[ccp4bb] Coot doesn't show Ramachandran spheres for residues insertion codes

Hi there, I’m using Coot 0.9.8.95 for OS X from CCP4. I notice that in real space refinement coot does not show Ramachandran spheres for peptide bonds that include an insertion code for one or more residues. See for example 3SOB//H/82-82A//. Best wishes Kevin -- Kevin Jude, PhD Structural Biol

Re: [ccp4bb] Attention APS users - where will you go?

Morning James, thanks for your attention to this issue. I don’t mean to hijack your thread, but I’d also like to point out that here in the US, the proposed DOE FY2023 budget request includes cutting a 10% funding *cut* to X-ray light sources (based on 2018 baseline). It seems the timing couldn

Re: [ccp4bb] Solubility of Aluminum Fluoride

I posted the following to ccp4bb in 2017 in response to a similar question about ADPBeF4. For AlF4 you’ll increase the NaF stoichiometrically: reagent[stock] (mM)final concentration (mM)volume (µl) BeCl2 100090 9 NaF750 450

Re: [ccp4bb] Solubility of Aluminum Fluoride

Sorry, I should have said ADPBeF3 (not ADPBeF4), and increase the NaF proportion for ADPAlF4. Which in practice means reducing the concentrations of everything else due to limited solubility of NaF. From: CCP4 bulletin board on behalf of Dr. Kevin M Jude Date: Wednesday, June 22, 2022 at 9

Re: [ccp4bb] PDBx-format utilities

Need I mention moleman and moleman2? Not trivial I suppose, but I will miss them…. From: CCP4 bulletin board on behalf of Paul Emsley Date: Thursday, September 8, 2022 at 12:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] PDBx-format utilities A spectre is haunting structural biology - it i

[ccp4bb] Dry shipper in limbo

My first adventure in international crystallography is off to an inauspicious start. On Monday, I sent a dry shipper “overnight” from California to Saskatchewan, but it has been stuck in the Memphis FedEx facility for a few days. I’ve gotten several conflicting explanations of the status from Fe

Re: [ccp4bb] Dry shipper in limbo

, for research purposes, with no commercial value (and don’t assign a high value to the shipment). When contacting FedEx ask for a supervisor in the international shipping division. Customs inspectors may be less tied up late at night. From: CCP4 bulletin board on behalf of Dr. Kevin M Jude

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

As suggested by the (conflicting) observations of Eleanor and Nicholas, it’s not clear whether you are showing data collection statistics for the full resolution range or just for the high resolution shell. If for the whole dataset, your Rmerge, I/sigma, and CC1/2 are high, low, and low, respect

Re: [ccp4bb] What could these crystals be?

It’s easy to do on a 0.2 µm spin filter, just pipet the crystals onto the filter with excess mother liquor, wash with several spins of mother-liquor, and elute with SDS loading buffer. Run all the washes and elution on a gel. -- Kevin M. Jude, PhD Structural Biology Research Specialist, Garcia

[ccp4bb] How to describe/correct modulated diffraction?

advice from the community on how to approach this. Best wishes to all, Kevin -- Kevin M. Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305

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: [ccp4bb]

[ccp4bb] Robert Langridge obit

His work was mostly before my time, but I just saw this obituary of Robert Langridge, founder of the UCSF computer graphics laboratory. https://www.berkeleyside.org/2024/01/08/robert-langridge-obituary

Re: [ccp4bb] Modeling Disulfide Bond Occupancies

I have done this in shelxl or phenix refinement, you can define occupancy groups (or free variables in shelxl) so that 472A and 384A are one group, 472B and 384B are another. Pretty sure there is a similar solution in refmac. Though also if the 384A rotamer doesn’t clash with the 472B rotamer, y

[ccp4bb] Contact: Hexclude doesn't work?

I’m trying to run contact on a protonated pdb file and want to ignore hydrogens, but when I use the HEXCLUDE keyword I still get hydrogen contacts. Is it a bug, or am I doing it wrong? Pasting the top of the log file below. Thanks Kevin ##

Re: [ccp4bb] Contact: Hexclude doesn't work?

. I’m measuring intermolecular contacts in the ASU. Best wishes Kevin From: Jon Cooper Date: Friday, August 30, 2024 at 1:06 PM To: Dr. Kevin M Jude Cc: CCP4BB Subject: Re: [ccp4bb] Contact: Hexclude doesn't work? Another thing could be if the atom type field is missing in the pdb file. It&#