[ccp4bb] 2025 Sealy Center for Structural Biology Symposium - Register NOW

omolecular structures to biological function" To register or for more information, visit: https://www.utmb.edu/scsb/symposium Abstract Deadline: Monday, March 24, 2025 Mark Andrew White, Ph.D. Professor of Biochemistry & Molecular Biology, Director, SCSB Macromolecular X

[ccp4bb] Assistant Professor in Structural Biology, University of Nebraska-Lincoln

, sex, pregnancy, sexual orientation, gender identity, religion, disability, age, genetic information, veteran status, marital status, and/or political affiliation. See https://www.unl.edu/equity/notice-nondiscrimination. Best regards, Mark Mark A. Wilson Professor Department of Biochemistry/Redox

Re: [ccp4bb] Extra density on Cysteine

physicist will likely have a better idea about this than me. Mark van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) > On 21 Jun 2024, at 11:02, hsyu11gmail wrote: >

Re: [ccp4bb] E. coli strain M15 or SG13009 - muchas gracias to all who replied

-escherichia-coli-strains/ we have just today obtained a plate with M15(pREP4) from someone at another lab in Madrid who also subscribes to ccp4bb. other people also offered the pREF4 plasmid Mark van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle

[ccp4bb] E. coli strain M15 or SG13009

Dear All. we are looking for E. coli strain M15 or SG13009 to use for expressing a protein from the vector pQE30. Are these strains still availabe commercially? If not, we'd be open for another way to obtain an aliquot. Wbw, Mark Mark van Raaij Dpto de Estructura de Macromoleculas, la

Re: [ccp4bb] Skimming crystal

into practice. Mark van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) > On 30 May 2024, at 13:16, 白雪慧 wrote: > > May I ask scientific researchers, how can they

Re: [ccp4bb] what happened to Molprobity

same here, the website http://molprobity.biochem.duke.edu/index.php <http://molprobity.biochem.duke.edu/index.php> loads, but when trying uploading a pdb file nothing happens. Hopefully it is just a temporary glitch. Mark van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Na

[ccp4bb] Room temperature change from 25ºC to 20ºC

. Mark J van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain To unsubscribe from the CCP4BB list, click the following link: https

[ccp4bb] Faculty Positions at UTMB Galveston

Biology Faculty Opportunities Assistant Professor of Biochemistry and Molecular Biology in Computational Systems Biology and Structural Biology University of Texas Medical Branch - Galveston, Texas Computational Systems Biology – Faculty Opportunity: UTMB Health is seeking junior faculty can

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

just came across this critique of that paper on Twitter: https://twitter.com/Robert_Palgrave/status/1730358675523424344 Robert Palgrave (@Robert_Palgrave) on X twitter.com https://twitter.com/Robert_Palgrave/status/1730358675523424344but I'm not enough of an expert to judge - perhaps some char

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

, but to find and model all the water molecules (metal ions, protein and everything else) with reasonable density and hydrogen bonds. - when you write "improve the data", I assume you mean "improve the model". Best wishes, Mark Mark van Raaij Dpto de Estructura de Macro

Re: [ccp4bb] Database for submitting unprocessed diffraction data

This months publication in Acta Cryst F by Loes Kroon-Batenburg may be of interest: https://journals.iucr.org/f/issues/2023/10/00/va5053/index.html <https://journals.iucr.org/f/issues/2023/10/00/va5053/index.html> Mark van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacio

Re: [ccp4bb] Assistant Professor in Structural Biology, University of Nebraska-Lincoln

Professor. Best regards, Mark Mark A. Wilson (he/him) Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine St. Lincoln, NE 68588 From: Gerlind Sulzenbacher Date: Sunday, October 15, 2023 at 10:15 AM To: Mark Wilson , CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Assistant Professor in Structural Biology, University of Nebraska-Lincoln

out of 12 each year. You can then pay yourself out of a grant for the other 3 months - if you get a grant that allows paying yourself of course. Still seems a bit unfair, but at least it is not just a 9 months one time contract. Best wishes, Mark J van Raaij Dpto de Estructura de Macromoleculas

