Re: [ccp4bb] Dual occupancy refinement in REFMAC5

Dear Martin, Sorry I did not see these emails until now. Glad it has been resolved. Kind regards, Kyle From: Martin Malý Sent: 22 November 2024 14:52 To: Kyle Gregory ; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Dual occupancy refinement in REFMAC5 You don&#

Re: [ccp4bb] Dual occupancy refinement in REFMAC5

From: James Holton Sent: 20 November 2024 15:00 To: Kyle Gregory ; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Dual occupancy refinement in REFMAC5 CAUTION: This email came from outside of the University. To keep your account safe, only click on links and open attachments if you know the

Re: [ccp4bb] Dual occupancy refinement in REFMAC5

Dear all, Thank you for your helpful replies. The keyword option worked fine for me. I think there is a bug in the GUI. Kind regards, Kyle From: CCP4 bulletin board on behalf of Kyle Gregory <3632e92fcc15-dmarc-requ...@jiscmail.ac.uk> Sent: 20 No

Re: [ccp4bb] Error in "Prepare and validate files for deposition" task"

Good morning, Sorry to hijack this post but I too am facing this issue with my structure that Maria faced with the error :-ERROR- adding_stats_to_mmcif_i2_gui:0 Error in wrapper Failed to adding_stats_to_mmcif:: No description available 204' I'm in the middle of depositing 8 structures and 5 ha

[ccp4bb] Tools for identifying possible contaminants

Dear all, We have a unit cell that is too small for our expected protein and suspect we have crystalised a contaminant. Does anyone have any recommendations on which tools we could use to identify the possible contaminant? I've tried SIMAD on ccp4cloud and it doesn't suggest anything reasonabl

[ccp4bb] Measuring angles between domains

Dear CCP4 bulletin board, I have two domains connected by a helix and I want to measure tilt angles between domains, for comparison purposes to other structures of the same protein. Does anyone have any tools they'd recommend? Kind regards, Kyle #

[ccp4bb] Tools for measuring RMSD of entire molecule when a single domain is aligned

Dear CCP4 bulletin board, I was wondering if there are any tools to determine the RMSD of the entire molecule (two domains) when only aligning one domain, the point i'm trying to make is a variation in domain positioning relative to one another but I'd like to quantify it. LSQ alignment in coot

[ccp4bb] Methods to improve ligand density of a homodimer?

Hello all, I have a homodimer structure in P1 21 1 spacegroup, the dimer is likely a crystallographic artefact, where it looks like the monomer is rotated by ~ 180 degrees around the Y axis. I am assessing ligand binding and each of the monomers display density at the site but it is not as cle

[ccp4bb] Increase in R-factor following REFMAC

Hello, I haven't seen this before but doing a round of refinment with REFMAC, after molecular replacement with phaser, my R factor and R free have increased? Also is it weird that my Rfree is smaller than my R factor? Result: Initial Final R factor0.3621 0.3761 R free 0.3108 0.4733

[ccp4bb] Calculating RMSD of a loop

Hi all, What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha aligned structures? Thought I could do this in Coot but I only see this if I align the specific loops, which I don't want to do. Thanks, Kyle