Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

2023-12-02 Thread Tim Grüne
Hi Mark, responsible people are resigning from X. Cheers, Tim Am 01.12.2023 23:24, schrieb Mark J. van Raaij: just came across this critique of that paper on Twitter: This exciting paper shows AI design of materials, robotic synthesis. 10s of new compounds in 17 days. But did they? This paper

Re: [ccp4bb] PDB redo R free

2023-04-27 Thread Tim Grüne
Dear Qixu Cai, the sets do not have to be identical, as long as refinement reaches a steady state. Best regards, Tim Am 28.04.2023 04:51, schrieb Qixu Cai: Dear all, I'm using the PDB-REDO server to refine my structure. I found that PDB-REDO said that 5% R-free set is too small and it

Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc

2019-07-01 Thread Tim Grüne
Dear Andre, easiest would be to select the FP and FC_ALL with sftools, write out the values to a text file and calculate the R-value with a scripting language like awk. Best, Tim Am 01.07.2019 15:02, schrieb Andre LB Ambrosio: Dear colleagues, Can a CCP4 program calculate r_work and

Re: [ccp4bb] [phenixbb] Copying mtz file

2019-06-25 Thread Tim Grüne
Dear Mirek, it is a stubborn myth the Free-R flags need to be conserved. You can simply regenerate a new set of flags. This does not compromise the free F-value. This is based on what I would call Tickle's conjecture, even though with one of his latest emails on the ccp4bb, where he explained

Re: [ccp4bb] Phenix / Coot neutron queries.

2019-06-21 Thread Tim Grüne
Dear Jonathan, since structure for neutron data are usually pre-refined and you are only interested in the small print, you can also use SHELXL for refinement (https://doi.org/10.1107/S1600576713027659). That gives you full control over what you want to achieve. With PDB2INS

Re: [ccp4bb] Mandatory mmCIF format for crystallographic depositions to the PDB

2019-02-20 Thread Tim Grüne
Dear John, dear CCP4, Is there a converter from CIF to mmCIF? Some structures are refined with Shelxl, which can output CIF. A converter would be very useful, even if they make only a small fraction of the PDB. Best regards, Tim On February 20, 2019 9:06:22 AM GMT+01:00, John Berrisford

Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

2018-11-29 Thread Tim Grüne
Hi Jacob, The idea of a scientific service being restricted by nationality is so strange to me that this possibility for misunderstanding did not occur to me. Best, Tim On November 29, 2018 10:24:49 PM GMT+01:00, "Keller, Jacob" wrote: >I saw explicitly that it is not limited to EU. > >JPK >

Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

2018-11-29 Thread Tim Grüne
Hi Graeme, I meant to say that the zenodo server sits in Europe, and the sbgrif server in the us. It was not meant to indicate any restrictions. Best, Tim On November 29, 2018 10:21:36 PM GMT+01:00, "graeme.win...@diamond.ac.uk" wrote: >Dear Tim, > >I do not think Zenodo is limited to

[ccp4bb]

2018-09-14 Thread Tim Grüne
Dear Daniel, Did you solve the structure of a small molecule, or do you have a small molecule ligand as part of a protein/ macromolecular complex? In the latter case you don't need checkCIF. Best, Tim On September 14, 2018 5:43:48 PM GMT+02:00, "Moss, Daniel L" wrote: >They say for small