Re: [PyMOL] Fit command for 24 vs 18 amino acids

Renuka, In this case the 'fit' command is detecting the residues that are common between your two sequences and fitting those. The operator in question here is "in". You can select atoms from one chain that are "in" another. For example, # load your two proteins p and q, then select the # resi

[PyMOL] Fit command for 24 vs 18 amino acids

I have binding site of two homologous crystallographic structures. PDB_01 contains 24 amino acids: Leu44, Gly45, Phe49, Val52, Ala65, Lys67, Glu89, Ile104, Leu120, Glu121, Arg122, Pro123, Val126, Asp128, Asp131, Glu171,

Re: Subject: Re: [PyMOL] fit command

Andre, * tree [2005-06-20 23:31] wrote: > > The Wiki (http://www.pymolwiki.org/) has some information about this. > It also shows you how to change some properties to make things easier to > fit. > > Intra_Rms (http://www.pymolwiki.org/index.php/Intra_Rms), and Fit > (http://www.pymolwiki.org/i

Subject: Re: [PyMOL] fit command

, -- Jason On Mon, 2005-06-20 at 20:13 -0700, pymol-users-requ...@lists.sourceforge.net wrote: > Message: 5 > Date: Mon, 20 Jun 2005 12:04:51 + > From: Andrea Spitaleri > Reply-To: Andrea Spitaleri > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] fit command >

Re: [PyMOL] fit command

> Fit only works with objects that are identical in terms of atom number, > chainID, atom name and what not. This is not the case for a protein on > one side and a protein plus ligand on the other. I've gotten away with some differences between chains. Sometimes you need to force it to fit using

Re: [PyMOL] fit command

Fit only works with objects that are identical in terms of atom number, chainID, atom name and what not. This is not the case for a protein on one side and a protein plus ligand on the other. Andreas > Thanks, > it worked. > So why fit did fail in doing that? -- --> Andreas Förster

Re: [PyMOL] fit command

Andrea Spitaleri wrote: Thanks, it worked. So why fit did fail in doing that? Well, I will leave it to some experts. I did spend sometime trying to understand that, but couldn't. I am still learning pymol!:)) -- :-) Ramesh K. Sistla May the wicked become good, may the good attain peace M

Re: [PyMOL] fit command

Thanks, it worked. So why fit did fail in doing that? Regards andre 2005/6/20, Ramesh Sistla : > Andrea Spitaleri wrote: > > Hi all, > > i have got two pdb files, ref.pdb and docked.pdb, where ref.pdb > > contains the protein A and docked.pdb the protein A + a docked ligand. > > when I try to r

Re: [PyMOL] fit command

Andrea Spitaleri wrote: Hi all, i have got two pdb files, ref.pdb and docked.pdb, where ref.pdb contains the protein A and docked.pdb the protein A + a docked ligand. when I try to run fit ref, docked I get: ExecutiveRMS-Error: No atoms selected. I tried to select the atoms or create a new object

[PyMOL] fit command

Hi all, i have got two pdb files, ref.pdb and docked.pdb, where ref.pdb contains the protein A and docked.pdb the protein A + a docked ligand. when I try to run fit ref, docked I get: ExecutiveRMS-Error: No atoms selected. I tried to select the atoms or create a new object but i get the same result