try this man!
awk 'NR==FNR {s = s $0 ORS; next} $0 == "ENDMDL" {$0 = s $0} 1'
./receptor.pdb ./docking.pdb >> together.pdb
пт, 7 янв. 2022 г. в 18:10, Saurabh Gayali :
> I guess we need to split the docking poses first and then merge them
> together.
> Hope I come up with a python script or
Dear Pymol users!
Working on the vizualisation of the protein-ligand interactions I
would like to switch from cartoon to the surface representation of the
protein, while still being capable to see the ligand-binding cavity
(as well as non-covalent interactions)
Could you suggest me some
Hi Enrico,
You can carve the protein surface around the ligand, i.e. show only the surface
behind the ligand, see this guide:
https://pymol.org/dokuwiki/doku.php?id=figure:carving_surfaces
You can also try and made the surface more transparent, but this doesn't always
give the best results,
Thank you very much,Ali!
just one question: when I do the surface calculations using bash
script operating with the command lines of the pymol it produces
correctly pse session with the surfaces. BUT if I save an image using
png, the surface is totally absent. Here are my commands directly from
Hi Enrico,
This is beyond my understanding, try and run this bash script without making
the surface transparent (to figure out if the issue comes from the transparency)
Also try the rebuild command before saving the image:
https://pymolwiki.org/index.php/Rebuild
Cheers,
Ali
Ali Kusay |
Hi Enrico,
You do not need the first line of your script.
This one-liner worked for me in the terminal.
pymol -c -d
"cmd.fetch('3nd3');cmd.show('surface');cmd.set('transparency','0.5');cmd.save('surf.pse');cmd.png('surf.png')"
You might test reversing the order of the cmd.png() and
Right, thank you, Blaine!
It works very well now! Actually there was a problem in the selection
from my part so..
I will play with the surfaces a little bit and then will update this
topic with my questions :-)
Cheers,
Enrico
пн, 10 янв. 2022 г. в 16:25, Mooers, Blaine H.M. (HSC)
:
>
> Hi Enrico,
