Re: [ccp4bb] program to complete (or to change) side chains to specific rotamers

2024-02-07 Thread Paul Emsley
I agree with James and for the record, the function that it seem to me that you want is set_residue_to_rotamer_name(imol, chain_id, res_no, ins_code, alt_conf, rotamer_name) Paul. To unsubscribe from the CCP4BB list,

Re: [ccp4bb] Calculation of energetics for many mutations

2024-02-07 Thread Krieger, James M
Hi Nick, This would probably be a better question for the CCPBioSim mailing list: ccpbio...@jiscmail.ac.uk There are several free energy simulation methods including alchemical ones that may help with mutations. Perhaps some docking-based approaches may be useful too. Best wishes James

Re: [ccp4bb] program to complete (or to change) side chains to specific rotamers

2024-02-07 Thread Jorge Iulek
Hi all, I answered/thanked Pavel privately for the more involving and expansive learning advice on getting better acquainted with cctbx. coot without the gui - scripting: I imagined that, after all, in general, underlying gui commands are the modules with their parameters/input data and

[ccp4bb] Reminder: School on Single molecule biophysics in cell lysates, 13-17 May 2024, IBT, Vestec, Czech Republic

2024-02-07 Thread Jan Dohnalek
Just a reminder - the registration to this course is open till *29 February.* Dear colleagues, The registration to a specialized course - Basic level school of MOSBRI is open. Find all the relevant details on this page https://www.mosbri.eu/training/basic-level-schools/bls2/ This basic-level

Re: [ccp4bb] what is isomorphous?

2024-02-07 Thread Robbie Joosten
Hi Carlos, In a practical setting you don't have to be very purist. The memory with respect to the reflection data is lost if you refine to convergence. Now there was are recent discussion on refinement convergence and again you can be quite purist here. However, if you go through a few cycles

Re: [ccp4bb] [EXT] Re: [ccp4bb] Crystallizing a tough target

2024-02-07 Thread kavyashreem
Dear Patrick, Thank you for the suggestions and for the detailed the statistics!! Regards Kavya On 2024-02-06 23:06, Patrick Shaw Stewart wrote: > Hi Kavya > > 1. Make a seed stock from the globules or anything else that you think might > be crystalline, and recreen. In other words,

[ccp4bb] Post-doc/staff openings: AAV structure, cell entry & gene therapy

2024-02-07 Thread Chapman, Michael S.
Post-doctoral and staff positions are open for structural studies of AAV, the gene therapy vector, and its host cell interactions, and separately, for computer methods development. Adeno-associated virus is the leading vector for human gene therapy and recently approved in treatments of SMA

Re: [ccp4bb] what is isomorphous?

2024-02-07 Thread Carlos Kikuti
Hello! I have to admit my maths is a bit lazy, but this discussion got me stitched up, because of a point I believe has not been addressed: the Rfree flags. I've been trained to import Rfree flags whenever the crystals have the same space group and similar cell dimensions to the search model for