Anyone who works with nucleic acids will certainly prefer the current situation.  From the PDB format guidelines:

* The asterisk (*) is used in place of the prime character (') for naming atoms of the sugar group. The prime was avoided historically because of non-uniformity of its external representation.

Eric



David A. Horita wrote:
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=1356&alloc_id=3438&op=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=1356&alloc_id=3438&op=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_id56&alloc_id438&op=click
_______________________________________________
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users

  

Reply via email to