Re: [PyMOL] APBS plugin for Sugars

Thank you so much for your quick answer! Now I can access the file and I was wondering how to get amber data for specific molecules. I know that the GLYCAM parameters exist, but as far as I understand I can see only bond information. If, for alanine, the amber.dat file has the following: ALA

Re: [PyMOL] Effect of different align method

Hello Julien Cappèle, Thank you for your response. I didn't mean to keep the input file in secrete. I have changed the access right to them, so you can download them freely. Best, Yeping Sun -- From:Julien CAPPELE Sent At:2020

[PyMOL] Install license file from CLI

Hi: I'm working with PyMol installed on a remote server, so I don't have access to the GUI. I already have an educational license. According to your FAQ at https://pymol.org/2/support.html?, the license file should be placed in $HOME/anaconda3/share/pymol/license.lic on a Linux computer. I

[PyMOL] Write the number of molecules for each state in a file

Hello PyMOLers I have PDB file that contains different frames ( or state or models) extracted from a MD simulation and I would like to select the number the water near (say 3.5 Angstroms) a protein for each state and write the results in the file. For instance like this where resid is a list

Re: [PyMOL] Effect of different align method

Hello Sunyeping, I would first point out that if you align on chain A of each molecule, then chain B of ASFV aligns with chain C of MTUB and vice versa. In other words you don't have the same assignment of chain ids in your trimer. The alignment of just alpha carbons of chain A with "align"

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

Hi, I would make one minor change to your script -- the command "run list_hb.py" needs to be run only once at the beginning of the script so: # multiple_hb.py from pymol import cmd from glob import glob cmd.do("run list_hb.py") for file in glob("model.000.*.pdb"): print(file) #file_list =

[PyMOL] Color by index

hello everyone! I am trying to color an explicit distribution by color (say blue to red) pls help me with the command color by index thanks! Vertika Gautam Research Assistant Drug Design and Development Research Group (DDDRG) Department of Chemistry, Faculty of Science University of Malaya

[PyMOL] help

hello everyone! I am trying to color an explicit distribution by color (say blue to red) pls help me with the command color by index thanks! -- Vertika Gautam Research Assistant Drug Design and Development Research Group (DDDRG) Department of Chemistry, Faculty of Science University of