Re: [ccp4bb] what happened to Molprobity

same here, the website 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 Nacional

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

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

Dear Mandar, - you may be able to find some more, less well-ordered, waters by looking at (difference) maps. These will probably refine to have higher B-factors, pushing your average up. - some of your best-ordered water molecules may in fact be metal ions, you can check the coordination.

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 Mark van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de

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

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] 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

[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

or 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 Biotecnologia

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

Re: [ccp4bb] Low resolution and high anisotropy

ltaneously 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) Sect

[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

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

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 3 E-28049 Madrid, Spain t

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

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

ed2a.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 Macromoleculas, lab 2

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

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 - CSIC

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

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 john wr

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

Re: [ccp4bb] unknown density

The ring looks too big to be imidazole or a nucleotide or a carbohydrate, so it’s probably mainly water molecules. Perhaps partially replaced by PEG to explain the density between them (i.e. water molecules in most copies of the protein and PEG in some other copies). I’ve seen horse-shoe shaped

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

that in 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, at 11

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

2.20A 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 22 Feb 2021, at 20:38, Gerard Bricogne wrote: > > Dear Patrick, Ma

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

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 Crystallographica F https://jou

[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

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://journals.iucr.

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

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

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, at 11:50, Trista

[ccp4bb] Commercial source of His-tagged protein

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 Macromoleculas

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

ot legal 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 of l

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

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 recent

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:

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 Nacional de

Re: [ccp4bb] High Rfree in last Shell

e 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, Stru

Re: [ccp4bb] ORCID being mandatory for PDB depositions

to 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

of the 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 Biotecnologia

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 Raaij

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

Re: [ccp4bb] Structure solution - hexapeptide

When I was at Santiago de Composrela Univ., we have had success with the CCP4 program ACORN even at around 1.2 Å resolution. Also peptides, no heavy atoms.Didn't do this myself though I have to admit, but could put you in contact with the people who did. Mark J van

[ccp4bb] Some sort of "closure"?

[it's about the famous case of fabricated structures and structure factors] 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 Crystallograp

Re: [ccp4bb] does 12 A diffraction worth optimization

ehydration: https://pubs.acs.org/doi/10.1021/cg500890r <https://pubs.acs.org/doi/10.1021/cg500890r>. 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/~m

Re: [ccp4bb] [Off-topic] Comparison of the same structure built by many people

This one?http://scripts.iucr.org/cgi-bin/paper?SE0260 Mark J van RaaijCNB-CSICwwwuser.csic.es/~mjvanraaij Original message From: Shintaro Aibara Date: 20/11/2017 21:25 (GMT+01:00) To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] [Off-topic] Comparison

Re: [ccp4bb] doubt regarding MR search model

, P2122, P2212, P2221, P21212, P21221, P22121 and P212121. Phaser can do this automatically for you by clicking the right box. If necessary, then try lower symmetry like P21 and perhaps P1. Programs like Xanuda can help. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de

Re: [ccp4bb] Protein rapidly precipitates when off ice

a sufficiently interesting protein fragment remains. 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 > On 14 Jul 2017, at 08:14, Debanu Das <

Re: [ccp4bb] weird diffraction pattern

rotating around the most problematic cell axis, which tends to be the shortest in the crystal. Bent loops might be helpful. 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 <h

Re: [ccp4bb] Se-Met and Se-Cys double labelling

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 > On 21 Jun 2017, at 17:46, Vito Calderone <calder...@cerm.unifi.it> wrote: > > I am worki

Re: [ccp4bb] in crystallo enzymatic activity

rhaps even important for natural regulation. And the mutant you make somehow lessened this requirement? 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 <http://www.cnb.csic.e

Re: [ccp4bb] waters with positive FoFc peaks?

Partially occupied Cs+ comes to mind. At lower resolution the difference may be more easily fudged away by the refinement lowering the B. Mark J van RaaijCNB-CSICwwwuser.csic.es/~mjvanraaij Original message From: Andrew Marshall Date:

Re: [ccp4bb] High Rfree: Phasing issue or partial crystal disorder

try placing the nearest structural homologue of the N-terminal domain as well as you can and see if some density appears, that way you have corrected the solvent envelope more or less and this could maybe help a bit. Greetings, Mark Mark J van Raaij Dpto de Estructura de Macromoleculas Centro

Re: [ccp4bb] Some problems in data processing

activated when necessary (at least I have rarely been able to improve on automatically processed data when doing it myself later...) Greetings, 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

Re: [ccp4bb] Using a codon-optimised gene to improve protein solubility

more details about your protein it's hard to give more help - you could try to contact other researchers studying similar proteins. Greetings, 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

Re: [ccp4bb] binding protein to nickel column

Could it be due to the fact that the protein is a histidine kinase - perhaps it is interacting with or even modifying its own his-tag? 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

Re: [ccp4bb] Large number of outliers in the dataset

-ordered aa from the input model, refine at different resolutions and compare the difference maps for that aa. Or calculate omit maps at different resolutions and compare those. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid

Re: [ccp4bb] Ramachandran statistics and referee responsibility

and not concealed…and authors and users of models refined against low-resolution data should be realistic about the conclusions one can draw from them. 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

Re: [ccp4bb] symmetry and pdb remark

the 6 equivalent ones of each that you want, un-showing or deleting the others by hand. Note that if you superpose 2zan onto 2zam and then include the CRYST1 card of 2zam, you are generating the packing for 2zam, not 2zan, so that does not make scientific sense. Mark J van Raaij Dpto de

