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@gmail.com> Date: Mon, Sep 13, 2010 at 10:46 AM Subject: Re: [Chimera-users] zone command between proteins To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@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@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@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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