Re: [ccp4bb] selenomethionine labeling
Hello Jerry,
We use the Van Duyne et al feedback inhibition method with BL21
and have never had a problem.
ho
UC Berkeley
--
Date:Thu, 26 Mar 2009 14:58:57 -0700
From:Jerry McCully for-crystallizai...@hotmail.com
Subject: selenomethionine labeling
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Content-Type: text/plain; charset=iso-8859-1
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Dear All:
I got a problem with the expression of one N-terminal His6 tagged pro=
tein in B834 cells when I tried to do selenomethionine labeling.=20
However=2C the protein can be expressed in BL21{DE3) cells.=20
Welcome any troubleshooting tips.
All the best=2C
Jerry
[ccp4bb] off topic - static laser light scattering
Dear all, The MALLS instruments on-line with an FPLC and with an RI detector, should provide an 'absolute MW', shape independent, and indeed in our hands they do well. Until yesterday, where a 21kD protein pretends to be 25 kD. We did the mass spec anyway, and its 21kD as we expected to the residue, but I am still puzzled by that result. One central assumption for the MALLS formulas, is that dn/dc, the specific refractive index increment, is constant for unmodified proteins, made by aa with no sugars etc. Literature suggests dn/dc values for proteins to be constant and between 0.189/0.190 is a good value, with minimal buffer dependence for aqueous buffers with 'the usual' salts. I am a rather bad physicist, but my reading tells me that dn/dc, and thus light scattering, depends to the laser-light induced dipole in the molecule. Is there any reason to believe that in theory a molecule with a very particular charge distribution (eg a small DNA binding protein which is already a 'dipole') would have significantly different dn/dc values? Is anyone aware of such an experiment? Literature searches were in vain ... Best - Tassos
[ccp4bb] Problems installing tasks to CCP4i - not yet solved.
Hi Tim, thankyou very much for the fast reply. Dear colleagues, Tim suggested: Hi Klaas ... Actually, you don't need to install arpwarp through the ccp4i interface. Once you setup your ccp4 environment, you can just run the install.sh (or install.csh in your case) which is in the arp-warp directory and everything should be set up for you. Tim Been there, done that. Ain't working. To be more specific, the installer is required to set up ARP/wARP, appears to run flawlessly and ends with lots of ok messages. Finally the script terminates with the remark: Installing GUI for ARP/wARP 7.0.1 CCP4 interface version detected is : 2.0.3 Using tarball ARP_wARP_CCP4I6.tar.gz (for ccp4 version 6 and newer). *** INSTALLATION OF ARP/wARP 7.0.1 GUI HAS BEEN SUCCESSFUL *** When I now try to run a ARP/wARP task in CCP4i after sourcing the arpwarp_setup.csh, I get the message: An interface to ARP/wARP is not available. The ARP/wARP interface doesn't appear to have been installed. Any further suggestions are most welcome. Cheers, Klaas --- Dr. Klaas Max MDC Berlin Buch Macromolecular Structures and Interactions Robert-Roessle-Strasse 10 13125 Berlin phone +49 30 9406 2265 fax +49 30 9406 2548 ---
[ccp4bb] XDS and ESRF ID23-1 images
Dear all, Not a CCP4 question. We seem unable to process with XDS a set of images collected at ESRF ID23-1. Images can be open and processed by other software (adxv, mosflm...) They have appropriate read permissions and so has the directory where we run XDS. We use the latest XDS binaries (VERSION January 30, 2009) or the previous one (expiring next week) for Mac OSX (Intel) and the input file for ID23-1 created at the beam line or the one in the XDSwiki. In all cases we get this error: !!! ERROR !!! Data image does not exist: x2-id23_1_001.img Any idea of where the problem may be? Cheers, Miguel -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée ) Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] XDS and ESRF ID23-1 images
I have seen this when the actual size of the image is different from what XDS expects. If you have now: NX=6144 NY=6144 QX=0.0513 QY=0.0513 try NX=3072 NY=3072 QX=0.10259 QY=0.10259 or the other way around. If the auto-generated input file doesn't match your images it might be because the binning has been changed. Cheers, Martin On Mar 27, 2009, at 2:46 PM, Miguel Ortiz Lombardia wrote: Dear all, Not a CCP4 question. We seem unable to process with XDS a set of images collected at ESRF ID23-1. Images can be open and processed by other software (adxv, mosflm...) They have appropriate read permissions and so has the directory where we run XDS. We use the latest XDS binaries (VERSION January 30, 2009) or the previous one (expiring next week) for Mac OSX (Intel) and the input file for ID23-1 created at the beam line or the one in the XDSwiki. In all cases we get this error: !!! ERROR !!! Data image does not exist: x2-id23_1_001.img Any idea of where the problem may be? Cheers, Miguel -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée ) Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. . B. Martin Hallberg, PhD Assistant professor Department of Cell and Molecular Biology Karolinska Institutet von Eulersv. 1 SE-171 77 Stockholm Sweden Fax: +46-8-339380
Re: [ccp4bb] Problems installing tasks to CCP4i - not yet solved.
