Hi James, paste the following piece of code into the PyMOL command line. It does more or less the same as "A > align > all to this" but with "super" instead of "align".
names = cmd.get_object_list() for name in names[1:]: cmd.super(name, names[0], object='aln') The first object in the list will be used as reference structure. The "aln" object which will be created represents the "all to reference" alignment. Cheers, Thomas James Starlight wrote, On 11/22/11 10:11: > By the way also I've tried use super_all script wich can do multiple > alignment via Super command > pldserver1.biochem.queensu.ca/~rlc/work/ > <http://pldserver1.biochem.queensu.ca/~rlc/work/>pymol/super_all.py > > but as the consequense the resulted sequence alignment in CGO in > pair-wise manner. How could I make something like this super all but for > just one reference ( similar to the align ) so I'd like to obtain > multiple sequence alignment on one reference based on the multiple > structure alignment. > > Thanks > > James > > 2011/11/21 James Starlight <jmsstarli...@gmail.com > <mailto:jmsstarli...@gmail.com>> > > Jason, > > but as I've understood super did alignment only for two structures, > Is there any way to do the same operation for ensemble ? (for CE as > I understood this could be done by alignto command but it lack for > seq alignment iin this case) > > > > James > > 2011/11/21 Jason Vertrees <jason.vertr...@schrodinger.com > <mailto:jason.vertr...@schrodinger.com>> > > Hi James, > > > set fetch_host, pdbe > > Your PyMOL looks to be outdated. This was added to the > open-source in > v1.3r1, I think. > > > By the way could you also help me with the alignment of my > structure ( I've > > posted this question today at this topic). I think that I > should use the > > combination of the structure alignment ( like CEalign) with > the common seq. > > alignment but I dont know exactly how :( > > You should use the 'cealign' or 'super' commands to do this. Cealign > uses only structure, whereas 'super' uses both structure and > sequence. > Please continue to post questions like this to the list for best > results: there are some very smart people on our PyMOL list. > > Cheers, > > -- Jason -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ 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
