[ccp4bb] map file specification

Hi, I am looking at the specifications of the ccp4 map file format and I am confused with the number of columns and the number of intervals. I assume that the number of columns is the grid size but what is the number of intervals (elements 8-9 in the header)? Regards, Pascal

Re: [ccp4bb] map file specification

On 09/15/2011 09:30 AM, Pascal wrote: I am looking at the specifications of the ccp4 map file format and I am confused with the number of columns and the number of intervals. Thanks for all the answers. I can almost write a map file. Only one problem remain: what is the machine stamp

Re: [ccp4bb] phaser openmp

can have much less than 5% of serial code. I have more problems with L2 misse cache events and memory bandwidth. A quad cores means 4 times the bandwidth necessary for a single process... If your code is already a bit greedy, the scale up is not good. Pascal

Re: [ccp4bb] phaser openmp

On 11/09/2011 11:53 AM, Francois Berenger wrote: On 11/09/2011 07:21 PM, Pascal wrote: I have more problems with L2 misse cache events and memory bandwidth. A quad cores means 4 times the bandwidth necessary for a single process... If your code is already a bit greedy, the scale up is not good

Re: [ccp4bb] writing scripts-off topic

ages that leverage your time most effectively. Low level languages have their advantages. It's not a good idea to stay away from them just because there is more work or it's more difficult. You cannot have 50M reflections*atoms*s^-1 processed for structure factor calculations in python. But it's true you probably won't need it every day. Brute force has some advantages over cool ideas sometimes ;) Pascal

Re: [ccp4bb] FORTRAN still rules?

for random numbers And so on... Pascal

[ccp4bb] pdb/mmcif to cif

Hi, Is anyone know how I can convert a pdb or mmcif file into the cif format ? I am trying to convert this file: http://pdb.org/pdb/explore/explore.do?structureId=3NIR Thanks, Pascal smime.p7s Description: Signature cryptographique S/MIME

Re: [ccp4bb] Structural Importance of Methionine

substrates in the protein binding clefts. I hope this helps you. All the best, Pascal On Fri, Aug 7, 2020 at 5:14 AM samer halabi < 30c2162795b2-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear All, > I am working on structures where Methionine is important in binding of > pept

Re: [ccp4bb] Cell disruption

up sometimes to just check the instrument for free . I have had this one for 10 years in my lab now. And before that was using one for 7 years during my post doc. I would not lyse bacteria by any other method now. I hope this helps. All the best. Pascal On Sat, Aug 15, 2020 at 9:08 PM Bernhard

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An Assistant or Associate Professor position has opened in the Department of Biochemistry at Université de Montréal: https://www.umontreal.ca/public/www/documents/offres_emploi_profs/MED_11-20_8_Biochemistry.pdf Enquiries and applications to: Lorraine Bidégaré Charette mailto:lorraine.bidegar

[ccp4bb] Subject: [ccp4bb] Soaking Kinase Crystals with ATP analogues

are not afraid of beryllium . Hope this helps Good luck -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry Boyer Hall room 356 611 Charles E Young Drive East Los Angeles CA 90095 office (310)-983-3515 lab (310)-983-3516 email

[ccp4bb] recombinant sources of N-glycanase

ourselves because the commercial sources are apparently too expensive. Thanks in advance. -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry Boyer Hall room 356 611 Charles E Young Drive East Los Angeles CA 90095 office (310)-983-3515 lab

Re: [ccp4bb] 24 well screw-cap crystallization plates

Hi Brad, I am afraid that there is no alternate source for these plates. The screw cap system , I believe, was patented by the canadian company NEXTAL that was then assimilated by Q...N and the patent is probably still holding. Pascal -- Pascal F. Egea, PhD Assistant Professor UCLA, David

Re: [ccp4bb] Lysis of Pichia pastoris

go, Bead beaters come in various sizes depending on the volumes you want to process. It is just a blender after all. Hope this helps. Best regards -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research

Re: [ccp4bb] off topic: GPCR membane insertion/orientation

sect the process of TM insertion, orientation and protein maturation quite well. Hope this helps, Best regards -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab

[ccp4bb] Protease inhibitor cocktails and protein crystallization.

