Hi Martin - ** Short answer:
Use `resn asp+glu` (although your original command actually works for me). ** Not-so-short answer, with a bonus question about comment syntax: The Asp/Glu line of your script can be condensed slightly using a plus sign, but the original syntax of that line actually works fine for me (PyMOL v.1.3, Fink/X11 build on Mac OS 10.6.6). However, for me, the lines to remove waters and add hydrogens fail. To elaborate, I've found that, with certain commands (but oddly not all of them -- for example, the `color` statements in your original script handle this just fine), adding a comment on the same line returns a "Malformed selection" error. I don't know if this is by design or an "unintended feature." I would expect these comments to be handled the same way as in Python code, but for whatever reason, they are not. (Query for the developers: Is there a specific reason some PyMOL functions attempt to include the hash mark and comment in the selection, rather than ignoring everything after the #? Perhaps it has something to do with the number of arguments--both the commands below that fail with an inline comment take only a single selection argument.) If you really want to keep the comment on the same line, add a semicolon between the command and the comment. The other option, of course, is to place the comment on the previous line. Also, you can use `remove solvent` to cover all the different ways of describing water (HOH, WAT, H2O). Try this: # remove water remove solvent; # or put the comment on the same line after a semicolon # add hydrogens h_add; # this one also requires a semicolon # basic view as surface color grey90 # color lys blue, cys yellow, asp/glu red color slate, resn lys # comments here seem to work without the semicolon color paleyellow, resn cys color tv_red, resn asp+glu Hope that helps, -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center New York, NY 10016 212-263-7898 On Mar 1, 2011, at 7:44 AM, Martin Hediger wrote: Dear all What is the selection syntax to select all GLU and ASP residues within an object? I'm trying it the way its written on the wiki: remove resn hoh # remove water h_add # add hydrogens as surface color grey90 color slate, resn lys # lysines in light blue color paleyellow, resn cys # cysteines in light yellow color tv_red, (resn asp or(resn glu)) # aspartic and glutamic acid in light red but, the selection kind of does not work for me (I'm assuming the operator for the logical AND is 'and'). What is it that I need to do differently? Kind regards Martin ------------------------------------------------------------------------------ Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= ------------------------------------------------------------------------------ Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
