visualization.
The structureViz context menus may be accessed by mouse
right-click in the Cytoscape network window.
The two sets of menus currently present the same options to the user,
except that Find modeled structures
and Select residues
are only available from the node context menu.
Open structure(s)&
Allow the user to specify which of the structures associated with the
currently selected node(s) should be opened in Chimera.
This action is enabled when structureViz detects
a node attribute with one of the recognized names for structure
annotations (see ).
PDB entries are fetched over the web from the
Small molecule structures are generated from SMILES strings
web service provided by the
at Indiana University.
When a structure has been opened in Chimera,
will appear.
Align structures
Open all structures associated with the currently selected node(s),
and if there are at least two,
invoke the Cytoscape/Chimera Structure Alignment Dialog
(To avoid opening all of the structures, instead open only the structures
of interest with the Open structure(s)&
action described above and align them with
Chimera&Align Structures& in the
Select residues (node context menu only)
The Select residues menu is present only when the node
has a value for the
FunctionalResidues or ResidueList
attribute.
In that case, the relevant structures are opened (if they
haven't been already)
and the associated residues are selected in both Chimera and the
Find modeled structures (node context menu only)
for homology-modeled structures that match the ID for this node.
The node ID must be a SwissProt, TrEMBL, GenPept or PIR sequence accession code.
If modeled structures are available for the sequence, they are fetched
over the web and opened in Chimera
Close structure(s)&
Allow the user to specify which of the open structures should be
removed from both Chimera and
Exit Chimera
Close all structures and quit from UCSF Chimera.
Figure 2. The
Molecular Structure Navigator dialog.
In this image, the Molecular Structure Navigator shows
three open structures (models): 1EZ2, 1QW7, and 1JGM.
The entry for 1JGM has been expanded to show the two chains, and the
second chain has been expanded to show the initial residues in the PDB entry.
When structureViz is used to open structures in Chimera,
the Molecular Structure Navigator appears (see Figure 2).
This dialog provides an easy and convenient way to interact with structures
regardless of a user's familiarity with Chimera.
Each structure has three levels:
The model& level corresponds to
a single opened structure.
The dialog reports the associated
node and the total numbers of chains and residues in the model.
The colored outline box reflects the default color of the model in Chimera.
The chain level corresponds to groups of residues within
a model that share a chain identifier.
The residue level reflects individual residues.
Residue names
and numbers are shown.
The levels in the hierarchy can be expanded and contracted.
Selecting a model, chain, or residue in the Molecular
Structure Navigator selects the corresponding structural element in Chimera.
In Figure 2, there are three entries at the model level, reflecting the three open structures.
model entry for 1JGM has been expanded to show the two chains that are part of this model
(phosphotriesterase is a dimer), and the second chain (B) has been expanded to show the residues
contained within that chain.
In addition to selection and navigation within the structural hierarchy,
the Molecular Structure Navigator provides menus
for aligning and analyzing structures and adjusting their display.
It serves as an alternative interface to UCSF Chimera, but the
standard Chimera menus, tools, and commands can also be employed.
The menu bar across the top of the
contains the following:
Align structures&
Invoke the Cytoscape/Chimera Structure Alignment Dialog
for aligning (superimposing) structures
by model or by chain.
In either case, the user must indicate one reference model (or chain)
and one or more other models (or chains) to match to the reference.
Results from each pairwise match can be used to create new edges in the
original Cytoscape network (see ).
Zoom out to include all structures in the UCSF Chimera display.
Presets are predefined combinations of display settings.
Choosing a preset
from the menu applies its settings.
The interactive presets are meant for
interactive manipulation and analysis.
They may change what items (atoms, ribbons, surfaces) are displayed and how
they are colored, and set the background color to black.
The publication presets are for generating
images for presentation and publication.
They do not change what items are displayed or their colors,
but may change their styles, and set the background color to white.
