[ccp4bb] postdoc position and lab manager, Halic lab, SJCRH

Dear all exciting new opportunities in Halic lab: postdoc position https://jobrxiv.org/job/st-jude-childrens-research-hospital-27778-chromatin-silencing-in-fission-yeast/ lab manager https://jobrxiv.org/job/st-jude-childrens-research-hospital-27778-lab-manager-in-cryo-em-chromatin-lab/ @LabHal

[ccp4bb] Open Position

We are searching for a post-doctoral associate with expertise in analytical chemistry and chemical biology and interest in a project entitled “Translatomics of Ribosome-Free Coded Peptide Bond Formation”. Thi

Re: [ccp4bb] coot & other graphics programs draw too many bonds

On Thu, 2021-04-01 at 15:02 +0200, Fred Vellieux wrote: > Hello there, > > After running autodock vina on certain small molecules, the graphics > software I am using (e.g. Pymol, Coot) draws far too many bonds on the > docked small molecule. See enclosed screen capture. > > Is there any way to

[ccp4bb] Improved support for extended PDBx/mmCIF structure factor files in OneDep

Extensions to the PDBx/mmCIF dictionary for reflection data with anisotropic diffraction limits, for unmerged reflection data, and for quality metrics of anomalous diffraction data are now supported in OneDep. In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group

Re: [ccp4bb] coot & other graphics programs draw too many bonds

Hi Fred, At least Schrodinder's PyMOL 2.3.2 can open Vina's PDBQR files (with multiple docked conformations) without any problems or additional CIFs in my experience. Different conformations of ligands are loaded as different states. It if is an older version you could try to convert Vina's PDBQR

Re: [ccp4bb] coot & other graphics programs draw too many bonds

Hi Fred, are you using the output from vina directly (I think it is called pdbrq)? If so, you could try converting it to mol2, before loading it into pymol. Cheers, Johannes Am Do., 1. Apr. 2021 um 15:59 Uhr schrieb Robbie Joosten < robbie_joos...@hotmail.com>: > Hi Fred, > > I think this is a

Re: [ccp4bb] coot & other graphics programs draw too many bonds

Hi Fred, I think this is a problem of not having the right description of the compound. Have you tried using a restraint file for the compound in Coot so the bonds are properly defined? Note sure if Coot uses them, but perhaps also remove all the CONECT records. Cheers, Robbie > -Original

Re: [ccp4bb] AW: [ccp4bb] High Rs

Agree with Herman except re using refined model as search model. This will almost always return the answer you started from.. Eleanor On Thu, 1 Apr 2021 at 13:49, Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > Dear Sam, > > > > The first thing that would come to my mind would be ic

[ccp4bb] coot & other graphics programs draw too many bonds

Hello there, After running autodock vina on certain small molecules, the graphics software I am using (e.g. Pymol, Coot) draws far too many bonds on the docked small molecule. See enclosed screen capture. Is there any way to prevent this from happening? This isn't very satisfactory of you wi

[ccp4bb] AW: [ccp4bb] High Rs

Dear Sam, The first thing that would come to my mind would be ice rings, but since you said you don't have them, there must be another reason for the high Rs. Zanuda will give you back the space group you used for MR and maybe a higher symmetry space group, but the program cannot be used to conf

Re: [ccp4bb] High Rs

Obviously something is wrong or missing but not enough info here to diagnose.. Check data processing very carefully. Look at plots of Rmerge v batch - did the crystal die at some point? At least in CCP4 you can restrict merging to a range of batches.. Wilson plot shapely? Spikes in the Second mo

[ccp4bb] High Rs

Dear all I have a dataset processed to 2.2 A, P212121, with no major issues identified by Xtriage (no tNCS, no twinning, no ice ring, good completeness). Phaser-MR gave a good solution except some loop regions are shifted. There is only 1 molecule in the ASU (and seemingly no more molecule can be