[ccp4bb] Assistant Professor in Structural Biology, University of Nebraska-Lincoln

, national origin, sex, pregnancy, sexual orientation, gender identity, religion, disability, age, genetic information, veteran status, marital status, and/or political affiliation. See https://www.unl.edu/equity/notice-nondiscrimination. Best regards, Mark Mark A. Wilson (he/him) Professor

Re: [ccp4bb] the structures of Nucleic acid

This just appeared and may be relevant: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad726/7272628 Critical Reviews and Perspectives When will RNA get its AlphaFold moment? Mark van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC

Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7

I reported this problem to Paul and to the group at least 2-3 months ago. It affects protein as well as nucleus acid.  I never heard back from Paul if a fix was in progress. Mark_Mark A. Saper, Ph.D.Visiting ProfessorFaculty of MedicineHebrew University of Jerusalem sa...@umich.

Re: [ccp4bb] Crystallisation textbook

e IUCr here: https://www.iucr.org/publications/iucr/buy Best wishes, Mark J van Raaij (Section Editor of Acta Cryst F) Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) > On 14 Jul

[ccp4bb] 27th Annual SCSB Structural Biology Symposium - Registration NOW OPEN

ie Zhang Ph.D. Texas A&M University To register or for more information, visit https://scsb.utmb.edu/symposium Mark Andrew White, Ph.D. Associate Professor of Biochemistry & Molecular Biology, UTMB, Galveston, TX 409.747.4747 https

[ccp4bb] Two postdoctoral positions open at CNB-CSIC

Two postdoctoral positions open at CNB-CSIC Two fully funded postdoctoral positions in the area of Structural Biology are available at Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain. PIs: Carmen San Martín, Mark J. van Raaij Starting on: June 2023 Contract length: 3 years Subject

Re: [ccp4bb] Renumber residues working PDB file - Applying a sequences numbering to PDB file

refinement, might be a nice little addition to ccp4. Mark J van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) Section Editor Acta Crystallographica F https://journals.iucr.org/f

Re: [ccp4bb] [EXT] Re: [ccp4bb] Regarding the diffraction image

in a similar condition to your protein - I don’t think you can conclude much more than that (unless there is some other difference like the TCEP being older this time and more oxidised, for example). Mark J van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecno

Re: [ccp4bb] [EXT] Re: [ccp4bb] Regarding the diffraction image

the unit cell in the c direction is quite long, 49 Å, this gives the relatively close spots in one direction. Mark J van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) Section

Re: [ccp4bb] Regarding the diffraction image

never know, it could be something interesting. Mark J van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) Section Editor Acta Crystallographica F https://journals.iucr.org/f

[ccp4bb] Last chance to nominate for the BCA Early Career Prize

@sussex.ac.uk<mailto:m@sussex.ac.uk>). Thanks, Mark Dr S.M. Roe, X-Ray Facility Manager, Tel. (+44) 01273 678863 (Office) School of Life Sc

[ccp4bb] BCA BSG Winter Meeting

able. Please note that we have tried to keep registration costs low. However, if you are a student and/or young researcher and are in need to support to attend this meeting then please contact our secretary Dr. Mark Roe (m@sussex.ac.uk<mailto:m@sussex.ac.uk>) to discuss your circum

Re: [ccp4bb] Low resolution and high anisotropy

simultaneously try to get a dataset from a better flash-cooled crystal while trying to get the most out of this dataset. Mark J van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092)

[ccp4bb] BCA BSG Winter Meeting

d this meeting then please contact our secretary Dr. Mark Roe (m@sussex.ac.uk<mailto:m@sussex.ac.uk>) to discuss your circumstances. Thanks BSG Committee. Dr S.M. Roe, X-Ray Facility Manager, Tel.

