Miguel,
here is what it is:
Jmol reads the indices of amino acid residues from pdb file - here is the
line, the N of ARG in chain A will have index 103 because of "ARG A 103"
ATOM 1 N ARG A 103 -15.318 8.439 62.436 1.00 25.84
RADA N
The renumber x in Rasmol allows you to change that read index to another
that starts from x (even negative values are sometimes necessary).
Everything else remains the same.
Why it is useful:
A. Protein X for which the structure is stored in pdb file is a sub-domain
of larger one Y. Y has e.g. 567 residues, domain X that was crystallized
(independently) only 70. Crystallographers retained Y- numbering of
residues in X. Now because X is molecule by its own, you analyze its 70-aa
sequence and have 5 tables of results indexed 1-70,because the analyzing
programs would index it based on the 70 aa sequence you input. To see what
the results mean means to add 103 to everything you want to see - source of
errors if you do not want to write a script to do that.
B. There is "conventional" numbering of proteins, based upon some alignment
etc. and again, that generates problem above.
C. Most difficult problem is to have "gaps" in the sequence data, which
happens if crystallography cannot provide coordinates for certain residues.
It can be identified by non-sequential "103's" in the "ARG A 103" segments
of the read line(s). That is not suitable for renumber command, with other
programs then RASMOL I usually correct for that by text-editing the pdb
file by filing the gaps by inserting lines with identifiable nonsense
coordinates, but that requires that the rest of the software recognizes
that.
Mostly, solving A and B with renumber is fine.
Regards, Petr
Dr. Petr Pancoska
Department of Pathology
SUNY Stony Brook, NY 11794
phone: (631)-444-3030
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"Miguel"
<[EMAIL PROTECTED]>
Sent by: To
jmol-users-admin@ jmol-users@lists.sourceforge.net
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.net
Subject
Re: [Jmol-users] renumbering in
12/21/2004 12:14 Jmol
PM
Please respond to
[EMAIL PROTECTED]
sourceforge.net
Petr wrote:
> Trying "renumber x" in the Rasmol Scripts console results in Script
> command not implemented: renumber.
True, that is not implemented.
A year ago when I was working on the scripting engine I did not understand
how it worked, and noone has asked for it.
> Cannot find any replacement functionality in the docs. This is relatively
> important function for transferring sequence analysis into 3D picture.
Please explain ... I do not understand what you mean.
> PDB files unfortunately sometimes contain numbering that starts not where
> one would like to so it is painful to re-calculate everything to the new
> indexing.
> renumber was an easy remedy for that - any suggestions how to do that?
I now understand that the residue sequence numbers are often not
sequential, and that insertion codes add to the complexity.
I can probably implement 'renumber' ... but the idea of changing the raw
data makes me nervous ... I fear it will have unforseen repercussions.
So first ...
I do not understand what the value of 'renumber' is. It seems to me that
it would break all of the scripts associated with that .pdb file.
Q: What is the benefit of using 'renumber'? What are you trying to
accomplish?
Miguel
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