Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Dear Prof. Dr. Dodson and all CCP4 community, Thanks for your reply. Just now, I used baverage. I found that it can average the B factor but not refine it. This function does not fit my requirement, because my resolution is low as 3 A. Many people said that Refmac5 overrefines the

Re: [ccp4bb] How to make GDP.BeF3 solution ?

Some blast from the past: Facility management came in full hazmat suits to decommission the old multiwire detectors with the large Be windows. https://www.ruppweb.org/Garland/gallery/Ch8/pages/Biomolecular_Crystallography_Fig_8-07.htm Anyhow, got one on the DOE Beryllium worker’s list.

Re: [ccp4bb] How to make GDP.BeF3 solution ?

Hi Firdous Can you ask Trilink biotechnologies if they can make it for you very good experience many speciality materials made Disclaim: i do not work with them or have any financial connections with them I think jena discontinued this item

Re: [ccp4bb] How to make GDP.BeF3 solution ?

Be aware that beryllium is also quite toxic. https://en.wikipedia.org/wiki/Acute_beryllium_poisoning Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm.

Re: [ccp4bb] How to make GDP.BeF3 solution ?

Nb, dissolution of BeCl2 in water is quite exothermic and releases HCl vapor, you will want to prepare that stock in a fume hood. Best wishes Kevin From: CCP4 bulletin board on behalf of Matthew BOWLER Date: Thursday, January 4, 2024 at 2:19 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re:

Re: [ccp4bb] [External] Re: [ccp4bb] alternatives to Consurf server

Hi Andre, I don't know if anyone mentioned Conservation-Colab, although it maps the conservation onto an AF model. https://zenodo.org/records/10062829 Cheers, Nick Nicholas Schnicker, PhD Director, Protein & Crystallography Facility Adjunct Assistant Professor, Molecular Physiology &

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Hmmm - I am not sure about the value of this - one expects the longer floppier side chains to have very different B values for the CB than the OE2.. The program BAVERAGE gives you a plot of mean B value residue by residue.. *baverage* - averages B over main and side chain atoms SYNOPSIS¶

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Re: [ccp4bb] RMSD per residue graph for multiple aligned PDB files

AFAIK the CCP4 tools “superpose” and “gesamt” both give tables of per-residue RMSD Harry > On 5 Jan 2024, at 10:49, Tomas Malinauskas > wrote: > > Dear All, > > I apologize for asking a somewhat off-topic question. > > I have multiple aligned PDB files loaded in PyMOL, each representing >

Re: [ccp4bb] RMSD per residue graph for multiple aligned PDB files

Dear Thomas, Just have a look at this paper where we have made three-dimensional sketches of both backbone and side chain RMSDs: https://pubmed.ncbi.nlm.nih.gov/34988429 The illustrations were done with Chimera, but "B-factor" plots with PyMOL can be generated,at least for the backbone

[ccp4bb] RMSD per residue graph for multiple aligned PDB files

Dear All, I apologize for asking a somewhat off-topic question. I have multiple aligned PDB files loaded in PyMOL, each representing different conformations of the same protein. I'm interested in creating a graph displaying RMSD per residue, similar to those shown at