Re: [ccp4bb] keyword for refmac to output coordinates in cif format

2021-10-29 Thread Ian Tickle
Hi Mark This tells you how to do it: https://www.wwpdb.org/deposition/PDBxDeposit Cheers -- Ian On Sat, 30 Oct 2021, 00:04 Mark J. van Raaij, wrote: > Dear All, > > this may be something simple but I can’t find it in the CCP4i GUI or > online. > Is there a keyword to make refmac output

Re: [ccp4bb] keyword for refmac to output coordinates in cif format

2021-10-29 Thread Mark J. van Raaij
sorry, you can ignore my question. The mmcif file is output all along, for some reason I had never noticed it. how stupid of me... Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain Section Editor Acta

[ccp4bb] keyword for refmac to output coordinates in cif format

2021-10-29 Thread Mark J. van Raaij
Dear All, this may be something simple but I can’t find it in the CCP4i GUI or online. Is there a keyword to make refmac output the coordinates as a cif file instead of a pdb file - or better, as both? Or is it some other program that converts the formats? Mark J van Raaij Dpto de Estructura de

[ccp4bb] Scientists positions open in Structural Genomics

2021-10-29 Thread Karla J. F. Satchell
The Northwestern Feinberg School of Medicine is seeking Two Protein Expression, Purification, and Crystallization Experts with an open rank for PostDoc, Research Associate, or Senior Research Associate to participate in a Structural Genomics Research Center addressing important biochemical

[ccp4bb] postdoc position cryo-EM available (Bajic lab, New York)

2021-10-29 Thread Goran Bajic
We are looking for a postdoctoral candidate with experience in single-particle cryo-EM and willingness to learn virology and immunology. Ph.D. in Biochemistry, Biophysics or a related discipline is required. Tomography (cryo-ET) experience is an asset but not a pre-requisite. The Bajic lab uses

[ccp4bb] LINXS Workshop-Structural Resolution of Membrane Proteins: From Sample Preparation to Structural Resolution"

2021-10-29 Thread Swati Aggarwal
Dear All, We are organizing the second part of the workshop series on 'Sample preparation of membrane proteins*'* along with the Lund Institute Of Advanced Neutron And X-Ray Science (LINXS). In our first online workshop in May 2021, we discussed several aspects of expression systems, protein

Re: [ccp4bb] what would be the best metric to asses the quality of a mtz file?

2021-10-29 Thread James Holton
Well, of all the possible metrics you could use to asses data quality Rfree is probably the worst one.  This is because it is a cross-validation metric, and cross-validations don't work if you use them as an optimization target. You can try, and might even make a little headway, but then

Re: [ccp4bb] what would be the best metric to asses the quality of a mtz file?

2021-10-29 Thread Clemens Vonrhein
On Thu, Oct 28, 2021 at 06:28:05PM +0530, Shipra Bijpuria wrote: > I would first look at the dataset stats and define a resolution range > mainly based on I/sigI >1 and cc1/2 >0.5. Based on this, would take the > good resolution datasets only. Some probably obvious word of caution here: these