Hi Klaas, I had exactly the same problem with opensuse 11.1. I installed the precompiled version of ccp4 6.1.1, so I don't think the problem is related to the compiler. I resolved the problem in a dirty way, simply copying the ccp4i configuration files for arp/warp from another installation of ccp4 on a machine running suse 9.1. Indeed, with suse 9.1 the installation of the arp/warp ccp4i interface is successful. I suspect that the problem is related to the new versions of tcl/tk. Try to use the one distributed on the ccp4 server ftp://ftp.ccp4.ac.uk/tcltk/TclTk-8.4 -- install it locally on your user account and set accordingly the variable CCP4I_TCLTK in the ccp4.setup-dist file. Hope it helps, Michele Max, Klaas wrote: Hi Tim, thankyou very much for the fast reply. Dear colleagues, Tim suggested: Hi Klaas ... Actually, you don't need to install arpwarp through the ccp4i interface. Once you setup your ccp4 environment, you can just run the install.sh (or install.csh in your case) which is in the arp-warp directory and everything should be set up for you. Tim Been there, done that. Ain't working. To be more specific, the installer is required to set up ARP/wARP, appears to run flawlessly and ends with lots of ok messages. Finally the script terminates with the remark: Installing GUI for ARP/wARP 7.0.1 CCP4 interface version detected is : 2.0.3 Using tarball ARP_wARP_CCP4I6.tar.gz (for ccp4 version 6 and newer). *** INSTALLATION OF ARP/wARP 7.0.1 GUI HAS BEEN SUCCESSFUL *** When I now try to run a ARP/wARP task in CCP4i after sourcing the arpwarp_setup.csh, I get the message: An interface to ARP/wARP is not available. The ARP/wARP interface doesn't appear to have been installed. Any further suggestions are most welcome. Cheers, Klaas --- Dr. Klaas Max MDC Berlin Buch Macromolecular Structures and Interactions Robert-Roessle-Strasse 10 13125 Berlin phone +49 30 9406 2265 fax +49 30 9406 2548 --- -- Dr. Michele Lunelli Department of Cellular Microbiology Max Planck Institute for Infection Biology Campus Charité Mitte Charitéplatz 1 D-10117 Berlin
Re: [ccp4bb] XDS and ESRF ID23-1 images
Hi Ronnie and others, Le 27 mars 09 à 15:02, Ronnie Berntsson a écrit : This might be a bit too obvious, but have you checked that the path to the images is correct? The path written in the input files generated on the beamline reflects where the images were located in the file tree there. Does it match where you have the files on your own computer? Yes and no... it looked the same, however there was a hidden extra character between the question marks '?' in the template! Not visible in 'vim' or 'less' but became apparent with: cat -tve XDS.INP So, next time I will read more carefully the error message (there were three '?' instead of the four I thought were written in the XDS.INP file) However, that was not all the story. Le 27 mars 09 à 14:57, Marija Backovic a écrit : I had a similar problem, and it was because I had played with changing some of the detector hardware parameters (NX, NY values in the XDS.INP). I know this has nothing to do with the availability of images :) Once I set the NX and NY back to the original value, defined by the XDS.INP file, the problem was solved. You can find the appropriate XDS.INP, corresponding to the detector you used, at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDS.INP Indeed, some of the detector hardware parameters (NX, NY) in the XDS.INP seemed to be incorrect in the input file generated at the beam line. The file from the XDSwiki for ID23-1 worked fine once the extra character was removed from the template name. Thanks to all who replied! Miguel -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée ) Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] off topic - static laser light scattering
