I now know that I can select specific residues to display the "volume data".
Something like `volume mol1-2MGyvol, mol1_2MGy, 1.0 blue .5 2.0 yellow 0,
resname CYS and mol1, 4.0, carve=4.0` works.
>From there I can choose to display the volume à la Fo-Fc
:)
El jue., 26 de jul. de 2018 a la(s) 10:
Dear PyMOL users.
I got a ccp4 difference map and a structure. If I load the structure in
Coot and then load the map (ticking the "Is a difference map" box). Coot
loads the map onto the structure, showing me the holes and peaks in
electron density.
How can I achieve this in PyMOL?
When I open the s
Thanks Marko and Thomas,
It works removing the lines at the end as indicated by Marko. I also
tried for other ligands. Indeed, I have the v1.5.0.5 version. Thanks a lot.
Cheers,
Baptiste
Le 26/07/2018 à 10:32, Marko Hyvonen a écrit :
Hi Thomas
Perhaps this is a Pymol version issue? I just t
Hi Thomas
Perhaps this is a Pymol version issue? I just tried this (with the
second command of yours) with the original coords and get the same
as Baptiste. I tried this on v. 1.8.2 open source Pymol in Win10
laptop.
With the fixed coords I j
Forget my last reply ;-) Marko is right, I didn't notice first because this is
fixed in PyMOL 2.1. Some PDBQT atom types were not imported correctly in
previous versions.
Cheers,
Thomas
> On Jul 26, 2018, at 10:21 AM, Marko Hyvonen wrote:
>
> Hi Baptiste,
>
> removing the data at the end
Hi Baptiste,
These files look good to me, I get:
PyMOL>rms Crystal_Rfp, Vina_Rfp
Executive: RMSD =0.032 (51 to 51 atoms)
Is it possible that you tried with a multi-model (multiple poses) pdbqt file
before? If that's the case, specify "mobile_state" and/or "target_state":
PyMOL>rms Crystal
Hi Baptiste,
removing the data at the end of the HETATM lines from ca.
character 70 onwards fixed it. Not sure what these are. According
to PDB 3.30 format, 67-76 should be empty. Some of the elements
were non-standard also (NA for N, OA for O), but looks
Thanks for your answers. The molecule is the rifampicin. Please find
attached the pdb from the crystal structure and the pdbqt from autodock
vina. May be the format of one or both files is not correct.
Best,
Baptiste
Le 25/07/2018 à 18:57, Markus Heller a écrit :
Not knowing what your molec
