[ccp4bb] School on Single molecule biophysics in cell lysates, 13-17 May 2024, IBT, Vestec, Czech Republic

/ <https://www.mosbri.eu/training/basic-level-schools/bls2/>* or contact directly the course organizers for more information zdenek.lan...@ibt.cas.cz (Scientific Organizer) magdalena.schneider...@ibt.cas.cz (Course Admin) Jan Dohnalek MoB-IBT centre of MOSBRI -- Jan Dohnalek, Ph.D Ins

[ccp4bb] Reminder: School on Single molecule biophysics in cell lysates, 13-17 May 2024, IBT, Vestec, Czech Republic

in this course is: Thursday 29th February 2024. Jan Dohnalek MoB-IBT centre of MOSBRI -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758

Re: [ccp4bb] Identify mysterious density in CryoEM map

Thanks Pavel! I tried, choosing Fobs and sigmaF as input variables, but sadly it returned an error message (see below). I don’t know if anything can be done to adapt the mtz file to their server. So I emailed them and will share if I get some feedback. > On Jan 26, 2024, at 2:45 PM, Pa

[ccp4bb] Identify mysterious density in CryoEM map

Dear all, We’re working on an unknown ligand density in our CryoEM structure. Is there a program that uses deep-learning to fill uncharacterized electron density similar to Checkmyblob but for CryoEM maps? Thanks, Jan

[ccp4bb] School on Single molecule biophysics in cell lysates, 13-17 May 2024, IBT, Vestec, Czech Republic

, etc., who want to learn a technique enabling high throughput screening for dynamic parameters of biochemical interactions on a single molecule level. The deadline for submission of an application to participate in this course is: Thursday 29th February 2024. Jan Dohnalek MoB-IBT centre of MOSBRI

Re: [ccp4bb] extra Fo-Fc density in two Cysteines

We have seen quite a few of these. Oxidation of S. Mostly in our case a result if reaction with beta-mercaptoethanol.. Jan On Mon, Dec 18, 2023 at 6:14 PM Liliana Margent < lmarg...@gradcenter.cuny.edu> wrote: > Hi there, We’ve been having an issue in trying to clear regions of Fo-Fc

[ccp4bb] MOSBRI - open call reminder

Structure under MOSBRI umbrella: CD, ITC, DSC, MST (labeled, non-labeled), BLI, nanoDSF, DLS, mass photometry, SPR, SAXS, FT-IR, fluorimetry, UV-Vis, optical tweezers See you at the instruments! Best regards, Jan Stransky, on behalf of CMS, MoB-IBT team

[ccp4bb] Is the PDBe deposition server broken?

. -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 To unsubscribe from the CCP4BB list, click

Re: [ccp4bb] Problems with CCP4i2 on WSL2 - crashes upon report

didn't really fit my error, but currently everything is running (again). Sorry for the spam... Best, Jan -- Dr. Jan Gebauer |  Head of C2f | Member of AG Prof. Baumann Institut für Biochemie | University of Cologne Zuelpicher Str. 47 | 50674 Cologne | Germany  +49 (221) 470 3212 Fax: +49

[ccp4bb] Problems with CCP4i2 on WSL2 - crashes upon report

If I delete my .CCP4* and CCP4I2_* directory to start fresh, the GUI fails immediately. Probably because it tries to open a view, which triggers the same error as above? Any help is highly appreciated... Best Jan -- Dr. Jan Gebauer |  Head of C2f | Member of AG Prof. Baumann Institut für Bi

Re: [ccp4bb] Dry shipper in limbo

for a good week. With simple tests one can identify dewars that are on their way out. Glad that your dewar turned up and that the great staff at CLS could fit you in. Cheers, Jan On Fri, Jul 28, 2023 at 1:09 PM Dr. Kevin M Jude wrote: > Hi all, thanks for the responses on and off l

Re: [ccp4bb] Dry shipper in limbo

to us ... Avoid FedEX!!! Jan Dohnalek On Fri, Jul 28, 2023 at 5:16 AM Dr. Kevin M Jude wrote: > 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 b

