[ccp4bb] X-ray equipment available
To all colleagues at CCP4BB: We have the following X-ray diffraction equipment to give away: I. Siemens X-1000 Multiwire Area Detector. It has been manufactured by Siemens Analytical X-ray Instruments Inc. in Madison, Wisconsin, USA. Equipment available includes multiwire area detector X-1000 itself, its Position Decoding Circuit, the 3-circle goniostat with the remote control and the set of collimators. This equipment is available free of charge except for the shipping costs. The detector needs a new gas-filling, however. II. A Siemens/Mac Science rotating anode X-ray generator with elongated table. The system is functional and in very good condition. Included are transformer and vacuum pumps to run the system, water cooling system not included. The generator will be given away free of charge, however freight costs are assumed to be taken by the purchaser. Spare parts include: A complete Cu-Target including the complete anode assembly. Filaments, O-rings The equipment is at Karolinska Institutet, NOVUM, Huddinge near to Stockholm, Sweden. For more information, please contact me outside the CCP4 bulletin, please. If you are interested in this equipment (in the described set or in any parts of it) please contact me directly using my email address rudolf.ladenst...@ki.se. Please do not respond to the ccp4bb address! With kind regards, Rudolf Ladenstein Professor of Structural Biochemistry Karolinska Institutet NOVUM 14157 Huddinge, Sweden Phone: +46 8 6089 222
Re: [ccp4bb] edit mtz cell in header?
There are many and various programs that do this. As Martin says - cad will do it - you can use the GUI to change each data set in the file.. if there is only one data set the easiest is this: mtzutils hklin old.mtz hklout new.mtz CELL 168.981 168.981 168.981 90 90 90 end eleanor martyn.w...@stfc.ac.uk wrote: Well, yes, that's how I would do it (but with Emacs). But I guess the official way would be with Reflection Data Utilities - Edit MTZ Datasets which will edit the dataset cells. It wraps keywords of CAD. Martyn -Original Message- From: CCP4 bulletin board on behalf of Ed Pozharski Sent: Fri 11/13/2009 9:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] edit mtz cell in header? You may be able to open mtz files in a primitive text editor such as nano (I just did). It's a little awkward, as there are no line breaks. MTZ header is in the end of the file and it is plain text, so should be easy to edit manually - just make sure you don't introduce extra space. There are plenty of hex editors out there: http://en.wikipedia.org/wiki/Comparison_of_hex_editors On Fri, 2009-11-13 at 15:52 -0500, Matt Warkentin wrote: Howdy folks I'm having an infuriating problem with an mtz file and sftools. I'm sure this is an easy fix. Here's the situation: phaser gave me an mtz and pdb file with bad cell information. It's I213, but the cell is listed as 168.981 168.981 168.982 i.e. NOT cubic - this creates an error with my crystallography software downstream (buster-TNT) So this looks like a bug in phaser, but I'm not worried about solving that problem right now, I just want to go in and manually change the cell info so its correct. This was easy for the pdb file obviously because its ASCII, but the mtz is binary and requires the use of programs that know how to read the header info. So I found sftools, which is the program to use for that right? Within sftools, I said READ blah.mtz LIST CELL - at this point the incorrect cell was listed SET CELL 168.981 168.981 168.981 - at this point the correct cell was listed LIST CELL - just to be sure, yes the correct cell is listed WRITE fixed.mtz QUIT Now, when I go open the new mtz file with my crystallography software, it still complains and reports the incorrect cell. If I open fixed.mtz with sftools and LIST CELL it also reports the incorrect cell. So it looks like sftools is not saving the correct cell to the mtz file. Any thoughts? Is there another way to change that header? thanks matt
Re: [ccp4bb] Twinning
Refmac refines against the original twinned data. Eleanor Bernhard Rupp wrote: Dear All, following the twinning threads as well as the refmac manual it is not quite clear to me yet whether refmac finds the twin operator and fraction, detwins the data, and refines against those detwinned data, or refines against the original twinned data like (I believe) phenix and shelxl. Thx, BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Eleanor Dodson Sent: Tuesday, August 04, 2009 1:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Twinning Try refinement with the newest REFMAC which will take twinning into account.
Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about
The rumblings here at the Univ. of Washington among the computational modelers is that some of their current models might be more representative of protein structures in solution than are the crystal structure models. It may take less than a couple of decades for a reduced emphasis on crystallographic studies. Has somebody determined P=NP, or come up with a provably global optimization algorithm (and sufficiently accurate force field) that can be run on available hardware in a reasonable amount of time for a protein of interesting size (this may vary, but in my case it's ~500 KDa)? Personally, I find the work that's being done on computational modeling fascinating, and follow it when I have the chance (although at the moment I'm out of date). But given the mathematical and computational issues, I expect crystallography to stick around for a while yet (at least until somebody comes up with an x-ray lens that works at ~1 Angstrom x-rays). Pete Ron Stenkamp On Sat, 14 Nov 2009, Van Den Berg, Bert wrote: I wonder, just as a side note, whether there will still be a (big) need for X-ray crystallography in a couple of decades? What will be the state of the art then in structure prediction? How much of structure space will have been covered by then, so that homology modeling can do most of the tricks? Bert van den Berg UMass Medical School -Original Message- From: CCP4 bulletin board on behalf of George M. Sheldrick Sent: Sat 11/14/2009 4:08 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about Apologies for the typo, I meant to say 'Bernhard'. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Sat, 14 Nov 2009, George M. Sheldrick wrote: I also think that it is a very nice video and I will certainly be showing it to my students (and relatives). However the little step between recording the X-ray reflections and getting a final refined map might be expanded a little. That is after all what CCP4 etc. is about! Otherwise, despite the suggestion in the film that an expert should be consulted, we are reinforcing the view held by many biologists and chemists that crystal structure determination is a routine analytical method and not suitable for an academic career. It worries me that in a couple of decades there will be few people still active who really understand how it works. On the other hand, Berhard's impressive new book may solve that problem (if people still read books). George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 13 Nov 2009, claude sauter wrote: Narayanan Ramasubbu a écrit : mb1pja wrote: Dear Fred A really nice video that would be great for giving non-crystallographers (including colleagues and 1st year students, and perhaps also friends and family) an overview of what we do. Thank you for pointing it out - and of course very many thanks to Dominique Sauter for making it. I am sure it will prove very popular. bet wishes Pete (Pete Artymiuk) On 11 Nov 2009, at 09:44, Vellieux Frederic wrote: Dear all, Thought I'd share this with you: I located this through Ms Ines Kahlaoui, from the Beja Higher Institute of Biotechnology in Tunisia (Ines has to teach and locates videos on the internet, which she then downloads and uses for teaching). Ines located this jewel: http://video.google.com/videoplay?docid=7084929825683486794ei=M3b5SvXqD6em2AK3jY33CQq=Plongee+coeur+vivant# This is the French version (explains everything about Structural Molecular Biology, but for the maths :-( , but also shows what we crystallographers have known for a long time, since the first colour ES graphics workstations in fact, that the electron are blue :-) ). Both French and English versions can be downloaded from http://cj.sauter.free.fr/xtal/Film/ No rights associated with the movie, and the Strasbourg group intends to release a higher quality version on DVD soon. Please contact them about that... I am only sharing what I thought was good for educational purposes. 18 minutes of your life, but worth it I think. So feel free to share this. Wish you all a nice day, Fred. Hi: Could someone point out the name and where to get these crystallization plates used in the video? By the way, this is a wonderful video. Subbu Dear Subbu and dear xtal lovers, the fancy plates used in the video are Nextal EasyXtal plates which are now sold by Qiagen. Concerning the video (thank you Fred for you kind advertisement!), the final version (English/French) will be available in DVD very soon, as well as divx and flash formats, we are working hard to get them ready by Christmas. This material will be released under the
