Re: [PyMOL] hydrogen bond list for a series of files

Thanks, Dr. Mooers. I modified a little. It seems the pdb files need be loaded. I put all the following lines in a file multifile_hb.pml run C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py import glob load

Re: [PyMOL] hydrogen bond list for a series of files

Hi Charles, Make sure that PyMOL's present working directory is where the pdb files are stored. Copy and paste each of the four lines below one at a time on the command line in PyMOL. run list_hb.py import glob chains = [('A','B'), ('A','C'), ('A','D'), ('A','E'), ('B','C'), ('B','D'),

Re: [PyMOL] renumber

Thank you Jared. From: Jared Sampson Sent: Monday, June 15, 2020 4:47 PM To: Oganesyan, Vaheh Cc: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] renumber Hi Vaheh - I wasn't saying it can't be done, just that pdbset is my preferred way to handle renumbering when going in the

Re: [PyMOL] renumber

Hi Vaheh -  I wasn't saying it can't be done, just that pdbset is my preferred way to handle renumbering when going in the insertion code --> integer direction. Within PyMOL, here is one way (you'll have to repeat for each chain you wish to renumber): ``` # see: 

Re: [PyMOL] renumber

Hi Vaheh, I susoect that your issue is an edge case for PyMOL. The resi variable is limited to integers (see https://pymolwiki.org/index.php/Property_Selectors). Atoms with letters in the resi field are invisible to PyMOL. You could write a python script to preprocess the coordinates, run the

[PyMOL] hydrogen bond list for a series of files

Hi, Pymol users Could you help me do this in an efficient way? Let me describe the task I try to do. I have a series of numerically ordered files, say model00.pdb model.01.pdb …… model.30.pdb All the pdb have the same protein composition, chain A, B, C, D, and E. Their relative position is

Re: [PyMOL] renumber (Oganesyan, Vaheh)

Coot is also an option. CCP4 is much better/flexible though. > On Jun 15, 2020, at 3:57 PM, pymol-users-requ...@lists.sourceforge.net wrote: > > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit

Re: [PyMOL] renumber

Jared, Are you saying it cannot be done within PyMOL? The ccp4 option is well known. Thanks. From: Jared Sampson Sent: Monday, June 15, 2020 2:41 PM To: Oganesyan, Vaheh Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] renumber Hi Vaheh - Try `pdbset` from the CCP4 suite.

Re: [PyMOL] renumber

Hi Vaheh - Try `pdbset` from the CCP4 suite. http://www.ccp4.ac.uk/html/pdbset.html#renumber ``` pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF renum 1 chain H renum 1 chain L end EOF ``` Hope that helps. Cheers, Jared From: Oganesyan, Vaheh Reply: Oganesyan, Vaheh Date: June 15,

Re: [PyMOL] renumber

Hi Vaheh, Thank you for the clarification. There are at least five numbering schemes (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198058). Which one are you following? Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of

Re: [PyMOL] renumber

Blain, The command will not change the numbering of amino acids starting from #1. But if you got missing ones, like in my case, it will. Except for those having also letter in the number field. I mean the numbering used for CDRs of antibodies, not alternatives. Hence, my question, is there a

Re: [PyMOL] renumber

Hi Vaheh, alter vh, resi=str(int(resi)+0) will not change the residue numbers because 0 is being added. Replace 0 with your desired residue number offset. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine

Re: [PyMOL] renumber

Thank you Jarrett, Then the command alter vh, resi=str(int(resi)+0) should work, right? But it doesn’t because there are residue numbers with letters. Is there a command that will either remove the letters or won’t pay attention to them and renumber sequentially. Regards, From: Jarrett

Re: [PyMOL] renumber

Hello, The command shown on this page https://pymolwiki.org/index.php/Renumber is not one that comes with PyMOL by default. Try downloading the script and importing it via the `run` command in the PyMOL command-line: *run renumber.py* and then you should be able to use the command as shown on

[PyMOL] renumber

Hello PyMOLers, Wiki uses renumber command to alter residue numbers, but PyMOL doesn't recognize it. Is it that Wiki is old, or my PyMOL version is dusty? Regards, Vaheh ___ PyMOL-users mailing list Archives:

Re: [PyMOL] User data

Hi Pedro, There is no designated infrastructure for this. Other plugins typically create their own directory in the user's home folder, like "~/.myplugindata". You could also create it inside the "~/.pymol" directory (like "~/.pymol/myplugindata"). This works on all platforms:

Re: [PyMOL] APBS plugin for Sugars

Hi Mario, Incentive PyMOL 2.x includes regular APBS and PDB2QPR. You should be able to manually edit the files there as well. For example with PyMOL 2.4.0 on Linux, the AMBER force field data files can be found like this: $ find . -name "AMBER.*"