[ccp4bb] EDR (Sophos) and CCP4 compatibility

breaking CCP4 and other necessary programs. Any comments and experience with EDR software in general and Sophos in particular is appreciated, both for OSX and Linux. Saludos cordiales, Mark Mark J van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle

[ccp4bb] Session on mix-and-inject serial crystallography at the SSRL/LCLS Users' Meeting

and results featuring this exciting technique. The agenda is here: https://events.bizzabo.com/SLAC-UsersMeeting-2022/agenda/session/910608 The meeting is fully remote this year and registration is still open (https://events.bizzabo.com/SLAC-UsersMeeting-2022/home). Best regards, Mark Mark A

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

un through. Price: we got very good deals on the two Akta systems we bought, not more expensive than a comparable Biorad. But Cytiva service/repair is very expensive. Good luck, Mark Mark J van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin

Re: [ccp4bb] Unidentified electron density

Could it be Tris? Mark J van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) Section Editor Acta Crystallographica F https://journals.iucr.org/f/ https://namedrop.io

[ccp4bb] Cryo-EM Core Director position, University of Nebraska-Lincoln

-EM that is underway. Consideration of applicants will begin on June 15th and continue until the position is filled. Additional information about the position is below the line. Best regards, Mark Mark A. Wilson (he/him) Professor Department of Biochemistry/Redox Biology Center University of

Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

tps://iupred2a.elte.hu <http://iupred2a.elte.hu/> (which a colleague here likes because it also tries to predict likelihood of protein interactions) Or perhaps it's just because you were going to run alphafold2 anyway? best wishes, Mark Mark J van Raaij Dpto de Estructura de Macrom

[ccp4bb] Sealy Center for Structural Biology and Molecular Biophysics Symposium

Sealy Center for Structural Biology and Molecular Biophysics Virtual Symposium 26th Annual Structural Biology Symposium Presented by the Sealy Center for Structural Biology and Molecular Biophysics Saturday April 30, 2022 Register online at https://www.utmb.edu/scsb/symposium for more detail

Re: [ccp4bb] MR solution not working

. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain Section Editor Acta Crystallographica F https://journals.iucr.org/f/ > On 3 Mar 2022, at 05:43, Shubhashish Chakraborty > <750c9a1ca48b-d

Re: [ccp4bb] Negative density

or perhaps something in the non-visible part of the ligand pulling electrons out of the rings? can this somehow be specified as ligand input? on the other hand, I guess this is near the "end" of refinement, so the Fo-Fc difference map is probably very flat - meaning that 3 sigma corresponds to ve

Re: [ccp4bb] the complex structure of protein and DNA

Hi, With this resolution and R-factors, I would guess you are not missing that much – certainly not large bits of DNA. Do you have Phosphate or Sulphate in the crystallisation buffer? If so, you may just be seeing Phosphate/Sulphate where the DNA would bind. Cheers, Mark Dr S.M. Roe, X-Ray

[ccp4bb] BCA BSG Early Career Prize

@sussex.ac.uk<mailto:m@sussex.ac.uk>). Thanks, Mark Dr S.M. Roe, X-Ray Facility Manager, Tel. (+44) 01273 678863 (Office) School of Life Sc

Re: [ccp4bb] keyword for refmac to output coordinates in cif format

sorry, you can ignore my question. The mmcif file is output all along, for some reason I had never noticed it. how stupid of me... Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain Section Editor Acta

[ccp4bb] keyword for refmac to output coordinates in cif format

Dear All, this may be something simple but I can’t find it in the CCP4i GUI or online. Is there a keyword to make refmac output the coordinates as a cif file instead of a pdb file - or better, as both? Or is it some other program that converts the formats? Mark J van Raaij Dpto de Estructura de

Re: [ccp4bb] Add hydrogens

Dear Sam, 1CDW is from 1996, when it was not obligatory (or common practice) to upload structure factors to the PDB. So I think you can't do any refinement, just perhaps some optimisation. Mark J van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia -

[ccp4bb] Postdoctoral research opportunity

encouraged to apply. Please email inquiries and CV's (including names of three referees) to Brian Mark (brian.m...@umanitoba.ca). All the best, Brian Mark == Brian Mark, MSc, PhD Dean, Faculty of Science Professor, Department of Microbiology & Depa

Re: [ccp4bb] Move fem map back to protein?

