Re: [ccp4bb] COOT 1.0 not showing content on MacOS

Hi Cheng, this a problem related to gtk+3 installation. There is a workaround to solve the issue. You need to install a previous version of gtk+3. All the instructions are here: https://github.com/pemsley/coot/issues/33#issuecomment-1374409909 Bw, Lucrezia On 2023-01-25 15:53, Cheng Zhang wr

Re: [ccp4bb] TEV vs HRV3C

Hi All, I agree with everything said and I also find 3C, my first choice, to cleave more efficiently/rapidly. But I remember all the folks working with membrane proteins were using TEV, so I wonder whether TEV may be more resistent to detergent? (but I never read/found any info about this).

Re: [ccp4bb] Question about CCP4 monomer dictionaries

Dear Stephen, The current monomer library is, for the most part, generated by running AceDRG - for non-metal containing entries at least. AceDRG [1,2] derives atom types using the cif files in the Crystallography Open Database [3], not the CSD. You can see which version of Acedrg has been using

Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

Hi Oleksiy, If the Akta Start is just for loading affinity columns (without air sensor or software), why not to get a Cyvita peristaltic pump for £3k rather than £9k? They

Re: [ccp4bb] Regarding the correct space group identification

Dear Sayan, For interest, the only other example I know of where diffraction images show two different space groups is presented in a paper by Zbyszek Dauter et al, Acta Cryst D61, 967-975, 2005, where crystals of the proteolytic domain of Lon contained superimposed orthorhom

[ccp4bb] Spam email after sending mail to ccp4bb

Every time I send an email to ccp4bb, I get a spam email from 295981...@qq.com that consists of a single line of Chinese (Japanese) characters, is anyone else getting this? Thanks, Andrew To unsu

Re: [ccp4bb] Regarding the correct space group identification

Boaz > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben Gurion University > Beer Sheva, Israel > > On Aug 1, 2022 18:24, Andrew Leslie - MRC LMB > wrote: > Dear Sayan, > >I believe that I have found the answer to your problem. > Wh

Re: [ccp4bb] Regarding the correct space group identification

ure solution is ~29/32%. For C2 structure > solution, it is a little higher, 32/35%. > > > With best regards, > Sayan Saha. > > > > > > On Fri, Jul 29, 2022 at 3:25 PM Andrew Leslie - MRC LMB > mailto:and...@mrc-lmb.cam.ac.uk>> wrote: > Dear

Re: [ccp4bb] Regarding the correct space group identification

22121 structure solution is ~29/32%. For C2 structure > solution, it is a little higher, 32/35%. > > > With best regards, > Sayan Saha. > > > > > > On Fri, Jul 29, 2022 at 3:25 PM Andrew Leslie - MRC LMB > mailto:and...@mrc-lmb.cam.ac.uk>> wrote: &g

Re: [ccp4bb] Regarding the correct space group identification

Dear Sayan, Using imosflm, based on the two images that you have uploaded, the cell appears to be orthorhombic (approx 80, 85, 111) and there is no evidence for the C2 unit call that you suggested. Using only the second image there is a C2 solution, but the prediction is ver

Re: [ccp4bb] Regarding the correct space group identification

Dear Sayan, I could be wrong, but perhaps Kay was asking you to provide the actual images, rather than jpeg images. One can usually get a lot more information by processing the actual images rather than looking at the jpegs. Best wishes, Andrew > On 28 Jul 2022, at 17:11,

Re: [ccp4bb] Comparing two datasets

I think that POINTLESS works with intensities rather than structure factors (I’m not sure if this can be changed). Also, SCALEIT gives a much more detailed breakdown (R factors as a function of resolution and differences in terms of sigmas etc) than POINTLESS WILL. Cheers, Andrew > On 26 Jul

Re: [ccp4bb] Comparing two datasets

I think that SCALEIT should be able to do this. This was originally designed to compare Fs for Native and heavy atom derivate data, but can compare any two similar datasets (ie those that can sensibly be scaled together). You will need to merge the two mtz files first. Cheers, Andrew > On 25

[ccp4bb] postdoctoral position in the MRC Laboratory of Molecular Biology

application closing date of 21st August 2022. For more details, see https://www.nature.com/naturecareers/job/postdoctoral-scientist-pnac-dr-roger-williams-lmb-1898-mrc-laboratory-of-molecular-biology-761415 Please contact me at r...@mrc-lmb.cam.ac.uk, if you have any questions. Roger Williams

Re: [ccp4bb] Strange crystal packing in twined crystal

Dear Florian, There have been previous examples where there are distinct “layers” of protein packing without any obvious density linking the layers, as it appears in the image you show. One is tyrosyl tRNA synthetase, where the layers were in fact linked by a disordered dom

