Dear colleagues, I tried renaming the residues. When I did so in chimeraX the file opens just fine but in pymol - it looks as a green hedgehog. I suppose that the pdb file is corrupted somehow. Is there a way to fix it? Kind regards, Dmitry
Hi Dmitry, We don't use Pymol so we don't know why it looks like that, sorry. If the file opens fine in ChimeraX it is probably not corrupted, but Pymol does not like something about how the residues are named. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 23, 2022, at 4:55 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues, I tried renaming the residues. When I did so in chimeraX the file opens just fine but in pymol - it looks as a green hedgehog.
I suppose that the pdb file is corrupted somehow.
Is there a way to fix it?
Kind regards, Dmitry
Hello Elaine and all, It seems that I partly realise the issue. So I used several monomers in 1 model. When I spit them into each individual, the issue is gone (at least in pymol). Kind regards, Dmitry
On 23. Sep 2022, at 17:39, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Dmitry, We don't use Pymol so we don't know why it looks like that, sorry. If the file opens fine in ChimeraX it is probably not corrupted, but Pymol does not like something about how the residues are named. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 23, 2022, at 4:55 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues, I tried renaming the residues. When I did so in chimeraX the file opens just fine but in pymol - it looks as a green hedgehog.
I suppose that the pdb file is corrupted somehow.
Is there a way to fix it?
Kind regards, Dmitry
participants (2)
-
Dmitry Semchonok -
Elaine Meng