Murpholino, You may want to consider where your protein is in relation to the Unit Cell and the Asymmetric Unit. Use the COOT File/Save Symmetry Coordinates/ to choose the symmetry molecule that fits the CCP4 map. Best regards, Mark Mark Andrew White, Ph.D. Associate Professor of

[ccp4bb] Register for the 2021 ACA Fundamentals of Single-Particle Cryo-EM Workshop

ere: https://www.acameeting.com/workshops Elizabeth (Liz) Kellogg (Cornell), Ed Twomey (Johns Hopkins), and I, Mark Herzik (UC San Diego) have assembled a panel of leading cryo-EM experts to present practical, technical advice used in their own groups and to answer questions from the audience. Confirmed speake

Re: [ccp4bb] Topology diagrams software

some info here: https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Topology_plots (haven’t done it myself for a while, so not sure which programs are still being maintained) Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E

Re: [ccp4bb] Analysis of NMR ensembles

input, you might get artificial “flexible” regions, and obtaining more NOEs, secondary structure restraints, measuring orientational restraints should shore these up. (Assuming that in the previous assignent phase all protons peaks could be properly assigned of course). Mark Mark J van Raaij Dpto de

Re: [ccp4bb] Unmodeled density

oh, 1.45 Å is a very short distance for metal coordination. perchlorate has a Cl to O distance of that length https://en.wikipedia.org/wiki/Perchlorate Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain Section Editor

Re: [ccp4bb] Unmodeled density

y the putative heavy(ish) atom that was co-crystallised. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain Section Editor Acta Crystallographica F https://journals.iucr.org/f/ > On 26 May 2021, at 15:08, leo joh

Re: [ccp4bb] Unmodeled density

the central blob looks too big for B or even for P or S. Perhaps Zn, Cd? (although you didn’t add it, it might have been in the protein buffer or dragged through the purification by the protein?) Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle

Re: [ccp4bb] sugestions on weak diffracting protein crystals

. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain Section Editor Acta Crystallographica F https://journals.iucr.org/f/ > On 18 May 2021, at 12:08, Deepak Deepak wrote: > > Dear all, > > I have got mu

[ccp4bb] Sealy Center for Structural Biology and Molecular Biophysics Virtual Symposium

Sealy Center for Structural Biology and Molecular Biophysics Virtual Symposium 25th Annual Structural Biology Symposium Presented by the Sealy Center for Structural Biology and Molecular Biophysics April 29-30, 2021 Register online at https://scsb.utmb.edu/symposium for more details. Invit

[ccp4bb] Fixing input anisotropic scale parameters in Refmac5

Dear Colleagues, I would like to run test refinements in Refmac5 where I can provide anisotropic scale parameters, fix them, and then proceed with restrained refinement of other model parameters. I could not find how to do this in the documentation-is this possible? Best regards, Mark Mark A

Re: [ccp4bb] unknown density

PEG in a high-res structure before, PEGs in several confirmations might explain a circle. Practically speaking, I’d first model five waters and see if they refine well. Mark > On 22 Mar 2021, at 14:58, Sam Tang wrote: > > Hello fellow colleagues > > Hope you are all well whil

Re: [ccp4bb] Can twinning be seen in the diffraction pattern?

this case the twinning is not (obviously) visible in the diffraction pattern - but detected through intensity statistics later. Best wishes, Mark Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain > On 12 Mar 2021,

Re: [ccp4bb] all of a sudden I cannot launch Coot nor ccp4i from the Terminal on my Mac laptop