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Hi, as previously suggested you can use AceDRG to generate a cif file for your ligand by input different type of files (SMILES, mmCIF, SDF/MOL, and SYBYL MOL2 files). You can use the AceDRG command line: https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/acedrg/acedrg.html or via ccp4i2, 'L

Re: [ccp4bb] H atoms in refined structure

Hi Luca, You should find that the hydrogens in the mmCIF file output by Refmac are flagged as riding hydrogens, not as an explicit part of the model. This behaviour is as intended, and should not pose a problem for deposition. They are not in the output PDB file because there is no way to flag

[ccp4bb] PostDoc position at MRC-LMB, Cambridge UK

engineering. Details of the position and how to apply can be found here: https://www.nature.com/naturecareers/job/postdoctoral-scientist-structural-studies-dr-suyang-zhang-lmb-1815-mrc-laboratory-of-molecular-biology-756703 Please feel free to contact me by email: szh...@mrc-lmb.cam.ac.uk Best

[ccp4bb] Postdoctoral position in the MRC Laboratory of Molecular Biology

, with an application closing date of 11 April 2022. For more details, please see https://www.nature.com/naturecareers/job/postdoctoral-scientist-pnac-dr-roger-williams-lmb-1798-mrc-laboratory-of-molecular-biology-755546 <https://www.nature.com/naturecareers/job/postdoctoral-scientist-pnac-dr-ro

Re: [ccp4bb] ligand binds to one molecule

I dont think it is necessary to prove what others have said so far, but if you would like some concrete evidence to support those statements: we cocrystallized a protein together with a small peptide, producing a crystal with for molecules in the AU but only one promoter showed clear density f

Re: [ccp4bb] SHELXD for help

Hi Fu, "The SCALEn (n = 1, 2, or 3) records present the transformation from the orthogonal coordinates as contained in the entry to fractional crystallographic coordinates." (please see here https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html) "The self-correlation co

[ccp4bb] Bug when running imosflm under Mac OS Monterey

When running imosflm under Mac OS Monterey, the program gives an X error: X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 45 (X_OpenFont) Value in failed request: 0x60005c Serial number of failed request: 1474 Current

[ccp4bb] Bug in starting the CCP4 distributed version of imosflm in latest CCP4 Updates (7.0.017 and 7.1.018)

n 7.4.0 of imosflm if this was installed using the LMB website (which uses a different startup script). Andrew Leslie To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?S

Re: [ccp4bb] freezing in ethane / propane - unipucks ?

Dear Guenter, Would the use of vials inside combi-pucks (https://www.mitegen.com/product/combipuck-system/) and some arrangements with your local contact at the other end, perhaps help with using propane remotely? BW, D On 26/01/2022 16:53, Guenter Fritz wrote: Dear all, we have some  de

Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

mmCIF) - scaled unmerged data (MTZ or XDS_ASCII) to this converter: https://project-gemmi.github.io/wasm/mxdepo.html and then you can upload the resulting cif file to the wwPDB deposition system. Best wishes Marcin On Thu, 13 Jan 2022 at 20:34, Dom Bellini - MRC LMB wrote: Dear Jasmine, But can w

Re: [ccp4bb] Improved support for extended PDBx/mmCIF structure factor files

Dear Jasmine, But can we now upload two mtz/mmcif files now for the structure factors? as in, the one from the processing software containing the raw data, as well as the one with the weighted amplitudes and the phases from Refinement software? Or do we still have to use CAD to create a single

Re: [ccp4bb] [External] [ccp4bb] High-order oligomers vs robust crystals - references?

Hi Frank, Once we could not crystallize a monomer protein, but we knew the structure of a homolog dimer. We made some educated guessed mutations to dimerize our monomer target, which were based on the structure of the dimeric homolog. Perhaps evidence or perhaps just luck? :-) https://pubmed

[ccp4bb] Postdoctoral positions in the MRC Laboratory of Molecular Biology

the position can be seen here: https://www.nature.com/naturecareers/job/postdoctoral-scientist-pnac-dr-roger-williams-lmb-1684-mrc-laboratory-of-molecular-biology-747391 <https://www.nature.com/naturecareers/job/postdoctoral-scientist-pnac-dr-roger-williams-lmb-1684-mrc-laboratory-of-molecular-

Re: [ccp4bb] am I doing this right?

