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

The Baker group has also reported substantial progress in all atom predictions Krishna et al., Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom bioRxiv 2023.10.09.561603 doi: 10.1101/2023.10.09.561603 https://www.biorxiv.org/content/10.1101/2023.10.09.561603v1.full

Re: [ccp4bb] mmciif pdb file editor.

PDBj has a nice web-based mmCIF editor that can help you edit mmCIF an validate the data entered. See https://pdbj.org/cif-editor/ Regards, Mitch Quoting Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk>: Hi There is no particular special editor from PDB (or from anywhere

[ccp4bb] Feb 9 Free Webinar: New Dimensions - How Computation Is Accelerating Structure Based Drug Design

Dear all, On Thursday, February 9, 2023 from 12:00 p.m. to 1:00 p.m. ET (17:00-18:00 UTC) Karen Akinsanya, President of Research & Development - Therapeutics, Schrödinger, Inc will present a zoom webinar titled New Dimensions - How Computation Is Accelerating Structure Based Drug

[ccp4bb] Jan 10 Free Webinar: Pandemic Preparedness: Accelerating the Discovery of New Therapeutics

Dear all, On Tuesday, January 10, 2023 from 12:00 p.m. to 1:00 p.m. ET (17:00-18:00 UTC) Ken Duncan, Deputy Director, The Bill & Melinda Gates Foundation will present a zoom webinar titled Pandemic Preparedness: Accelerating the Discovery of New Therapeutics This zoom webinar

Re: [ccp4bb] Na vs K

You can also look at your anomalous maps. For most energies/wavelengths used to collect protein data, f" for K will be just under 2x the f" for S while for Na f" will be much less (0.2-0.25 of S). So you can use S atom anomalous as an internal reference. If you see anomalous peaks at your S

[ccp4bb] Online Workshop Series on Structural and Crystallographic Databases -- Registration Open

On behalf of The U.S. National Committee for Crystallography (USNC/Cr) of the National Academies of Sciences, Engineering, and Medicine, I am happy to announce that registration is now open for "EXPLORING STRUCTURAL DATABASE USE IN CRYSTALLOGRAPHY: WORKSHOP SERIES".  The topics will focus

Re: [ccp4bb] any issues getting through to the CCP4 servers?

Hi, I just noticed that there is a page -- https://www.ccp4.ac.uk/?page_id=2593 that allows downloading various versions. It notes there is an issue with the Package Managers for Mac and Linux due to a server error. It sounds like this page was added as a workaround until things are back to

Re: [ccp4bb] A strange problem related to MR

You can also use phaser.famos to compare MR solutions to see if they are related -- https://www.phaser.cimr.cam.ac.uk/index.php/Famos phaser.famos moving.pdb=pdbfile1 fixed.pdb=pdbfile2 (from the it looks like there is also a phenix GUI to access this functionality as well --

Re: [ccp4bb] cryptic error message trying to use LigPlot on an unknown ligand

What about coot? Have a look at https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/coot-may-2017-ligands-madrid-mcs2017-csic.pdf pp28-40 and Emsley P. (2017). Tools for ligand validation in Coot. Acta Crystallogr. D73, 203–210. https://doi.org/10.1107/S2059798317003382

Re: [ccp4bb] (scattering factors) f and f" for Sr Heavy atom

You can also use the ccp4 legacy program crossec --- http://legacy.ccp4.ac.uk/html/crossec.html for your case -- echo -e "NWAV 1 1.2782\nATOM Sr\nEND\n" | crossec | grep SR Atom symbol and number SR 38 $TABLE:Wave length v F' and F"- SR : $GRAPHS:Lambda v F' and F" SR :A:2,3,4:

Re: [ccp4bb] refinement of 0.73A data in shelxl

I am not sure about in the PDB format or mmCIF format. However, other refinement programs have this ability too, e.g. the occupancy groups of refmac http://www.ysbl.york.ac.uk/refmac/data/refmac_keywords.html#Occupancy buster refine has a tool pdb2occ to help generate appropriate groupings in

Re: [ccp4bb] Unusual monomer-monomer interface in crystal

When the JCSG was in production, we would routinely collect X-ray emission spectra from our samples to look for metals. We also saved all crystals after data collection and if we saw extra anomalous peaks in the maps during refinement, we would put the crystal up again and collect quick low

Re: [ccp4bb] A Max Perutz question

You can also do a reverse image search with tineye https://www.tineye.com/search/153d902d2e4567ccb3299daefa3cef8d207d197a/ or google image search

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

We used to use dichlorodimethylsilane in toluene to siliconize both coverslips and the special glass capillaries for crystal mounting. I don't have the protocol we used anymore, but the one listed on protocolpedia sounds familiar.

Re: [ccp4bb] How big are my solvent channels in my protein crystal?

As Ditlev points out, measuring the channels ignores the flexibility / dynamic nature of proteins in crystals. Also, if you have any disordered tag residues or loops, they also occupy space in the solvent channels. That said, I have found the Doug Juers' lab's program map_channels very useful

[ccp4bb] Zebra Bar code printer power supply recall.

The power supply on the Zebra brand bar code printer we have for labeling plates is part of a recall. I thought I would pass on the details in case others are affected. The recall was expanded to include 1.3 million units manufactured between 2006 and 2012 for the North American market.