Publication presets may decrease interactive performance because finer
divisions are used to render atoms, ribbons, and surfaces.
in Chimera
interactive 1 (ribbons)
interactive 2 (all atoms)
interactive 3 (hydrophobicity surface)
publication 1 (silhouette, rounded ribbon, sticks)
publication 2 (silhouette, licorice, sticks)
publication 3 (depth-cued, rounded ribbon, sticks)
publication 4 (depth-cued, licorice, sticks)
Clash detection&
Identify steric conflicts (close contacts) involving the selected atoms
and show them with lines.
Find all clashes
Identify clashes between the selected atoms and all other atoms.
Find clashes within models
Identify clashes between the selected atoms and other atoms in the
same model.
Clear clashes
Remove lines showing clashes.
(For full access to clash options and settings, instead use the Chimera
Hydrogen bond detection&
Find hydrogen bonds&
identifies hydrogen bonds involving the currently selected atoms,
restricted as follows:
Between models
- inter-model hydrogen bonds only (note that different chains in the same
structure are still in the same model)
Within models
- intra-model hydrogen bonds only
- both inter- and intra-model hydrogen bonds
The hydrogen bonds are shown with lines, which can be removed by
subsequently choosing Clear hydrogen bonds.
(For full access to hydrogen-bond options and settings, instead use the Chimera
Quit from UCSF Chimera and close the Molecular Structure Navigator.
Collapse model tree
Collapse models to hide residues and chains in the
Molecular Structure Navigator tree.
Expand all models
Expand models to show all chains in the
Molecular Structure Navigator tree.
Expand all chains
Expand to show all chains and residues in the
Molecular Structure Navigator tree.
Refresh model tree
Refresh model tree
Refresh model tree
Refresh the Molecular Structure Navigator tree.
Show residues as...&
Set how amino acids are listed in the Molecular Structure Navigator:
single letter
Use single-letter abbreviations for amino acid residues.
three letters
Use three-letter abbreviations for amino acid residues.
Use the full names of amino acid residues.
Select parts of structures in UCSF Chimera and the
Molecular Structure Navigator.
Select all amino acid residues.
Nucleic acid
Select all nucleic acid residues.
Select all ligand residues.
Select all monatomic ions.
Select all solvent residues.
Secondary structure&
Select amino acid residues according to their secondary structure assignments:
&&(non-helix, non-strand amino acid residues)
Functional Residues
Select functional residues (available when the appropriate
has been assigned).
Invert selection
Invert the current selection (select the unselected atoms and deselect
the selected atoms).
Clear selection
Clear the selection (deselect all atoms).
Two categories of context menus can be accessed by mouse
right-click in the
those with ,
and those which also include special actions
depending on the context level (,
residue, or chain).
Generic actions are always available, although the scope of the action
depends on the context of the pop-up menu.
When the mouse cursor
is placed on a specific item (model, chain, or residue)
when the menu is popped up, the action applies specifically
to that item.
If the mouse pointer is placed over an empty area,
the action applies to any selected models, chains, or residues.
Note that when nothing is selected, the context menu can not be popped up
in an empty area.
Control the display of atoms and bonds in the current context.
Show all atoms.
Backbone only
Show backbone atoms only (these may be obscured by ribbons).
Show the sequence of each chain in a separate window (Chimera's
In the residue context, the entire chain sequence will still be shown,
but with any residue(s) selected in Chimera and the
highlighted in bright green.
Hide all atoms.
Adjust the view and center of rotation in Chimera to focus on
the models, chains, or residues specified by the context.
Rainbow by chain
(only available in the model context)
Assign each chain in the model a separate color.
Rainbow by residue
(only available in the model or chain context)
Rainbow-color-code the residues in each chain, starting from blue
and ending at red.
Atoms/Bonds&
Change atom/bond color.
By element
Color-code atoms by element: grey for carbon, red for oxygen,
blue for nitrogen, yellow for sulfur, etc.
By heteroatom
Use the model default color for carbon, color-code
other atoms by element.
Change ribbon color.
Change surface color.
Change label color.
Control display styles.
Different styles can serve to highlight different aspects of a structure,
from overall shape to specific atomic interactions.
Show bonds as wir this style is the simplest
and least computationally demanding.
Show bonds as sticks and atoms as endcaps (rounded ends).
Ball & Stick
Show bonds as sticks and atoms as balls.
