[Chimera-users] pdb-l: Selecting phytols in Chimera?

[Elaine Meng]

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 at 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 at 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 at c=; disp :cla at c?a,c?b,c?c,c?d
>
> It undisplays all the carbons in the chlorophyll (:cla at 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 at cgl.ucsf.edu) since there
> will be more people able to answer there.
>
> --Eric
>                          Eric Pettersen
>                          UCSF Computer Graphics Lab
>                          pett at cgl.ucsf.edu
>                          http://www.cgl.ucsf.edu