Dear Tassos, Your assumptions are right, if (1) your dn/dc is accurate, or (2) your machine is calibrated. We recently measured a protein of a similar size to yours, and when a 700 Da ligand was added to the buffer, the measured protein mass was increased accordingly. So MALS can be pretty accurate. For our dn/dc, for pure proteins, we always use 0.185 (not 0.19). For sugar groups, we assume a dn/dc of 0.14, and estimate a mass-averaged value for the glycoprotein (usually somewhere between 0.175 to 0.18). For DNA and RNA, the values will be different, again. You may also realize that by changing a simple calibration constant, you can modify your measured molar masses anyway you want. It may be time for a recalibration (it is not difficult, you can do it yourself). We tend to regularly run BSA, and see if everything is as expected with our equipment. Good luck, Engin Anastassis Perrakis wrote: Dear all, The MALLS instruments on-line with an FPLC and with an RI detector, should provide an 'absolute MW', shape independent, and indeed in our hands they do well. Until yesterday, where a 21kD protein pretends to be 25 kD. We did the mass spec anyway, and its 21kD as we expected to the residue, but I am still puzzled by that result. One central assumption for the MALLS formulas, is that dn/dc, the specific refractive index increment, is constant for unmodified proteins, made by aa with no sugars etc. Literature suggests dn/dc values for proteins to be constant and between 0.189/0.190 is a good value, with minimal buffer dependence for aqueous buffers with 'the usual' salts. I am a rather bad physicist, but my reading tells me that dn/dc, and thus light scattering, depends to the laser-light induced dipole in the molecule. Is there any reason to believe that in theory a molecule with a very particular charge distribution (eg a small DNA binding protein which is already a 'dipole') would have significantly different dn/dc values? Is anyone aware of such an experiment? Literature searches were in vain ... Best - Tassos
Re: [ccp4bb] Problems sourcing
Dear List, I am trying to install the latest CCP4 6.1.1 binaries on Linux and running into sourcing problem. I could source the ccp4.setup file as root (c-shell) and ccp4 ran just fine. But as a user, with the same shell, I could not source the setup file. The error is setenv: Too many arguments. There are so many environment variables in that file it's impossible to find the culprit. Could someone help me out? Thanks, Jason This transmission may be confidential or protected from disclosure and is only for review and use by the intended recipient. Access by anyone else is unauthorized. Any unauthorized reader is hereby notified that any review, use, dissemination, disclosure or copying of this information, or any act or omission taken in reliance on it, is prohibited and may be unlawful. If you received this transmission in error, please notify the sender immediately. Thank you.
Re: [ccp4bb] Fwd: [ccp4bb] Crystal vacuum cleaner
I think Dr. Loll has expressed my reasons for my original suggestion. When there are skins, evaporation, etc., crystal catching can be a real pain, and then you break your best crystal... What if you could just go up to your intended crystal and vacuum it up, and whisk it away to the dewar? Jacob - Original Message - From: Patrick Loll To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, March 27, 2009 8:35 AM Subject: [ccp4bb] Fwd: [ccp4bb] Crystal vacuum cleaner Pretty cool, but the examples shown are all gigantic. Having just spent a frustrating several hours chasing 5 um crystals, I'd give half my kingdom for a simple way to catch THOSE little buggers (damn you, surface tension!). Begin forwarded message: From: Patrick Shaw Stewart patr...@douglas.co.uk Date: March 27, 2009 8:41:53 AM EDT To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Crystal vacuum cleaner Reply-To: Patrick Shaw Stewart patr...@douglas.co.uk Jacob Have you seen the Crystal Catcher system, developed in Japan? http://adsabs.harvard.edu/abs/2008APExp...1c7002K Some of us saw it at a recent IUCr meeting, but I don’t know anyone who has tried it with their own proteins Patrick --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
Re: [ccp4bb] off topic - static laser light scattering
