Jmol/Visualizing large molecules: Difference between revisions
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<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== | ||
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===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]). | ||
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The number of non-hydrogen atoms in the average amino acid in a protein is about 8. Where did this value come from? | The number of non-hydrogen atoms in the average amino acid in a protein is about 8. Where did this value come from? | ||
<blockquote> | <blockquote> | ||
The | The average molecular weight of an amino acid, weighted by amino acid frequencies in proteins, is 110<ref>Average molecular weight of an amino acid is about 138. When the average is weighted according to the occurrences of amino acids in proteins, it is about 128. Subtracting 18 for the weight of water removed when a peptide bond is formed, the average is 110. This is explained in [http://books.google.com/books?id=5Ek9J4p3NfkC&pg=PA84&lpg=PA84&dq=average+amino+acid+molecular+weight&source=bl&ots=ZxHCOzsnjL&sig=we53bW4b7kLuy53LL2BHNDd8CwU&hl=en&sa=X&ei=SD81UdatGo6B0AHy8oHwDQ&ved=0CFEQ6AEwBA#v=onepage&q=average%20amino%20acid%20molecular%20weight&f=false Lehninger Principles of Biochemistry].</ref>. Half of the atoms in protein are hydrogen<ref>There are approximately 1.01 hydrogens per non-hydrogen atom in proteins. The source of this value is given in the article [[Hydrogen in macromolecular models]].</ref>, and the other half are mostly carbon (12), with some oxygen (16) and nitrogen (14). So if we take 13 as the average weight of a non-hydrogen atom, and average that with 1 for the other 50% of the atoms (hydrogen), we get (13 + 1)/2 = 7 as the approximate molecular weight of the average atom in protein. 110/7 is about 16 atoms for the average amino acid in protein. But half of those are hydrogen, missing from most PDB files. So the number of non-hydrogen atoms in the average amino acid is about 8. | ||
</blockquote> | </blockquote> | ||
Since the maximum number of atoms in a single model in a PDB file is 99,999 (see above), dividing by 8 non-hydrogen atoms per amino acid gives a '''maximum of about 12,500 amino acids in a single model in a single PDB file''' (containing nothing but protein and no hydrogen atoms). In fact, longer chains can be represented if only the alpha-carbon atoms are present in the PDB file. | Since the maximum number of atoms in a single model in a PDB file is 99,999 (see above), dividing by 8 non-hydrogen atoms per amino acid gives a '''maximum of about 12,500 amino acids in a single model in a single PDB file''' (containing nothing but protein and no hydrogen atoms). In fact, longer chains can be represented if only the alpha-carbon atoms are present in the PDB file. | ||
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Suppose that you want the alpha carbons for a subset of models in the published ensemble. You can get 16 models from the 184 models in 2hyn by taking either the first 16 | Suppose that you want the alpha carbons for a subset of models in the published ensemble. You can get 16 models from the 184 models in 2hyn by taking either the first 16 | ||
:<tt>load models {1 16 1} =2hyn filter "*.ca"</tt> | :<tt>load models {1 16 1} =2hyn filter "*.ca"</tt> | ||
or by taking every 12th model plus the last model | |||
:<tt>load models {1 184 12} =2hyn filter "*.ca"</tt> | :<tt>load models {1 184 12} =2hyn filter "*.ca"</tt> | ||
