Re: [ccp4bb] ATP analogues

://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> -- Matthew Bowler Project Leader MASSIF1@ESRF European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 G

[ccp4bb] Best practices for making metal fluoride complexes for structural biology

udies plus some case studies on their uses - it is now available on BioRxiv (see https://www.biorxiv.org/content/10.1101/2024.03.25.586559v1) - I hope people find it useful, any feedback would be highly appreciated. Happy Easter to all, Matt. Matthew Bowler Project Leader MASSIF1@ESR

Re: [ccp4bb] How to make GDP.BeF3 solution ?

: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> -- Matthew Bowler Project Leader MASSIF1@ESRF European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 G

Re: [ccp4bb] Can ALF3OH mimic the transition state?

Can anyone explain this to me, have you ever encountered this before? Your answer is much appreciated! Jinyu - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- Matthew Bowler Project Leade

[ccp4bb] [DEADLINE EXTENDED] Advanced Methods for Ambient Crystallography at ESRF-EBS Workshop - 21-23 November 2023

Jude) Daniel Keedy (CUNY) Silvia Russi (SSRL) Chia-Ying Huang (PSI) Sasha Popov (ESRF) Clemens Vonhrein (GPhL) Nicolas Coquelle (IBS) -- Matthew Bowler Project Leader MASSIF1@ESRF European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 Grenoble France

[ccp4bb] Advanced Methods for Ambient Crystallography at ESRF-EBS Workshop - 21-23 November 2023

speakers and tutors include: Robert Thorne (Cornell) Marcus Fischer (St Jude) Daniel Keedy (CUNY) Silvia Russi (SSRL) Chia-Ying Huang (PSI) Sasha Popov (ESRF) Clemens Vonhrein (GPhL) Nicolas Coquelle (IBS) -- Matthew Bowler Project Leader MASSIF1@ESRF European Molecular Biology Laboratory 71 avenue

[ccp4bb] PostDoc position at EMBL Grenoble to work on ESRF beamline MASSIF-1

/searchjobs/index.php?nPostingID=1225&nPostingTargetID=2879&ID=QHPFK026203F3VBQB688N79SB Closing date is the 12th October and interviews will be early November 2020. Best wishes, Matthew. -- Matthew Bowler Synchrotron Crystallography Group European Molecular Biology Laboratory 71 avenue des Ma

[ccp4bb] PostDoc position at EMBL Grenoble to work on ESRF beamline MASSIF-1

&nPostingTargetID=2879&ID=QHPFK026203F3VBQB688N79SB Closing date is the 12th October and interviews will be early November 2020. Best wishes, Matthew. -- Matthew Bowler Synchrotron Crystallography Group European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 Grenobl

Re: [ccp4bb] dewar horror stories

-1192 USA (215) 762-7706 pj...@drexel.edu <mailto:pj...@drexel.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- Matthew

[ccp4bb] PostDoc position at EMBL Grenoble to work on ESRF beamline MASSIF-1 - closing date 15/12/19

here https://www.embl.fr/jobs/searchjobs/index.php?ref=GR00140&newlang=1&loc[]=4 Closing date is the 15th December and interviews will be 27th January 2020. Best wishes, Matthew. -- Matthew Bowler Synchrotron Crystallography Group European Molecular Biology Laboratory 71 avenue des Ma

[ccp4bb] PostDoc position at EMBL Grenoble to work on ESRF beamline MASSIF-1

;loc[]=4 Closing date is the 15th December and interviews will be 27th January 2020. Best wishes, Matthew. -- Matthew Bowler Synchrotron Crystallography Group European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 Grenoble France ===

Re: [ccp4bb] channels in crystal packing

Hi Jean-Luc, Doug Juers wrote a program for this called MAP_CHANNELS, see http://scripts.iucr.org/cgi-bin/paper?S160057671402281X Cheers, Matt On 2019-05-11 09:39, ferrer wrote: Dear all, I am looking for a software to measure channels diameter and larger volumes along these channels in a c

Re: [ccp4bb] Thoughtful remark...

m the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- Matthew Bowler Synchrotron Crystallography Group European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 Grenob

Re: [ccp4bb] Name that protein!