[ccp4bb] Postdoc position in structural cell biology at the MRC Laboratory of Molecular Biology, Cambridge UK

constriction through focussed ion beam (FIB) milling and electron cryotomography (cryo-ET) of Gram-positive bacteria. The new 3-year position will be located at the MRC Laboratory of Molecular Biology (LMB) in Cambridge, UK within the group of Jan Löwe, working in collaboration with the groups of Séamus

Re: [ccp4bb] Structure prediction - waiting to happen

We are getting the same feeling from discussions with (non-structural) biologists around us. I also agree that AlphaFold models are a great tool but they do not tell everything and cannot exactly replace experiments. Is the development mainly in the hands of journals' reviewers...? Best, Jan

Re: [ccp4bb] Alexey Vagin

So sad. Alexei was a great scientist and a good friend. I will have only good memories of him. Jan On Mon, Mar 27, 2023 at 5:20 AM Nukri Sanishvili wrote: > Sad news indeed for so many of us, those who knew Alexei personally and > those who benefited professionally from his se

Re: [ccp4bb] anomalous data usage

h and easy. Jan On Wed, Mar 15, 2023 at 3:52 PM Randy John Read wrote: > Hi Jon, > > My understanding of the philosophy is that new users would prefer to think > about crystallographic data objects, rather than worrying about the arcana > of MTZ files and the many diff

[ccp4bb] Postdoc positions in cryo-EM development at the MRC Laboratory of Molecular Biology, Cambridge UK

*Postdoctoral positions available in cryo-EM methods development at the MRC Laboratory of Molecular Biology, Cambridge UK, in the groups of Chris Russo and Jan Löwe* We have one position each available, funded for two years as part of the LMB’s Blue Sky collaboration with AstraZeneca

Re: [ccp4bb] Problem downloading models maps in from PDBe in Coot

This has been quite variable in (several?) last versions of Coot. I have some three latest versions available and when one does not work I start another one. Sad but true. Jan On Thu, Sep 15, 2022 at 11:39 AM Robbie Joosten wrote: > Not sure if this is a PDBe bug or a Coot

Re: [ccp4bb] PDBx-format utilities

, i.e. most of the time used to see "what really happened" during the last refinement run. Jan On Thu, Sep 8, 2022 at 9:29 PM Paul Emsley wrote: > A spectre is haunting structural biology - it is the spectre of the PDBx > format. > > We at CCP4 are interested in providing tool

Re: [ccp4bb] Lower b-factors with increasing T

. Jan On Thu, Sep 8, 2022 at 3:03 AM Tom Peat wrote: > I think the basic question being asked is why are the B-factors going the > 'wrong' way? > That is, as the temperature increases, one might expect higher B-factors > (at least that is what we are taught) whereas what Ma

Re: [ccp4bb] Polymer ligand (Jefffamin) modeling in low resolution maps

ting option. Our lab consensus is to keep the atoms, but reduce occupancy to almost 0. I think, I could do that for the methyl groups in Jeffamin. Best regards, Jan On 8/19/22 11:42, Matthew Snee wrote: Hi It is likely that your density is a consensus of multiple different jeffamines binding at

[ccp4bb] Polymer ligand (Jefffamin) modeling in low resolution maps

, but the contacts  are nothing great, e.g. position of the oxygens in the polymer is  not clear. Calculating Polder maps does not clear things  up. How would you deal with interpretation such maps? Thank you for your ideas :-) Jan

[ccp4bb] Postdoc opening in Berkeley

be found here: https://lbl.referrals.selectminds.com/jobs/xfel-postdoctoral-fellow-crystallography-spectroscopy-4991 https://lbl.referrals.selectminds.com/jobs/chemist-postdoctoral-fellow-4992 Do not hesitate to contact me directly in case of any questions. Jan Kern Staff Scientist - Head

Re: [ccp4bb] Checking X-ray sequence (no more protein).

