Yep, that was it and will take care of most of the issues I encountered. Just
stumbled upon colorbyrmsd.py, which contained that function a couple of minutes
ago as well.
Thanks for all the suggestions and pointers!
Cheers,
Carsten
-----Original Message-----
From: Thomas Holder [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(). 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_alignment
Example:
fetch 1ubq 2lgd, async=0
super 1ubq & guide, 2lgd & guide, object=aln
python
pairs = cmd.get_raw_alignment('aln')
for pair in pairs:
print pair, cmd.get_distance(pair[0], pair[1]) python end
Hope that helps.
Cheers,
Thomas
On 19 Jan 2015, at 14:47, Shane Caldwell <shane.caldwel...@gmail.com> wrote:
> 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 their
> benefits and drawbacks. Which you use will depend on what you are trying to
> do.
>
> Depending on what information you have, the strategy will change and CA-CA
> distances may or may not be reasonable to compare. The underlying challenge
> is the question of how to know which parts of structures are functionally
> equivalent, and the answer gets philosophical once the sequences diverge a
> lot. With drift of sequence, geometry and function can drift as well.
>
> I'd have a look into the various algorithms detailed at
> http://www.rbvi.ucsf.edu/home/meng/grpmt/structalign.html and see if one fits
> your situation. Of course, if you're just looking for a few values, PyMol's
> Measurement Wizard is a low-tech way to get a few distances.
>
> Sorry if this isn't too helpful, but without knowing more about your
> situation it's difficult to make recommendations.
>
> Cheers,
>
> Shane Caldwell
> McGill University
>
> On Sun, Jan 18, 2015 at 9:12 PM, Schubert, Carsten [JRDUS]
> <cschu...@its.jnj.com> wrote:
> 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 match structurally
> superimposed CA's besides a distance criterion, which does not seem to be to
> reliable in the case of large deviations. I tried to snoop around in the
> alignment object created by the align command, but did not make much inroads.
>
> Anyone have any experience with this?
>
> Thanks
> Carsten
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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