[Chimera-users] Fwd: zone command between proteins

[Elaine Meng]

Hi Francesco,
Sure, you could also use model numbers, alone or in combination with residue numbers and/or chain IDs, as described in the documentation:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 13, 2010, at 6:44 AM, Francesco Pietra wrote:

> Hello Elaine:
> Is it not possible to refer to the two different models (protein #0,
> peptide #1)?
> francesco
> 
> 
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret at gmail.com>
> Date: Mon, Sep 13, 2010 at 10:46 AM
> Subject: Re: [Chimera-users] zone command between proteins
> To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> 
> 
> 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
> number.
> 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).
> 
> thanks
> francesco
> 
> 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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