Re: [ccp4bb] NCS axis detrmination

Hi Vandna, Assuming you have two copies, chain A and B. In UCSF chimera: 1) open two copies of the pdb (model #0 and #1) 2) in command line, type: match #1:.B@CA #0:.A@CA showMatrix true Besides moving model #1 chain B to model #0 chain A, the match command also outputs the

Re: [ccp4bb] Correcting 3-letter codes based on protonation states in a PDB file

Thanks to Dave, Tristan and David for the suggestions. The code Tristan posted is similar to what I had been thinking about doing, and probably will do in the future, although not being familiar with ChimeraX, I'll likely end up using Biopython. For this particular round, for expediency

[ccp4bb] Postdoctoral Position in Biophysical Studies of Neuronal Membrane Proteins at Yale University

JOB DESCRIPTION A postdoctoral position at Yale University School of Medicine is available immediately for highly motivated, creative individuals with a strong interest in the conformational dynamics of neuronal membrane proteins. The lab employs a combination of steady-state flux kinetics,

[ccp4bb] NCS axis detrmination

Hi every one , I am looking for a tool to perfectly determine the NCS axis. I have two forms of crystals where diamer is with NCS but on a comparison of both forms, it looks like NCS axis is little off when i superpose two forms, i would like to measure rotation or

Re: [ccp4bb] Questionable Data collection and refinement statistics for 5XQL

Hi Pavel, Similar results in PDB-REDO https://pdb-redo.eu/db/5xql, nothing wrong but clear room for improvement. That said, I would hope that the epositors set the record straight on the data completeness or conjur up the missing reflection data. Cheers, Robbie Sent from my Windows 10 phone

Re: [ccp4bb] Questionable Data collection and refinement statistics for 5XQL

I agree with Dominika, I can't see major problems with this entry (I also did some quick refinement and briefly looked at maps). Reported R factors match re-calculated values using data from PDB, which is good. Smaller issues I see are: - no solvent (water) in the model, while density suggests

Re: [ccp4bb] Questionable Data collection and refinement statistics for 5XQL

Dear C-Daddy, Did you look at the maps? Do you see any astonishing misinterpretations there? Do you think that the completeness in the last resolution shell would affect the maps and the model? If so, why? There are many possible reasons for the discrepancy you pointed out. In I422 a=b,

[ccp4bb] Questionable Data collection and refinement statistics for 5XQL

Dear colleagues, I am really astonished by a recently released structure 5XQL. This structure was just published in BBRC with a super fast process (accepted overnight). Significant inconsistences were observed when I compared the Data collection and refinement statistics in the paper and at

Re: [ccp4bb] Correcting 3-letter codes based on protonation states in a PDB file

This can be done in a few lines of script in any structural biology package that provides a Python (or other) shell. Here's how I'd do it in ChimeraX, for example: Assuming your model is the only one loaded and atom names are all standard: m = session.models.list()[0] histidines =

Re: [ccp4bb] Correcting 3-letter codes based on protonation states in a PDB file

I believe the ProPka or Pdb2pqr webservers can do this. ProPka.org http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ HTH, Dave -- Dr David C Briggs Hohenester Lab Department of