Re: [ccp4bb] To Trim or Not to To Trim

Hi, Probably a stupid question. Could you multiply a, b and c cell dimensions by 2 or 3 (to give 8 or 27 structures) and restrain well defined parts of structure to be ‘identical’ ? To give you a more NMR like chemically sensible ensemble of structures? Ben > On 18 Mar 2023, at 12:04, Helen

Re: [ccp4bb] TWIN?

Hi, I have had twinning with P61, which makes it look like P6122. This is with slightly asymmetric dimer. You could try mol replacement in P65, and refine with twinning on. Maps should look better if correct. Ben Sent from my iPhone > On 9 Jun 2021, at 10:13, Randy John Read wrote: > >

Re: [ccp4bb] superimposition of 3D structures with the DNA part only

eic acids. If this is no longer true, I’m happy to learn of it. Charlie > On Apr 28, 2020, at 6:40 AM, benjamin bax <mailto:ben.d.v@gmail.com>> wrote: > > > HI Fred, > > I still use command line version of lsqkab to do this kind of DNA fitting - > script below only uses maincha

Re: [ccp4bb] superimposition of 3D structures with the DNA part only

HI Fred, I still use command line version of lsqkab to do this kind of DNA fitting - script below only uses mainchain atoms (not bases) which helps if you have different DNAs. Chain E and F are DNA. Ben ./lsq-hinge-6fqv-bin-EV-B.com > lsq-hinge-6fqv-bin-EV-B.log cat

[ccp4bb] REMARK 280 in mmcif?

In PDB files you could put all information about protein delivery buffer, crystallisation conditions and cryo conditions in REMARK 280 (and pull it through in refmac with keyword pdbout copy remarks 280 ) Where are you meant to put all the information about what could be in your crystal in

Re: [ccp4bb] Potential weak binding ligand in the active site

Hi Katherine, One possibility could be that you have occupancy of 0.5 and that ligand binding at one site in the crystal distorts a second site so it cannot bind ligand. Occupancy refinement is not always very stable. If you are looking at two structures on top of one another - refinement

Re: [ccp4bb] photograph of Enraf-Nonius FAST detector

Hi Harry, I think some old stuff from Birkbeck crystallography teaching labs. went to science museum. However, picture of Enraf-Nonius Weissenberg X-ray camera, model Y809, (X-ray diffraction camera) - from 1968 - does not look quite like what I remember.

[ccp4bb] Fwd: Senior Laboratory Technician - Protein Purification - in the Medicines Discovery Institute at Cardiff University.

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Re: [ccp4bb] query of B chain model of protein

Hi, Looks like you have some density for same conformation as in A chain. It could be you have two (or more) conformations for some parts of the structure in MolB. It is often tricky to sort out when you have two conformations for residues and map is ambiguous (and at 2.8A). I would rigid

Re: [ccp4bb] Incorrect Structure in the PDB

Hi Trevor, Some of my colleagues came across a misinterpreted structure published in Acta D., a couple of years ago. They raised the issue with the editors of Acta D., who were most helpful in getting the issue sorted out. My impression is that the journals are the responsible for the papers

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Hi Khoa, How many rounds of refine and rebuild have you gone through on the graphics? Have you tried Lorestr in CCP4 (Automated refinement of macromolecular structures at low resolution using prior information, Oleg Kovalevskiy, Robert A. Nicholls and Garib N. Murshudov). Ben [At 2.9A

Re: [ccp4bb] Conserved water

How about WONKA and OOMMPPAA: analysis of protein–ligand interaction data to direct structure-based drug design? Ben On 7 Jun 2017, at 07:59, Eleanor Dodson wrote: Many years ago I wrote code to label waters with a code related to the residue/atom they were

Re: [ccp4bb] CH-bond length discrepancies

'Most distances between bonded atoms weresettled longago to highaccuracy, but,in the caseof hydrogens, the values in common use often differ by as muchas 20%.' Phenix / MolProbity

Re: [ccp4bb] Ligand electron density

Hi, A think a detailed discussion is off topic for CCP4 bb. https://www.quantiki.org/wiki/quantum-sock-theory Ben On 2 Apr 2017, at 00:31, Phoebe A. Rice wrote: At long last, a brilliant theoretical framework for observations previously dismissed as mere

Re: [ccp4bb] Twinning and R-Free

Hi Alun, 1. What does phenix.xtriage think of the dataset? 2. What kind of redundancy do you have in the dataset? 3. Sometimes with a large crystal and a small beam the twin fraction varies as you rotate the crystal and illuminate different parts of the crystal (which can have different twin

Re: [ccp4bb] Bad density for chains

You could try the diffraction anisotropy server: http://services.mbi.ucla.edu/anisoscale/. Sometimes it helps maps become more interpretable. Ben On 26 Jan 2017, at 14:11, Pooja Kesari wrote: We have a 2.6 A structure showing four chains in an asymmetric unit.