Is it possible, as I have heard about some DNA-binding proteins, that it is at least partially intrinsically disordered (ID), which might change the Stokes radius? You could cross-check by SDS-PAGE or SEC (ID's run larger). CD, with careful protein quantification, might also do the trick. ID itself might also change the dn/dc value, perhaps due to hydration (about that I am not sure, though--I have read that this has an effect on PSV for AUC, though). 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 *** - Original Message - From: Engin Ozkan eoz...@stanford.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, March 27, 2009 9:57 AM Subject: Re: [ccp4bb] off topic - static laser light scattering Dear Tassos, Your assumptions are right, if (1) your dn/dc is accurate, or (2) your machine is calibrated. We recently measured a protein of a similar size to yours, and when a 700 Da ligand was added to the buffer, the measured protein mass was increased accordingly. So MALS can be pretty accurate. For our dn/dc, for pure proteins, we always use 0.185 (not 0.19). For sugar groups, we assume a dn/dc of 0.14, and estimate a mass-averaged value for the glycoprotein (usually somewhere between 0.175 to 0.18). For DNA and RNA, the values will be different, again. You may also realize that by changing a simple calibration constant, you can modify your measured molar masses anyway you want. It may be time for a recalibration (it is not difficult, you can do it yourself). We tend to regularly run BSA, and see if everything is as expected with our equipment. Good luck, Engin Anastassis Perrakis wrote: Dear all, The MALLS instruments on-line with an FPLC and with an RI detector, should provide an 'absolute MW', shape independent, and indeed in our hands they do well. Until yesterday, where a 21kD protein pretends to be 25 kD. We did the mass spec anyway, and its 21kD as we expected to the residue, but I am still puzzled by that result. One central assumption for the MALLS formulas, is that dn/dc, the specific refractive index increment, is constant for unmodified proteins, made by aa with no sugars etc. Literature suggests dn/dc values for proteins to be constant and between 0.189/0.190 is a good value, with minimal buffer dependence for aqueous buffers with 'the usual' salts. I am a rather bad physicist, but my reading tells me that dn/dc, and thus light scattering, depends to the laser-light induced dipole in the molecule. Is there any reason to believe that in theory a molecule with a very particular charge distribution (eg a small DNA binding protein which is already a 'dipole') would have significantly different dn/dc values? Is anyone aware of such an experiment? Literature searches were in vain ... Best - Tassos
Re: [ccp4bb] Crystal vacuum cleaner
Does your system eliminate the need for cryoprotection? Also, how do you time the buffer-removal/freezing steps? JPK *** 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 *** - Original Message - From: Watanabe Nobuhisa nobuh...@nusrc.nagoya-u.ac.jp To: CCP4BB@JISCMAIL.AC.UK Cc: Jacob Keller j-kell...@md.northwestern.edu Sent: Thursday, March 26, 2009 10:50 PM Subject: Re: [ccp4bb] Crystal vacuum cleaner I am not sure this is the answer for your question, but please check, http://www.nusrc.nagoya-u.ac.jp/WatanabeLab/XtalMount/index.html We named it as a loopless mounting method in the paper, but now we leave the loop... The vacuum cleaner I have used for the method is my mouth. But we have just developed a semi-automatic equipment. I hope we will be able to submit the manuscript soon. Nobuhisa Watanabe, PhD. === Synchrotron Radiation Research Center Department of Biotechnology and Biomaterial Chemistry, Graduate School of Engineering Nagoya University C1-3(651) Furo-cho Chikusa-ku, Nagoya 4648603 Japan Email: nobuh...@nagoya-u.jp Fax: +81-52-789-5286 On 2009/03/27, at 4:43, Jacob Keller wrote: Dear Crystallographers, Has anybody ever heard of mounting crystals in tiny crystal-sized capillaries, such as are pulled by patch-pipet machines, or those used in microfluidics? The material could be either glass or plastic, and one could have some method of continuous positive or negative pressure, perhaps through a hole in the crystal cap. Anyway, once safely inside the tiny capilary, one could freeze it at leisure, without concern for evaporation. It would really make harvesting easy--just vacuum up the crystal, then plop in LiqN2/ propane as per usual. I guess it could also really be done with appropriate modification of a micro-manipulator. 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] SBGrid Computing School - May 5th-8th 2009
