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. ------------------------------------------------------------------------------ New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
