[ccp4bb] Online Workshop Series on Structural and Crystallographic Databases -- Registration Open

On behalf of The U.S. National Committee for Crystallography (USNC/Cr) of the National Academies of Sciences, Engineering, and Medicine, I am happy to announce that registration is now open for "EXPLORING STRUCTURAL DATABASE USE IN CRYSTALLOGRAPHY: WORKSHOP SERIES".  The topics will focus

Re: [ccp4bb] Ligand occupancy refinement

Hi Akanksha, years ago I tried to refine, using refmac, an inhibitor only with partial occupancy bound to HIV-1 PR and was not that happy (probably a biased view) with the outcome. In a next step I included water molecules with partial occupancies that normally occupy the binding site in the

Re: [ccp4bb] Why there are two solutions about heavy atoms in SHELXD

On Wed, 2 Mar 2022 22:56:28 +0800, fu wrote: >Dear Colleagues, > I get two solutions after running SHELX C/D. In both results, the > coordinates of the heavy atoms are centrosymmetric. Why there are two > solutions? > >Best wishes, >Fu Xingke >Institute of Physics CAS Hello Fu, SHELXD

Re: [ccp4bb] Why there are two solutions about heavy atoms in SHELXD

On Wed, 2 Mar 2022 22:56:28 +0800, fu wrote: >Dear Colleagues, > I get two solutions after running SHELX C/D. In both results, the > coordinates of the heavy atoms are centrosymmetric. Why there are two > solutions? > >Best wishes, >Fu Xingke >Institute of Physics CAS Hello Fu, SHELXD

Re: [ccp4bb] Ligand occupancy refinement

Thank you for the suggestions I will try again by setting the occupancy of the entire ligand to the single average occupancy and re-do the refinement with Buster, Phenix refine and Remac5 with full positional and B-factor refinement and check the B-factor of the neighbouring residues. The ligand

[ccp4bb] AW: [ccp4bb] Ligand occupancy refinement

PS: this does not work for very small atoms, e.g. waters. Here I let the temperature factor take care of the occupancy as well. Von: Schreuder, Herman /DE Gesendet: Donnerstag, 3. März 2022 16:23 An: CCP4BB@JISCMAIL.AC.UK Betreff: AW: [ccp4bb] Ligand occupancy refinement Dear Ankanksha, The

[ccp4bb] AW: [ccp4bb] Ligand occupancy refinement

Dear Ankanksha, The ligand is either present, or it is not present. It cannot be that some atoms are present and others not. For ligands, I always use a single group occupancy using the program Buster from global phasing. In my hands, this always works. There is a correlation between occupancy

Re: [ccp4bb] Ligand occupancy refinement

Dear Akanksha Tomar, By default, phenix.refine will assign a single occupancy for the ligand as long as all atoms have the _same_ occupancy (0https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

Re: [ccp4bb] Ligand occupancy refinement

Hello, the ligand needs to be treated as one occupancy group since refining individual occupancies would be a case of refining too many parameters, unless it was a very fragmentary compound!! It is one keyword in refmac, but I can't remember for phenix, sorry! Ta jc Sent from ProtonMail mobile

Re: [ccp4bb] Ligand occupancy refinement

Hello, at 2.1 A resolution, atomic temperature factors and occupancy are strongly correlated. So you have to be very careful with the results. So the best is just to set the inhibitor to the average occupancy and then to include it into a full positional and B-factor refinement. You can check

Re: [ccp4bb] Ligand occupancy refinement

Hello, What about refining using refmac5 ? it may yield to different results Mahmoud Rizk On 03/03/2022 15:15, Akanksha Tomar wrote: Hi everyone, I am trying to refine the occupancy of a bound ligand. After fixing the protein model and water I fitted the ligand into it. Currently, I

[ccp4bb] Ligand occupancy refinement

Hi everyone, I am trying to refine the occupancy of a bound ligand. After fixing the protein model and water I fitted the ligand into it. Currently, I am using Phenix Refine with occupancy refinement for individual atoms switched on. After the refinement, the overall occupancy of the ligand is

[ccp4bb] Structural Biologist Wanted at the Franklin

https://opportunities.rfi.ac.uk/vacancy/postdoctoral-research-scientist-in-protein-science-477711.html Dear All, Just a note to say Ray Owens and I have a vacancy to work on the structural

Re: [ccp4bb] MR solution not working

Dear Shubhashish, in most cases the "just doing rigid body refinement" is working. But, depending on the space group, there are multiple possibilities for indexing the same set of reflections and then your simple refinement strategy will fail. Check the section "Alternative indexing" in

Re: [ccp4bb] MR solution not working

if the spacegroup is the same as wt and the cell params are similar, just do rigid body refinement and forget about MR (I’ll never understand people running MR needlessly in these cases…apart from wasting computer time it risks placing the new solution in a different place than the wt) if the

Re: [ccp4bb] MR solution not working

Hello, I have a maybe naive question, did you check the results for the Matthew Probabilities calculation ? Are you 100% certain that's your protein of interest in the crystal? Sometimes we can have surprise. Nicolas On 03/03/2022 05:43, Shubhashish Chakraborty wrote: Hello, I am trying

[ccp4bb] AW: [ccp4bb] MR solution not working

Hi Shubhashish, How many molecules do you assume are in the asymmetric unit? You may have a very high solvent content and by trying to find multiple molecules, you spoil your solution. Also, did you do a thermal shift assay to make sure your protein is properly folded? Best, Herman Von: CCP4