[Chimera-users] zone command between proteins

Francesco Pietra chiendarret at gmail.com
Mon Sep 13 01:46:58 PDT 2010

Hello Elaine:
As far as I can understand, the software output does not allow any of
the CHIMERA possibilities, except for non-standard residues in the
peptide.  Perhaps renaming all peptide residues as non-standard
residues; not tried if CHIMERA can accept that format.

The protein is three chains, A, B, C, each chain beginning with
residue number 1. What only goes in sequence throughout is the atom
The peptide is chain A, beginning with residue number 1.

I cannot intervene in the output format, which derives from a complex
sequence of steps, including removal of all Hs and replacement by
REDUCE. To deal with non-standard residues, I have to arrange such as
the procedure stops, allowing me to replace a file with all-Hs with
the non-standard residue, which is less easy than one can imagine.

This is why I could only map for the non-standard residue of the
peptide vs the protein. And this is why I thought to rename the
peptide residues in the final file with names of my random choice.

Of course, my obvious interest is in peptide.residue-protein.residue
mapping (just about a curious intervention by ops in this thread).


On Sun, Sep 12, 2010 at 6:36 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Francesco,
> You would have to use residue numbers and/or chain IDs.  Actually the
> peptide is also "protein" (at least the standard residues) so you would not
> want to use that specifier anyway.  If your peptide was chain B and the
> protein was chain C, for example:
> sel :.c & :.b z<5
> Or if everything was chain A and your protein is residue numbers 3-455 and
> the peptide is residues number 456-462:
> sel :3-455.a & :456-462.a z<5
> There are several ways to figure out the numbers and chain IDs, including
> looking at the balloon help that pops up when you hold the cursor over some
> atoms on the screen, or using the Sequence tool, or using a text-editor to
> look at the PDB file.
> See "atom specification" for details on using model, residue, chain IDs etc.
> in the command line.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
> Best,
> Elaine
> -----
> 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 Sep 12, 2010, at 7:28 AM, Francesco Pietra wrote:
>> Hello:
>> How to map the residues at a given distance (<5A) between a protein
>> and its 5-residues peptide ligand? I could only use the zone command
>> for a non-standard residue in the peptide:
>> sel protein & :non-standard_residuename_of_peptide
>> All other peptide residues are standard residues.
>> thanks
>> francesco pietra

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