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 Malay
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
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" g
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 = [f'{m
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 of
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 already
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 Ju
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