[ccp4bb] Fwd: [ccp4bb] Calculation of generalised R-factor?

Dear CCP4ers, many thanks to all of you who replied to my request! I wish you a Merry Christmas and a Happy New Year! Dirk. Forwarded Message Subject:[ccp4bb] Calculation of generalised R-factor? Date: Tue, 20 Dec 2016 14:47:00 +0100 From: Dirk Kostrewa

Re: [ccp4bb] Calculation of generalised R-factor?

On Tuesday, 20 December 2016 10:28:44 PM Pavel Afonine wrote: > Hi Dirk, > > > I want to check the validity of the refinement of anisotropic B-factors vs. > > TLS + isototropic B-factors using the Hamilton R-value ratio test as > > described in Ethan Merritt's paper "To B or not to B", Acta

[ccp4bb] Dna model

Dear All, I want to built a 3d model of DNA to be used to show the path of genome transfer in a tailed phage electron density map, during infection. It will be helpful if The model can be generated as an mrc file or of a similar file format. Any suggestions? Thanks Andy Sent from my

Re: [ccp4bb] Calculation of generalised R-factor?

Hi Dirk, I want to check the validity of the refinement of anisotropic B-factors vs. > TLS + isototropic B-factors using the Hamilton R-value ratio test as > described in Ethan Merritt's paper "To B or not to B", Acta Cryst. D, Vol > 68, pp 468. This test uses the generalised R-factors (assuming

Re: [ccp4bb] Atom clashes in active site?

Hi Scott, That would be great if you have some references handy? Thanks very much, Andrew Marshall PhD Candidate Laboratory of Protein Crystallography Dept. of Molecular and Cellular Biology School of Biological Sciences The University of Adelaide On Wed, Dec 21, 2016 at 1:48 AM, Scott Horowitz

Re: [ccp4bb] Atom clashes in active site?

Hi Pavel, That worked a treat! Thanks again for your help, Andrew Marshall PhD Candidate Laboratory of Protein Crystallography Dept. of Molecular and Cellular Biology School of Biological Sciences The University of Adelaide On Tue, Dec 20, 2016 at 3:18 PM, Pavel Afonine

Re: [ccp4bb] Ubuntu Mate for Pymol and Coot 3D

Thanks Nicolas and Paul! I am using active 3D with Quadro 5000 graphics card and Nvidia 3D kit in Fedora system (Fedora 23). Everytime I update the kernel (dnf update), I lost the 3D in both the updated new kernel and the old kernel, I have to reinstall the driver again, but can not make every

Re: [ccp4bb] Ubuntu Mate for Pymol and Coot 3D

Dear Paul, I am currently not working under Ubuntu OS, so I can't try your fix. But if my memory is still good, it was exactly the problem (the dynamic menus). And I am sure that some ccp4bb reader will be happy to find and try this solution. Thank you. Nicolas Nicolas Foos PhD Structural

Re: [ccp4bb] Ubuntu Mate for Pymol and Coot 3D

On 20/12/16 16:21, Nicolas FOOS wrote: Dear Lei, I already try : Ubuntu Mate (no problem), Xubuntu (no problem), Ubuntu (standard) (I had problem with coot due to unity desktop). A shot in the dark, but maybe your problem is with dynamic menus? If so, try this: $ export

Re: [ccp4bb] Ubuntu Mate for Pymol and Coot 3D

Dear Lei, I already try : Ubuntu Mate (no problem), Xubuntu (no problem), Ubuntu (standard) (I had problem with coot due to unity desktop). Also alternatively : Mageia5 (no problem), Manjaro (python3 as default in environment create some difficulty for several Macromolecular X-ray soft).

Re: [ccp4bb] Atom clashes in active site?

Hi Andrew, Based on the atoms and distances you are mentioning, these don't sound like steric clashes, but like a chalcogen bond between the S and O atoms, and CH...O hydrogen bonds between the O and CH3. These are common and well-accepted interactions, but unfortunately aren't usually treated as

Re: [ccp4bb] Calculation of generalised R-factor?

Hi Dirk, You need the "Overall weighted R2 factor". The reference for the paper I meant is http://onlinelibrary.wiley.com/doi/10.1107/S056773947293/abstract Cheers, Robbie > -Original Message- > From: Dirk Kostrewa [mailto:kostr...@genzentrum.lmu.de] > Sent: Tuesday, December 20,

Re: [ccp4bb] Calculation of generalised R-factor?