Show atoms as spheres using their VDW radii.
A ribbon is a cartoon-like representation that traces the
backbone of a protein or nucleic acid.
It is particularly useful for
viewing the secondary structure of a protein.
Hide ribbon.
Show flat ribbon.
Show edged ribbon (rectangular cross-section).
Show rounded ribbon (rounded cross-section).
Molecular surfaces highlight the overall shapes of structures and
their binding pockets.
Hide molecular surface.
Show surface as solid. To reveal underlying objects,
adjust Transparency (below).
Show surface as mesh.
Show surface as dots.
Transparency&
Adjust surface transparency.
Hide atom and residue labels.
Label atoms by name.
Label atoms by element symbol.
IDATM type
Label atoms by .
Label residues by identifier.
Clear selection
Clear the selection (deselect all atoms).
This action applies to all selected items,
regardless of the context of the pop-up.
Delete selection
Delete all atoms in the current selection.
This action applies to all selected items,
regardless of the context of the pop-up.
Note that deleted
atoms cannot be restored except by reopening the original structure,
and that deletion will also remove any corresponding ribbon or surface.
Close model(s)
Close all of the models in the current context.
This will remove them from the
Molecular Structure Navigator as well as closing them in Chimera
Select parts of the models in the current context.
Select all amino acid residues.
Nucleic acid
Select all nucleic acid residues.
Select all ligand residues.
Select all monatomic ions.
Select all solvent residues.
Secondary structure&
Select amino acid residues according to their secondary structure assignments:
&&(non-helix, non-strand amino acid residues)
Functional Residues
Select functional residues (available when the appropriate
has been assigned).
If the ID of a node
is a SwissProt, TrEMBL, GenPept or PIR sequence accession code,
can be searched for homology-modeled structures
of the corresponding sequence using
Find modeled structures
If ModBase contains modeled structures of that sequence,
they are fetched over the web and opened in Chimera.
Chimera also displays a dialog, the
that lists the models and some associated information.
There may be a large number of modeled structures,
whereas a user may want only one.
Clicking a row in the
shows just the corresponding model (hides the others in the list),
and the scores and other information in the list can help to identify
an appropriate model for further analysis.
To close all other models in Chimera, select the desired model in the
invert the selection (Select&Invert selection),
and then use Close model(s) in the
Figure 3. Importing modeled
structures.
In this image, the Molecular Structure Navigator shows the result of
finding modeled structures for node MSL1, which has the ID YIR009W.
UCSF Chimera has queried
and retrieved the results.
Structures can be spatially aligned (superimposed) and the corresponding
alignment scores assigned to edges in the Cytoscape network.
The Cytoscape/Chimera Structure Alignment Dialog can be invoked
In the latter menu, Align structures
includes suboptions by chain
for choosing specific chains to use in the alignment,
versus by model for choosing whole models.
In the dialog, it is necessary to specify one reference model
(chain, if aligning by chain)
and one or more models (chains) to match.
Each structure to match is superimposed on the reference
structure by first creating a sequence alignment and then fitting the aligned
residue pairs.
The sequence alignment is constructed using a score based both
on residue type (as in a traditional sequence alignment) and on
secondary structure assignments (preferentially aligning helix with helix
and strand with strand).
If models were chosen rather than specific chains, all pairwise combinations
of chains in the two models are aligned and the chain pair with the best score
is used for the fit.
The fit is iterated to remove far-apart residue pairs
so that only a well-superimposed structural core is used for the final fit.
(For details, see the Chimera
default alignment and matching settings are used.)
Additional dialog options:
Show sequence panel for each alignment - whether
Chimera should display the sequence alignment used to superimpose each
pair of structures.
In the sequence alignment window
(Chimera's
the residue pairs used in the final fit are indicated with light orange boxes.
Assign results to Cytoscape edge attributes
- whether to add an edge between the nodes associated with each
reference-match pair of structures, and to assign the alignment scores as
attributes of that edge.
Alignment Pairs is the number of residue pairs used in the final fit.
RMSD is the &-carbon RMSD of that set of residues in the final fit.
Score is the score of the sequence alignment
(based on both residue types and secondary structure as described above)
used to align the structures.
