[PyMOL] sampling from the protein data bank

I'm looking for a python script to sample from the entire pdb. I want to select pdb's with a certain attribute, or rule out a certain attribute, for example membrane proteins. I also want to rule out pdb's that have metal atoms in them. I would appreciate all of your help. Sincerest regards.

[PyMOL] get area as a sequence area pair

I have used the script in example 4 here https://pymolwiki.org/index.php/Get_Area to get the areas for a certain pdb. I want to be able to distinguish though which residue has which area. I can get the sequence using get_fastastr, but I want to modify the above script to iterate over the sequence

[PyMOL] Calculating center of mass for the entire protein

I find the documentation about the python api here to be a bit lacking. https://pymolwiki.org/index.php/Centerofmass I would appreciate more info on how to use this: cmd.centerofmass() returns a list of 3 floats. -- Check

Re: [PyMOL] Calculating center of mass for the entire protein

ass as a list of > 3 floats, presumably in that order? > > Is there another question? The page describes the arguments and their > defaults so I am unsure what is lacking. > > -David > > On Apr 5, 2017, at 10:29 PM, Ahmad Abdelzaher > wrote: > > I find the docume

Re: [PyMOL] Calculating center of mass for the entire protein

with a selection. > E.g.: > > x,y,z = cmd.centerofmass('byres n. ca') > print "COM of protein:", x, y, z > > Hope it helps, > > Tsjerk > > On Thu, Apr 6, 2017 at 6:30 AM, Ahmad Abdelzaher > wrote: > >> Well I'm assuming the selectio

Re: [PyMOL] Calculating center of mass for the entire protein

every > command in pymol operates on selections, so it is a fundamental concept you > should spend time to understand if you are planning to use pymol. > > https://pymolwiki.org/index.php/Category:Selecting > > > On Thu, Apr 6, 2017 at 1:13 AM, Ahmad Abdelzaher > wrote: >

Re: [PyMOL] Calculating center of mass for the entire protein

I don't fully get what you mean, however, with or without the .pdb, I get the same error. On Thu, Apr 6, 2017 at 3:28 PM, João M. Damas wrote: > When you do the load, the .pdb is stripped off. The selection is 1a5m and > not 1a5m.pdb > > On Thu, Apr 6, 2017 at 3:18 PM, Ahmad Ab

Re: [PyMOL] Calculating center of mass for the entire protein

te: >> >> When you do the load, the .pdb is stripped off. The selection is >> 1a5m and not 1a5m.pdb >> >> On Thu, Apr 6, 2017 at 3:18 PM, Ahmad Abdelzaher >> mailto:underoath...@gmail.com>> wrote: >> >> In the documentation, it

Re: [PyMOL] Calculating center of mass for the entire protein

Script > > Cheers, > Thomas > > On 06 Apr 2017, at 16:01, Ahmad Abdelzaher wrote: > >> I did remove it. I get the same error. >> >> Regards. >> >> On Thu, Apr 6, 2017 at 3:59 PM, Jed Goldstone wrote: >> centerofmass 1a5m >> works j

Re: [PyMOL] which PyMOL to open?

That's not a dumb question AJ. I have been using Pymol for a while and I haven't got a clue. :D On Fri, Apr 21, 2017 at 8:15 PM, AJ Vincelli wrote: > Hello all, > > I hate to ask a dumb question, but I need some seriously novice help. I > just installed educational-use-only PyMOL (version 1.7.4.

[PyMOL] get_area algorithm and dot_density accuracy

Hello, Does the get_area command use the rolling ball algorithm? Which dot_density corresponds to the best accuracy 1 or 4? Is there a reason why it consumes more time to compute sasa? Dssp takes significantly less time to do the calculations, however compared to Pymol dot_density of 3, the areas

Re: [PyMOL] get_area algorithm and dot_density accuracy

I would appreciate any help regarding this. On Tue, Apr 25, 2017 at 12:36 PM, Ahmad Abdelzaher wrote: > Hello, > > Does the get_area command use the rolling ball algorithm? Which > dot_density corresponds to the best accuracy 1 or 4? Is there a reason > why it consumes more time

Re: [PyMOL] get_area algorithm and dot_density accuracy

differences in the algorithm > used to calculate the SASA. The speed differences could be the result > of different algorithms and how they are implemented. > > You might want to check out FreeSASA ( http://freesasa.github.io ) to > perform your SASA calculations. > > Emilio >

[PyMOL] Using API to select resi, and return some information within a certain distance

Hello, I'm still a bit new to the API so I'm not sure which commands to use. At least I know I will start with cmd.select(string name, string selection). How can I tell Pymol to: 1) look within a certain radius distance, and return resi's within that distacne. 2) find all polar interactions wit

Re: [PyMOL] Using API to select resi, and return some information within a certain distance

Thanks Jared. A lot of fantastic tips there. Much appreciated. Regards. On Sat, Apr 29, 2017 at 6:03 AM, Jared Sampson wrote: > Hi Ahmad - > > Here are a few suggestions: > > I'm still a bit new to the API so I'm not sure which commands to use. > At least I know I will start with cmd.select(stri

Re: [PyMOL] Using API to select resi, and return some information within a certain distance

I forgot to ask, how to retrieve residues within my selection to a list or something. Also, what does cmd.get_pdbstr do? On Mon, May 1, 2017 at 10:54 PM, Ahmad Abdelzaher wrote: > OK I finally tried some of Jared suggestions, I'm not sure why > util.cnc doesn't work I get "

Re: [PyMOL] Using API to select resi, and return some information within a certain distance

(bare_name, resname, resnumber)) cmd.hide('everything', 'all and not %s_%s%s' % (bare_name, resname, resnumber)) cmd.zoom('%s_%s%s' % (bare_name, resname, resnumber), 5) cmd.png('%s_%s%s.png' % (bare_name, resname, resnumber), ray=1) On

[PyMOL] Is there a way to "count" hydrogen bond interactions?

I know I can can find the hydrogen bond interactions between a selection and surrounding residues within a certain radius. I would like to find a way to retrieve the actual count of those interactions per residue. How can I do it in the API? Regards. --

[PyMOL] Why does Pymol display the chain as disconnected?

http://www.rcsb.org/pdb/explore.do?structureId=1ax8 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot_

[PyMOL] Installing Edupymol on centos 7

I just downloaded the free Edupymol version, EduPyMOL-v1.7.4.5-Linux-x86_64.tar.bz2. I untarred using tar -xvjf EduPyMOL-v1.7.4.5-Linux-x86_64.tar.bz2. Now I have a folder called pymol with the following files / directories: data examples ext modules pymol pymol.exe scripts setup.sh Ho

Re: [PyMOL] Installing Edupymol on centos 7

why you don't use PyMOL 2.0 instead? We do provide an > edu license file for PyMOL 2.0 on the Edu PyMOL download page. > > Cheers, > Thomas > > > On Nov 5, 2017, at 11:49 PM, Ahmad Abdelzaher > wrote: > > > > I just downloaded the free Edupymol version, E

[PyMOL] Editing PDB to remove flexible loop

Hello, Is there a way to keep the sequence of structure, but remove the modelling of some flexible loop? Meaning, Pymol should show the entire sequence, but the strcuture should not show this sequence. A side question, how else can I compare two structures in Pymol besides aligning them and compa

[PyMOL] Installing Pymol API on linux for Anaconda Python 3.5

*Hello,* *I'm trying to nstall the Pymol API on linux for Anaconda Python 3.5. * *I tried the commands here: https://anaconda.org/schrodinger/pymol , this is what I got. * *I would appreciate if someone helps me install it.* *[labusr@luxor Downloads]$ con