Hello, There are available spots remaining for the 2009 SBGrid Computing School, please see below for more information. Please Note: SBGCS registration fees will increase for any attendee who registers after Friday, April 3, 2009. Starting April 4th Nanocourses will increase to $119.00, and Super Tutorials will increase $35.00. The 2009 SBGrid Computing School will offer three (3) Nanocourses: 1. Python Programming for Scientists (Registration Closed for Python) 2. Molecular Visualization (Limited Space Available) 3. OS X Programming for Mac and iPhones (Limited Space Available) Nanocoruses will offer an intensive two-day training and will be concluded by a take-home assignment. Participants who successfully complete a nanocourse will receive a certificate. Please Note: You can only take one (1) of the three (3) nanocourses being offered (nanocourses will run concurrently). In addition to the nanocourses we will also offer several lecture and workshop sessions: 1. Software Showcase Session- Will feature a keynote presentation by Frank Delaglio (Pymol). 2. Quo Vadis Structural Biology? Session- Will include presentations by members of the SBGrid consortium: -Anna Pyle from Yale University -Dinshaw Patel from Memorial Sloan-Kettering Cancer Center -Brandt Eichman from Vanderbilt University We will also have four (4) Super-Tutorials Sessions: 1. Phenix (Limited Space Available) 2. CCP4 (Limited Space Available) 3. SHARP (Limited Space Available) 4. NMR for Crystallographers (Limited Space Available) Please Note: You can take all four Super-Tutorials! Please visit http://school.sbgrid.org for a list of invited speakers. Visit the SBGrid Computing School website at http://school.sbgrid.org to register. If you have any questions please email sch...@sbgrid.org We're looking forward to seeing you in May! -- SBGrid Computing School Harvard Medical School http://school.sbgrid.org sch...@sbgrid.org
Re: [ccp4bb] Crystal vacuum cleaner
As an undergrad late in the last century, I used a micromanipulator, quartz capillaries, and a device similar to a patch pipet (manually operated via a screw) to do just this. It was just about the time that nylon loops were coming into wide use, though, and I gladly abandoned he capillary method in favor of loops. For microcrystals, I favor using micromesh mounts from MiTeGen. -- Kevin M. Jude Berger Lab California Institute for Quantitative Biosciences University of California, Berkeley On 3/26/09 12:43 PM, Jacob Keller wrote: Dear Crystallographers, Has anybody ever heard of mounting crystals in tiny crystal-sized capillaries, such as are pulled by patch-pipet machines, or those used in microfluidics? The material could be either glass or plastic, and one could have some method of continuous positive or negative pressure, perhaps through a hole in the crystal cap. Anyway, once safely inside the tiny capilary, one could freeze it at leisure, without concern for evaporation. It would really make harvesting easy--just vacuum up the crystal, then plop in LiqN2/propane as per usual. I guess it could also really be done with appropriate modification of a micro-manipulator. 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 mailto:j-kell...@northwestern.edu ***
Re: [ccp4bb] Problem sourcing
Dear Ian,
I got bumped out at this line:
Setenv PATH ${PATH}:${XIA2CORE_ROOT}/Test
Could you shed some light on this? I'm using C shell. It can't be the
syntax since I could source as root.
Thanks,
Jason
-Original Message-
From: Ian Tickle [mailto:i.tic...@astex-therapeutics.com]
Sent: Friday, March 27, 2009 12:39 PM
To: Phan, Jason
Cc: CCP4BB@jiscmail.ac.uk
Subject: RE: [ccp4bb] Problems sourcing
Hi Jason
Type 'set verbose' (without the apostrophes) and trying sourcing again,
it should stop just before the offending line.
Cheers
-- Ian
-Original Message-
From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
Behalf Of Phan, Jason
Sent: 27 March 2009 16:24
To: CCP4BB@jiscmail.ac.uk
Subject: RE: [ccp4bb] Problems sourcing
Dear List,
I am trying to install the latest CCP4 6.1.1 binaries on Linux and
running into sourcing problem. I could source the ccp4.setup file as
root (c-shell) and ccp4 ran just fine. But as a user, with the same
shell, I could not source the setup file. The error is setenv: Too
many
arguments. There are so many environment variables in that file it's
impossible to find the culprit. Could someone help me out?
