[ccp4bb] SUMMARY: displaying residues (as a surface perhaps) for one component of a p-p-i

Dear bb members, My question from yesterday is repeated at the bottom of this email. What worked is the suggestion by Jan Dohnalek (IBT and CMS, BIOCEV Vestec): opening a structure file in CCP4MG with the option "interfaces" then selecting "residues". A simplified display of the proteins appea

Re: [ccp4bb] Regarding R factor value (R Free)

Hi! The R factor describes agreement between the refined model and the processed diffraction data. Without the diffraction data, one cannot calculate an R factor just from atomic positions. To me, it seems like your best bet would be to try and retain the R factor information in the PDB file

Re: [ccp4bb] Regarding R factor value

Depending on how you process the model, the reported R-value becomes invalid. So you need to get it from the PDB entry before processing or recalculate it with respect to the experimental data. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of > Abhilasha Tha

[ccp4bb] Regarding R factor value (R Free)

Hii!! I have 1500 processed PDB files and I need the R factor value for each pdb files. How I get this R factor value, because it's there initially but, after processing, some data from PDB is deleted only the atom and coordinate information is there no header information in the PDBs. Manually to

[ccp4bb] Regarding R factor value

Hello!! I have 1500 processed PDB files and I need the R factor value for each pdb files. How I get this R factor value, because it's there initially but, after processing, some data from PDB is deleted. Manually to get R factor is not possible. Please suggest me, how to get this R factor value f

[ccp4bb] Eiger images and XDS

Hi all, Apologies for the non-CCP4 question: I’m attempting to use XDS to process some data from the Eiger detector at the AMX beamline (NSLS-2 17-ID-1). To read in the Neggia library, my XDS.INP contains the line “LIB=/…path.../dectris-neggia-mac.so" I’ve successfully used the same dectris

[ccp4bb] Notebooks for CryoEM and Crystallography

Dear Community, I published some notebooks in order to help students, PhDs, and all colleagues to better organize CryoEM and Crystallography data! After discussing this with colleagues and friends, I found that it is difficult to get reproducibility of results due to a lack of the right informat

Re: [ccp4bb] displaying residues (as a surface perhaps) for one component of a p-p-i

So does PISA with great detailed info on interface residues available. VO From: CCP4 bulletin board On Behalf Of Jan Dohnalek Sent: Tuesday, May 31, 2022 2:48 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] displaying residues (as a surface perhaps) for one component of a p-p-i Dear Fred, C