Re: [ccp4bb] Data Processing questions

2024-05-22 Thread Tom Peat
Hello Marco, There are schools that will teach you about the software (and theory) used in crystallography and they tend to be very good, so one suggestion is to enroll in one of these 1-2 week courses to learn everything properly. You should process all of your data sets- it is only after havi

[ccp4bb] Data Processing questions

2024-05-22 Thread Marco Bravo
Hi All, I just collected a lot of data for native crystals and Seleno-methionine derivative crystals. I have a couple of questions 1. How do I know which images to process and which ones to exclude which might be radiation damaged and not be good to further process? I have been told it is possib

Re: [ccp4bb] Search for similar geometric arrangement in PDB database

2024-05-22 Thread Ezra Peisach
May I point you towards the shape similarity search available at the rcsb.org site? https://www.rcsb.org/news/feature/63933da0e543b6038c4fc5dd The news suggests that you need to upload via URL - but there is a file upload option in the source pull down. On 5/22/24 5:03 PM, Das, Abhinaba wro

[ccp4bb] Search for similar geometric arrangement in PDB database

2024-05-22 Thread Das, Abhinaba
Dear community, Is it possible to conveniently search the PDB for specific geometrical shapes, disregarding the input residues and specifically focusing on finding similar topologies? Thanks in advance To unsubscribe fro

[ccp4bb] ccp4um broken on EL8

2024-05-22 Thread Oliver H . Weiergräber
Dear community, It seems a recent update has broken ccp4um on EL8 (reproduced this on RHEL8 and AlmaLinux v8). The tool crashes with [...]ccp4um-bin: symbol lookup error: /lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b This usually results from an incompatibi

[ccp4bb] Program Available - The inaugural Gateway Ion Channel Symposium (the deadline for registration is May 31)

2024-05-22 Thread Juan Du
Dear Colleagues, This email is to remind you to register or support your trainees in registering for the inaugural Gateway Ion Channel Symposium (GICS). The deadline for registration is May 31, 2024. https://www.vai.org/event/gateway-ion-channel-symposium/ GICS is designed to feature junior fa

Re: [ccp4bb] ccp4 monomer library atom name change

2024-05-22 Thread Keitaro Yamashita
Dear Charis, Please see: https://www.wwpdb.org/news/news?year=2023#654a801dd78e004e766a96bd Because wwPDB has changed these atoms names, the monomer library was updated accordingly. More than 800 monomers were affected. We have added the old atom names in _chem_comp_atom.alt_atom_id to help progr

[ccp4bb] Out from May 21 to May 28 (no internet)

2024-05-22 Thread Yousif Shamoo
Hi, I will be out of the office from May 21 to May 28. I will not have access to the internet during this time. Thanks Yousif Yousif Shamoo, Ph.D. Rice University Ralph and Dorothy Looney Professor Professor, Department of Biosciences MS-140 P.O. Box 1892 Houston, TX. 77251-1892 (Ph

[ccp4bb] ccp4 monomer library atom name change

2024-05-22 Thread Harris Georgiou
Dear colleagues, We have recently discovered a change in the monomer library and specifically a change in the atom names of PYR.cif. The atom names of this monomer were changed between ccp4 version 8.0.016 and version 8.0.018. We were wondering if this change was on purpose and if these new ato