Thanks,
Jason
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Re: [ccp4bb] Crystal vacuum cleaner
Jacob, Although the use of patch-clamp pipettes and micromanipulators come to mind, I just wonder about what would happen to the pipette and the fluid in it when you flash-froze it. Nonetheless, the idea of a means to transfer small crystals easily and quickly has some merit. In another incarnation many years ago, I dabbled in developmental biology. To select out small invertebrate eggs (from sea urchins and sand dollars), which were about 80-100 microns in diameter, we used a braking pipette to them pick them up, one at a time. Even smaller single amoeba cells (like amoeba) can be handled in this way. While you could attach one to a micromanipulator, I always used it by hand as it was much faster. There are several different types, and they could be used to handle objects/cells as small as 20 microns in diameter. A Google book search will bring up Methods in Cell Physiology, Volume 1 by David M. Prescott,1964. See Chapter 8, page 128, (G. E. Stone and I. L. Cameron) for a description of one style of braking pipette. The primary concept is that a narrow constriction/aperture within the pipette causes enough air flow resistance to increase markedly the amount of suction needed to move a small volume of liquid. Hence, we could mouth pipette single cells trivially without sucking them clear through the pipette or taking in too much fluid. For those who have done wet mounts of crystals in capillaries, we know how difficult it can be to control the suction. We made our braking pipettes out of two pieces: (1) a sampling capillary with one end pulled the make the narrow aperture and (2) a holder made out of a cut-off Pasteur pipette. The sampling capillary was placed inside the cut-off Pasteur pipette so the sampling tip stuck out. Then the junction was sealed with the old main-stay: sealing wax. Attaching a tube to the other end of the Pasteur pipette allowed for mouth pipetting. It's about a 10 min job to prepare. Cheers, Michael Also see: Lloyd Claff, C. ''Braking'' Pipettes Science, Volume 105, Issue 2717, pp. 103-104 R. Michael Garavito, Ph.D. Professor of Biochemistry Molecular Biology 513 Biochemistry Bldg. Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: garav...@msu.edu On Mar 27, 2009, at 12:34 PM, Jacob Keller wrote: I think Dr. Loll has expressed my reasons for my original suggestion. When there are skins, evaporation, etc., crystal catching can be a real pain, and then you break your best crystal... What if you could just go up to your intended crystal and vacuum it up, and whisk it away to the dewar? Jacob - Original Message - From: Patrick Loll To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, March 27, 2009 8:35 AM Subject: [ccp4bb] Fwd: [ccp4bb] Crystal vacuum cleaner Pretty cool, but the examples shown are all gigantic. Having just spent a frustrating several hours chasing 5 um crystals, I'd give half my kingdom for a simple way to catch THOSE little buggers (damn you, surface tension!). Begin forwarded message: From: Patrick Shaw Stewart patr...@douglas.co.uk Date: March 27, 2009 8:41:53 AM EDT To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Crystal vacuum cleaner Reply-To: Patrick Shaw Stewart patr...@douglas.co.uk Jacob Have you seen the Crystal Catcher system, developed in Japan? http://adsabs.harvard.edu/abs/2008APExp...1c7002K Some of us saw it at a recent IUCr meeting, but I don’t know anyone who has tried it with their own proteins Patrick --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
[ccp4bb] Adding Non-natural Base to RNA Model in Coot
Dear All, I'd like to add substitute a natural base (adenine) for a non-natural base (2-aminopurine), in a molecular model of an RNA molecule. I'd like to do this with CCP4 and Coot. Could I ask for some help please? Thanks! and all the best, --Buz
[ccp4bb] Phaser SAD+MR followed by CNS
Hello all, I have a structure that has been solved by MR and now have experimental SAD phases that I hope will improve the map. I used Phaser for this from within the CCP4i suite but I would like to take the solution and work with it further in CNS. Is there a way to generate a .hkl file from the Phaser output .mtz file? -- Kelly-Anne
Re: [ccp4bb] Phaser SAD+MR followed by CNS
The CCP4 mtz2various will do this. A sample script and instructions for using the CCP4i GUI can be found at http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Phase+Solution#File_preparation. The example cited is for preparing a file for EPMR, which is a simple hklF listing. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu Kelly-Anne Twist wrote: Hello all, I have a structure that has been solved by MR and now have experimental SAD phases that I hope will improve the map. I used Phaser for this from within the CCP4i suite but I would like to take the solution and work with it further in CNS. Is there a way to generate a .hkl file from the Phaser output .mtz file? -- Kelly-Anne
Re: [ccp4bb] Phaser SAD+MR followed by CNS
Dear Kelly-Anne 2009/3/27 Kelly-Anne Twist wils...@rockefeller.edu: Hello all, I have a structure that has been solved by MR and now have experimental SAD phases that I hope will improve the map. I used Phaser for this from within the CCP4i suite but I would like to take the solution and work with it further in CNS. Is there a way to generate a .hkl file from the Phaser output .mtz file? There is also the possibility to check the CNS pages at http://cns-online.org/v1.21/ (also nice to have if you get further problems) and they also have a page on converting to hkl format: http://cns-online.org/v1.21/tutorial/sf_convert/mtz_to_cns/text.html Best regards, Folmer
[ccp4bb] !RE: [ccp4bb] Problem sourcing
Hi Jason
Nothing obviously wrong there (I assume that the capital 'S' in 'Setenv'
is just your mail client being silly?). Is that the last line printed?
