[Chimera-users] Detecting residue from command line

Francesco Pietra chiendarret at yahoo.com
Fri Nov 30 13:01:19 PST 2007

Mysteriously it works nicely. Mysteriously as I had to rename HETATM -> ATOM
and remove all CONECTs from Chimera's membrane_aligned.pdb and
complex_aligned.pdb in order to have them accepted by leap. Probably, the atom
renaming that I had to carry out in transferring pdb written by Chimera to
Amber would have requested editing CONECTs too (which was out of my
possibilities for a CONECT list so long that it took time to delete it).

The combined pdb only has

RecordName, AtomNumber, AtomName, resName, resSeq, and xyz coordinates. Column
22 (chainID) does not exist. All residues (including WAT) separated from one
another by TER.

This rudimentary situation notwithstanding,

select :3-##.water

or color ... :#-##.water

work fine. What I found extraordinary is that  for a pdb arranged:

1-76 POPC
77-520 protein
521 ligand
522-9999 WAT
0-4759 WAT

with only TERs separating the residues, the colored groups do not overlap

color hot red pink :0-521.water

relegates such water as two separate well ordered groups in the external layer,
the one of TIP3P water added to build the box.

There is some overlapping with lipid (I don't yet master that taskbar command)
so that I don't yet know what will happen during Amber minimization because of
that overlapping. At any event, the few commands you suggested clarified the
situation quite a lot.


--- Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Francesco,
> In the command line, ":" means residue number and the following "." 
> indicates the chain ID.  You could select the residues with
> select :0-521.water
> if they are in the "water" chain, or use that same specification in 
> many other commands, for example
> color hot pink :0-521.water
> Probably the most tricky thing is that :0-521 without specified chain 
> ID would include residues in any chains with single-character IDs 
> (A,B,C ...) but not the special chains "water" and "het"
> Details on command-line atom specifications:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.htm
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> On Nov 30, 2007, at 9:51 AM, Francesco Pietra wrote:
> > Sorry for a question that was surely answered many times.
> >
> > How to detect on the screen (from command line) residues from their 
> > resSeq
> > number?. I have two different sets of WAT: 522-9999 and 0-4759 and 
> > want to
> > check where 0-521 are located in a protein-ligand-POPC membrane.
> >
> > Thanks
> > francesco pietra

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