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@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

Elaine: 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 macroscopically. 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. Thanks francesco --- Elaine Meng <meng@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@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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