(sorry I got it wrong before, I just checked the source will stop
*after* the offending line, not before as I said, so it's the last line
you want). If you paste the bad line at the shell prompt do you get the
same error? Try 'set echo' source again (you can turn both verbosity
and echoing on for max info!). This will expand the variables ($PATH
etc).
Are you actually using C shell (csh) or TC shell (tcsh)? csh has some
rubbish features I wouldn't recommend it! If you have actually
installed csh I would install tcsh instead! I think the CCP4 shell
script actually assumes you have tcsh not csh.
Hope this helps!
Cheers
-- Ian
-Original Message-
From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
Behalf Of Phan, Jason
Sent: 27 March 2009 18:52
To: Ian Tickle
Cc: CCP4BB@jiscmail.ac.uk
Subject: RE: [ccp4bb] Problem sourcing
Dear Ian,
I got bumped out at this line:
Setenv PATH ${PATH}:${XIA2CORE_ROOT}/Test
Could you shed some light on this? I'm using C shell. It can't be the
syntax since I could source as root.
Thanks,
Jason
-Original Message-
From: Ian Tickle [mailto:i.tic...@astex-therapeutics.com]
Sent: Friday, March 27, 2009 12:39 PM
To: Phan, Jason
Cc: CCP4BB@jiscmail.ac.uk
Subject: RE: [ccp4bb] Problems sourcing
Hi Jason
Type 'set verbose' (without the apostrophes) and trying sourcing
again,
it should stop just before the offending line.
Cheers
-- Ian
-Original Message-
From: owner-ccp...@jiscmail.ac.uk
[mailto:owner-ccp...@jiscmail.ac.uk]
On
Behalf Of Phan, Jason
Sent: 27 March 2009 16:24
To: CCP4BB@jiscmail.ac.uk
Subject: RE: [ccp4bb] Problems sourcing
Dear List,
I am trying to install the latest CCP4 6.1.1 binaries on Linux and
running into sourcing problem. I could source the ccp4.setup file as
root (c-shell) and ccp4 ran just fine. But as a user, with the same
shell, I could not source the setup file. The error is setenv: Too
many
arguments. There are so many environment variables in that file
it's
impossible to find the culprit. Could someone help me out?
Thanks,
Jason
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Disclaimer
This communication is confidential and may contain privileged
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If
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Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies
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traffic in compliance with its corporate email policy. The Company
accepts no liability or responsibility for any onward transmission or
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domain.
Unless expressly stated, opinions in this message are those of the
individual sender and not of Astex Therapeutics Ltd. The recipient
should check this email and any attachments for the presence of
computer
viruses. Astex Therapeutics Ltd accepts no liability for damage caused
by any virus transmitted by this email. E-mail is susceptible to data
corruption, interception, unauthorized amendment, and tampering, Astex
Therapeutics Ltd only send and receive e-mails on the basis that the
Company is not liable for any such alteration or any consequences
thereof.
Astex Therapeutics Ltd., Registered in England at 436 Cambridge
Science
Park, Cambridge CB4 0QA under number 3751674
This transmission may be confidential or protected from disclosure and
is
only for review and use by the intended recipient. Access by anyone
else
is unauthorized. Any unauthorized reader is hereby notified that any
review, use, dissemination, disclosure or copying of this information,
or
any act or omission taken in reliance on it, is prohibited and may be
unlawful. If you received this transmission in error, please notify
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Disclaimer
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except for the
Re: [ccp4bb] Problem sourcing
On Fri, Mar 27, 2009 at 02:52:10PM -0400, Phan, Jason wrote:
I got bumped out at this line:
Setenv PATH ${PATH}:${XIA2CORE_ROOT}/Test
What does $PATH expand to? If you had a directory with a space in it,
that would generate the error you're seeing.
Could you shed some light on this? I'm using C shell. It can't be the
syntax since I could source as root.
root might well have a different PATH.
