[ccp4bb] AlphaFold Protein Structure Database update - changes to PAE JSON format

Dear All, You may have seen our announcement today about expanding the AlphaFold Protein Structure Database to 214M predicted models. To enable this expansion, we’ve updated the Predicted Aligned Error (PAE) JSON format to make it compact (about 4x smaller): The PAE JSON numbers are now

Re: [ccp4bb] Regarding the correct space group identification

Dear Sayan, On Thu, 28 Jul 2022 15:12:30 +0530, Sayan Saha wrote: >Dear Sir, > >1. There are no ice-rings. However, diffraction spots seem to be >overlapping. This can be seen during the data processing, as the space >group (C2 or P222) varies even in the consecutive frames. spot overlap

[ccp4bb] Yes, there are now 214 *million* structures in the AlphaFold Protein Structure Database

Hi all, I thought Sameer was burying the lead a tad in his message... :-) So, for those of you who -like me- are not on social media: ==> As of today, the AlphaFold Protein Structure Database contains 214 million models predicted with AlphaFold, covering almost all of UniProt. <== So, if

[ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

Dear Sayan, your options left, as far as I can see, are: - check if your structure is not twinned, or if not, correct for twinning - refine using the Zanuda space group. - try to find a better crystal that does not produce multiple diffraction images. Best, Herman Von: Sayan Saha Gesendet:

Re: [ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

I cant see how the C2 cell can be reindexed to the P/mmm one? Am I right to assume these are different processing of the same diffraction? And how many molecules do you have in each cell? Eleanor On Thu, 28 Jul 2022 at 12:52, Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > Dear

Re: [ccp4bb] Regarding the correct space group identification

Sorry - meant to add this: I know that (of the “free” programs) Mosflm, DIALS and Eval15 can process multiple lattices. Harry > On 28 Jul 2022, at 14:36, Harry Powell wrote: > > Hi Sayan > > If you have multiple lattices showing in your diffraction pattern, it may be > worthwhile using one

[ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

Dear Sayan, Thank you for this information. Why are your spots overlapping? The axes of your crystal are not particularly long. Did you put the detector very close to the crystal, or are there multiple diffraction patterns? Did you run Zanuda on your P1 structure? What Rfactors do you get when

Re: [ccp4bb] Regarding the correct space group identification

Dear Sir, The crystal-to-detector distance was set to 190 mm. Yes, multiple diffractions seem to be present. We have not yet tried Zanuda on the P1 structure. However, the Rw/Rf of P1 structures are little higher (31/34%). With best regards, Sayan Saha. On Thu, Jul 28, 2022 at 5:22 PM

Re: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

Hi Nick, Thanks a lot for that advice, directing Phenix to the new coot.app location appears to have fixed the amino acids restraints issue! Though still having issue with Phenix not connecting to Coot, perhaps i will post this issue on the Phenixbb and see what the community has to say.

Re: [ccp4bb] Regarding the correct space group identification

Dear Sayan, I could be wrong, but perhaps Kay was asking you to provide the actual images, rather than jpeg images. One can usually get a lot more information by processing the actual images rather than looking at the jpegs. Best wishes, Andrew > On 28 Jul 2022, at 17:11,

Re: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

Hi Paul, I seemed to have fixed the amino acid dictionary issue by following Nick's suggestion to direct Phenix to the new coot.app location in my ccp4 applications folder. Though I am still having the issue that Phenix is not connecting to Coot, is this a known/common issue? Would you please

Re: [ccp4bb] Regarding the correct space group identification

Dear Sir, image1.osc image2.osc The detector-to-crystal distance was 190 mm. The Oscillation range was 1.0 degree. Please

Re: [ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

Dear Madam, The data were processed in C2 and P222 independently from the same diffraction. There are two protomers in the ASU. With best regards, Sayan Saha. On Thu, Jul 28, 2022 at 7:25 PM Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > I cant see how the C2 cell

[ccp4bb] job opening: Scientist, X-ray Crystallography - San Diego, CA

*Scientist, X-ray Crystallography - San Diego, CA* Pharmaceuticals *Job Description * Janssen Research & Development, L.L.C., a division of Johnson & Johnson's Family of Companies is recruiting for a Scientist, X-ray Crystallography, located in La Jolla, CA! At the Janssen Pharmaceutical

[ccp4bb] Workshop on Big Data Neuroscience Sept 15-16 Austin TX

Dear Colleagues, We are excited to announce the 7th annual Big Data Neuroscience (BDN) workshop organized by the Advanced Computational Neuroscience Network. The BDN workshop brings together researchers in neuroscience, computer

Re: [ccp4bb] Regarding the correct space group identification

Hi Sayan If you have multiple lattices showing in your diffraction pattern, it may be worthwhile using one of the programs that can process multiple lattices for your integration. It may also be a good idea to share a few of your images that show the problem with an expert (don’t post the

[ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

Dear Sayan, If a subunit is correctly oriented, but the translation is incorrect, density for a ligand may still show up in the binding site of the protein. It might be that one of the 2-fold axes, you think is crystallographic, is in fact non crystallographic and a few Angstroms away from the

[ccp4bb] Regarding the correct space group identification

Dear All, We have collected home-source X-ray intensity data for a protein at 2.6 Angstrom. The data can be processed in either C2 (a=120, b=80, c=85 and beta=115) or P222 (P22121, a=80, b=85, c=110). MR solution can be obtained in both the space groups. However, the solution can be refined with