Re: [ccp4bb] [EXTERNAL] [ccp4bb] refmac same residue different names

Hi Diana, At the risk of thread-jacking Ed’s question, yes, PHENIX handles this seamlessly for us as well. However, REFMAC5 doesn’t like this scenario, with or without alt. confs. or insertion codes. There are some models where I’d really like to use REFMAC5 for refining these mixed species

Re: [ccp4bb] [EXTERNAL] [ccp4bb] refmac same residue different names

The scenario I presented earlier works like a charm in refinement with the Phenix program suite. For example, I have used it for both mixed populations of ligands (e.g., AAMP and BADP) as well as phosphorylation (ASER and BSEP). Diana ** Diana R.

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

I agree. We have encountered refinement problems similar to those Ed describes for models with mixtures of modified cysteine species, which is a fairly common occurrence. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska

Re: [ccp4bb] [EXTERNAL] [ccp4bb] refmac same residue different names

Herman, thanks - however, it seems like I have poorly worded my question. I do know how to generate alternate conformers, what the PDB ATOM record format is etc. The point was that when I have alternate conformers that carry the same residue ID but different residue types, Refmac exits with the

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

The situation might not be so rare, if you consider 50% Lys and 50% Acetyl-Lys or other post-translational modifications. Gottfried On Wednesday, 06-02-2019 at 18:05 Diana Tomchick wrote: If you have the odd case where one residue (of the same number in the polypeptide chain) is a Leu and the

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

If you have the odd case where one residue (of the same number in the polypeptide chain) is a Leu and the alternative residue is a Phe, then it would be ALEU and BPHE, both residues would have the same residue number, and reset the occupancies to fractions that sum to 1.0. Diana

[ccp4bb] 2 Postdoctoral Fellowships in Structural Biology and Drug Development at the University of Oslo, Centre for Molecular Medicine Norway (NCMM)

Structural Biology and Drug Development at the University of Oslo [cid:45310D88-A655-46CE-828B-07D61B8B9026] 2 Postdoctoral Fellowships Inhibitor discovery targeting the Helicobacter pylori pH acclimation system (a pH-gated urea channel and a cytoplasmic urease)1 1Strugatsky et al. “Structure

[ccp4bb] X-ray generator and imaging plates available

Dear CCP4bb readers, we are in the process of decommissioning our in-house X-ray source and would like to offer it to the community: Bruker MicroStar X-ray generator (non-functional, i.e. for repair or replacement parts) 2 Helios Mx Cu X-Ray optics for Microstar Mardtb Imaging Plate Detector

Re: [ccp4bb] Live stream of CCP4 Study Weekend?

All the videos from the CCP4 Study Weekend 2019 are now available on the CCP4 YouTube channel. Only the videos where the speakers have expressly given permission for them to be uploaded are there. Regards Karen McIntyre Science & Technology Facilties Council Scientific Computing Department –

[ccp4bb] New Technical staff position at PPSCF facility EPFL Lausanne Switzerland

Dear CCP4 community, The Protein Production and Structure Core Facility has a new open position for a technical staff (CDI, 80-100%, location EPFL Lausanne Switzerland). The main duties will be to advise, assist and follow-up X-ray crystallisation projects for various users; as well as to