law...@jic.ac.uk> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- Matthew Bowler Synchrotron Crystallography Group European Molecular Biology Lab

[ccp4bb] Fully automated intelligent data collection : MASSIF-1@ESRF

ther questions please don't hesitate to contact me (mbow...@embl.fr <mailto:mbow...@embl.fr>) or Didier Nurizzo (nuri...@esrf.fr <mailto:nuri...@esrf.fr>). Best wishes, Matthew. Web:http://www.esrf.eu/MASSIF1 Mail: mass...@esrf.fr <mailto:Mail:mass...@esrf.fr> FAQ:http

[ccp4bb] Fully automated intelligent data collection : MASSIF-1@ESRF

X For any further questions please don't hesitate to contact me (mbow...@embl.fr) or Didier Nurizzo (nuri...@esrf.fr). Best wishes, Matthew. Web:http://www.esrf.eu/MASSIF1 Mail: mass...@esrf.fr FAQ:http://www.esrf.eu/MASSIF_FAQ -- Matthew Bowler Synchrotron Crystallography Group European M

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

lling -> 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/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij -

Re: [ccp4bb] cryo condition

-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 - -- Matthew Bowler Synchrotron Crystallography Group European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 Grenoble

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

ssion 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-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 24 Apr 2015, at 12:45, Matthew BOWLER

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

e for the suggestions! William --- The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 215 Euston Road, London NW1 2BE. -- Matthew Bowler Synchrotron Diffraction

[ccp4bb] ECM29 microsymposium on Crystallization and Crystal Treatment

two 30-min talks from invited speakers, three 20-min talks chosen from the submitted abstracts, and poster presentations. Looking forward to many interesting contributions. With best regards, Matthew Bowler and Terese Bergfors (co-chairs) -- Matthew Bowler Synchrotron Crystallography Group

[ccp4bb] ECM29 microsymposium on Crystallization and Crystal Treatment

presentations. Looking forward to many interesting contributions. With best regards, Matthew Bowler and Terese Bergfors (co-chairs) -- Matthew Bowler Synchrotron Crystallography Group European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 Grenoble France

Re: [ccp4bb] Absence of contact between layers in a crystal

(GNU/Linux) iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi j0JFZac4kAh8twpov71MG84= =XN57 -END PGP SIGNATURE- -- Matthew Bowler Synchrotron Diffraction Group European Molecular Biology Laboratory 71, avenue des Martyrs CS 90181 F-38042 GRENOBLE Cedex 9 FRA

Re: [ccp4bb] ligand bonds (AlF3) breaking up after refinement in refmac

oded AlF3. Also, no such warning, mentioning the actual bond length, is there in the log file of Refmac. regards, Ansuman On Saturday, 17 January 2015 8:51 PM, Matthew BOWLER wrote: Dear Ansuman, I agree with Matthew that the refinement seems to be OK - the reason the bonds are longer

Re: [ccp4bb] ligand bonds (AlF3) breaking up after refinement in refmac

Dear Ansuman, I agree with Matthew that the refinement seems to be OK - the reason the bonds are longer is because what you actually have bound is MgF3- and not AlF3. MgF3- is a much better transition state analogue as it is isosteric and isoelectronic with a transferring phosphoryl group. At p

Re: [ccp4bb] equivalent osmotic pressures for xtal transfer

Hi Frank, I have never tried this for soaking but all the conversions that you need between any salt and any other ppt can be found here http://go.esrf.eu/RH, the RH matching is the same process as osmolarity so it could work, best wishes, Matt. On 2014-07-26 21:42, Frank von Delft wrote

Re: [ccp4bb] Crystals Disappearing Overnight

Ng4dZzXQG5+LQiPwZVdXXQ= =LbR6 -END PGP SIGNATURE- -- Matthew Bowler Synchrotron Science Group European Molecular Biology Laboratory BP 181, 6 rue Jules Horowitz 38042 Grenoble Cedex 9 France === Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.88.2

Re: [ccp4bb] Non-catalytic Rossmann fold domain

: 573-884-1280 fax: 573-882-2754 http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html [2] Links: -- [1] mailto:tanne...@missouri.edu [2] http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html -- Matthew Bowler Synchrotron Science Group European Molecular Biology Laboratory BP

Re: [ccp4bb] Large Conformational Change Upon Binding Ligand...

