Hi Morgan, More generally, to figure out Chimera selection strings for atoms in unusual residues, display an example of that residue and label its atoms to see their names. Then, using the names to specify, you can either (1) display the whole residue and then undisplay certain atoms or (2) undisplay the whole residue and then display certain atoms (as in Eric's example). You may be able to incorporate partial wild cards (? for single character, = for completion). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ atom_spec.html#wildcards Another way to see the names that will be used in remediated PDB files is to look up that residue in the chemical components dictionary. In structure 2axt, there are many chlorophyll A residues (CLA). To see its atom names, you could look at the PDB's component definition, http://remediation.wwpdb.org/pyapps/ldHandler.py?query=CLA http://remediation.wwpdb.org/data/C/CLA/CLA_D3L1.gif or you could use the following commands in Chimera open 2axt color byhet show :1.het focus la :1.het It looks like the phytol moiety of CLA is C1-C20. If I were working repeatedly with this structure, I'd probably use the "alias" command to alias the phytol selection string to something short and easy to type, for example alias phytol :cla@c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,c 18,c19,c20 (add/subtract atom names as desired). A range (c1-c20) will not work because names are treated as characters rather than numbers. After using that alias command, you can simply use "phytol" as the command- line specifier, for example ~disp phytol For subsequent use, you could put the alias in a command file (simply a text file containing one or more commands). Opening a command file executes its commands, and you can even designate it as a startup file to be automatically executed when the command line is first started. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ indexcommand.html#cmdfile http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Midas Of course, this approach depends on a consistent set of atom names being used in the various structures you use, which it should be in the remediated PDB files. I hope this helps, 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 Jul 9, 2007, at 1:15 PM, Eric Pettersen wrote:
On Jul 9, 2007, at 6:39 AM, Morgan Ryan wrote:
Is it possible to write a selection string that will select all the phytol substituents in a model? I'm looking at photosystem II. I would like to select all the phytol side chains of the many chlorophyll molecules and hide them, so that only the porphyrin-like chlorin ring structures are visible. Can that be done? Thanks! Morgan
Hi Morgan, I think the only direct way is to use the command line (Favorites-
Command Line). This command should do it:
~disp :cla@c=; disp :cla@c?a,c?b,c?c,c?d
It undisplays all the carbons in the chlorophyll (:cla@c=) and then redisplays the carbons involved in the porphyrin ring (all of which have 3-letter names that end in A-D). You might want to consider posing Chimera-specific questions to the Chimera users mailing list (chimera-users@cgl.ucsf.edu) since there will be more people able to answer there.
--Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu