Dear Pymol Users!
I am working on the visualization of the ligand binding poses
predicted by protein-ligand docking. Having 88 solutions I split these
states into different states and then set transparency=0.8 to each of
them, in order to visualize them as the "cloud" of the conformational
space of
Dear Pymol Users!
Is it possible to visualize protein-ligand interactions (which
normally is achieved in GUI via a - > present -> ligand sites
using some combination of the pymol commands, which could be scripted
using cmd. syntax ?
I've found this explanation
https://pymolwiki.org/index.php/Displa
Thank you very much Jared!
Could you tell me if you have some cool present for the surface
representations ?
For example I am using the following script to visualize the surface
of the protein around the ligand binding site:
cmd.show('surface', 'polymer within 15 of complex* and not polymer')
cmd
Dear Pymol users!
Here is the chain of the pymol commands that I am using to label the
visible amino-acids shown as lines in the current pymol session.
cmd.select('name CA and rep lines')
cmd.label('sele', 'resn')
cmd.set('label_font_id', '14')
cmd.set('label_color', 'indigo')
cmd.set('label_positi
I've just found the list of the presets:
https://pymolwiki.org/index.php/Preset
so a new question is still about preset.ligand_cartoon.
It works well, but shows me too much information. Is it possible to
limit the set of the identified residues e.g. to indicating only the
residues involved in the