[ccp4bb] Beta OG cif definition and PDB deposition
Hello everyone, Perhaps this is a newbie question, so I apologize. After much work and a lot of thanks to the ccp4 bulletin board I just tried to submit my first structure to the pdb database. It is a membrane protein and therefore has some detergent molecules bound to it. I received an email back from the lady who authorizes the structures indicating that the stereochemistry of many of my beta octylgluside molecules are incorrect. Needless to say I am not a chemist, and therefore the subtleties of sugar ring enantiomers were not immediately apparent to me, however I now understand how the hydroxyls must be pointing for the molecule to satisfy the BOG criteria. My question is that shouldn't the .cif file, in this case libcheck_BOG.cif (COOT generated when I get the monomer from the coot library) contain these enantiomeric restrictions? Even if I change the carbons of the beta glucoside manually, shouldn't the correct stereochemistry be restrained during the refinement? Thanks so much for any help with this complicated question. Drew This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
[ccp4bb] CCP4 Study Weekend Januay 6th-8th 2010
Dear All, A quick reminder to you all about this coming January's CCP4 Study Weekend entitled From Crystal to Structure with CCP4 (January 6th-8th 2010). The deadline for the first round of registrations will be the 21st of November after which the registration price will increase from £210 to £260. So please get your registration in before then. After the success of this year's event, the meeting will be held again at the East Midlands Conference Centre in Nottingham University in the UK. For more details and to register please see the Study Weekend website at: http://www.cse.scitech.ac.uk/events/CCP4_2010/ We hope to see you there. Best wishes, Ronan Ronan Keegan CCP4 Group -- Scanned by iCritical.
[ccp4bb] IMAC and Low Ionic Strength
Dear Crystallographers, Recently I incubated a small amount of His-select resin with bacterial lysate in (50 mM TRIS-HEPES pH 8.0, 10 mM CaCl2), and washed the resin, for certain experimental reasons, with (50 mM TRIS-HEPES pH 8.0, 0.2 mM CaCl2), at which point a significant amount of my protein fell off the column. The ratio of my protein : background proteins was much higher in these washes, implying that my protein probably had bound, but was now falling off the column due to the 10mM==0.2mM CaCl2 transition. Has anyone had problems using such low ionic strength wash buffers? Is it possibly necessary for the his-metal-ion interaction? Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
[ccp4bb] updating refmac
I wanted to update refmac5 to the latest version in CCP4. I downloaded v5.5.0105 and unpacked the tarball. The three files are named refmacgfortran, libcheckgfortran and makecifgfortran. So, I moved the corresponding files refmac5, libcheck and makecif in ccp4-6.1.2/bin/ to another folder and created symbolic links with the old names (e.g., refmac5) to the new files (e.g., refmacgfortran). Is this correct, or is there some better way to do this? Thanks. Tom -- Thomas J. Magliery, Ph.D. Assistant Professor Department of Chemistry Department of Biochemistry The Ohio State University 1043 Evans Laboratory 100 West 18th Ave. Columbus, OH 43210-1185 (614) 859-5743 phone (Google Voice) (614) 292-1685 fax magli...@chemistry.ohio-state.edu http://www.chemistry.ohio-state.edu/~magliery
[ccp4bb] Postdoctoral Positions UCSF/Stroud Lab
The Stroud Lab at UCSF (http://www.msg.ucsf.edu/stroud/index.htm) is looking to fill multiple post-doctoral positions in 1. membrane protein crystallography and 2. structure and function of RNA-modifying enzymes. Applicants should have background in biochemistry, molecular biology, and/or crystallography. The position in membrane proteins will be in close affiliation with MPEC (http://mpec.ucsf.edu/index.htm) and CSMP (http://csmp.ucsf.edu/index.htm). Candidates with experience with membrane proteins is highly preferred for this position. If interested, please email your cover letter and CV to: beth...@msg.ucsf.edu Please specify the position that you are applying to. -- John K. Lee, Ph.D University of California, San Francisco Genentech Hall 600 16th. Street, S414 San Francisco, CA 94158-2517 USA