If you know at least something about your protein, organism, type of molecule, ..., you could try mass spectrometry peptide mapping to known sequences, this may give you some answers for the ambiguities you might be seeing, if nothing else .. Jan On Fri, Jul 29, 2022 at 12:15 PM Jon Cooper

Re: [ccp4bb] Discrepancy in His library used by CCP4 and Molprobity?

convinced would be the right ones. Now, Jan's question triggered mine .. Anybody else had similar experience with such ligands? Jan Dohnalek On Fri, Jul 29, 2022 at 11:54 AM Jan Stransky wrote: > Hi all, > > while validating X-ray structure using Molprobity (web service), we got > sy

[ccp4bb] Discrepancy in His library used by CCP4 and Molprobity?

and Molprobity is happy, but when Bong Angels are called in Coot (Regularize zone button :-)) the bond length goes to 1.36A and Molprobity  is unhappy again. So I would like to ask, who is right or where else the problem can be. Best regards, Jan P.S. CCP4 is version 8.0.002

[ccp4bb] EMBO practical course on “Practical Integrative Structural Biology” 06 – 13 November 2022

behalf of the organisers, Jan Kosinski Arjen Jakobi Maya Topf To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to m

Re: [ccp4bb] displaying residues (as a surface perhaps) for one component of a p-p-i

particular interface and display it. I hope it works for you, Jan On Tue, May 31, 2022 at 8:12 AM Fred Vellieux wrote: > Dear bb members, > > I am quite certain that someone must have needed to do this already. I > looked at publications but no details were given concerning how f

[ccp4bb] coot 0.9.8.1 and phenix mtz files

*mydata*.mtz will only open up the PDB but ont the mtz file. The latter can be opened via the Load menu. - The Coot window launched from the phenix gui does not displany the pdb or the map. Any pointers would be appreciated. Thanks! Jan -- Jan Abendroth UCB BioSciences Seattle

[ccp4bb] Reminder and Extension - Survey on Data Standards and Databases in Molecular Biophysics

;* We appreciate your answers The survey will close on 4 March 2022 *Feel free to contact us at mosbri-d...@ibt.cas.cz * Jan Dohnálek & Jan Stránský for the team of Standards for data archiving & exploitation MOSBRI -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Science

[ccp4bb] Job at EMBL Hamburg - Senior Scientific Software Engineer: New Methods for Structural Modeling

ations <https://www.embl.org/groups/kosinski/publications/>. We offer access to superb computational infrastructure, experimental data from electron microscopy and other techniques, competitive salaries, and excellent working conditions. Best, Jan -- Group leader at European Molec

Re: [ccp4bb] PDB deposition of structure solved with a Robetta model

select domains from various sources, etc. Cheers, Jan On Mon, Feb 7, 2022 at 5:24 AM Loll, Bernhard wrote: > Dear all, > > I have recently solved a structure by molecular replacement with a > search model calculated by the Robetta server. > > I am in the process to deposit the coor

[ccp4bb] Survey on Data Standards and Databases in Molecular Biophysics

e your answers The survey will close on 4 March 2022 *Feel free to contact us at mosbri-d...@ibt.cas.cz * Jan Dohnálek & Jan Stránský for the team of Standards for data archiving & exploitation MOSBRI -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech R

Re: [ccp4bb] Validation of structure prediction

he density is actually not that appropriate. The only "improvement" to this I think is the multiple model approach. My 2 c. Jan On Sat, Jan 15, 2022 at 9:29 PM James Holton wrote: > > On 1/13/2022 11:14 AM, Tristan Croll wrote: > > (please don’t actually do this)

[ccp4bb] Computational modeling job opportunities in the Kosinski lab at EMBL Hamburg

s of the job opportunities <https://www.embl.org/groups/kosinski/open-positions/>. We offer access to superb computational infrastructure, experimental data from electron microscopy and other techniques, competitive salaries, and excellent working conditions. Best regards, Jan Kosinski -- Gr

[ccp4bb] LMB Kendrew Lecture on AlphaFold

With best wishes, Jan To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a ma

[ccp4bb] Search for a particular motif [off-topic]

that? Thanks, Jan To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted

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

This is good to know indeed. Will improve my teaching now, I also did not know this is now done automatically. Thanks for pointing it out. Jan On Mon, Aug 30, 2021 at 9:44 PM Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > Dear Eleanor, > > Thanks for pointing out that

