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Results tagged with pymol
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user 10049
A python-based scripting language to visualise 3-D structures, especially of proteins.
0
votes
How to Calculate Delta Phi Psi between aligned pair of residue between Reference and Target ...
I made a test answer showing how to get the delta-phi , delta-psi between two structure aligned with PyMOL, here my code , not sure it is the fastest/cleanest way but only one I could figure out. … from pymol import cmd
from pymol import stored
import time
pymol.finish_launching()
# get two structures
# fetch from remote
cmd.fetch('3hr8 ')
cmd.fetch('3hr8 1xp8')
# load from locale
# cmd.load …
- 1,299
2
votes
Building the structure of the viral capsid from the monomer protein alphafold structure pred...
Try alphafoldserver with your mutated sequences and look for 180 copies
You need tokens though and dont know if it works as
alphafold-multimer does , alphafoldserver should be powered by alphafold3
- 1,299
3
votes
Loop Pymol command get_area
from https://www.blopig.com/blog/2019/08/how-to-iterate-in-pymol/
Example 1: Print the names of all the selected objects
You’ve selected several objects in PyMOL, and you want to see their names. …
- 1,299
1
vote
Loop Pymol command get_area
Ok went back to this question having pymol within a hand's reach this time. … Question is not really clear to me so I am posting a reasonable (to me) version of the question into a new code snippet;
I am using two PDBs containing ATP as ligand '3dgl.pdb', '2p09.pdb'
code:
import pymol …
- 1,299
1
vote
Align two different structures with respect to their active sites or heme cofactor
With PyMOL I tried to use Pair/Pair_fit command with two heme proteins :
2d0t https://www.rcsb.org/structure/2d0t and 4zv8 (https://www.rcsb.org/structure/4ZV8) :
pair hem_2d0t , hem_4zv8, same as pair_fit … Using parKVFinder (https://github.com/LBC-LNBio/parKVFinder , https://www.softxjournal.com/article/S2352-7110(20)30319-8/fulltext) pymol plugin on both proteins stripped of all their HETATM, I calculated …
- 1,299
0
votes
Visualise multiple disappearing pdb files in Pymol
try:
import time
def trial(pathname, num_files):
for i in range(num_files):
filename = (pathname + str(i + 1) +'.pdb')
print(filename)
# print(i)
cmd.load(filena …
- 1,299
1
vote
How can I measure the distance between each pair of carbon alphas in overlayed protein struc...
import math
from pymol import (
cmd ,
stored
)
print('########## PYMOL VERSION #################################### … peptide_2_moved')
cmd.load('peptide_2_moved_CA_alphatoall.pdb' , 'peptide_2_moved_CA_alphatoall')
cmd.spectrum('b', 'rainbow_rev' , 'peptide_2_moved_CA_alphatoall' , '0' , '1')
output:
########## PYMOL …
- 1,299
2
votes
Accepted
how to add a custom elements into PyMOL visualization?
my attempt :
import pymol
from pymol.cgo import *
from pymol import (
cmd ,
)
print('########## PYMOL VERSION ########################## …
- 1,299
1
vote
Accepted
Connecting and merging multiple RNA 3D structures in PyMol/Chimera
in PyMol use, from menu :
File ---> Export Molecule... ---> and before hitting Save
select the molecules you want to save toghether (in the same .pdb file)
with the Selection drop down list either all … (all the loaded mols are saved) or enabled (you can enable the ones you want to be saved toghether)
Examples of Save menu :
For command line see Thread: [PyMOL] independent positioning of two proteins …
- 1,299