Have you tried
getproperty chaininfo ?
or
x = getProperty("chaininfo")
?
On Thu, Mar 21, 2013 at 2:54 PM, Eric Martz <[email protected]>wrote:
> Does someone know an easy way to query Jmol for the residue sequence
> numbers (atom property resno) for the first and last residues in each
> chain? Something less brute force than scanning the ATOM records directly?
>
> One issue is that ligands are often assigned to chains and given high
> numbers, but they are not standard amino acids or nucleotides (so
> they are HETATM not ATOM). Many are not covalently bound to a protein
> or nucleotide chain, but some are. For example in 1igt
> (immunoglobulin) the heavy chains end at residue 474. The ASN-bonded
> sugars are then numbered 475-483 for each chain.
>
> So its not sufficient to look for the highest resno assigned to a named
> chain.
>
> Take 1igt as an example. I want an easy way to have Jmol tell me that
> Chains B and D start at 1 and end at 474, and chains A and C start at
> 1 and end at 214.
>
> The lengths I have already parsed out from SEQRES (using
> jmolGetPropertyAsString('fileInfo', 'seqres')).
>
> (Although the heavy chains are numbered from 1-474, their length is
> only 444 with gaps in the numbering, and there are many insertion codes.)
>
> Thanks, Eric
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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