getting crystals of these inhibitors. Does anyone have extended experience in this matter. Many thanks in advance. -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515

Re: [ccp4bb] reproducibility of protein crystals

a little bit of practice) to characterize what is in your crystal or if you have a mass spec at hand look at the content of a crystal. How long did those crystals take to grow? Is there a skin covering your drops? Hope this helps -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen

Re: [ccp4bb] highly glycosylated protein

. -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 356 Boyer Hall office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu

Re: [ccp4bb] crystallization of a weird protein

tend to yield more salt crystals at the screening stage. Hope this helps. > -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 356 Boyer Hall office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu

Re: [ccp4bb] Hydrophobic protein surface and SDS page

an SDS-PAGE gel. Phosphorylation and glycosylation will also affect the apparent MW as estimated from the SDS-PAGE experiment. What you observe is not unusual at all. If you want to be sure of your MW, Mass Spec will tell you what you want to know. Hope this helps, good luck -- Pascal F. Egea

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A Postdoctoral Research Position is available in the Structural Cell Biology Laboratory of Dr. John Pascal at Thomas Jefferson University. Current research projects focus on nucleic acid enzymes involved in genome maintenance/DNA repair, transcriptional regulation, and innate immunity. The

[ccp4bb] expression of membrane proteins as GST fusions

share with us. Many thanks in advance. -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 364 Boyer Hall Molecular Biology Institute office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu -- Pascal F. Egea

Re: [ccp4bb] GTP Agarose Resin

and no magnesium during purification helps. If your GTPase has a very low basal GTPase activity ( and some do as they require a cognate GAP to really get in the mood to hydrolyze) this might be enough to minimize hydrolysis on this resin. Good luck, -- Pascal F. Egea, PhD Assistant Professor

Re: [ccp4bb] Nanodrop versus Nanophotomter Pearl versus good old Bradford.

ks well in micro-titre plates etc. It is > certainly very superior to Bradford. (Smith, P.K., et al. (1985). > "Measurement of protein using bicinchoninic acid". Anal. Biochem. 150 (1): > 76–85. doi:10.1016/0003-2697(85)90442-7). > > cheers > > Shaun > -- Pascal F. Egea

[ccp4bb] Bad geometry for alt. conformation refined in Refmac5

98 63.372 48.403 0.50 31.24 AO John Pascal, PhD Thomas Jefferson University Department of Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ph 215.503.4596 fx 215.923.2117

[ccp4bb] Post Doctoral Position at UCLA. Membrane Protein Complexes.

-mail, address, phone), a list of experimental expertise and a brief research statement describing your past research and future goals. Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310

Re: [ccp4bb] Expression of large proteins in E. coli

Best -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu

Re: [ccp4bb] UV microscope for screening

much cheaper and as efficient. Hope this helps. -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu

[ccp4bb] continuous flow centrifuge

anyone had experience with this type of instrument and would be willing to share his/her thoughts about it. Thank you very much in advance. -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building

Re: [ccp4bb] question - GFP fusion - cleavage sites

Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu n Mon, May 24, 2010 at 5:05 AM, Celina R. wrote: > Dear CCP4er's, >

[ccp4bb] metal-chelating affinity chromatography and FosCholine detergents

experience the same quite systematic (so far in my hands) problem with this class of detergents. I would appreciate any comments or advices from biochemists that face(d) the same situation. Thanks in advance -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of

Re: [ccp4bb] SAXS on a coiled coil protein

eolysis in solution, if your protein is so floppy you would expect it to be rather sensitive to some proteases in solution? my guess is that by now you would have observed this during your purification. - NMR? Hope this helps, All the best -- Pascal F. Egea, PhD Assistant Professor UCLA, David Gef

Re: [ccp4bb] problem in annealing

should go through. HTH -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu

Re: [ccp4bb] how to optimize crystallization of a membrane proteinf

ially with alkylosides (personal experience). Good luck, -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu

Re: [ccp4bb] Confirming expression of a GPCR in HEK293

really great, however it is not that great, in my hands, when it comes to purification of a membrane protein (in presence of detergent) I prefer his-tags to flag-tags in this case. You can use a his-flag to combine both advantages. Hope this helps -- Pascal F. Egea, PhD Assistant Professor UCLA

