Re: [ccp4bb] Please share your experience about "ugly" crystals showing good diffraction

Hi Anirban, It would be great if you could share the compilation of relevant responses to your request. I think many others in the community could use these examples for educational purposes. Best, Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science

Re: [ccp4bb] COOT: adding xylose to a plant glycosylation chain

Dear Marilyn, On 05/07/2018 15:00, Yoder, Marilyn wrote:     On Windows, WinCoot 0.8.9     On Mac, Phenix version 1.13-29998-000  (Coot is version 0.8.9) This is probably the reason... old coot. Get your fresh WinCoot from here (well, the stable release, anyway) ht

Re: [ccp4bb] Oxford University Press

Dear Bernhard, To conclude our conversation, the person who determined and deposited the most small-molecule structures was not a 'poor Russian' but almost certainly Prof. Allan White of UWA, Perth with 5372. He died in 2016. I don't know how many papers he had to review as a punishment. Bes

Re: [ccp4bb] RMS bond and angle

I'm not quite sure what is "wrong" here except perhaps for the idea of "manual correction". If you calculate the rmsd for thousands of angles and you change four of them it is unlikely there will be a large change in its value. The reason programs disclose both the overall rmsd and the individ

Re: [ccp4bb] AW: COOT: adding xylose to a plant glycosylation chain

Hi Marilyn, if 'some luck' happens not to be the case you may be able to create a good cif file for the covalent protein-sugar bond with the JLigand tool (CCP4 suite). that tool allowed me to connect an isoaspartate residue at both ends with my protein chain so that neither coot nor refma

[ccp4bb] AW: COOT: adding xylose to a plant glycosylation chain

Hi Marilyn, I have been struggling with carbohydrates in the pre Glyco module era, which was *not nice*. However, the following strategy works reasonably well: 1) Get the XYP monomer with the "get monomer" command. 2) Move the XYP manually in its electron density. This can be very ap

[ccp4bb] COOT: adding xylose to a plant glycosylation chain

Hello, I'm having problems adding XYP (beta-xylose) to my glycosylation chain in a plant protein. I have a 1.87 Angstrom map, 4 molecules in the asymmetric unit. I have two primary N-glycosylation sites, per protein. I am not using NCS for refinement or model building. The density for the NA

[ccp4bb] Last few months updates, updated coot, ccp4i2, imosflm, etc

For those of you not applying updates, the last few months updates have included * phaser 2.8 * ccp4i2 * dials 1.9 (1.10 coming soon) * ccp4mg * coot 0.8.9.1 * imosflm/ipmosfm 7.2.2 plus interfaces to simbad, ample arcimboldo, and a dials gui DUI Update ID: 7.0.050 Date: 17.01.18 Component

Re: [ccp4bb] Clear segid

I found the solution by myself: open pdb file in vim and replace segid by regexp :%s/\S\S\S\s\s\(\S$\)/ \1/g 2018-07-05 14:33 GMT+03:00 Eugene Osipov : > Hello everyone, > is there any simple way in CCP4 to clear segid field? > I used phenix.pdbtools but version 1.13 does not work anymore. >

[ccp4bb] CCP4 release 7.0 update 059

Dear All update 059 contains * fix for ccp4i2 issue when running xia2 from interface * workaround for phaser FPE issues on OSX * updated crank2 Current plans for future updates are 060 * aimless, pointless, rabdam, fragon, molrep 061 * update to xia2 and dials All the best Charles on beha

[ccp4bb] Clear segid

Hello everyone, is there any simple way in CCP4 to clear segid field? I used phenix.pdbtools but version 1.13 does not work anymore. -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering Research Center of Biotechnology Russian Academy of Sciences Leninsky pr. 33, 119071 Mos

[ccp4bb] AW: Re: [ccp4bb] disulfate bond ?

Hi Shijun, Unfortunately, it happens very often that a ligand (in your case Chloramphenicol) does not bind to the protein in the crystal. If you look into the twilight gallery, there is a large number of crystal structures where people desperately tried to fit their precious ligand in what turn

Re: [ccp4bb] disulfate bond ?

Hi Thanks for all your suggestions . It is out of our hope even though it is disulfide bond, so I wondering what's the biological meaning for this kind of disulfide bond. I used AcCOA and Chloramphenicol when I screen crystal, but I could only put a COA in the election density even that the el

Re: [ccp4bb] Oxford University Press

> there is an error in your computation No, the computation is correct. The model parametrization is oversimplified and the input data are uncertain. Sort of the climate model of review. Cheers, BR From: Sanishvili, Ruslan Sent: Thursday, July 5, 2018 02:07 To: CCP4BB@JISCMAIL.AC.UK;

[ccp4bb] RMS bond and angle

Hi all Just finishing up a new structure at 2.4A. Buster refine gives RMS bond 0.008 and angle 1.13, while MolProbity gives 0.01 and 1.83 degree. I checked the 4 outliers from molprobity……>4sigma. After manual correction, warning goes off, but RMS angle only goes down to 1.82 I am using Phenix 1.