Hi Ian, James, I have a strong feeling that I have seen this result before, and it was due to Andy Hammersley at ESRF. I’ve done a literature search and there is a paper relating to errors in analysis of counting statistics (se below), but I had a quick look at this and co

[ccp4bb] Re-Release of iMosflm version 7.4.0

Dear All, Version 7.4.0 of iMosflm has just been re-released and can be downloaded from: https://www.mrc-lmb.cam.ac.uk/mosflm/imosflm/ver740/introduction.html *** Note that the Windows version will not process HDF5 images (

Re: [ccp4bb] Double covalent ligand

Dear Rens, CCP4i2 now contains a CIF dictionary accumulator, which should help with handling such problems (note it's also available as standalone to be used via command line if that's useful). This is used automatically when providing multiple ligand CIF dictionaries to the Refinement interfac

[ccp4bb] iMosflm version 7.4.0 release withdrawn

A bug has come to light in reading some hdf5 files (from Eiger detectors) in the latest version of mosflm (7.4.0) . the program will stop with an error message when attempting to read the hdf5 file. I have therefore blocked the download site until this has been fixed. I will send a new message

[ccp4bb] New iMosflm release, version 7.4.0

Dear All, A new version of iMosflm (7.4.0) has just been released. It can be downloaded from: https://www.mrc-lmb.cam.ac.uk/mosflm/imosflm/ver740/introduction.html This version has improved integration for very weak images

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

Dear Kay and Jon, I cannot remember Ian Tickles original posting on this (assuming that it was made to the bulletin board), but surely the resolution of the data is also a very important factor in the danger of over-fitting. The lower the resolution, the worse the experimental data to refined p

[ccp4bb] Postdoctoral positions in structural biology

application closing date of 26 August 2021. For more details, please see https://mrc.tal.net/vx/mobile-0/appcentre-ext/brand-3/candidate/so/pm/4/pl/1/opp/1625-Postdoctoral-Scientist-PNAC-Dr-Roger-Williams-LMB-1625/en-GB <https://mrc.tal.net/vx/mobile-0/appcentre-ext/brand-3/candidate/so/pm/4/pl/1/

Re: [ccp4bb] Problems with refining covalently linked heme cofactor

Dear Vera, In my experiences I had no problems to link protein atoms to a ligand in Coot. Did you check that you merged the cofactor to the protein molecule first? otherwise that could be one reason why Coot is not creating the link. BW, D On 13/07/2021 14:33, Vera Pfanzagl wrote: Hello,

Re: [ccp4bb] How to process two datasets 45 degrees apart?

Dear Murpholino, Assuming that the two datasets are from the same crystal, and collected without moving the crystal in-between, then when processing with mosflm I recommend processing both sweeps in the same mosflm run. This is because you will get more accurate cell

Re: [ccp4bb] help needed with link description

Dear Gerlind, I'm glad that we were of help! I should point out that the "Make link (click 2 atoms)" is dangerous as it only generates a LINK record but not a full link dictionary - it should only be used for common known links that are present in the monomer library. This issue is discussed in

Re: [ccp4bb] help needed with link description

Dear Gerlind, Where did you get your mad_monlib.cif file? It shouldn't be neccesary for you to be manually modifying such restraint dictionaries (any more). You can generate these using AceDRG, either via CCP4i2 or Coot. Shameless plug: https://journals.iucr.org/d/issues/2021/06/00/ir5021/index

Re: [ccp4bb] unknown density in 1.6 A structure

Hi Peer, If I understand you correctly you are saying that you do not know what substance may be in the density; then perhaps you only need to extend by an extra atom to create a new kind of symmetrical molecule that will fit the density? BW, D On 03/06/2021 11:55, SHEPARD William wrote:

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP

... and don’t forget the Mg++ ion Sent from my iPad > On 23 Jul 2020, at 20:10, LMB wrote: > > One way of approaching such modelling uncertainties is to build explicitly a > number of likely models, refine them and examine the difference maps > carefully to see whether y

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP

One way of approaching such modelling uncertainties is to build explicitly a number of likely models, refine them and examine the difference maps carefully to see whether you can convince yourself that one model is clearly better than the others. At least then you will know whether the alternati

Re: [ccp4bb] Question about P3, H3 and R3 space groups

When I was writing Pointless I had to do all sorts of kludgy things to cope with the different “conventions” used by ccp4, clipper and cctbx libraries, scalepack etc. The PDB should have stuck to established conventions to avoid confusion. And lots of people for some reason seem not to like sp

Re: [ccp4bb] What resolution - X-ray diffraction round this time

Ask the referee - (apart from the other suggestions here) ‘How would removing data Improve my model?” Sent from my iPad > On 28 Feb 2020, at 08:22, dusan turk wrote: > > Hi, > > Browsing through the recent discussion on EM data resolution cutoff it > occurred to me that the X-ray diffractio