? I don't think a Mac, not running Gnome desktop, would create such config files) Good luck, Mark [1] https://discourse.gnome.org/t/there-is-a-way-to-set-gnome-apps-to-prefer-dark-theme-through-command-line/3160 [2] https://unix.stackexchange.com/questions/8922/where-does-gsettings-stor

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

for not checking this well enough at the time and not knowing enough about mmcif standards. Or if there were later conversions/adaptations to the format that introduced these non-standard additions of 0 and o? Could it affect other entries? Ours, but also others? Mark J van Raaij Dpto de

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

53.98 112.75 90.00 100.43 90.00 Space group: C2 Average mosaicity: 0.68 Minimum and maximum SD correction factors: Fulls 1.04 6.74 Partials 1.63 13.05 Dataset: D9-25/nat/rm written as averaged data to output file /tmp/mark/D9-25_14_2_mtz.tmp M

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

uggested by the positive density. In any case, happy that this thread serves to learn something more from the comments by the experts. Mark Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain Section Editor Acta Crysta

[ccp4bb] Windows 10 and loggraph utility

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

[ccp4bb] Fwd: [ccp4bb] Postdoc position, Plant Hormone Transporting Membrane Proteins (Denmark)

in case it might be of interest for someone @CNB: > Begin forwarded message: > > From: Bjørn Panyella Pedersen > Subject: [ccp4bb] Postdoc position, Plant Hormone Transporting Membrane > Proteins (Denmark) > Date: 5 February 2021 at 17:20:38 GMT+1 > To: CCP4BB@JISCMAIL.AC.UK > Reply-To: Bjørn

Re: [ccp4bb] (scattering factors) f and f" for Sr Heavy atom

ly to give good phase info 9.7 kEV, values of f' = -0.65 and f" = 1.3, if I calculated/looked it up correctly Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain Section Editor Acta Crystallographica F https:/

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

a monomer. It will be interesting to see how well future iterations of the method can assemble the complete protein chain and the complete protein chains into the correct heteromer. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28

[ccp4bb] Log graphs not opening with CCP4i and Windows 10

Anyone run into the loggraph utility not opening on Windows 10? If not then any ideas what to check if it does not open? Mark To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi

Re: [ccp4bb] protein oligomer

), so the difference can be quite large. You can determine the real pI by iso-electric focussing. Best wishes, Mark Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 Section Editor Acta

Re: [ccp4bb] Quote source inquiry

I think most of us are such "excellent" cryo-coolers that for every beamline shift we have multiple crystals with ice ring diffraction :-) Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 9

Re: [ccp4bb] Commercial source of His-tagged protein

ey are happy to be named) Best wishes, Mark Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 Section Editor Acta Crystallographica F https://journals.iucr.org/f/ > On 2 Jul 2020, a

[ccp4bb] Commercial source of His-tagged protein

/expertise of a molecular biology lab (except us :-). We can and will make the His-tagged proteins of interest for them, but if there is an economical and reliable commercial source, it might be worth using that for initial tests. Best wishes, Mark Mark J van Raaij Dpto de Estructura de Macr

[ccp4bb] LCLS Project Scientist for Sample Delivery Posting

Job ID 4077 SLAC National Accelerator Laboratory (SLAC) is one of the world’s premier research laboratories, providing an internationally leading capability in t

[ccp4bb] NIH+DOE request for information for advancing high resolution bioimaging technologies

iscuss this in detail with you or answer any questions related to this RFI and LCLS capabilities. Please contact Mark Hunter (mhunt...@slac.stanford.edu<mailto:mhunt...@slac.stanford.edu>). We look forward to having an active discussion with you about how y

[ccp4bb] Call for submissions of interest in coronavirus research using LCLS

e SLAC/Stanford Cryo-EM<https://sites.slac.stanford.edu/cryo-em/> facilities is welcome. Please contact Mark Hunter (mhunt...@slac.stanford.edu<mailto:mhunt...@slac.stanford.edu>) for additional information and guidance. For more general information about LCLS, p

