Jmol/Visualizing large molecules: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) No edit summary |
||
| (9 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
<Structure size='400' frame='true' align='right' caption='Half-capsid of human hepatitis B virus displaying only the alpha carbon atoms for the [[biological assembly]] of [[2g33]].' scene='Jmol/Visualizing_large_molecules/Backbone_by_chain/1' /> | <Structure size='400' frame='true' align='right' caption='Half-capsid of human hepatitis B virus displaying only the alpha carbon atoms for the [[biological assembly]] of [[2g33]].' scene='Jmol/Visualizing_large_molecules/Backbone_by_chain/1' /> | ||
<center><table style="background-color:#d8ffd8;" class="wikitable"><tr><td> | |||
This page was written in 2011 and '''needs major revisions''' to take into account (i) that Proteopedia now automatically shows [[biological unit]] 1, simplified as needed (try [[4v60]] or [[1sva]]<ref>Page [[1sva]] uses the [[Molstar]] viewer instead of [[JSmol]].</ref>); (ii) the 2022 ability of [http://firstglance.jmol.org FirstGlance in Jmol] to automatically simplify and display very large [[biological units]]; | |||
and (iii) the ability of JSmol to generate biological units. Please see: | |||
*[[Biological_Unit#Visualizing_the_Biological_Unit|Visualizing the Biological Unit]] | |||
*[[FirstGlance/Virus_Capsids_and_Other_Large_Assemblies]] | |||
*[[Biological_Unit:_Showing]] | |||
[[User:Eric Martz|Eric Martz]] 21:27, 22 September 2024 (UTC) | |||
</td></tr></table></center> | |||
==Inadequate Memory May Preclude Display== | ==Inadequate Memory May Preclude Display== | ||
| Line 28: | Line 36: | ||
===62 Chains=== | ===62 Chains=== | ||
In the | In the final update of the PDB data format specification ([https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM Version 3.3]) and the current remediation of PDB data, chain IDs (names) must be single alphanumeric characters (A-Z, a-z, 0-9). This permits a maximum of 62 chains. This limit is not much of a problem for [[asymmetric unit|asymmetric units]]. In January, 2011, there is only one PDB entry with 62 chains ([[2zkr]]), and 4 more with 55-60 chains. | ||
Generally, the first 26 chains are given IDs A-Z. Above 26, it is apparently arbitrary whether numerals or lower case letters are used first. For example, for the 28 chains in [[3krd]] or [[3hln]] or [[3gpt]], those beyond A-Z are 1-2. Alternatively, for the 28 chains in [[3lo3]], the extra two are identified a-b, and in the 42-chain [[3jqo]], lower case ID's are present but no numerals. Also, when numerals are used, they may begin with 1, or with 0 ([[3fic]]). Occasionally, the letters A-Z are not used up before lower case ID's are employed: [[1tzn]] has 28 chains with ID's A-O and a-o. | Generally, the first 26 chains are given IDs A-Z. Above 26, it is apparently arbitrary whether numerals or lower case letters are used first. For example, for the 28 chains in [[3krd]] or [[3hln]] or [[3gpt]], those beyond A-Z are 1-2. Alternatively, for the 28 chains in [[3lo3]], the extra two are identified a-b, and in the 42-chain [[3jqo]], lower case ID's are present but no numerals. Also, when numerals are used, they may begin with 1, or with 0 ([[3fic]]). Occasionally, the letters A-Z are not used up before lower case ID's are employed: [[1tzn]] has 28 chains with ID's A-O and a-o. [[7sya]] has 12 chains a-l, with no chains having upper case names. | ||
Jmol can automatically apply a distinct color to each chain, up to 36 chains ([http://jmol.sourceforge.net/jscolors/#Chains Jmol Colors]). However, it can distinguish 62 chains by selection (see [http://chemapps.stolaf.edu/jmol/docs/#setmisc set chainCaseSensitive]). | Jmol can automatically apply a distinct color to each chain, up to 36 chains ([http://jmol.sourceforge.net/jscolors/#Chains Jmol Colors]). However, it can distinguish 62 chains by selection (see [http://chemapps.stolaf.edu/jmol/docs/#setmisc set chainCaseSensitive]). | ||
