Re: [PyMOL] Superimpose small non-protein molecules?

Looks like PymolWiki is down. On Tue, May 5, 2015 at 1:59 PM, Osvaldo Martin wrote: > Hi Jorge, > > You are right align is only for proteins. You can use the Fit > command > > Cheers, > Osvaldo. > > On Tue, May 5, 2015 at 3:38 PM, Jorge Fernandez de Cossi

Re: [PyMOL] Superimpose small non-protein molecules?

Hi Jorge, You are right align is only for proteins. You can use the Fit command Cheers, Osvaldo. On Tue, May 5, 2015 at 3:38 PM, Jorge Fernandez de Cossio Diaz < cos...@cim.sld.cu> wrote: How can I superimpose two small non-protein molecules in PyMol? I

Re: [PyMOL] superimpose option

Just to quickly add... probably the easiest way to run CE at the present might be through the new protein comparison tool at RCSB-PDB web site: http://www.rcsb.org/pdb/workbench/workbench.do Andreas On Tue, Dec 8, 2009 at 8:12 AM, Michael Zimmermann wrote: > Dr. Vertrees, thank you for the th

Re: [PyMOL] superimpose option

Michael, You are correct. Users can just download the CE program and use that. The CEAlign that I was talking about is a C++ extension that I wrote just for PyMOL. It plugs directly into the PyMOL system so you can just type: cealign protA, protB and the proteins are aligned and the results a

Re: [PyMOL] superimpose option

Dr. Vertrees, thank you for the thorough reply to Saeid's question. I just wanted to note that you don't have to install all of PyMol from source to use CE. You can set up CE and just run it when you want it, like other python add-ons. That might not be the case for the most recent version thoug

Re: [PyMOL] superimpose option

Saeid, If you know exactly which atoms in protein A are to be paired with atoms in protein B, then this is "fitting" and PyMOL can do it with the "fit" family of commands. In PyMOL type, "help fit" to get help and "fit ?" for fit's syntax. (A neat trick in PyMOL: "commandName ?" will show you in

Re: [PyMOL] superimpose option

Hey Saeid, use the 'super' command. Type super protein1, protein2 For more information, check teh wiki. Andreas On Tue, Dec 8, 2009 at 7:07 AM, saeid mirzaei wrote: > Hi everyone, > > could some one tell me I can use Pymol for superimposing two protein or not > if so how can I use it? >

Re: [PyMOL] Superimpose

Hi Michael, I notiuced no-one has posted anything so here goes. Start with align 1abc, 1target which will superimpose 1abc onto 1target then from here you can select the non homologous regions (using display sequence and highlight from here and colour to your hearts content. I'm sure there are

RE: [PyMOL] superimpose

Michael, The 'fit' command will do atom-for-atom RMS alignments, but all atom attributes must match within each object (segment, chain, residue id, residue name, atom name, etc.) for this to succeed. As a result, the 'fit' command can be tricky to use. Several 'alter' commands and a 'sort', a