Re: [ccp4bb] Covalent Cysteine Aduct

this resolution (and with good phases from the refined model). In the CME case that Jack Tanner and other mentioned, you’d expect to see two peaks. Best regards, Mark Mark A. Wilson Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street

[ccp4bb] 25th Annual Structural Biology Symposium, May 2nd, Galveston TX - Registration is now OPEN

Best regards, Mark A. White, Ph.D. Associate Professor of Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics Macromolecular X-ray Laboratory, Basic Science Building, Room 6.658A

[ccp4bb] BCA Biological Structures Group Early Career Prize

o:m@sussex.ac.uk>). Thanks, Mark To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

[ccp4bb] Positions available at Evotec

Many thanks, Mark [cid:image002.png@01D514C2.B80E8D30] Dr. Mark Brooks Project Leader, mark.bro...@evotec.com<mailto:mark.bro...@evotec.com> www.evotec.com<http://www.evotec.com/> Evotec (U.S.) Inc Building 303B, College Road East, Princeton, NJ 08540, USA. STATEMENT OF CONFIDENTIA

[ccp4bb] Postdoctoral position in molecular image analysis methods development, University of Nebraska

Dear Colleagues, There is a postdoctoral position at the University of Nebraska in methods development for molecular image analysis. Application review has started and will remain open until the position is filled. Please see details below. Best regards, Mark Mark A. Wilson Associate Professor

Re: [ccp4bb] not solely pdb issue: need someone to officially settle the pdb dispute

Another problem is that the structure was apparently originally not cited properly, and now still cited as work from the lab of B, rather than as work of A... Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel

Re: [ccp4bb] not solely pdb issue: need someone to officially settle the pdb dispute

. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 > On 21 Aug 2019, at 11:22, Anastassis Perrakis wrote: > > If the structure has been deposited in the PDB and thus is pu

Re: [ccp4bb] need someone officially settle a pdb dispute for a publication

egal rulings, but are considered by their members (most respectable journals) as a strong guideline. This case may have similarities: https://publicationethics.org/case/claim-stolen-data-and-demand-retractions <https://publicationethics.org/case/claim-stolen-data-and-demand-retractions> Best

Re: [ccp4bb] challenges in structural biology

A recent paper in my favourite journal :-) suggests there is no correlation in crystallisation conditions even for similar proteins: http://scripts.iucr.org/cgi-bin/paper?S2053230X19000141 As you write, surface loops are likely to be diffe

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

The validation reports are pretty bad, so it seems to be a case where the referees and editor have not checked them. And, like Herman wrote, the models do not appear to agree well enough with the maps - in all three cases. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de

Re: [ccp4bb] MR for coiled coil structure

<https://journals.iucr.org/d/issues/2018/03/00/cb5097/> Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 > On 10 Jul 2019, at 10:00, Shengyang Jin wrote: > > Dear all, > > We recently

Re: [ccp4bb] resolution

much more info and maps should look better than at 3.0Å, even if the Rs are a bit higher. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 > On 5 Jul 2019, at 15:48, Sam Tang wrote:

[ccp4bb] Fwd: Domainex is hiring a Structural Biologist

Posted on behalf of Domainex. Begin forwarded message: From: Stefanie Reich mailto:s.re...@domainex.co.uk>> Date: 31. May 2019 at 17:04:20 CEST To: "ccp4bb@jiscmail.ac.uk" mailto:ccp4bb@jiscmail.ac.uk>> Subject: Domainex is hiring a Structural Biologist https:

Re: [ccp4bb] High Rfree in last Shell

Send your manuscripts to any of the IUCr journals! Might still get the occasional referee like that, but the editors should ignore those comments. plus you'd be supporting a scientific society [sorry for the advert...] Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacion

Re: [ccp4bb] High Rfree in last Shell

e, the only improvement you could make is collect better data. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://wwwuser.cnb.csic.es/~mjvanraaij Section Editor of Acta Crystallographica F,