Re: [ccp4bb] IMAC and Low Ionic Strength
Hello Jacob, I am not entirely sure why this has happened to you... A couple of suggestions that may help: 1. dial down the TRIS to 20 mM - you can also use TRIS-HCl (unless the second buffer is there for some other reason). 2. try a 'stronger' resin. I know in the past I've always strongly advocated selectivity over binding strength (i.e. HIS-Select resin over Ni-NTA and its many versions) but in this particular case there may be something weird going on between HIS-Select and Calcium (such as gradual displacement of bound ions, perhaps?). So in this case the use of His-Trap or Ni-NTA etc. may be justified. Let us know how it goes! Artem -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob Keller Sent: Monday, November 16, 2009 3:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] IMAC and Low Ionic Strength Dear Crystallographers, Recently I incubated a small amount of His-select resin with bacterial lysate in (50 mM TRIS-HEPES pH 8.0, 10 mM CaCl2), and washed the resin, for certain experimental reasons, with (50 mM TRIS-HEPES pH 8.0, 0.2 mM CaCl2), at which point a significant amount of my protein fell off the column. The ratio of my protein : background proteins was much higher in these washes, implying that my protein probably had bound, but was now falling off the column due to the 10mM==0.2mM CaCl2 transition. Has anyone had problems using such low ionic strength wash buffers? Is it possibly necessary for the his-metal-ion interaction? Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] IMAC and Low Ionic Strength
Hi Jacob, an alternative explenation might be your protein does not bind via the tag to the resin but unspecifically. What happens if you add the recommended NaCl concentration? Does it fall off too? Just a thought, Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Nov 16, 2009, at 16:05, Jacob Keller j- kell...@md.northwestern.edu wrote: Dear Crystallographers, Recently I incubated a small amount of His-select resin with bacterial lysate in (50 mM TRIS-HEPES pH 8.0, 10 mM CaCl2), and washed the resin, for certain experimental reasons, with (50 mM TRIS-HEPES pH 8.0, 0.2 mM CaCl2), at which point a significant amount of my protein fell off the column. The ratio of my protein : background proteins was much higher in these washes, implying that my protein probably had bound, but was now falling off the column due to the 10mM==0.2mM CaCl2 transition. Has anyone had problems using such low ionic strength wash buffers? Is it possibly necessary for the his-metal-ion interaction? Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] edit mtz cell in header?
All true - but knowing that unit cell is stored as text, direct edit seems to require fewer keystrokes. Obviously, this is so that I can happily use the keystrokes I saved to write this :) On Sun, 2009-11-15 at 23:01 +, martyn.w...@stfc.ac.uk wrote: Well, yes, that's how I would do it (but with Emacs). But I guess the official way would be with Reflection Data Utilities - Edit MTZ Datasets which will edit the dataset cells. It wraps keywords of CAD. Martyn -Original Message- From: CCP4 bulletin board on behalf of Ed Pozharski Sent: Fri 11/13/2009 9:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] edit mtz cell in header? You may be able to open mtz files in a primitive text editor such as nano (I just did). It's a little awkward, as there are no line breaks. MTZ header is in the end of the file and it is plain text, so should be easy to edit manually - just make sure you don't introduce extra space. There are plenty of hex editors out there: http://en.wikipedia.org/wiki/Comparison_of_hex_editors On Fri, 2009-11-13 at 15:52 -0500, Matt Warkentin wrote: Howdy folks I'm having an infuriating problem with an mtz file and sftools. I'm sure this is an easy fix. Here's the situation: phaser gave me an mtz and pdb file with bad cell information. It's I213, but the cell is listed as 168.981 168.981 168.982 i.e. NOT cubic - this creates an error with my crystallography software downstream (buster-TNT) So this looks like a bug in phaser, but I'm not worried about solving that problem right now, I just want to go in and