[PyMOL] Placing pseudo atom on COM and saving it as pdb

Hi There, I am looking to automate the calculation of centre of mass and placing a pseudo atom on the COM and save it as a pdb file . Going through the forum [ https://sourceforge.net/p/pymol/mailman/message/34458943/] , I found some useful scripts for this, but, I am having trouble getting it don

Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

#x27;).readlines(): > pdb = pdb.strip() > cmd.load(pdb,'tmp') > cmd.pseudoatom('tmp',name='pseudo') > cmd.save(pdb[:-4]+'-pseudo.pdb','pseudo') > cmd.delete('tmp') > cmd.delete('pseudo')

Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

ot name='pseudo'. > Should've tested it first. > > Cheers, > > Tsjerk > > On Wed, Oct 12, 2016 at 9:56 PM, Subha K wrote: > >> Thanks David and Tsjerk for the kind reply and suggestion. >> >> I Figured a solution by combining both of your sugges

[PyMOL] Iterating through all objects and calculate RMS

Hi There, I am trying to calculate the rmsd of all ligands loaded in the pymol with reference to a reference ligand using a script. My current script looks like this, myobjects = cmd.get_object_list() print myobjects cmd.select('sele', "F60_target_14 and resn UNK") cmd.create('obj01', 'sele')

Re: [PyMOL] Iterating through all objects and calculate RMS

Regards, > Gabriel Marques > > On Oct 18, 2016, at 1:57 PM, Subha K wrote: > > Hi There, > > I am trying to calculate the rmsd of all ligands loaded in the pymol with > reference to a reference ligand using a script. My current script looks > like this, > > &g

[PyMOL] problem saving the transformed coordinate after alignment

Hi there, I am trying to save the transformed coordinates of an object after performing an alignment. I came across the save_transformed.py [ https://pymolwiki.org/index.php/Modeling_and_Editing_Structures], but, this seems to give a completely different coordinate of the object and not the one th

Re: [PyMOL] problem saving the transformed coordinate after alignment

Thanks Gabriel and David for the useful suggestion. Best Regards, Subha On Wed, Oct 19, 2016 at 12:11 PM, David Hall wrote: > I think the answer is to just use save, not that save_transformed function. > > -David > > On Oct 19, 2016, at 1:47 PM, Subha K wrote: > > Hi ther

[PyMOL] loading a file whose name is stored in a variable

Hi there, If the base name of my file is stored in a variable, how can I load the file using the variable? Eg., My filename is "File10.pdb" and I have, X = File10 I tried loading it using, cmd.load ( X+".pdb", X), but it doesn't seem to work. Sorry for posting a very basic question. Thanks, Su

Re: [PyMOL] loading a file whose name is stored in a variable

t.py command. > > Regards, > Gabriel Marques > > > > On Oct 20, 2016, at 1:06 PM, Subha K wrote: > > > > Hi there, > > > > If the base name of my file is stored in a variable, how can I load the > file using the variable? > > > > Eg., My file

[PyMOL] Pair_fit syntax

Hi there, Could somebody please help me with the correct syntax for pair fit? I tried this, but this doesn't work. pairfit (obj2 and resi 256-510), (onj1 and resi 1-255), [(obj2 and resi 1-255), (obj1 and resi 256-510), [(obj2 and resi 766-1020), (obj1 and resi 511-765), [(obj2 and resi 511-765)

Re: [PyMOL] Pair_fit syntax

020/CA, /obj1///511-765/CA, > /obj2///511-765/CA, /obj1///766-1020/CA > > Note that if you have any missing residues you might get an error 'Atom > counts between selection sets don't match'. In this case you should make > sure that the obj2 selections have the same number

[PyMOL] Atom Order when Saving

Hi There, Just wondering if there is a way to have the same order of atoms (with that of the initial loaded file) while saving a pdb file with pymol? I came across an old post on this [ https://sourceforge.net/p/pymol/mailman/message/7561093/] and not sure if there is a direct way now to do this.

Re: [PyMOL] Atom Order when Saving

Great! Thanks heaps. Subha On Mon, Nov 14, 2016 at 1:06 PM, David Hall wrote: > https://pymolwiki.org/index.php/Retain_order > > > On Nov 14, 2016, at 3:04 PM, Subha K wrote: > > Hi There, > > Just wondering if there is a way to have the same order of atoms (with >