[mailto:thomas.hol...@schrodinger.com]
Sent: Monday, January 19, 2015 3:33 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] How to determine distance of matching atoms in aligned
nonidentical structures?
Hi Carsten & Shane,
I assume Carsten is looking for cmd.get_raw_alignment(). Re
Hi Carsten & Shane,
I assume Carsten is looking for cmd.get_raw_alignment(). Recent versions of
PyMOL can create an alignment object with all alignment commands (align, super,
cealign). get_raw_alignment returns the (model, index) keys for all pairs.
http://pymolwiki.org/index.php/get_raw_align
Hi Carsten,
This sounds like a non-trivial problem, my understanding is that it's still
an ongoing challenge to best align dissimilar structures. Other ways of
aligning structures involves using the vectors from secondary structure
elements, or feeding in (multiple) sequence alignments. All have t
Hi,
How can I best determine the distance between matching pairs of atoms in two or
more aligned structures? Fairly easy to do when the two aligned structures are
the same, but how does one go about when the structures are not the same? The
problem is that I cannot figure out how to dependably
