Hi Dimitry if you add an "object=<some name>" to your align command, then the sequences are shown correctly aligned. The residues used in the alignment are shown in their normal colors, the excluded onses are shown in gray, eg:
align obj01////CA, obj02////CA, object=alignment I think you should be able to save the alignment by this command: save alignment.aln, alignment Best Regards Esben Peter Friis Research Scientist Novozymes A/S Krogshoejvej 36 2880 Bagsvaerd Denmark Phone: +45 44461334 E-mail: e...@novozymes.com Novozymes A/S (reg. no.: 10007127). Registered address: Krogshoejvej 36 DK-2880 Bagsvaerd, Denmark This e-mail (including any attachments) is for the intended addressee(s) only and may contain confidential and/or proprietary information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information herein is strictly prohibited. If you are not an intended recipient you should delete this e-mail immediately. Thank you. -----Original Message----- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of DimitryASuplatov Sent: 22. august 2008 12:40 To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Sequence alignment editing Hello, I have two structures of related organisms. I want to align them in 3D with pymol and be able to view their sequences aligned as well (corresponding to structure alignment). Right now when using Display->Sequence mode sequences are displayed simply 'as is' even after 3D 'align' command. Could something be done? Thanks. Thanks! SDA. ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
