Thank you very much to both of you for your help. Have a good day. Fred
> Matt, > > There isn't an escape sequence, but PyMOL will automatically disable the > asterisk as a wildcard for atom names if any PDB file loaded contains an > asterisk in that field. > > To manually choose another wildcard for that field, issue something like > > set atom_name_wildcard, % > > As for coloring atoms by element, use of wildcards should be avoided -- > use the "elem" operator instead. > > color red, elem o > color blue, elem n > color green, elem c > > etc. > > Cheers, > Warren > > -- > Warren L. DeLano, Ph.D. > Principal Scientist > > . DeLano Scientific LLC > . 400 Oyster Point Blvd., Suite 213 > . South San Francisco, CA 94080 USA > . Biz:(650)-872-0942 Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:war...@delsci.com > > >> -----Original Message----- >> From: pymol-users-ad...@lists.sourceforge.net >> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of >> matthew.frank...@imclone.com >> Sent: Monday, April 03, 2006 8:37 AM >> To: Kerff Frédéric >> Cc: pymol-users@lists.sourceforge.net; Warren DeLano >> Subject: Re: [PyMOL] Atom type selection with the * >> >> >> pymol-users-ad...@lists.sourceforge.net wrote on 04/03/2006 >> 09:49:51 AM: >> >> > Hi Pymol users, >> > >> > I'm experiencing some trouble with the selection of atom type using >> > the "*". Sometimes it works and sometimes it doesn't... >> > I used for example: >> > color red, object////o* >> > 'color red, name o*' give the same result. >> > Any idea why it's happening and more interesting what >> should I do to >> > fix >> it. >> > Thank you very much. >> > >> > Fred >> > >> >> Hi Fred - >> >> I don't have the answer to your question, but I did want to >> point out that "*" is a perfectly valid part of the atom name >> in some PDB files - the PDB expects you to use it for atoms >> in the ribose ring of nucleotides. For example, this is from >> a structure I did a while ago: >> >> HETATM 8021 O5* TTP 1 0.035 48.396 15.975 1.00 50.15 >> O >> HETATM 8022 C5* TTP 1 -0.048 49.462 14.957 1.00 40.93 >> C >> HETATM 8023 C4* TTP 1 0.565 50.743 15.416 1.00 38.78 >> C >> HETATM 8024 O4* TTP 1 -0.194 51.219 16.565 1.00 36.44 >> O >> HETATM 8025 C3* TTP 1 1.977 50.628 15.948 1.00 38.12 >> C >> HETATM 8026 O3* TTP 1 2.988 50.525 14.996 1.00 44.69 >> O >> HETATM 8027 C2* TTP 1 2.084 51.848 16.841 1.00 33.48 >> C >> HETATM 8028 C1* TTP 1 0.693 51.871 17.477 1.00 33.26 >> C >> >> >> So watch out! >> >> >> >> Warren - is there a way of escaping the "*" if you want to >> use it for selection? Let's say I wanted atom C5* but not C5M. >> >> Thanks, >> >> Matt >> >> -- >> Matthew Franklin phone:(917)606-4116 >> Senior Scientist, ImClone Systems fax:(212)645-2054 >> 180 Varick Street, 6th floor >> New York, NY 10014 >> >> >> Confidentiality Note: This e-mail, and any attachment to it, >> contains privileged and confidential information intended >> only for the use of the >> individual(s) or entity named on the e-mail. If the reader >> of this e-mail is not the intended recipient, or the employee >> or agent responsible for delivering it to the intended >> recipient, you are hereby notified that reading it is >> strictly prohibited. If you have received this e-mail in >> error, please immediately return it to the sender and delete >> it from your system. Thank you. >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by xPML, a groundbreaking >> scripting language that extends applications into web and >> mobile media. Attend the live webcast and join the prime >> developer group breaking into this new coding territory! >> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&; > dat=121642 >> _______________________________________________ >> PyMOL-users mailing list >> PyMOL-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> >> >