Re: [ccp4bb] off-topic: structural motif / domain comparison

Like PDBeFOLD search? https://www.ebi.ac.uk/msd-srv/ssm/ Jan On Fri, Aug 6, 2021 at 8:43 AM Sam Tang wrote: > Dear all > > Sorry for an off-topic question here. I wonder if anyone may be aware of > any search program which allows one to 'blast' a protein domain just like

[ccp4bb] Joint webinar of Centre of Molecular Structure and Excillum - 28th April

-capabilities-at-cms/ Best regards, Jan Stransky P.S. You can now follow news from Centre of Molecular Structure at Twitter, @CmsIbt (https://twitter.com/CmsIbt) -- Jan Stránský, PhD. Institute of Biotechnology, AS CR Centre of Molecular Structure Průmyslová 595 252 50 Vestec Czech Republic Email

[ccp4bb] postdoctoral position in cryo-EM at LMB in Jan Löwe's group

here: https://www.nature.com/naturecareers/job/postdoctoral-scientist-structural-studies-dr-jan-lowe-lmb-1485-medical-research-council-laboratory-of-molecular-biology-736334 <https://www.nature.com/naturecareers/job/postdoctoral-scientist-structural-studies-dr-jan-lowe-lmb-1485-medical-resea

Re: [ccp4bb] Open position - data management in biophysics

r 10 years ..." Fineprint - assuming nobody asks for reports, further applications, silly record tables, appraisal documents, in that period .. Back to real world. Jan On Fri, Jan 22, 2021 at 11:49 AM Pearce, N.M. (Nick) wrote: > "If you do your work well, you will get more ..”

Re: [ccp4bb] Open position - data management in biophysics

On Fri, Jan 22, 2021 at 10:54 AM Pearce, N.M. (Nick) wrote: > Academia, one of the only careers where _success_ is rewarded with > perpetual impending employment every two+ years. > > Which translates "If you do your work well, you will get more .." Jan > Nick >

[ccp4bb] Up-to-date 3D stereo solution

to controls. We played a bit with PS VR, VR solutions prsented last year at CCP4 weekend seem to be still far from usable. Did anyone try AR? Best regards, Jan To unsubscribe from the CCP4BB list, click the following link: https

Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

involve more machine learning. Jan On 04/12/2020 00:49, Paul Adams wrote: I agree completely Tom. Having been recently involved in some efforts to identify interesting compounds against SARS-CoV-2, I can say that the current AI/ML methods for docking/predicting small molecule binding have

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

We also recently encountered this way of coordinates treatment - did not find it useful but just left it as it was (life has other more exciting adventures waiting ...). I strongly support the solution suggested by Luca, A nice day to all, Jan Dohnalek On Fri, Dec 4, 2020 at 8:48 AM Luca

Re: [ccp4bb] (off-topic) beamline for XAFS

Dear Banu, I would recommend looking also at SSRL beam line 7-3 and 9-3 as they are well set up for protein EXAFS. Greetings, Jan On Tue, Nov 10, 2020 at 11:03 AM PULSARSTRIAN wrote: > Dear all, > Sorry for the off topic. > Looking for suggestions on beamlines for XAFS on

Re: [ccp4bb] metal coordination at low resolution - restraints

It is the active site which is very well defined, with high occupancy and tight binding. We also have high resolution structures of these .. However, restraints (for protein-metal contacs) were not necessary to refine these sites. Atoms site where they should be ... Jan On Tue, Sep 8, 2020 at 2

Re: [ccp4bb] metal coordination at low resolution - restraints

Hi Garib, > > On 8 Sep 2020, at 11:39, Jan Dohnalek wrote: > > These are structural. > > > Are they tetrahedral or octahedral? From the list of neighbours they do > not look like tetrahedral. Some of them do look like octahedral. > > They are involved in reaction

Re: [ccp4bb] metal coordination at low resolution - restraints

These are structural. They form the active site of our enzyme. Normally there is no need to restrain these, they "behave". But in general having such standard "restraint angles" available would be of use, I agree. Jan On Tue, Sep 8, 2020 at 12:22 PM Garib Mursh

[ccp4bb] diffdump in CCP4 7.1

Hi all, It looks as if the utility ‘diffdump’ is no longer part of the standard linux CCP4 7.1 distribution. It has been a very handy tool for preparing XDS input files. Does anyone know if there is an equivalent script in CCP4 7.1? Thanks, Jan -- Jan Abendroth UCB BioSciences Seattle

[ccp4bb] Power supply for a Phillips CM10 Electron Microscope?

