Re: [ccp4bb] neophyte PyMol question

hah! On Fri, Mar 21, 2025, 6:44 PM Harry Powell < 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi Gottfried (and Karl!, and Andrew Gnann off-board) > > Many thanks. It seems that if I don’t have the “set_view()” as the last > thing I do before I save the picture, then I get my “almost

[ccp4bb] CBMS Structural Biology Workbench - May 27 through 30, 2025 - registration deadline approaching

Dear Colleagues, The CBMS Structural Biology Workbench will take place May 27 through 30, 2025. The first two days, May 27 and 28, are dedicated to MX and the following days May 29 and 30 to Solution Scattering and X-ray Footprintig. This is an IN-PERSON workshop. DEADLINE to REGISTER APRIL

Re: [ccp4bb] Assembling a structure given phi, psi angles

Bob diamond wrote the first? Model building/ refinement program using this approach. The trouble was that small deviations in angles resulted in large positional errors farther down the chain and methods correcting the local Map features replaced it.. But the algorithms to go from angles to coordi

Re: [ccp4bb] Assembling a structure given phi, psi angles

Seems phenix could help: https://phenix-online.org/archives/list/pheni...@phenix-online.org/thread/HHG4R6JUWRBVUD3VLXEOPMFSQBLUYKJQ/?sort=date Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android Original Message On 04/04/2025 12:19, Harry Powell

Re: [ccp4bb] Assembling a structure given phi, psi angles

Hi Charlie Not sure if this is at all relevant (or even right - I expect others to correct me...), but Helen Ginn’s “Vagabond” does a refinement based on torsion angles rather than atomic positions, so she might have something that does what you are after. Harry > On 4 Apr 2025, at 11:27, Car

[ccp4bb] Assembling a structure given phi, psi angles

Does anyone know if there is a program that will take a sequence file associated with phi and psi angles and produce a 3D coordinate set in pdb format? I know this can be done in the sense that Byron Rubin’s bender did the same thing in analog fashion. Many thanks Charlie Carter ##

Re: [ccp4bb] Words to avoid

On 20/03/2025 12:28, Andrew Gnann wrote: Look into options like lockdown mode on Android. ... and if you have a Pixel phone (6, 7, 8 or 9) or Pixel tablet also consider switching to GrapheneOS. On Thu, Mar 20, 2025, 7:26 PM Goldman, Adrian wrote: Oh, and on the same topic: if I rem

Re: [ccp4bb] POTUS and the PDB

Thank you, Robbie. I think this analysis is perhaps even more timely given the rumours emanating from the White House regarding an executive order covering macromolecules. Draft text (smuggled out over the US-Canadian border in a dry shipper) as follows: By the authority vested in me as Presid

Re: [ccp4bb] Assembling a structure given phi, psi angles

Many years ago I wrote something to do this (sadly I never published anything and can't find the old code). I'm not saying it's not possible to produce useful structures this way, but in my hands the results were not good. I did a little investigation and it appeared that backbone bond length

[ccp4bb] Designing Cryo-ET teaching module for students

Hello everyone I am planning to teach a Cryo-ET course module for undergraduate students at an introductory to intermediate level next year. The course will cover image processing and 3D reconstruction, including tilt series alignment, segmentation, and subtomogram averaging, aiming to achieve a r

Re: [ccp4bb] Designing Cryo-ET teaching module for students

Hi Firdous A good starting point is the Relion STA tutorial - https://relion.readthedocs.io/en/release-5.0/STA_tutorial/ Best regards Rangana On Fri, Apr 4, 2025 at 11:08 AM Firdous Tarique wrote: > Hello everyone > > I am planning to teach a Cryo-ET course module for undergraduate students >

Re: [ccp4bb] Assembling a structure given phi, psi angles

Dear Charles, This is related to an old classical technique in computational chemistry, called the Z-matrix, for switching from Cartesian to internal coordinates and back: see https://en.wikipedia.org/wiki/Z-matrix_(chemistry) A problem with using this for macromolecules is t

Re: [ccp4bb] Assembling a structure given phi, psi angles

XPLOR can do it or NAB from David case I believe Also rosetta stores its structures (silent.out) most as phi psi chi angles + Calpha coords I believe Regards Gary Dr Gary S Thompson NMR Facility Manager CCPN CoI & Working Group Member Wellcome Trust Biomolecular NMR Facility School of Bioscienc

[ccp4bb] Post doc position CXFEL project / Arizona State

Dear CCP4bb Community, I wanted to draw your attention to this post doc opportunity at Arizona State’s CXFEL project: https://apply.interfolio.com/164848

Re: [ccp4bb] POTUS and the PDB

Well done and an excellent read! Jürgen > On Mar 31, 2025, at 5:31 PM, Robbie Joosten > wrote: > > Dear CCP4bb members, > > This month on the CCP4bb we discussed the effect of the current US president > on the science and society in quite a lot of detail. I think a fair > comparison between