Menu
▾
▴
Re: [PyMOL] about super_all.py Plugin installation.
|
From: PAVAN P. <pav...@gm...> - 2011-12-30 06:21:15
|
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 On Fri, Dec 30, 2011 at 2:15 AM, Thomas Holder < sp...@us...> wrote: > 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/Align> > http://pymolwiki.org/index.**php/Cealign<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 <zj...@ma... <mailto: >> zj...@ma...>**> 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> >> <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 >> <sp...@us... >> <mailto:speleo3@users.**sourceforge.net<sp...@us...> >> > >> <mailto:speleo3@users.**sourceforge.net<sp...@us...> >> >> <mailto:speleo3@users.**sourceforge.net<sp...@us...>>>> >> 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 > |
