Re: [PyMOL] H-bonds representation

Thanks Jason. It works quite well in case of not very compliated ligands ( e.g bonds beetween aa-tRNA and the aa-tRNA syntase were correct ) but in the sugar-bound enzyme there were some mistakes in representation of the H-bonds netween water/ligand/active center ( some water also partisipate in

Re: [PyMOL] ray - volume

Hi David, > Since I happen to be playing with volumes right now, I tried that and > it causes my sticks to pop out of the volumes (see attached).  This is > on a build of the latest open source code in SVN. You have found the reason why this isn't turned on by default. There are still some proble

Re: [PyMOL] ray - volume

On Wed, Nov 30, 2011 at 12:25 AM, Jason Vertrees wrote: > Hi David, > > Are your data and color ramp points correct? If you send me the data, > I can double-check what we've done. I am also confusing how to put the quasi-center of volume on some certain atom. Even I only chose one atom, but the

Re: [PyMOL] ray - volume

Hi David, Are your data and color ramp points correct? If you send me the data, I can double-check what we've done. Cheers, -- Jason On Tue, Nov 29, 2011 at 10:56 AM, David Hall wrote: > Since I happen to be playing with volumes right now, I tried that and > it causes my sticks to pop out of t

Re: [PyMOL] ray - volume

On Tue, Nov 29, 2011 at 11:56 PM, David Hall wrote: > Since I happen to be playing with volumes right now, I tried that and > it causes my sticks to pop out of the volumes (see attached).  This is > on a build of the latest open source code in SVN. Thanks for confirmation. There are some unmet d

Re: [PyMOL] Get number of residues in model

Hi Martin, Here's a fourth option (and the technique worth noting :p ): print len( set( [(i.chain,i.resi,i.resn) for i in cmd.get_model(selection).atom] ) ) Cheers, Tsjerk On Tue, Nov 29, 2011 at 4:26 PM, Jason Vertrees wrote: > Hi Martin, > > You get three options: > > (1) You can count alph

Re: [PyMOL] ray - volume

On Tue, Nov 29, 2011 at 11:34 PM, Jason Vertrees wrote: > Hi Lina, > > set ray_volume, on Thanks, is the ray_volume some new feature in latest version? seems Version 1.4. no ray_volume feature. Best regards, > > Cheers, > > -- Jason > > On Tue, Nov 29, 2011 at 10:27 AM, lina wrote: >> Hi, >> >

Re: [PyMOL] ray - volume

Hi Lina, set ray_volume, on Cheers, -- Jason On Tue, Nov 29, 2011 at 10:27 AM, lina wrote: > Hi, > > a quick question, how to keep the volume during ray. > > the volume is here, > > but after ray, > > it's gone, > > what's kinda of special settings I need to take care? > > Thanks with best reg

[PyMOL] ray - volume

Hi, a quick question, how to keep the volume during ray. the volume is here, but after ray, it's gone, what's kinda of special settings I need to take care? Thanks with best regards, -- All the data continuously gene

Re: [PyMOL] Get number of residues in model

Hi Martin, You get three options: (1) You can count alpha carbons: fetch 1rx1, async=0 count_atoms n. CA (2) But, a protein could be missing alpha carbons then this is more complete (and the technique worth noting): n=0 select qq, polymer select pp, None python while cmd.count_atoms("qq"):

[PyMOL] Get number of residues in model

Dear List How can I compute the numbers of residues in a model? Martin -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threat

Re: [PyMOL] H-bonds representation

James, > Is there any semi-avtomated way to find ligand binding pocket and do all > such things ? For your given object, click A > preset > ligands sites > cartoon. Try other options under that menu. Cheers, -- Jason > 2011/11/28 Thomas Holder >> >> Hi James, >> >> most trivial manner: >> >>

Re: [PyMOL] H-bonds representation

Thanks, Thomas, Jason both of the methods are useable :) By the way I've forced with the problem of the representation of the active sites of different enzymes. I need to view all my protein as the cartoons and the ligand as the shpere in the ligand binding pocket. Besides I need to mark residues

Re: [PyMOL] RMSD between two structures

Hi Martin, It should be RMSD indeed. Mind that the final RMSD from align is obtained after optimizing the fit by leaving out outliers. Cheers, Tsjerk On Nov 29, 2011 10:07 AM, "Martin Hediger" wrote: Is the RMS the same as RMSD? PyMOL writes "RMS" when using align. Martin Am 11.11.11 14:

Re: [PyMOL] RMSD between two structures

Is the RMS the same as RMSD? PyMOL writes "RMS" when using align. Martin Am 11.11.11 14:59, schrieb Thomas Holder: > Hi Martin, > > is it the transform=0 argument what you are looking for? > > http://pymolwiki.org/index.php/Align#PYMOL_API > > x = cmd.align('foo', 'bar', transform=0) > print '