Re: [ccp4bb] off topic -- pymol error message

; 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! > > Chen > &g

[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! Chen -- Cheng Chen, Associate ProfessorSchool of Life Sciences, Building 15, Tianjin University No.92 Weijin Road, Nankai

[ccp4bb] AW: [ccp4bb] off-topic: pymol map

-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

Re: [ccp4bb] off topic: pymol

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

Re: [ccp4bb] off topic: pymol

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

Re: [ccp4bb] off topic pymol

. 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

Re: [ccp4bb] off topic pymol

A C Hope that helps, Sam -- *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

Re: [ccp4bb] off topic pymol

: 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 connected

Re: [ccp4bb] off topic pymol

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

[ccp4bb] off topic pymol

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

Re: [ccp4bb] Off-topic - PyMol map sampling at unit cell boundary

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,

Re: [ccp4bb] Off-topic - PyMol map sampling at unit cell boundary

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

[ccp4bb] Off-topic - PyMol map sampling at unit cell boundary

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.

Re: [ccp4bb] Off-topic PyMOL Issue

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

Re: [ccp4bb] Off-topic PyMOL Issue

Dear Greg, The following might work: set cylinder_shader_ff_workaround, on Best regards, Takanori Nakane