Dear folks,
I have a couple of questions about the alignment and fitting functions
of pymol.
I've been using the 'align' and 'fit' functions of pymol apparently
quite successfully, but I found it difficult to make the 'rms' or
'rms_cur' functions actually report anything. I can take a structure
with identical sequence in two conformations and 'fit' it properly or I
can use 'align' and get an RMS value, but 'rms' doesn't report anything
directly. Now I did find that I could get the value with:
print cmd.rms('selection1','selection2')
but I was surprised that I couldn't get it directly. After looking in
the code, I found I could do:
rms (selection1),(selection2),quiet=0
and then the value was reported. Should that not be the default?
Second question: Is it possible to get the identity of the the atoms
used by 'align'? I know from 'help align' that
"If object is not None, then align will create an object which
indicates which atoms were paired between the two structures"
but could we possibly have access to a list of atoms or residues
matched?
Cheers,
Robert
--
Robert L. Campbell, Ph.D. <r...@post.queensu.ca>
Senior Research Associate phone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-633-2497
Kingston, ON K7L 3N6 Canada
PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
(out of date web site:http://biophysics.med.jhmi.edu/rlc)
