Hi Nat,
I don't think PyMOL natively handles something that slick. I would
then start scripting:
fetch 3edx, async=0
# start a Python block
python
# import stored
from pymol import stored
# create a set to hold residue identifiers
stored.resiList = set()
# this set will contain those residues ids w/letters
badList = set()
# populate the residue list
cmd.iterate("3edx", "stored.resiList.add(resi)")
# foreach residue in the list, look for anything resembling
# a number followed by a non-number (eg. letter)
# and add it to the bad list
for x in stored.resiList:
if None != re.search("\d+\D", x):
#print x
badList.add(x)
# the set difference will be what you're looking for
print "Good residues are"
print stored.resiList - badList
python end
Cheers,
-- Jason
On Tue, Feb 15, 2011 at 5:22 PM, Nat Echols <[email protected]> wrote:
> On Tue, Feb 15, 2011 at 2:07 PM, Jason Vertrees
> <[email protected]> wrote:
>>
>> Interesting question. PyMOL's wildcards can help here:
>>
>> select allButInsertionsA, not (i. *A)
>>
>> This will look for all residue NUMBERS that end in "A" and select
>> everything but that.
>
> Thanks, that definitely helps a lot. I just realized that my original
> question was poorly formulated, however: the insertion code often (maybe
> always?) changes from residue to residue (PDB ID 3edx is one example). So I
> could build up a list of all insertion codes, or just use all uppercase
> characters, but I'm worried about the size of the resulting selection
> strings. (I managed to crash PyMOL for the first time in years last week
> with a very long selection.) Can I instead select for a *blank* insertion
> code?
> -Nat
> ------------------------------------------------------------------------------
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) [email protected]
(o) +1 (603) 374-7120
------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
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