*** -- Matthew Bowler Synchrotron Science Group European Molecular Biology Laboratory BP 181, 6 rue Jules Horowitz 38042 Grenoble Cedex 9 France === Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.88.29.04 http://www.embl.fr/ ===

Re: [ccp4bb] crystals with large solvent content -dehydratation

al. So it would seem that equilibrating at a certain RH in the FMS vs in a droplet could have very different results. is there any data on this? Matthew Bowler wrote: Hi Andre, a very effective method is the use of a humidity control device. It has the great advantage that you can characterize cha

Re: [ccp4bb] crystals with large solvent content -dehydratation

all salt?, should I keep the additive concentration?, how much precipitant should I add? how many steps?). crystal condition: 23% PEG 3350, 0.2M NaCl, 0.1M Tris pH 8.5, 3% galactose (orthorhombic crystals, with about 0.6 x 0.6 mm) all the best, Andre Godoy -- Matthew Bowler Synchrotr

Re: [ccp4bb] cryo condition

Ed. On Thu, 2013-05-23 at 14:38 +0200, Matthew BOWLER wrote: Hi Faisal, if your solvent channels are smaller than 40A in the largest dimension (most are) you can use a mesh loop to pick up the crystal and then wick away all of the mother liquor. You can then flash cool your crystal witho

Re: [ccp4bb] cryo condition

olatile mother liquor components, which shouldn't be happening here to the same degree. Cheers, Ed. On Thu, 2013-05-23 at 14:38 +0200, Matthew BOWLER wrote: Hi Faisal, if your solvent channels are smaller than 40A in the largest dimension (most are) you can use a mesh loop to pick u

Re: [ccp4bb] cryo condition

Sciences JNU -- Matthew Bowler Synchrotron Science Group European Molecular Biology Laboratory BP 181, 6 rue Jules Horowitz 38042 Grenoble Cedex 9 France === Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.88.29.04 http://www.embl.fr/ ===

Re: [ccp4bb] cryo condition

of Life Sciences JNU -- Matthew Bowler Synchrotron Science Group European Molecular Biology Laboratory BP 181, 6 rue Jules Horowitz 38042 Grenoble Cedex 9 France === Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.88.29.04 http://www.embl.fr/ ===

Re: [ccp4bb] How to generate a complete viirus PDB

d I use to generate a complete virus PDB using the NCS? Thank you Hong Hsiang -- Matthew Bowler Synchrotron Science Group European Molecular Biology Laboratory BP 181, 6 rue Jules Horowitz 38042 Grenoble Cede

Re: [ccp4bb] seeking help from a bioinformatics guru

, How many unique transmemberane protein structure have by far been solved by X-ray? 2, How many X-ray structures of water-soluble domains in which their membrane-anchoring alpha helices have been removed? I tried PDB search and PDBe search, but no success by far? Thank you very much! Mike

Re: [ccp4bb] crystal dehydration

AM, Matthew BOWLER wrote: Hi Judith, a very effective method is the use of a humidity control device - this was actually the reason we developed the equations that predict the RH in equilibrium with precipitant solutions. It has the great advantage that you can characterize changes that occur

Re: [ccp4bb] crystal dehydration

dehydration of protein crystals. Thanks! Best, Judith -- Matthew Bowler Synchrotron Science Group European Molecular Biology Laboratory BP 181, 6 rue Jules Horowitz 38042 Grenoble Cedex 9 France === Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.88.29.04

Re: [ccp4bb] Equilibrium Relative Humidity matching

work in batch, e.g. people making crystals for X-FEL data collection. You can download it as a program from http://www.douglas.co.uk/vdtomb/vdtomb.htm - it seems to work pretty well. Best wishes Patrick On 22 November 2012 12:11, Matthew Bowler <mailto:mbow...@embl.fr>> wrot

[ccp4bb] Equilibrium Relative Humidity matching

er in the crystallisation drop by a controlled amount. Hope it is useful, cheers, Matt. -- Matthew Bowler Synchrotron Science Group European Molecular Biology Laboratory BP 181, 6 rue Jules Horowitz 38042 Grenoble Cedex 9 France === Tel: +