Dear Robbie, thanks for your reply. According to the REFMAC5 manual, the weighted R-factor is just: weighted R factor = sum w ||F_o -|F_c ||/sum w |F_o | So, unfortunately, it is not the generalised R-factor. Do you have a reference for that follow-up paper? PDB_REDO does too much for my

Re: [ccp4bb] Calculation of generalised R-factor?

The value for the Hamilton test is written by Refmac as the weighted R-factor. There was a follow-up paper that showed that you shouldn’t use the normal R-factor for the Hamilton test. PDB_REDO does the Hamilton test automatically, but you can also feed two Refmac logfiles to the bselect

Re: [ccp4bb] Calculation of generalised R-factor?

I'd be interested as well. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa Sent: Tuesday, December 20, 2016 8:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Calculation of generalised R-factor? Dear CCP4ers, I want to check

[ccp4bb] Coot crashes on starting baton mode.

Hi all, I'm running Coot 0.8.7 (as distributed with the CCP4 package) on OSX 10.11.6. As soon as I click to enter CA-baton mode, coot crashes (terminal output pasted below). All I have done prior to this is load a pdb and an mtz, build skeletons and pick a start point. Has anyone seen this

[ccp4bb] Calculation of generalised R-factor?

Dear CCP4ers, I want to check the validity of the refinement of anisotropic B-factors vs. TLS + isototropic B-factors using the Hamilton R-value ratio test as described in Ethan Merritt's paper "To B or not to B", Acta Cryst. D, Vol 68, pp 468. This test uses the generalised R-factors

[ccp4bb] Postdoctoral position in protein crystallography available at The Institute of Cancer Research, London UK

The Institute of Cancer Research, London, is one of the world’s most influential cancer research institutes, with an outstanding record of achievement dating back more than 100 years. We provided the first convincing evidence that DNA damage is the basic cause of cancer, laying the foundation

[ccp4bb] Post-doctoral position in Structural Biology of Cilia, Astbury Centre, Leeds, UK

Dear All, A post-doctoral position is available immediately in the laboratory of Dr Joe Cockburn, at the Astbury Centre, University of Leeds, UK to perform structure-function studies on ciliary proteins. The position is funded by The Wellcome Trust and is available immediately for a period of

Re: [ccp4bb] unusual monoclinic relation?

Dear Andy, You've mentioned that MR doesn't work in any of the space groups you've tried, but there are different scenarios that you might be able to recognise from where the MR fails. 1. You might have the wrong protein, e.g. crystallised from a contaminant. In that case, I would expect to

Re: [ccp4bb] Atom clashes in active site?

Hi Pedro, quick answer: no. Longer answer: see article "13 typical occupancy refinement scenarios and available options in phenix.refine" here: http://phenix-online.org/newsletter/ Pavel On Tue, Dec 20, 2016 at 12:29 AM, Pedro Matias wrote: > Hi Pavel, > > If the

Re: [ccp4bb] Atom clashes in active site?

Hi Andrew, One of the atoms should be in altconf A and the other in B. Otherwise the problem remains. Pedro Às 01:48 de 20/12/2016, Andrew Marshall escreveu: > Hi all, > > Thank you for your suggestions. I tried the pdb file edit (making the > offending atoms of both the ligand and the protein

Re: [ccp4bb] Atom clashes in active site?

Hi Pavel, If the occupancies are 1 does phenix still refine them? Anyway, they can be explicitly fixed if necessary. Pedro Às 03:00 de 20/12/2016, Pavel Afonine escreveu: > Hi Perdo, > > technically this should work too with the caveat that non-blanc altid > will trigger occupancy refinement

Re: [ccp4bb] unusual monoclinic relation?

Dear Andrew, If you're sub 2 Angstrom - give Archimboldo a shot. We recently solved the crystal structure of a unknown protein this way. You perhaps have the advantage of knowing what be in there. Antony. --- Antony W Oliver --- --- sent from my mobile account --- On 20 Dec 2016, at 08:18,

Re: [ccp4bb] unusual monoclinic relation?

Thanks Tim, Yes, I may give that a go next time (the wild-type was actually solved by S-SAD, very nice ordered bridge) Orperhaps time to seed / derivitize / mutate and get different packing. Still, not before xmas! Andy -Original Message- From: Tim Gruene

[ccp4bb] Change of Email address

I am in the mailing list of subscribers for ccp4bb with current yahoo mail account. I am going to discontinue this mail account. kindly change my email account to my gmail account, ranvirsin...@gmail.com Ranvir SinghDept cum NCHGSRPanjab UniversityChandigarhINDIA.