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Re: [Jmol-users] renumbering in Jmol
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From: <ppa...@no...> - 2004-12-21 19:08:17
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Miguel,
please see my additional e-mail.
Rest below in #############
Petr
Dr. Petr Pancoska
Department of Pathology
SUNY Stony Brook, NY 11794
phone: (631)-444-3030
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"Miguel"
<mi...@jm...>
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Subject
Re: [Jmol-users] renumbering in
12/21/2004 01:23 Jmol
PM
Please respond to
jmol-users@lists.
sourceforge.net
Petr wrote:
> 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.
OK.
Q: Does it renumber all groups in all chains, or just the selected set?
#####################################
well, good question.
I think minimally painful (from the conceptual point of view, maybe not by
implementation.. :-))) is to let the renumber act upon the selection.
Then the user is responsible for results. If one does "select
all","renumber x" all chains are renumbered sequentially.
Potential problem is, if you have a selection that is somehow internaly not
compatible with the natural residue numbering - say "select Polar
Residues", then an attempt to renumber the selection in the strict sense
might have unwanted consequences.
Easiest way out would be to renumber all by default.
Next level might be to be able to renumber different chains in multi-chain
polymers after selecting them.
Final level alternative is to renumber the residues in the complete chain
which has at least one atom selected. Meaning e.g., that by clicking on one
atom in a chain, you selected a residue in a chain and if the renumber x
command is issued after that, the whole chain that contains the selected
atom(s) is renumbered. To be sure that user renumber all chains,
combination of select all, renumber x is needed.
###################################
> 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.
OK, I think I understand that
> B. There is "conventional" numbering of proteins, based upon some
> alignment etc. and again, that generates problem above.
OK
> 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.
I did not really understand what you meant by 'non-sequential "103's" '
Q: Are you saying that there may be some sequence numbers missing? as in
101,102,103,110,111,112 ?
##############################
Yes, e.g. in cases when segments of the polymer chain in the crystal are
too flexible - it is still 70-80% water in there for proteins - so the
reflections of x-rays are not measurable and the analysis software cannot
convert them into any useful electron densities, so the atoms in the
structural model cannot be fit into them. No data=no "sequence numbers" in
the pdb file and "101,102,103,110,111,112" is the result
##############################
Q: So, in this case are you saying that you would like to renumber a
chain, but retain any 'gaps' that might exist?
###########################
Yes, please see my second e-mail
########################
Jmol has some recognition of polymers. So if two residues are too far
apart to bond then Jmol can recognize that ... even if they are in the
same chain.
Q: Would that be useful in trying to calculate whether or not the sequence
should retain the previous 'gap'?
Q: Should there be any type of 'renumbering' based upon polymer chains?
################################
I think this is too complicated and more appropriate for different kind of
programs (structural alignment etc.) outside the scope of viewer.
#################################
The complicated scenarios are probably more than I can handle
Q: Should 'renumber' only work on the selected set of atoms. Then you can
select the subsets that you want and renumber them as you like them.
################################
PLease see the answer above
#################################
Q: Please confirm that after 'renumber', all insertion codes are set set
to space/null.
###############################
Do not understand this because I do not know what insertion code is. In
rasmol and other viewers, if there are missing atoms, result on screen
depends on rendering mode. Some (wireframe) gives weird structures by
trying to connect distant atoms, some are "interpolating", some (cartoon)
are leaving space gaps in the rendering.
It is overkill to try to do something with this at this level I believe.
######################################
One minor problem that occurs to me is this ... If the user has previously
turned on labels that contain the residue number then those labels will
continue to hold the previous values. To correct this one would have to
reexecute the 'label' command.
##################################
Well, that's the price I would happily pay in exchange for removing those
mind-boogling re-indexing calculations :-))
##################################
Miguel
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