Dear all, We’re looking for a 24 h.t. and 24 fil. power supply for a Phillips CM10 Electron Microscope. Does anyone know how to get such component separately? Used is fine too. Thanks, J. To unsubscribe from the CCP4BB

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] dewar horror stories

, there is a lot more value being shipped in each shipment. Cheers, Jan On Thu, Jun 25, 2020 at 6:47 AM Syun-Ru Yeh wrote: > We had a similar experience with a CX100 a few years ago. We found some > small chunks of white powder leaking out of the inner chamber of the dewar, > which was a

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] dewar horror stories

ty (which can be determined by the S/N number printed on the dewar). > > Best, > Syun-Ru > > --- > Syun-Ru Yeh, Professor > Department of Physiology and Biophysics > Albert Einstein Collage of Medicine > Bronx, NY 10461 > > > ------ >

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] dewar horror stories

The trouble is no other company does international LN2 shipments here ... So we stopped shipping dewars completely. Jan On Thu, Jun 25, 2020 at 2:27 PM Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > I had a similar one-sided discussion with FEDEX about their ignoring

Re: [ccp4bb] dewar horror stories

these issues - they even did not reply ... Jan On Wed, Jun 24, 2020 at 9:27 PM Patrick Loll wrote: > Hello community, > > We recently had a dry shipping dewar fail catastrophically (while en route > to the beam line, so, major trauma). I sent it to a company that > specia

[ccp4bb] Project applications to CMS, IBT Biocev - Covid-19

*, and no financial contribution will be requested for the measurement/service. Stay safe The CMS team http://www.ibt.cas.cz/core-facility/CMS/index.html -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech

Re: [ccp4bb] powdery residue on pucks?

We call this 'synchrotron dust', but our suspicion is the same that is is a breakdown product of the foam. It happens more often with old dewars than with newer ones. Once this happens, it is a good time to test the dewars. Cheers, Jan On Fri, Feb 21, 2020 at 4:40 PM Diana Tomchick

[ccp4bb] Coot on Macosx Catalina

Hi everyone, I'm running into issues installing coot on Macosx Catalina. When install the system using BINARY.setup the following message shows up: Does anyone else faced this problem? Is there a way to work around it? Thanks, J.

Re: [ccp4bb] Figure of merit in refinement

iple reflections - I guess this is possible but I wonder if you could get easily say a 25 sigma I in this way. And as we often end our beer-discussions - may be all protein space groups are actually true P1, just close enough to satisfy the high symmetry rules .. but this is getting a bit philosop

[ccp4bb] Postdoctoral position for XFEL crystallography/spectroscopy at Berkeley Lab

We are looking for a postdoctoral fellow to study metalloenzymes using X-ray crystallography and spectroscopy at X-ray free electron lasers. The fellow will work in the Kern/Yachandra/Yano group ( http://www2.lbl.gov/vkyachan/ and http://biosciences.lbl.gov/profiles/jan-florian-kern/) at Berkeley

[ccp4bb] Rescuing CCP4i2 projects after a loss of CCP4 installation

to expect compressed database files, which presumably needs to be exported. Unfortunately, I only have the folder structure left. Is there a way to do that? Best, Jan PS: I can easily import ccp4i (old) projects - but that's of no help for the new projects. -- Dr. Jan Gebauer AG Prof.

