; To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] off topic -- pymol error message
>
> Hi all,
>
> What does this message means when loading a pdb file in pymol:
>
> 'utf-8' codec can't decode byte 0xd6 in position 37: invalid continuation byte
>
> Thank you!
>
>
Hi all,
What does this message means when loading a pdb file in pymol:
'utf-8' codec can't decode byte 0xd6 in position 37: invalid continuation byte
Thank you!
Chen
--
Cheng Chen, Associate ProfessorSchool of Life Sciences, Building 15, Tianjin
University
No.92 Weijin Road, Nankai Di
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Emilia
C. Arturo (Emily)
Gesendet: Montag, 20. Juli 2015 21:30
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] off-topic: pymol map
This is a hot topic, and the answer is not straightforward. It was recently
Hi Almu -
It's actually even easier than what Vincent wrote as well. :) You don't need
to create multiple objects or worry about backbone selections--PyMOL has some
built-in settings that will do this for you.
# the PDB from your example
fetch 3bwp
# color however you like
color blue, resi
Dear Almu,
very easily:
#load the same pdb twice and give it two different names:
load xx.pdb, molA
load xx.pdb, molB
# show one as cartoon, the other as sticks:
hide everything
show cartoon, molA
show sticks, molB
#hide the backbone sticks of molB
hide sticks, molB and name c+n+o (this is for
.
Best,
D
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Almudena Ponce
Salvatierra [maps.fa...@gmail.com]
Sent: 12 February 2015 15:30
To: ccp4bb
Subject: Re: [ccp4bb] off topic pymol
Dear all,
thank you very much for all your suggestions. The
.33 A
>C
> ATOM381 CD ARG A 49 -14.933 -23.259 -30.207 1.00104.16 A
>C
>
> Hope that helps,
>
> Sam
> --
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Almudena
> Ponce Salvatierra
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Almudena Ponce
Salvatierra [maps.fa...@gmail.com]
Sent: 04 February 2015 17:07
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] off topic pymol
Dear all,
does anyone know why if I open a pdb in pymol (that appears normal and fully
connect
Hi Almudena,
some graphic programs connect atoms based on distance only (draw a line
between two atoms that represents the covalent bond). I suspect this is
what PyMol does. Some may employ more information such as one encoded in
Monomer Library CIF files. Some try to do both. I suspect this is wh
Dear all,
does anyone know why if I open a pdb in pymol (that appears normal and
fully connected in coot) it appears as if it was broken into pieces?
Thanks,
Almudena.
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical C
Hi all,
To follow up on my question from last week, Dr. Emsley's work-around worked
great for me. Increase map sampling in coot, export, and then proceed in
pymol without using the map_double command. I end up with gigantic map file
sizes (~160MB), and it's more work to make all my maps this way,
On 09/01/15 21:08, Shane Caldwell wrote:
Hi ccp4bb,
Apologies for a cross-post. I previously asked this question on the
pymol-users mailing list, but I thought I'd ask here as well, in case
someone who doesn't follow that bb might have run into my problem
rendering maps in PyMol. I'm starting
Hi ccp4bb,
Apologies for a cross-post. I previously asked this question on the
pymol-users mailing list, but I thought I'd ask here as well, in case
someone who doesn't follow that bb might have run into my problem rendering
maps in PyMol. I'm starting to think it's a non-trival problem to solve.
Hi Greg,
Takanori Nakane's suggestion should work for you, which is our workaround
for non-compliant video cards/drivers. If it doesn't or you see performance
or stability problems, please try these two settings:
unset use_shaders
unset sphere_mode
These two settings are usually only necessary f
Dear Greg,
The following might work:
set cylinder_shader_ff_workaround, on
Best regards,
Takanori Nakane
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