Re: [ccp4bb] RMSF calculation in pymol

I don’t have one for pymol, but there is a function in prody for it. Best wishes James On 14 Dec 2023, at 21:41, Srivastava, Dhiraj wrote:  Hi All sorry for off topic question. does anyone have script for rmsf calculation of multistate pdb file in pymol? There used to be a

[ccp4bb] RMSF calculation in pymol

Hi All sorry for off topic question. does anyone have script for rmsf calculation of multistate pdb file in pymol? There used to be a script rmsf_states written by Robert Campbell but with newer version of pymol, it's not working. Thank you Dhiraj

Re: [ccp4bb] solvent mask for partial ligands, addendum

You guessed right.  Bulk solvent does not get a localized "occupancy". It is set to "0" anywhere near modeled atoms, even if those atoms have an occupancy of 0.01.  Yes, it might seem sensible to do "occupancy" for the bulk, but in practice it is tricky.  I tried my hand at a "fuzzy" bulk

[ccp4bb] BCA 2024 Spring Meeting Abstracts Open Now!

Dear CCP4BB, Register now for the British Crystallographic Association's (BCA) Spring Meeting (University of Leeds 25th-28th March 2024)! Abstract submission deadline: 19th January (09:00

Re: [ccp4bb] solvent mask for partial ligands

Dear Gottfried Assuming your modelling is correct you can always try occupancy refinement of your ligand (or simply test alternative values). Maybe that will help. You can also play with bulk solvent mask parameters. Keywords (both occupancy and mask parameters) can be found in

[ccp4bb] solvent mask for partial ligands, addendum

Dear all,   I have a modelling problem, which probably has something to do with the solvent mask. There is a positive density blob at the surface of my protein, which I can more or less satisfy with a Hepe (EPE). Hepes is in the buffer, the sulfonic acid H-bonds to a lysine side chain and a

[ccp4bb] solvent mask for partial ligands

Dear all,   I have a modelling problem, which probably has something to do with the solvent mask. There is a positive density blob at the surface of my protein, which I can more or less satisfy with a Hepe (EPE). Hepes is in the buffer, the sulfonic acid H-bonds to a lysine side chain and a