Re: [ccp4bb] Off-topic question

Hi, there is a guide here, but you should get the proper script for Pymol from the Consurf server. http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/suzuki/jpxtal/Katsutani/en/consurf.php Jan On 6/22/19 10:24 PM, khaja faisal tarique wrote: > Hi everyone, > > I was wondering can anyon

Re: [ccp4bb] A ccp4I2 question

I can comfirm, it is my favourite feature of i2. I would like to see it automated (or -able using CLI) for flawless backup recovery. Cheers, Jan On 16/04/2019 14:22, Christian Roth wrote: > yes one can > > Cheers > Christian > > On Tue, Apr 16, 2019 at 1:19

Re: [ccp4bb] High Rfree in last Shell

ments of Biophysics and Biochemistry > UT Southwestern Medical Center > 5323 Harry Hines Blvd. > Rm. ND10.214A > Dallas, TX 75390-8816 > diana.tomch...@utsouthwestern.edu <mailto:diana.tomch...@utsouthwestern.edu> > (214) 645-6383 (phone) > (214) 645-6353 (fax) >

[ccp4bb] High Rfree in last Shell

Hi everyone, I’m trying to publish two structures at 3.1Å resolution with the following refinement statistics: Resolution range (Å) 49.2-3.1 49.3-3.1 Rfactor (%)24.0 (32.4)

Re: [ccp4bb] map rotation

100 228 112 MODE to AVER rota euler 1 0 0 TRANS 0 0 0 end eof Cheers, Jan On Mon, Mar 25, 2019 at 3:49 AM Eleanor Dodson wrote: > Hmm - I find maprot extremely confusing, but remember a wrkmap does not > use any symmetry so maybe that is why some is lost. > > I woul

Re: [ccp4bb] map rotation

ng something in maprot. Any input would be appreciated. This is public data, so I would be happy to share the data. Cheers, Jan On Wed, Mar 20, 2019 at 9:26 PM Jan Abendroth wrote: > Hi all, > this should be easy, scripting the rotation of a map. > Purpose for this is: Superimpo

[ccp4bb] map rotation

molecule A and B (not a big deal), more importantly, it cuts of certain areas on both molecules. Molecule A and B have low RMSDs (0.5Å). I must be missing something fairly obvious, have not been able to see what. Feedback would be much appreciated. Scripts are below. Thanks! Jan mapmask \ mapin

Re: [ccp4bb] 3D

We have tried PS VR, and it works even with coot. It has some obvious drawbacks with toolbars, so it is not perfect for model building, unless you have good set of keybindings configured and perfect muscle memory. I could also imagine to configure a gamepad, but we are not there yet. Jan On 3/11

[ccp4bb] Visualisation software supporting ChromaDepth

the viewer in Chimera -- I could write my own python script then... Thanks for all help, Jan Gebauer -- Dr. Jan Gebauer Structural Biologist px.uni-koeln.de / c2f.uni-koeln.de / pipc.uni-koeln.de To unsubscribe from the C

Re: [ccp4bb] Fwd: [ccp4bb] SO4 or PO4

This can be done at Diamond I23 beamline. https://doi.org/10.1016/j.nimb.2016.12.005 Best regards, Jan Dne 16.02.2019 v 18:49 Patrick Loll napsal(a): > S has about 0.56 anomalous electrons at 8 keV, whereas P has about > 0.44. This is a small difference between two weak signals—un

Re: [ccp4bb] 3D stereo and (pymol) Win 10

. I will let you know, once I know the results. Best regards, Jan On 2/1/19 3:19 PM, Pedro Matias wrote: > Hi all, > > Thanks Philippe, for the comprehensive discussion of the problem. > > I may also add that about 2 years ago I inquired our local DELL reseller > about laptops

Re: [ccp4bb] AW: [ccp4bb] 3D stereo and pymol

Awesome solution :-) I am sure, users will appreciate it. And I don't need stereo personally :-) Jan On 1/31/19 9:26 AM, Hughes, Jon wrote: > ...just open pymol, go to display - stereo mode - cross-eye then click > stereo. it might need a little practice and it makes one look even > sil