Re: [ccp4bb] Visualization system for a Mosquito Robot

those, one at room temperature and one in the cold. They seem to work OK. I said OK not great so you can consider this type of system for your setup, depending on what level of high-throughput you are willing or able to reach. Hope this helps Best Pascal Egea Post Doctoral Fellow Robert

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, PA 19107. Email: [EMAIL PROTECTED] Thomas Jefferson University is located in center city Philadelphia, adjacent to a variety of cultural, entertainment and historical attractions. Affirmative Action/Equal Opportunity Employer. John Pascal, PhD Thomas

[ccp4bb] Job Announcement - FACULTY POSITION IN X-RAY CRYSTALLOGRAPHY

FACULTY POSITION IN X-RAY CRYSTALLOGRAPHY Department of Biochemistry and Molecular Biology Thomas Jefferson University in Philadelphia USA Job Description: The Department of Biochemistry and Molecular Biology at Thomas Jefferson University in Philadelphia invites applications for tenure-track o

Re: [ccp4bb] Se oxidation

Biol Crystallogr. 2001 Sep;57(Pt 9):1337-40. Epub 2001 Aug 23. Cheers, Pascal Egea, PhD Post Doctoral Researcher UCSF Department of Biochemistry and Biophysics Stroud laboratory On Mon, Feb 9, 2009 at 10:27 AM, aka akaka wrote: > Dear All > I would like to know whether oxidation

Re: [ccp4bb] Off topic: Mammalian gene expression in E. coli

of another expression plasmid encoding two " chaperones ", the trigger factor and GroES/EL. This is worth trying too. Hope this helps, cheers. Pascal Egea, PhD University of California San Francisco Department of Biochemistry and Biophysics Stroud Lab

Re: [ccp4bb] Purification with ligand

er, keep also in mind that you will contaminate your columns and it can be hard to get rid of some ligands sometimes. Sorry, if all this was a little bit too long. Hope this helps, Pascal Egea, PhD University of California San Francisco Department of Biochemistry and Biophysics Laboratory of Rob

Re: [ccp4bb] precipitation of deglycosylated protein

ou express it. This depends on what your expression system is. You can try to add stabilizing agents like glycerol, ethylene glycol or some di-sugars like trehalose. I hope this helps, Cheers, Pascal F. Egea, PhD University of California San Francisco Department of Biochemistry and Biophysics O

Re: [ccp4bb] precipitation of deglycosylated protein

poor defined. Pascal Egea

Re: [ccp4bb] OT: Crystallisation compatible detergents

sulfo-betaines they can sometime have the same protective effect without the trouble of detergents. I hope this helps, Cheers Pascal F. Egea, PhD University of California San Francisco Department of Biochemistry and Biophysics >

Re: [ccp4bb] Acrylamide in RNA crystallization

type column) to try to clean it up. If you have an NMR spectroscopist friend around, try to look at the presence of acrylamide before and after these steps and see what works the best for you. Hope this helps Pascal Egea, PhD University of California San Francisco Department of Biochemistry and

Re: [ccp4bb] Tips on fitting poorly defined loop regions

ps at least partially. There is another program called XPLEO (and a derivation of it called LoopTK) and is available from the Stanford site at the Synchrotron Linear Accelerator that has been helpful in our lab in the case of a loop region in a membrane protein. Hope this helps. Good luck Pas

Re: [ccp4bb] citrate blocks the active site

and also the magic carboxylate malonate; a little bit like the Hofmeister series. You maybe able to find a surrogate to citrate that will able you to either soak your crystals or co-crystallize successfully with your substrate(s). Hope this helps Cheers, Pascal Egea University of California San

Re: [ccp4bb] detergent crystals

microscopes are getting more and more popular so maybe you have one next by. It is very convenient. Hope this helps Pascal Egea, PhD University of California Los Angeles Department of Biological Chemistry

[ccp4bb] Electron Density Maps

between those programs? Can differences in the way to perform bulk solvent correction account for those differences? Thanks in advance for your suggestions. Pascal Egea