Re: [ccp4bb] glycosylated density blob?

well yes, looks like a glycosylation to me too. However, at 2.75Å resolution I think it will be impossible to know which one from the density alone. Perhaps mass spectroscopy can give a clue? Or get clues from what is known about your protein and your expression system. Mark J van Raaij Dpto de

[ccp4bb] PhD fellowships in Spain

demic records, reference letters and a B2 level certificate in english need to be supplied (nationals of english-speaking countries are exempted). Greetings, 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] Need suggestion for protein solubility

afterwards and hopefully it would not precipitate because the non-protein impurities are removed. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij <h

Re: [ccp4bb] R/Rfree values

. Greetings, 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 > On 14 Dec 2016, at 16:02, rohit kumar <rohit...@gmail.com> wrote: >

Re: [ccp4bb] Skin on the drop

Microbatch under oil in Terasaki plates or perhaps microdialysis might be an option. Then you don’t have a liquid/air interface. It is harder to do very small volumes then, especially with microdialysis. Or free interface diffusion in thin tubes (or with specialised equipment). Mark J van Raaij

Re: [ccp4bb] merge different crystal data

the short axis of your crystals, which is observed often, you may need to use bent loops). 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 > O

Re: [ccp4bb] suggestion for structure solution of a protein with low sequence identity

. - residues 1-49 and 370-377 may be genuinely disordered and not modellable, how hard did you try? Hope this helps, 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

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

model building (Auto)BUSTER for structure refinement Uppsala Software Factory programs (Mapman, etc.), manipulation of maps and PDB files Cryo-EM software (EMAN2, BSOFT) Available in Windows but with important limitations: Phenix (no MR-Rosetta, no parallelization) DIALS (no parallelization) Mark J

[ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

Phenix (no MR-Rosetta, no parallelization) CCP4 (limitations on file-names) Please correct me if pertinent and provide additional examples if possible. Gratefully yours, Mark Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid

Re: [ccp4bb] strange X-ray diffraction diagram――RNA Or Complex？

brooms? The stick part of the broom may be the single crystal. 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 > On 12 Oct 2016, at 08:54,

Re: [ccp4bb] Retraction of 2HR0

not be aware of the problems of the original structure…of course, MR with a made-up structure is not very likely to work... Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://wwwuser.cnb.csic.es

[ccp4bb] Easy way to generate symmetry-related protein chains?

be easier ways. in the CCP4bb archive I found the following tip for COOT: Extensions - Modelling - Symm Shift Reference Chain Here. but that does not appear to be available in COOT, or not anymore. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c

Re: [ccp4bb] Easy way to generate symmetry-related protein chains? (summary)

It seems the easiest way is to Save Symmetry Coordinates in COOT and then assemble the desired chains in a text editor. Extensions - Modelling - Symm Shift Reference Chain Here. is present if you build COOT yourself, but is not in the pre-built releases (for now). Mark J van Raaij Dpto de

Re: [ccp4bb] HIS related crystallography issue

the side-chain needs flipping. At even higher solution you may see difference density in wrongly oriented His/Asn/Gln side-chains. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http

Re: [ccp4bb] Online server for generation of topology cartoons

the output from one or more of these programs as guide. It is than also easier to change them upon suggestions of collaborators or referees. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http

Re: [ccp4bb] Protein precipitation

a third way to use the information would be to reclone the part before and/or after the protease cleavage site, i.e. you may have identified (a) stable domain(s) that may crystallize much better than the full-length protein. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional

Re: [ccp4bb] Gadolinium complexes- phosphate buffer

to the drop and fish crystals after different incubation times. Greetings, Mark Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 18 May 2015, at 11:42

[ccp4bb] Question for those who use AutoSharp via CCP4i on MacOSX Yosemite

this? Greetings, Mark J van Raaij mjvanra...@cnb.csic.es mailto:mjvanra...@cnb.csic.es http://www.cnb.csic.es/~mjvanraaij http://www.cnb.csic.es/~mjvanraaij

Re: [ccp4bb] Maximising anomalous signal in helical/line scan

Hi Matthew, William seems to want to increase the x-ray intensity gradually during the experiment by augmenting the transmission gradually. It that possible? If so, would it be advisable? Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E

[ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

The abstract of the papers says they used MIR. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 23 Apr 2015, at 18:57, Todd Jason Green wrote

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

The abstract of the papers says they used MIR. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 23 Apr 2015, at 18:57, Todd Jason Green wrote: My

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

conclusions in the paper than what is supported by the medium-resolution data, the structure provides useful information. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es

[ccp4bb] CrystalClear tape rolls

. Greetings, Mark Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij

Re: [ccp4bb] CrystalClear tape rolls

you are right, I must have been looking with my ears when I checked this morning. https://hamptonresearch.com/product_detail.aspx?cid=10sid=88pid=271 Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34

Re: [ccp4bb] Balbes

models and are easier to use than Amore, but usually take a bit longer. Balbes is overkill for a problem like this. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es

Re: [ccp4bb] Merge PDB chains

program to do it, or already have one lying around... Mark Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 23 Oct 2014, at 12:51, luzuok wrote

[ccp4bb]

, if appropriate. Or increase the allowed overlap. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 27 Sep 2014, at 13:34, rohit kumar wrote: Dear All

Re: [ccp4bb] Enigmatic electron density attached to Cys residue

What odds to you give us? ...I bet on disordered DTT covalently bound to the protein. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 19 Aug

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