Re: [ccp4bb] 3D stereo and pymol

, and it seems that 3d vision is not very supported by NVIDIA, even for gamers... Was anybody able to mke it work with Geforce cards, to save few bucks? Best regards, Jan Dne 03.01.2018 v 10:42 Wim Burmeister napsal(a): > I answer a bit late, but I repost a message on 3D graphics from Mai > 2017 : >

Re: [ccp4bb] Can H-clashes be ignored ?

serious H-clash is checked, otherwise mostly not. Jan Dohnalek On Fri, Aug 17, 2018 at 6:27 PM Firdous Tarique wrote: > Hello everyone. > > I have a basic question. When a validation report of a coordinate is > generated we often come across a term known as "Too-Close Co

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

Dear Charles, is there a plan to release new base package of CCP4 which would contain all updates, so we don't have to go through the already quite lengthy update process with new installations? Best regards, Jan On 07/05/2018 03:15 PM, Ballard, Charles (STFC,RAL,CSE) wrote: > For those of

Re: [ccp4bb] Unidentified electron density blob

e? For example HEPES has a group with sulphur, which might be seen in anomalous map. If you see anomalous peaks on sulphurs of your protein, it might not be that unreasonable even on 1.0A-ish wavelength. Best regards, Jan Dne 06.07.2018 v 16:02 Robbie Joosten napsal(a): I'd like to add t

[ccp4bb] Acrimboldo BORGES standard libraries

/destination/BORGES_LIBS I selected 'edit set up file' while running 'ccp4sm'. Still, the standard libraries show in ccp4i remain greyed out, only CUSTOM is an option. The ccp4.setup-sh file does not seem to have a reference to BORGES. I wonder what I am missing to get this installed. Thanks, Jan

Re: [ccp4bb] Salt or protein?

Thanks your suggestions! I tried Dials but couldn’t get any further. There just too few spots like Artem suggested. I’ll follow Patrick’s advice to seed a new screening with this crystal. This one was really tiny. I may get a bigger one. Jan > On Feb 17, 2018, at 2:43 PM, Harry Powell <h

[ccp4bb] Course on fragment screening using crystallography laboratory equipment

://www.biocev.eu/event/instruct-ciisb-fragment-screening-course/ or the attached file for details. *Apply before February 9 2018 to frederic.velli...@ibt.cas.cz <frederic.velli...@ibt.cas.cz>.* Jan Dohnalek Institute of Biotechnology, Biocev Centre of Molecular Structure -- Jan Dohnalek

[ccp4bb] Senior Scientist (M/F) in Protein Crystallography at ZoBio

-Jan Waterreus

[ccp4bb]

You could try Xenon derivation chamber. DOI: 10.1107/S0907444902011010 Cheers, Jan On 29/11/17 13:05, Eleanor Dodson wrote: > That depends on the quality of your data and your model! > > I play with refinement and rebuilding - check indicators v > resolution., etc etc (I look at the

[ccp4bb] What is the easiest/cheapest way to obtain a library of proline derivatives?

Sorry for being a bit off-topic, but I’m looking to transform the catalytic properties of a protein I’m working on by adding an aromatic moiety on one of its prolines. However none of the proline derivatives I find commercially are really interesting. Does anyone know what would be the cheapest

[ccp4bb] Speaker opportunity at ACA 2018, session: Current state of instrumentation, automation, status and future

com> Jan Abendroth, Beryllium Discovery, jabendr...@be4.com<mailto:jabendr...@be4.com> Thanks and best wishes, Matt Clifton Jan Abendroth JAN ABENDROTH, Dr. Core Leader, CrystalCore P 206-780-8925 F 206-780-8547 Seattle | Boston | USA | be4.com [cid:image001.png@01D350FE.EE91E390]

[ccp4bb] Two openings for postdoctoral fellows at Berkeley National Lab

/ and http://biosciences.lbl.gov/profiles/jan-florian-kern/) at Berkeley Lab’s Molecular Biophysics & Integrated Bioimaging Division. We have been conducting a number of XFEL experiments on several different systems and some recent publications include: Fuller et al, Nature Methods 2017

