[PyMOL] selecting multiple atoms ie oxygen
I wish to select multiple oxygens (labelled O1, O2 etc.. within my pdb file) and colour them red for example. Is there any easy way of doing this other than typing out a list of all the oxygens I wish to select? eg. color red, (5paa and (name o1+o1a+o2+o3+o4+o5+o1p+o2p+o3p)) I know in molscript its posible to use a o* label to select all oxygens, is such a switch possible in pymol. It doesn't work, or I am using the wrong syntax if its possible. Any thoughts would be appreciated. John
RE: [PyMOL] selecting multiple atoms ie oxygen
John, color red, 5paa and elem o The problem with using asterices as wildcards in atom names is that some ill-conceived PDB files actually use them in atom names. However, PyMOL does support the use of a terminal wildcard in some cases, such as with the delete command... create obj01, none create obj02, none delete obj* And with residue names color red, as* color blue, gl* color pink, hi* Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of John Berrisford Sent: Wednesday, February 18, 2004 3:42 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] selecting multiple atoms ie oxygen I wish to select multiple oxygens (labelled O1, O2 etc.. within my pdb file) and colour them red for example. Is there any easy way of doing this other than typing out a list of all the oxygens I wish to select? eg. color red, (5paa and (name o1+o1a+o2+o3+o4+o5+o1p+o2p+o3p)) I know in molscript its posible to use a o* label to select all oxygens, is such a switch possible in pymol. It doesn't work, or I am using the wrong syntax if its possible. Any thoughts would be appreciated. John --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
FW: [PyMOL] selecting multiple atoms ie oxygen
Warren, Personally, I'd much rather have wild-card selections in atom names and have to deal individually with the ill-conceived PDB files than the other way around. Regards, David Horita -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Warren DeLano Sent: Wednesday, February 18, 2004 10:56 AM To: 'John Berrisford'; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] selecting multiple atoms ie oxygen John, color red, 5paa and elem o The problem with using asterices as wildcards in atom names is that some ill-conceived PDB files actually use them in atom names. However, PyMOL does support the use of a terminal wildcard in some cases, such as with the delete command... create obj01, none create obj02, none delete obj* And with residue names color red, as* color blue, gl* color pink, hi* Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of John Berrisford Sent: Wednesday, February 18, 2004 3:42 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] selecting multiple atoms ie oxygen I wish to select multiple oxygens (labelled O1, O2 etc.. within my pdb file) and colour them red for example. Is there any easy way of doing this other than typing out a list of all the oxygens I wish to select? eg. color red, (5paa and (name o1+o1a+o2+o3+o4+o5+o1p+o2p+o3p)) I know in molscript its posible to use a o* label to select all oxygens, is such a switch possible in pymol. It doesn't work, or I am using the wrong syntax if its possible. Any thoughts would be appreciated. John --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] selecting multiple atoms ie oxygen
-Original Message- From: Charlie Sent: Wednesday, February 18, 2004 8:56 AM To: Warren DeLano Subject: Re: [PyMOL] selecting multiple atoms ie oxygen Warren DeLano wrote: John, color red, 5paa and elem o The problem with using asterices as wildcards in atom names is that some ill-conceived PDB files actually use them in atom names. However, PyMOL does support the use of a terminal wildcard in some cases, such as with the delete command... create obj01, none create obj02, none delete obj* And with residue names color red, as* color blue, gl* color pink, hi* Cheers, Warren Hi Warren, I've struggled with this a couple of times. Could it be worth finding another way round, so that a consistent role for * exists. Might it not be better to require users to somehow escape *'s in atom names and then allow * as a wildcard. Although this might be less clear for newbies, the lack of * as a wilcard in atom names is currently unclear. I don't know much about python, but the unix system of escaping special chars with a backslash would be an option, then one could select foo,(bar//A/50/*1\*) to get atoms O1* and C1* from the molecule. You've probably been through this and have a perfectly sound reason for not doing it ! The newbie issue is what troubled me. Unix hacks know how to edit PDB files to replace asterisks with something more benign, and they know to escape common wildcards -- but the ordinary person does not. Clearly we can't make everyone happy, so perhaps consistency should be the guide? But on the other hand, we are talking about a huge portion of the PDB. Nearly every nucleic acid structure seems to suffer from this unfortunate naming convention (~5000 PDB entries contain C1\* according to grep of a recent copy of the PDB). It is true that well-established conventions already exist for handling asterisks, but I don't believe in following conventions blindly, particularly when so many people would be negatively affected. I welcome further discussion on this point. Guidance from the community will be crucial, since I don't have a good solution in mind yet. Some food for thought: 1) Are atom name wildcards really needed when a more precise way of selecting by element symbol already exists? 2) If so, then what are the proposals? a. Escape non-wildcard asterisks with backslash? (regexp convention, but would trip-up newbies, break current PyMOL scripts, and inconvenience a whole field of research) b. Escape wildcard asterisks in atom names with a backslash (that would be very backwards from the standard convention and create further confusion). c. Add a configurable atom_name_wildcard toggle? d. Support alternative wildcards for atom names? Would . or .* work? Also note that currently PyMOL doesn't have a regexp engine, and it doesn't support full wildcards -- just terminal astericks in a few situations. Full regexps matching (and thus full convention adherence) would be a nice addition in the future, but it will need to be configured somehow as well, probably via some global setting like regexp_based_matching. Cheers, Warren