Users should be aware that the scores may not correlate well with
structural similarity or superposition quality when the sequences are
dissimilar and hard to align.
Successful superposition only requires the sequence alignments to be partly
correct, as incorrect regions tend to be omitted during fit iteration.
Omitting parts of the sequence alignment from the fit will affect
the number of residue pairs used and the RMSD, even if the resulting
superposition is entirely correct.
However, in typical usage, the proteins are similar
and their sequences easy to align.
Figure 4. Using UCSF Chimera's
MatchMaker capabilities to perform an alignment of two structures.
In this image
two structures: 1PSC and 1DPM had been loaded into Chimera and
aligned (Chimera&Align structures&by chain).
In order to facilitate the use of structureViz and UCSF Chimera from other plugins, the
structureViz plugin exports a number of commands using the CyCommand mechanism.
commands may be used by other plugins, or as part of scripts that are executed using the
There are a number of arguments which are repeated for several of the commands.
In particular:
structurelist, atomspec, and structuretype are defined here and referenced from each of the commands
outlined below:
This a list of structures which may be specified as either a list of open PDB identifiers, model numbers,
or Cytoscape nodes that are associated with open structures.
As with other lists, these values are comma-separated
and enclosed in quotes.
"1tup,1gzh,1tsr"
Note the special keywords selected, which will be converted into all of the models which are
selected or partially selected, and all which refers to all currently open structures.
An atomspec is the specification for an atom in Chimera, however structureViz will
only allow specification to the residue level.
The general form of the atomspec is:
#model.submodel:residuelist.chain
where model and submodel are the model and submodel numbers,
residuelist is a comma-separa and chain is the chain identifier,
which is usually a letter (e.g. 'A').
The model is required, but all other specifiers are optional.
For example, to specify chain 'A' for the first model, all that is required is #0:.A or even
#0.A (this form is not legal in Chimera, but it is allowed in structureViz).
structurelist a special form of the atomspec is the selected keyword, which refers
to the currently selected models, chains, or residues.
More information on the Chimera atom specification syntax is available
structureViz supports only a limited set of the full specification provided by Chimera.
This argument is used to control the selection or display of structural components based on
the class or chemical attribute of the component.
The legal keywords are:
full: Display or select the full backbone.
minimal: Display or select the minimal backbone.
ions: Display or select ions
ligand: Display or select ligands
main: Display or select the main structure
nucleic acid: Display or select nucleic acids
protein: Display or select proteins
solvent: Display or select the solvent
helix: Display or select components with helical secondary structure
strand: Display or select components with strand (or sheet) secondary structure
coil: Display or select components that are neither helix nor strand
with CA/C1': Display or select atoms in side chains including the CA (for amino acids) and C1' (for nucleic acids)
without CA/C1': Display or select atoms in side chains excluding the CA and/or C1'
In general, all of the commands include several arguments, which are described below the
command description.
The arguments and their values are specified as name, value pairs separated
by an equals sign (=).
For example, to align two structures, the user might enter:
align structures reference="1tup" structurelist="1gzh,1tsr" assignattributes=false showsequences=true
Note that the text arguments are placed within quotes.
If the argument has a default value, that value is shown below in brackets ([]).
Literal values, such as the booleans true and false or the keyword selected are
shown in bold, while descriptions of the argument type such as atomSpec or chainSpec
are shown in italics, usually with an example following in parentheses.
structureviz align chains
Perform sequence-driven structural superposition on a group of structures by chain.
Arguments:
referencechain=chainSpec: This is the chain to be used as the reference
for the pairwise alignments.
The format is the same as an
except that only the chain component is used.
chainlist=chainlist: The list of chains to align to the referencechain, where
each element in the list is an
from which only the model
and chain component are extracted.
showsequences=[false]: If true, the sequence alignment for each
pair of structures is shown.
createedges=[false]: If true new edges will be created in the
Cytoscape network that represent the similarity of each structure with the reference
assignattributes=[true]: If true the RMSD, Alignment Score, and
number of aligned pairs are added to the Cytoscape network as attributes.
structureviz align structures
Perform sequence-driven structural superposition on a group of structures.