Re: [ccp4bb] ORCID being mandatory for PDB depositions

really be fully responsible, because it would imply checking (i.e. redoing) much of it, but at least in the paper byline it should say who did what, giving some "safety" if something turns out wrong with the omics or the mice, but the structure(s) being fine. Mark J van Raaij D

Re: [ccp4bb] ORCID being mandatory for PDB depositions

with it (which I might not necessarily be able to judge). Similarly, as a structural biologist I might prefer not to be on the knock-out mice database entry in case there was something wrong or unethical in the way the mice were made... Mark J van Raaij Dpto de Estructura de Macromoleculas Centro

Re: [ccp4bb] ORCID being mandatory for PDB depositions

corresponding paper are also on the PDB entry, and there is nothing wrong with that, but if a (non-crystallographer?) collaborator really doesn't want an ORCID, he or she doesn't have to be an author of the PDB entry. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Bio

Re: [ccp4bb] problem with the symmetry water molecule

and set the occupancy of that water molecule to 0.50 > On 11 Mar 2019, at 17:17, Phil Jeffrey wrote: > > Hello Firdous > > You are seeing two because you are displaying crystallographic symmetry and > you are seeing its symmetry mate. Coot only places one (check the PDB file) > but displays

Re: [ccp4bb] Nitril groups not present on compounds

Hi Maria, from the picture, it looks like disorder to me. Note that the three non-H atoms at the top of the ring also have significantly less density than the five non-H atoms that are closer to the protein. Perhaps the compounds is just quite wobbly in it's binding site. Mark J van

[ccp4bb] Cryo-EM Data Processing Workshop, May 6-9, 2019 - Structural Biology Symposium, May 4, 2019

mic Resolution" Liang Tong, Ph.D., Columbia University "Structural Insights into RNA Processing and Quality Control" To register or for more information, visit http://scsb.utmb.edu/s

[ccp4bb] 24th Annual Structural Biology Symposium, May 4th, Galveston TX - Registration is now OPEN

Columbia University "Structural Insights into RNA Processing and Quality Control" To register or for more information, visit http://scsb.utmb.edu/symposium -- Yours sincerely, Mark A. White, Ph.D. Associate Professor of Bioch

Re: [ccp4bb] [EXTERNAL] [ccp4bb] refmac same residue different names

models, and it’s not clear to me how to do so. It sounds like Ed is encountering similar issues. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

I agree. We have encountered refinement problems similar to those Ed describes for models with mixtures of modified cysteine species, which is a fairly common occurrence. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska

Re: [ccp4bb] Live stream of CCP4 Study Weekend?

vation/webinars/ Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://wwwuser.cnb.csic.es/~mjvanraaij Editor of Acta Crystallographica F, Structural Biology Communications http://journals.iu

[ccp4bb] Structural Biology Position at Evotec (U.S.)

Zip Recruiter & please do not send applications through to me directly. https://www.ziprecruiter.com/jobs/evotec-473c889a/senior-scientist-protein-purification-structural-biology-f3e5dcbf Best wishes, Mark www.evotec.com<http://www.evotec.com/> Evotec (U.S.) Inc Building 303B, College

Re: [ccp4bb] anisou cards and refmac

BS”D Dear Garib, This is a deposited structure, not something I did. They used REFMAC 5.8.0107 Harry On 15 Oct 2018, at 12:25 PM, Garib Murshudov mailto:ga...@mrc-lmb.cam.ac.uk>> wrote: Dear Harry, Could you please send the script or log file from refmac. It should have not happened, bu

[ccp4bb] anisou cards and refmac

BS”D Dear All, I would just like to know how refmac handles the following setup. A deposited structure (2.8Å resolution) is a homotrimer protein (chains A, B,C) with bound dsDNA (chains D, E), and some water molecules. There is NCS (type: local) defined between the three protein chains (A t

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

issues with the exact physical nature of these interactions, particularly at short donor-acceptor distances. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472

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