Re: [ccp4bb] three letter codes for buffer components

/ The University of Dundee is a registered Scottish charity, No: SC015096. The University of Dundee is a registered Scottish Charity, No: SC015096 -- Matthew Bowler Structural Biology Group European Synchrotron Radiation Facility B.P. 220, 6 rue Jules Horowitz F-38043 GRENOBLE CEDEX FRANCE

Re: [ccp4bb] IUCr committees, depositing images

; thunderingly absent from this thread has been the chorus of volunteers who will write the grant. phx -- Matthew Bowler Structural Biology Group European Synchrotron Radiation Facility B.P. 220, 6 rue Jules Horowitz F-38043 GRENOBLE CEDEX FRANCE === Tel

Re: [ccp4bb] Methods for dehydrating crystals

am trying to push the resolution of my crystals. Thanks, Andrea -- Matthew Bowler Structural Biology Group European Synchrotron Radiation Facility B.P. 220, 6 rue Jules Horowitz F-38043 GRENOBLE CEDEX FRANCE === Tel: +33 (0) 4.76.88.29.28 Fax: +33

Re: [ccp4bb] identifying hinges in flexible proteins

-domain protein in which domain movements of up to 30 degrees are observed. Is there a programme available which attempts to determine rigid-body units and hinge regions in an 'unbiased' way? thanks for your suggestions, Stephen Cusack -- Matthew Bowler Structural Biology Grou

Re: [ccp4bb] Homology modelling

esidues. Does anyone know of another program that I could use to do this step? Similarly if anyone knows other software tools/methods I could use to try and work out the implications of sequence changes I would be grateful for advice. Thanks, Simon -- Matthew Bowler Structural Biology Group

[ccp4bb] Solvent channel volume measurement

Dear All, does anyone know of a program that can measure the volume or largest dimension of the solvent channels in crystals? Cheers, Matt. -- Matthew Bowler Structural Biology Group European Synchrotron Radiation Facility B.P. 220, 6 rue Jules Horowitz F-38043 GRENOBLE CEDEX FRANCE

[ccp4bb] Post-doctoral position in membrane protein structure at the ESRF

me with informal enquiries. Many thanks, Matt. -- Matthew Bowler Structural Biology Group European Synchrotron Radiation Facility B.P. 220, 6 rue Jules Horowitz F-38043 GRENOBLE CEDEX FRANCE === Tel: +33 (0) 4.76.88.29.28 Fax: +33 (0

[ccp4bb] Post-doctoral position in membrane protein structure at the ESRF

laboratory facilities you could need. Please follow the instructions below to apply but feel free to email me with informal enquiries. Many thanks, Matt. http://www.esrf.eu/Jobs/Research/2320 -- Matthew Bowler Structural Biology Group European Synchrotron Radiation Facility B.P. 220, 6 rue Jules

Re: [ccp4bb] Dehydration treatments

makrishnan-lab MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK -- Matthew Bowler Structural Biology Group European Synchrotron Radiation Facility B.P. 220, 6 rue Jules Horowitz F-38043 GRENOBLE CEDEX FRANCE === T

Re: [ccp4bb] database-assisted data archive

UsersAndScience/Experiments/MX/Software/ispyb Enrico. -- Matthew Bowler Structural Biology Group European Synchrotron Radiation Facility B.P. 220, 6 rue Jules Horowitz F-38043 GRENOBLE CEDEX FRANCE === Tel: +33 (0) 4.76.88.29.28 Fax: +33 (0) 4.76

Re: [ccp4bb] Blue color upon X-ray exposure?

