Beware of sweeping statements - I work with nucleic acids (mostly
bound to proteins) and I am continually irritated by the use of * in
nucleic acid names, and I think I qualify as anyone.
Now that the ASCII code has settled down somewhat, " ' " could take
it's rightful place in PDB files, liberating " * " to its otherwise
universal role as wild-card.
Laurence Pearl
On Wednesday, February 18, 2004, at 05:25 pm, Eric Zollars wrote:
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
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Laurence H. Pearl
Section of Structural Biology, Institute of Cancer Research
Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
Phone +44-207-970 6045 : Secretary +44-207-970 6046
FAX +44-207-970 6051 : E-Mail laurence.pe...@icr.ac.uk
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" Live Simply and do Serious Things .. " - Dorothy Crowfoot Hodgkin
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