manually change the cell info so its correct. This was easy for the pdb file obviously because its ASCII, but the mtz is binary and requires the use of programs that know how to read the header info. So I found sftools, which is the program to use for that right? Within sftools, I said READ blah.mtz LIST CELL - at this point the incorrect cell was listed SET CELL 168.981 168.981 168.981 - at this point the correct cell was listed LIST CELL - just to be sure, yes the correct cell is listed WRITE fixed.mtz QUIT Now, when I go open the new mtz file with my crystallography software, it still complains and reports the incorrect cell. If I open fixed.mtz with sftools and LIST CELL it also reports the incorrect cell. So it looks like sftools is not saving the correct cell to the mtz file. Any thoughts? Is there another way to change that header? thanks matt -- -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
[ccp4bb] The use of TFE and analogs in protein crystallization
We are trying to crystallize a small fragment (approximately 120aa) of a membrane protein. We encounter many problems in solubilizing the protein and would like to know if any one has experience in crystallizing proteins in the presence of TFE (Tetrafluoroethylene) (I understand that high concentration might have a problems with secondary structure), HFIP (Hexafluoro-2-propanol), TFA (Trifluoroacetic acid) etc. Appreciate any feedback, suggestion
Re: [ccp4bb] Oxidation, again!
Hi Jeremiah -- the short answer is Yes You Must! Don't whether you need that high concentration generally, but if it's not too osmotically active, the crystals should be fine; test it. But when mounting SeMet crystals, it's always a good idea to add fresh DTT or TCEP or whatever, it seems to be rather effective at reversing oxidation. (Are you sure it's oxidized? I assume you've checked the crystals by mass spec?) phx Jeremiah Farelli wrote: Hello all, I posted here a few months ago. My post dealt with a protein crystal that was very sensitive to oxidation (with the SeMet derivative even more so). The protein grows in 24% PEG 1500, no more than 1 mM DTT, 0.05 M Hepes, pH 7.5, 1% glycerol. TCEP will not work, even at very low concentrations. Does anyone have any experience with soaking the crystals in high concentrations (10-50 mM?) of DTT or TCEP before freezing? Could this feasibly be used to reverse any protein oxidation right before freezing?
Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about
Kjeldgaard Morten wrote: On 14/11/2009, at 20.17, Miguel Ortiz Lombardia wrote: Le 14 nov. 09 à 19:15, Kjeldgaard Morten a écrit : On 14/11/2009, at 18.55, Ronald E Stenkamp wrote: The rumblings here at the Univ. of Washington among the computational modelers is that some of their current models might be more representative of protein structures in solution than are the crystal structure models. It may take less than a couple of decades for a reduced emphasis on crystallographic studies. Molecular models are the result of numbers emerging from computer programs. The results of such computations do not reflect anything in nature. There's no experimental evidence whatsoever, making modelling a very theoretical -- in my eyes uninteresting -- exercise. For what it's worth, protein molecules in crystal structures, with typically 50% solvent, are already in solution to the extent that protein molecules are ever in solution in their natural environment. Hi, I think that strong statements and future foretelling are probably not very useful to a discussion that is indeed interesting and that will be put forward more and more often. Crystal structures are actually models themselves. Yes, but models that can be validated against experimental data. The defining characteristics of computational models is that they (A) are 100% dependent on the algortihm, (B) can't be validated at all. Cheers, Morten Sorry, they can be validated to some extend using biochemical data! - J. - -- Dr. Jeroen R. Mesters Gruppenleiter Strukturelle Neurobiologie und Kristallogenese Institut für Biochemie, Universität zu Lübeck Zentrum für Medizinische Struktur- und Zellbiologie Ratzeburger Allee 160, D-23538 Lübeck Tel: +49-451-5004065, Fax: +49-451-5004068 Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.selfish-brain.org Http://www.opticryst.org -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) --