Minnesota Dept. of Medicinal Chemistry 308 Harvard St. SE, #8-101WDH Minneapolis, MN 55455 Office 2-163 WDH / Lab 2-160 WDH Phone: 612-624-2448 -- Matthew Bowler Structural Biology Group European Synchrotron Radiation Facility B.P. 220, 6 rue Jules Horowitz F-38043

Re: [ccp4bb] Crystal rescue

ns or comments? Thanks a lot! Best, Zhiyi -- Matthew Bowler Structural Biology Group European Synchrotron Radiation Facility B.P. 220, 6 rue Jules Horowitz F-38043 GRENOBLE CEDEX FRANCE === Tel: +33 (0) 4.76.88.29.28 Fax

Re: [ccp4bb] FW: [ccp4]: TDS upon flashcooling

ng re-annealing times lead to cracking of the crystal. My two questions would be: - any thoughts on cryo solutions? - does the result from the re-annealing experiment ring any bells? Would this be an indication that I need the cooling to be faster or slower? Cheers, Rafael. -- Matthew B

Re: [ccp4bb] sulfur sad phasing

, calcium, sulfate in already phased structures? Thanks in advance, Matthias -- Matthew Bowler Structural Biology Group European Synchrotron Radiation Facility B.P. 220, 6 rue Jules Horowitz F-38043 GRENOBLE CEDEX FRANCE === Tel: +33 (0

[ccp4bb] PhD position at the ESRF Structural Biology Group

complex with metallofluorides * ^19 F --NMR spectroscopy of protein metallofluoride complexes *Place of Work:* ESRF in Grenoble *Supervisors:* Dr. Matthew Bowler, T: +33 (0)4 76 88 29 28, email: bow...@esrf.fr <mailto:bow...@esrf.fr> P

[ccp4bb] shelxl LS refinement problem: summary

Dear BB, after very quick replies from George Sheldrick and Kay Diederichs we recompiled shelxh setting JW to 1200 and IM to 32000 and it worked beautifully. Thank you both very much for your help, regards, Matt. -- Matthew Bowler Structural Biology Group European Synchrotron

[ccp4bb] shelxl LS refinement problem

THIS PROBLEM ** even though I have added the line BLOC 1 N_1001 > LAST. Is there a way round this? I really only want the errors on a ligand so would it help to do the full matrix refinement only on a selected set of atoms? Many thanks, yours, Matt. -- Matthew Bowler Structural Biology Gr

[ccp4bb] EMBO / MAX INF2 Practical Course on Structure Determination in Macromolecular Crystallography, ESRF, June 15-19, 2009.

r of participants is limited to 20 and the deadline for application is May 1^st , 2009. More detailed information, the course programme and instructions as to how to apply to attend the course can be found in the webpages at the URL: http://cwp.embo.org/pc09-05/. -- Matthew Bowler Macromolec

[ccp4bb] EMBO / MAX INF2 Practical Course on Structure Determination in Macromolecular Crystallography held at the ESRF, June 15-19, 2009.

is limited to 20 and the deadline for application is May 1^st , 2009. More detailed information, the course programme and instructions as to how to apply to attend the course can be found in the webpages at the URL: http://cwp.embo.org/pc09-05/. -- Matthew Bowler Macromolecular Crystal

[ccp4bb] Postdoctoral Fellow, Membrane protein structure at the ESRF

rable. Only candidates holding a Ph.D. obtained less than 3 years ago are eligible for Post-doctoral positions. Post-doctoral fellows are employed for a two year-period with a possibility of extension to three years. The contract will start as soon as possible. Contact person: Matthew Bowler

[ccp4bb] Workshop Announcement: Biological physics at large facilities: From molecules to cells

/* */ /* *//* *Abstracts for Oral or Poster presentations : Deadline 12 September 2008.**//* */A few bursaries are available for financial help to attend the workshop/* -- Matthew Bowler Macromolecular Crystallography Group European Synchrotron Radiation Facility

[ccp4bb] Summary: Refmac unrestrained refinement on ligands only

. Many thanks to all who replied, cheers, Matt. Matthew BOWLER wrote: Dear All, I have looked everywhere for answers on this one with no luck... I have several structures at reasonable resolution 1.7 to 1.1A. I have performed unrestrained refinement on the model which is fine for the

[ccp4bb] Refmac unrestrained refinement on ligands only

. So what I would like to do is unrestrained refinement only on the ligands and leave the protein restraints in place. I have a feeling that if I cannot do it in Refmac I can in phenix but I cannot find anything out about that either. All help greatly appreciated, yours, Matt. -- Matthew