Arguments:
reference=structure: This is the structure to be used as the reference
for the pairwise alignments.
The format is the same as an
except that only a single structure may be specified.
structurelist=:
The list of structures to align to the reference structure.
showsequences=[false]: If true, the sequence alignment for each
pair of structures is shown.
createedges=[false]: If true new edges will be created in the
Cytoscape network that represent the similarity of each structure with the reference
assignattributes=[true]: If true the RMSD, Alignment Score, and
number of aligned pairs are added to the Cytoscape network as attributes.
structureviz clear clashes
Clear the clashes shown in the display and disable clash detection.
No arguments
structureviz clear hbonds
Clear the hydrogen bonds shown in the display.
No arguments
structureviz clear selection
Clear all selections.
No arguments
structureviz close
Close some or all of the currently opened structures.
Arguments:
structurelist=[selected]: This is the list of structures (in the
to be closed.
structureviz color
Color part or all of a structure.
This command allows the user to specify the
color for residues, labels, ribbons, and surfaces.
is specified as a recognized Chimera
a hexidecimal RGB value: #rrggbb.
Arguments:
preset=preset_type: One of the recognized Chimera
(e.g. preset="interactive 1").
If this argument is used, no structurelist or atomspec
argument is required (and if provided, is ignored)..
All other color arguments require either a sturcturelist or an
atomspec, or an atomspec of "selected" is assumed.
residues=color: set the color of the targeted residues to color.
labels=color: set the color of the targeted labels to color.
ribbons=color: set the color of the targeted ribbons to color.
surfaces=color: set the color of the targeted surfaces to color.
structurelist=structurelist: This is the list of structures (in the
to apply the specified colors to.
atomspec=atomspec: This is the list of models, chains, or residues (in the
form of a list of s to apply the specified colors to.
structureviz depict
Change the depiction (display style) of a structure.
Arguments:
preset=preset_type: One of the recognized Chimera
(e.g. preset="interactive 1").
If this argument is used, no structurelist or atomspec
argument is required (and if provided, is ignored)..
All other depict arguments require either a sturcturelist or an
atomspec, or an atomspec of "selected" is assumed.
style=[none|wire|stick|bs|sphere|cpk]: This is the style of depiction
to use for residues in the specified structurelist or atomspec argument, but does not change the visibility
of those items.
If all of the resides of a structure are hidden (for example because a ribbon representation is being
used) this command will appear to have no effect.
You will need to first
the sidechains for those residues.
ribbonstyle=[none|flat|edged|round]: This is the style of depiction
to use for ribbons in the specified structurelist or atomspec argument.
Unlike the style argument
setting the ribbonstyle acts to display the ribbon for the selected structural elements.
Setting the
ribbonstyle to none hides the ribbon.
surfacestyle=[none|solid|mesh|dot]: This is the style of depiction
to use for surfaces in the specified structurelist or atomspec argument. Like ribbonstyle this
argument causes the surface to be calculated and displayed.
structurelist=structurelist: This is the list of structures (in the
to change the depiction of.
atomspec=atomspec: This is the list of models, chains, or residues (in the
form of a list of s to change the depiction of.
structureviz exit
Exit Chimera.
No arguments
structureviz find clashes
Find clashes between two models or parts of models.
Arguments:
structurelist=structurelist: This is the list of structures (in the
to detect classed between.
atomspec=[selected]: This is the list of models, chains, or residues (in the
form of a list of s to detect clashed between.
continuous=[true]: This argument tells Chimera to continually update the clash
detection and the display of the clashing residues.
structureviz find hbonds
Find hydrogen bonds between two models or parts of models.
Arguments:
structurelist=structurelist: This is the list of structures (in the
to look for hydrogen bonds between.
atomspec=[selected]: This is the list of models, chains, or residues (in the
form of a list of s to look for hydrogen bonds betwee.
structureviz focus
Focus the Chimera display on a structure or part of a structure.
If no arguments are supplied, the entire
scene is focused.