Re: [ccp4bb] DNA binding protein

with subsequent crystallization trials in presence of the bona-fide target DNA sequence. 4-Precipitation of the DNA with streptomycine sulfate. You could also loss some protein. 1 and 2 are in my opinion the less invasive soutions. Hope this helps. Best regards Pascal Egea

Re: [ccp4bb] Cryoprotection in > 3M ammonium sulfate

Hi Brenda, You can try sugars like glucose, trehalose and sucrose for high AS contents. It has been succesfully used in really hard cases such at protein RNA crystals grown in AS. see Acta Cryst (2002) D58 1664-1669 Garber et al. HTH Pascal Egea

Re: [ccp4bb] Adding a transmembrane segment

and look for your protein in there. Is your ectodomain N or C-terminal (I assume it is N from your message)? Have you looked at the targeting sequences present in the protein (signal sequence, reverse anchoring motifs)? Hope this helps Pascal F. Egea, PhD

Re: [ccp4bb] lysozyme

s the rare tRNA genes). If they don't have the plasmid at hand you can still grow the cells and make a miniprep of the plasmid (low copy) to have a lysozyme gene in your hands. Hope this helps. Let me know if you can't find it. -- Pascal F. Egea, PhD Assistant Professor UCLA, David G

Re: [ccp4bb] Phase separation to crystals

are protein crystals then I would try to lower the polymer concentration and increase salt concentration to try to get out of this region of the phase diagram. Hope this helps -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314

Re: [ccp4bb] small molecule library

I can suggest the following reading Discovering novel ligands for macromolecules uisng X-ray crystallographic screening Nienaber VL et al, Nature Biotechnology vol 18 october 2000 pp1105 -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological

Re: [ccp4bb] off topic, design of a self-cleaving tag

is for expression and purification purposes only. Hope this helps -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu

[ccp4bb] post-doctoral in membrane protein structural biology

addresses of three references. I will be attending the ACA-2013 meeting in Hawaii this coming week and will present a poster presented from 5:30-07:30pm on Sunday, July 21. Motivated individuals are invited to directly contact with me. Pascal F. Egea, PhD

[ccp4bb] membrane protein and phase separation

ome of you have already observed? Many thanks in advance, -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry Boyer Hall room 356 611 Charles E Young Drive East Los Angeles CA 90095 office (310)-983-3515 lab (310)-983-3516 em

Re: [ccp4bb] off-topic: bug busting

with this since my post-doc Hope this helps. Best regards, Pascal Egea On Tue, Feb 4, 2014 at 8:49 AM, Phoebe A. Rice wrote: > Some time ago, there was a nice discussion of cost-effective, wimpy > protein-friendly ways to break open E. coli. We're thinking about > replacing an a

Re: [ccp4bb] Difficult MR with MBP fusion protein

going on in your crystals. Good luck Pascal Egea On Fri, May 16, 2014 at 8:03 AM, Niu Tou wrote: > Dear All, > > Recently we collected some data of a MBP fusion protein, at around 4A > resolution. The protein itself is about half of the MBP size. However when > we tried to solve

Re: [ccp4bb] suggestions for cryoprotectant

ually easier to cryo-protect. Hope this helps Pascal Egea On Fri, Oct 19, 2018 at 2:57 PM Firdous Tarique wrote: > Dear members > > I have got beautiful crystal hits in SaltRx screens which are not > diffracting to a good resoultion. All of them are salt based condition and >

Re: [ccp4bb] Should I optimize these crystals?

Lab > > Department of Biochemistry and Molecular Biology > > The University of Chicago > > 929 E. 57th Street > > Chicago, IL 60637 > > Lab: GCIS W229 > > Lab phone: 773-834-0660 > > > -- > > To unsubscribe from the CC

[ccp4bb] Post Doctoral Position at UCLA

three potential references to *pe...@mednet.ucla.edu .* Thanks. All the best, Pascal Egea -- Pascal F. Egea, PhD UCLA, David Geffen School of Medicine Department of Biological Chemistry Boyer Hall room 356 611 Charles E Young Drive East Los Angeles CA 90095 office (310)-983-3515 lab (310

