PAVAN PAYGHAN wrote, On 12/29/11 13:23: > Dear , > > "A > align > all to this" and "alignto" both are the same or different? > If different in what context.
It's different. The first method uses "align" and gives you an alignment object (uses util.mass_align function). The second uses "cealign" and cannot make an alignment object. http://pymolwiki.org/index.php/Align http://pymolwiki.org/index.php/Cealign "align" does sequence based alignment and RMSD minimization, "cealign" is a more sophisticated structure based alignment. Cheers, Thomas > Pavan Payghan > > > On Thu, Dec 29, 2011 at 4:23 PM, zjxu <z...@mail.shcnc.ac.cn > <mailto:z...@mail.shcnc.ac.cn>> wrote: > > Dear Pavan, > > > align 4-5 structures at a time (with low sequence identity). > > check cealign: http://www.pymolwiki.org/index.php/Cealign > <http://www.pymolwiki.org/index.php/Cealign> > > In pymol1.4, you could use 'alignto': > PyMOL>help alignto > DESCRIPTION > NOTE: This feature is experimental and unsuspported. > "alignto" aligns all other loaded objects to the given selected object > using the CEalign algorithm. > USAGE > alignto target [, quiet ] > EXAMPLE > # fetch some calmodulins > fetch 1cll 1sra 1ggz 1k95, async=0 > alignto 1cll > > Hope this helps, > > Zhijian Xu > > > PAVAN PAYGHAN wrote: > > > Dear, > > > Thanks a lot for the information. As you mentioned super is only > for aligning two structures while with super_all to align the > multiple structures, but the most important thing is to obtain > the alignment file out of all this excercise, can it be possible > with super, super_all? > > If not which option exist in Pymol wherein one can align 4-5 > structures at a time (with low sequence identity). > > > Pavan Payghan > > > > On Wed, Dec 28, 2011 at 6:11 PM, Thomas Holder > <spel...@users.sourceforge.net > <mailto:spel...@users.sourceforge.net> > <mailto:spel...@users.sourceforge.net > <mailto:spel...@users.sourceforge.net>>> wrote: > > Hi Pavan, > > > Thank you very much for the modified script. > > Its working fine, only thing I am facing is that it can > not be > used for aligning more than two structures at a time(I > want it > for around 4 -5 structure alignment). The command used to do > so is > > super abc,def,XYZ > > > "super" is for two structures, "super_all" (from the script) is > for many structures. But the syntax is without comma in mobile > selection: > > super_all abc, def ghi jkl > > for the third structure its giving error like ,ValueError: > invalid literal for float (): XYZ. > > Apart form this could you please explain > > 1. Number of alignment residues should match exactly in > all the > structures. > > > you can't influence this with super_all. > > 2. How to get alignment file for super, super_all > command after > alignment has been done. > > > this is not possible with super_all. > > But PyMOL can do this even without the super_all script. On the > button-panel to the right, try: "A > align > all to this" > > You'll get an new object called like "aln_all_to_XYZ", this you > can save: > > save file.aln, aln_all_to_XYZ > > > > Cheers, > Thomas > > -- Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen -- 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