Arguments:
structurelist=structurelist: This is the list of structures (in the
to focus on.
atomspec=atomspec: This is the list of models, chains, or residues (in the
form of a list of s to focus on.
structureviz hide
Hide parts of a structure.
Arguments:
structurelist=structurelist: This is the list of structures (in the
atomspec=[selected]: This is the list of models, chains, or residues (in the
form of a list of s to hide.
structuretype=structuretype: The
to narrow the selection to or to implicitly select for hiding.
structureviz list chains
List the chains in a structure.
Arguments:
structurelist=[all]: This is the list of structures (in the
to list the chains for.
structureviz list residues
List the residues in a structure.
Arguments:
structurelist=[all]: This is the list of structures (in the
to list the residues for.
chainlist=chainlist: The list of chains to show residues for, where
each element in the list is an
from which only the model
and chain component are extracted.
Only one of structurelist or chainlist may be specified.
structureviz list selected chains
List all of the currently selected chains in Chimera.
Arguments:
structurelist=[all]: This is the list of structures (in the
to list the selected chains for.
structureviz selected models
List all of the currently selected models in Chimera.
No arguments
structureviz list selected residues
List the currently selected residues in Chimera.
Arguments:
structurelist=[all]: This is the list of structures (in the
to list the selected residues for.
chainlist=chainlist: The list of chains to show selected residues for, where
each element in the list is an
from which only the model
and chain component are extracted.
Only one of structurelist or chainlist may be specified.
structureviz list structures
List all of the open structures.
No arguments
structureviz move
Move (translate) a model.
Arguments:
x=x location: The x coordinate to move the model to.
y=y location: The y coordinate to move the model to.
z=z location: The z coordinate to move the model to.
structurelist=[selected]: This is the list of structures (in the
to be moved.
structureviz open structure
Open a new structure in Chimera.
Arguments:
pdbid=pdbid: The ID of the structure in the PDB.
This will cause Chimera to fetch
the designated structure from the PDB.
modbaseid=modbaseid: The ID of a modeled structure in
Chimera will fetch the modeled structure from
ModBase and display it.
nodelist=nodelist: A list of nodes in Cytoscape to attempt to find attributes with
structural identifiers and open all the identifiers for those nodes.
showdialog=[false]: if true show the Molecular Structure Navigator dialog after
opening the structure in Chimera.
structureviz rainbow
Color part or all of a structure in a rainbow scheme.
Arguments:
structurelist=structurelist: This is the list of structures (in the
to color in a rainbow.
atomspec=[selected]: This is the list of models, chains, or residues (in the
form of a list of s to color in a rainbow.
structureviz rotate
Rotate a model.
Arguments:
x=angle: The amount (in angles) to turn around the x axis.
y=angle: The amount (in angles) to turn around the y axis.
z=angle: The amount (in angles) to turn around the z axis.
center=centerspec: The center of the rotation.
This may be one of the
keywords: view, models, or front or an x,y,z value representing
a point in the scene, or an
for designating a
portion of the structure to rotate around.
structurelist=[selected]: This is the list of structures (in the
to be rotated.
structureviz select
Select a structure or parts of a structure.
Arguments:
structurelist=structurelist: This is the list of structures (in the
to select.
atomspec=[selected]: This is the list of models, chains, or residues (in the
form of a list of s to select.
structuretype=structuretype: The
to select.
structureviz send
Send a command to Chimera.
Arguments:
command=chimera command: The command to send to
No special parsing or handling is done on the string.
For a list of Chimera commands and syntax, see the
Show parts of a structure.
Arguments:
structurelist=structurelist: This is the list of structures (in the
atomspec=[selected]: This is the list of models, chains, or residues (in the
form of a list of s to show.
structuretype=structuretype: The
to narrow the selection to or to implicitly select for displaying.
small sample network annotated with PDB structures:
(phosphotriesterases)
larger sample network annotated with PDB structures:
(the amidohydrolase superfamily from the
a node attribute file providing known linkages between GI numbers and protein structures:
structureViz publication:
structureViz: Linking Cytoscape and UCSF Chimera. Morris JH, Huang CC, Babbitt PC, Ferrin TE. Bioinformatics 2007. [PMID:]