Re: [ccp4bb] Zinc binding protein expressed from insect cells

ve managed to purify some protein I would try to do some emission spectroscopy to see what ions are bound (zinc and or iron ) you may be surprised by what you will see. sorry for the lengthy response but I hope this helps. all the best, Pascal Egea On Fri, Aug 15, 2014 at 8:03 AM, Harvey

[ccp4bb] fluorescence question

’ fluorescence that interferes severely with our measurements (we are using tetramethyl rhodamine as fluorescent reporter). I was curious to know if anyone else had encountered this problem and figured out a solution. Any suggestion will be greatly appreciated. Many thanks in advance. Pascal Egea Assistant

[ccp4bb] MR phasing using Negative Stain EM reconstruction

resolution cryoEM maps for MR as described in the review from Jackson et al in Nature Protocols but I was wondering if there is an intrinsically impossibility for negative stain reconstructions. Any thoughts or advice will be greatly appreciated. Best, -- Pascal F. Egea, PhD Assistant Professor UCLA

Re: [ccp4bb] Off-topic: heterologous co-expression in yeast

this helps. Best of luck -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry Boyer Hall room 356 611 Charles E Young Drive East Los Angeles CA 90095 office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu

Re: [ccp4bb] Thrombin cleavage of membrane protein with fusion tag

ratio and incubation time and temp. you can do trials on small scale digests in PCR tubes at different temperatures. we usually cut at 4 or room temp. I hope this helps, Best regards, -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological

[ccp4bb] gelification of a pure protein

thanks in advance . -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry Boyer Hall room 356 611 Charles E Young Drive East Los Angeles CA 90095 office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu

Re: [ccp4bb] gelification of a pure protein

, Pascal -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry Boyer Hall room 356 611 Charles E Young Drive East Los Angeles CA 90095 office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu

Re: [ccp4bb] Membrane Protein Optimisation

trying to concentrate. too much detergent staying around is a major cause of trouble (i.e. poor diffraction and phase separation competing with productive crystal growth) besides many other parameters Hope this helps -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine

Re: [ccp4bb] Data 3 A

offense intended). Best, Pascal Egea On Tue, Jan 12, 2021 at 3:22 PM rohit kumar wrote: > Dear all, > > I am trying to solve a data with 3 A resolution, however data quality is > very bad and mathews coffi. suggest two molecules per ASU but It always > gives one molecule in AU after

Re: [ccp4bb] crystallizing fusion proteins

should be bright yellow so that speeds up the screening process a bit. I hope this helps. Good luck Best regards, Pascal Egea, PhD UCLA School of Medicine > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscma

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Postdoctoral Research Position in Structural Biology at University of Montreal A postdoctoral research position is available in the laboratory of Dr. John Pascal at the University of Montreal. Current research projects focus on the structural biology, biochemistry, and cell biology of proteins

Re: [ccp4bb] the purification process of protein, used for crystallization

advantage to remove some large molecular weight contaminants ( usually DNA) and some aggregates that are annoying. These choices depend on your target of course and the level of abundance too. Best, Pascal Egea, PHD UCLA Geffen School of Medicine On Fri, Nov 17, 2017 at 5:46 AM Liuqing Chen <519

Re: [ccp4bb] Protein toxicity or low expression

the pre and post induction > lysate on SDS PAGE. Out of so many option available in the literature I am > confused what to try first. Any general idea? > > Your suggestions can help a lot. > > Kahkashan > Ph.D student > Delhi University > India > -- Pascal F. Egea, PhD

Re: [ccp4bb] Structural biologist and modeler opportunity in Boston area

On Dec 17, 2024, at 1:36 PM, Yanfeng Zhou wrote: Hi all, Our team is growing and we are looking for an experienced structural biologist and modeler to join us in Cambridge, Massachusetts. Please click the link to learn more or share the link if someone needs this opportunity. https://www.l

[ccp4bb] Assistant/Associate Professor in Cryo-EM, Université de Montréal (Canada)

Please take note of the following employment opportunity: Assistant or Associate Professor in Cryo Electron Microscopy Université of Montréal, Québec, Canada Department of Biochemistry and Molecular Medicine Center for Biomedical Innovation Faculty of Medicine Find out more about the position and