Hi, I put a new script on the PyMOLWiki that is more flexible than the other all-to-one solutions:
http://pymolwiki.org/index.php/Extra_fit Cheers, Thomas Thomas Holder wrote, On 12/30/11 10:50: > Dear Pavan, > > I'm sorry that this appears to be so complicated. The "super" command in > PyMOL is structure based (not as good as cealign) and can create > alignment objects. > > The closest solution to your request that I can think of at the moment > is the piece of script below. You can copy-paste this into the PyMOL > command line (including the "python"/"python end" lines). > > python > > # example structures > cmd.fetch('1e4y 1ake 4ake 3hpq', async=0) > > # all to one alignment > target = '1ake' # <-- you can change this > sele = ' and name CA' > models = cmd.get_object_list() > for model in models: > cmd.super(model + sele, target + sele, object='aln') > > # save alignment to file > cmd.save('all-to-one.aln', 'aln') > > python end > > > Hope that helps. > > Cheers, > Thomas > > PAVAN PAYGHAN wrote, On 12/30/11 07:21: >> Dear, >> >> cealign,super,super_all cannot make an alignment object , as the most >> important thing is to obtain >> the alignment file out of all this exercise remains unresolved >> ,Please suggest me structure based alignment method in PyMol wherein I >> can use multiple structures at a time (with low sequence identity) . >> Pavan Payghan -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox _______________________________________________ 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
