Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

2024-06-06 Thread Ben Bax
Hi, I am just re-refining an old twinned dataset - which I will redeposit (refinement is never finished). The pdb seem to have automagically detwinned my data. Where do I find my original twinned data (F and SIGF)? (or will I have to redeposit my original un-detwinned structure factors). Tha

Re: [ccp4bb] RES: [ccp4bb] Rwork and Rfree the same?

2024-03-03 Thread Ben Bax
Fcalc maps look fantastic. Are you sure they were not using an Fcalc for the missing 35% of the data? Ben On 29 Feb 2024, at 21:33, Rafael Marques wrote: Sorry for jumping into the post, but I would like the community’s opinion about completeness, once this topic was raised here. W

Re: [ccp4bb] Regarding the diffraction image

2023-02-06 Thread Ben Bax
Hi Kavya, More than one crystal? Epitaxial growth (protein crystal growing on salt crystal or vice versa) Did you try IZIT? (https://hamptonresearch.com/product-Izit-Crystal-Dye-33.html). I have seen salt and protein crystals in the same drop before now - but not growing together. Ben On 3

Re: [ccp4bb] symmetry possibilities

2022-07-23 Thread Ben Bax
Hi Jorge, I have had some similar cases. The twin fraction can vary during data collection on the synchrotron (different areas of the crystal can have different twin fractions). Sometimes this is not a problem and twin refinement works fine - sometimes it is a problem and it is hard to get a cle

Re: [ccp4bb] Refmac automatically handles twinning?

2022-03-30 Thread Ben Bax
The twin fraction can vary during data collection - if the beam is smaller than the crystal For example you could have crystals which are like two very short ends of pencils - with flat ends together (in your case these might pencils could be in P3) In some orientations you could have the beam g

Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)]

2015-06-24 Thread Ben Bax
(and protonated) forms of AMPPNP the same. When I tried to deposit a specific AMPPNP tautomer in 2013, they would not accept it. The PDB also seems to believe, as I understand it, that the overall charge on AMPPNP is zero and that the phosphates do not carry negative charge. Ben Bax Senior

Re: [ccp4bb] Residual density feature

2015-06-15 Thread Ben Bax
pdb header. Regards, Ben Ben Bax Senior Scientific Investigator BioMolecular Sciences UK RD Platform Technology & Science GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK Email benjamin.d@gsk.com<mailto:benjamin.d@gsk.com> Mobile +44 (0) 7912