[ccp4bb] Two openings for postdoctoral fellows at Berkeley National Lab

/jan-florian-kern/) at Berkeley Lab’s Molecular Biophysics & Integrated Bioimaging Division. We have been conducting a number of XFEL experiments on several different systems and some recent publications include: Fuller et al, Nature Methods 2017 http://www.nature.com/nmeth/journal/v14/n4/abs/n

Re: [ccp4bb] Coot: changing scroll map keybinding

So, thanks to pointing by Paul, I have found the keybinding definition in "python/template_key_bindings.py" on coot's github. It is called "Step scrollable map number" with suggested key "M" Jan On 07/12/2017 10:33 AM, Jan Stransky wrote: Hi, I believe, I ha

[ccp4bb] Coot: changing scroll map keybinding

st regards, Jan

Re: [ccp4bb] XDS on Windows

Hi Jan, Hi Rob, hi Gustavo, thanks for you answers. I totally missed the thread in the bb and couldn't find anything in the archive also the wiki entry - frankly I havn't checked that one for a while ... Great to know that the CU update solves most of the issues regarding the openMP

Re: [ccp4bb] HETATM record after Refmac

Indeed, even from i2. The issue is somewhere else, sorry for blaming refmac. Jan On 05/03/2017 01:09 PM, Robbie Joosten wrote: Hi Jan, That could be a postprocessing thing, because that version of Refmac works fine from the command line or from CCP4i (at least in my hands on Linux). Cheers

[ccp4bb] HETATM record after Refmac

Dear ccp4ers, is there way to retain HETATM keyword for ligands when running refmac? It apparently changes HETATM to ATOM which spoils some nice ligand features in Coot... Best regards, Jan

Re: [ccp4bb] Glycoprotein expression question

We had experience with a relatively small glycoprotein - when glycosylation sites were deleted, solubility went drastically down - we could not express soluble any more. Back to eukaryotic expression system which worked. So may be you were really lucky. Jan On Tue, Apr 11, 2017 at 10:34 PM

Re: [ccp4bb] Helium-Temp Cryo-Cooling

this geometry is difficult to achieve in most standard MX beam lines. I thought there was some initiative maybe 8-10 years ago at APS and at ESRF to get a He cryo jet running at one of their MX beam lines but I do not remember the details. Greetings, Jan On Tue, Apr 4, 2017 at 2:14 AM, Colin Nave <coli

Re: [ccp4bb] Proline derivatives

Thanks everyone for all the suggestion! I have plenty of options now! > On Mar 31, 2017, at 11:06 AM, Lakshmi SwarnaMukhi Pidugu > <swarna.pid...@gmail.com> wrote: > > You could try scifinder. > > Swarna > > On Wed, Mar 29, 2017 at 6:07 PM, Jan van Agthoven <

[ccp4bb] Proline derivatives

Hi Everyone, Does anyone know what’s the fastest way the find all commercially available proline derivatives on carbon gamma? Thanks, Jan

Re: [ccp4bb] Run on remote server

t the data are there in temp directory. Any ideas? Developers, any idea how to help you track down the bug? Is it possible to import resulting data back, including database entry? Jan On 02/13/2017 03:21 PM, Jan Stransky wrote: Good to know, it works indeed. Just worth noting, that the remote w

Re: [ccp4bb] Run on remote server

Good to know, it works indeed. Just worth noting, that the remote working dir must exist. Thanks Jan On 02/13/2017 02:10 PM, Stuart McNicholas wrote: Dear Jan, I see the same error message when doing "Test server group". However, when I actually run a job, all seems OK. I

[ccp4bb] Run on remote server

ile system is working outside CCP4.) On "Test server group" GUI ask for login credentials anyway. When giving htem, I get following: """ Testing server_hostname Failed connection 'NoneType' object has no attribute 'sshThreadRemoteFiles' """ Any ideas? Jan

Re: [ccp4bb] XDS questions

I had some cases, when path INTEGRATE.HKL -> Aimless gave data, from which it was not possible to solve structure by Phaser. It looked like structure solved, but then I got 45-50% Rwork/free. There were no problems with XDS_ASCCI.HKL -> Aimless (Not scale, just merge) path. Jan On 11/2

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