-ben
--
Ben Eisenbraun
Structural Biology Grid Harvard Medical School
http://sbgrid.org http://hms.harvard.edu
Re: [ccp4bb] Problem sourcing
On Mar 27, 2009, at 11:52 AM, Phan, Jason wrote:
Setenv PATH ${PATH}:${XIA2CORE_ROOT}/Test
try replacing this with
setenv PATH ${PATH}:${XIA2CORE_ROOT}/Test
setenv needs to be all lower case, and the double quotes permit spaces
in the path (assuming that is the problem)
Re: [ccp4bb] Problem sourcing resolved
Thank you, Ian, Ben and Bill.
My apology for the S in setenv, a typo.
I expanded the variables in $PATH and found the culprit: set PATH =
(/usr/lib /usr/lib64 /usr/local/lib /usr/local/lib64) in my /etc/cshrc
file. I have the line source /etc/cshrc at the top of my ~/.cshrc
file. After commenting it out, voila!!!
Thank you, Gentlemen. It'll be a good weekend. One less thing to think
about.
Jason
-Original Message-
From: Ian Tickle [mailto:i.tic...@astex-therapeutics.com]
Sent: Friday, March 27, 2009 5:38 PM
To: Phan, Jason
Cc: CCP4BB@jiscmail.ac.uk
Subject: !RE: [ccp4bb] Problem sourcing
Hi Jason
Nothing obviously wrong there (I assume that the capital 'S' in 'Setenv'
is just your mail client being silly?). Is that the last line printed?
(sorry I got it wrong before, I just checked the source will stop
*after* the offending line, not before as I said, so it's the last line
you want). If you paste the bad line at the shell prompt do you get the
same error? Try 'set echo' source again (you can turn both verbosity
and echoing on for max info!). This will expand the variables ($PATH
etc).
Are you actually using C shell (csh) or TC shell (tcsh)? csh has some
rubbish features I wouldn't recommend it! If you have actually
installed csh I would install tcsh instead! I think the CCP4 shell
script actually assumes you have tcsh not csh.
Hope this helps!
Cheers
-- Ian
-Original Message-
From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
Behalf Of Phan, Jason
Sent: 27 March 2009 18:52
To: Ian Tickle
Cc: CCP4BB@jiscmail.ac.uk
Subject: RE: [ccp4bb] Problem sourcing
Dear Ian,
I got bumped out at this line:
Setenv PATH ${PATH}:${XIA2CORE_ROOT}/Test
Could you shed some light on this? I'm using C shell. It can't be the
syntax since I could source as root.
Thanks,
Jason
-Original Message-
From: Ian Tickle [mailto:i.tic...@astex-therapeutics.com]
Sent: Friday, March 27, 2009 12:39 PM
To: Phan, Jason
Cc: CCP4BB@jiscmail.ac.uk
Subject: RE: [ccp4bb] Problems sourcing
Hi Jason
Type 'set verbose' (without the apostrophes) and trying sourcing
again,
it should stop just before the offending line.
Cheers
-- Ian
-Original Message-
From: owner-ccp...@jiscmail.ac.uk
[mailto:owner-ccp...@jiscmail.ac.uk]
On
Behalf Of Phan, Jason
Sent: 27 March 2009 16:24
To: CCP4BB@jiscmail.ac.uk
Subject: RE: [ccp4bb] Problems sourcing
Dear List,
I am trying to install the latest CCP4 6.1.1 binaries on Linux and
running into sourcing problem. I could source the ccp4.setup file as
root (c-shell) and ccp4 ran just fine. But as a user, with the same
shell, I could not source the setup file. The error is setenv: Too
many
arguments. There are so many environment variables in that file
it's
impossible to find the culprit. Could someone help me out?
Thanks,
Jason
This transmission may be confidential or protected from disclosure
and
is
only for review and use by the intended recipient. Access by anyone
else
is unauthorized. Any unauthorized reader is hereby notified that any
review, use, dissemination, disclosure or copying of this
information,
or
any act or omission taken in reliance on it, is prohibited and may
be
unlawful. If you received this transmission in error, please notify
the
sender immediately. Thank you.
Disclaimer
This communication is confidential and may contain privileged
information intended solely for the named addressee(s). It may not be
used or disclosed except for the purpose for which it has been sent.
If
you are not the intended recipient you must not review, use, disclose,
copy, distribute or take any action in reliance upon it. If you have
received this communication in error, please notify Astex Therapeutics
Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies
of the message and any attached documents.
Astex Therapeutics Ltd monitors, controls and protects all its
messaging
traffic in compliance with its corporate email policy. The Company
accepts no liability or responsibility for any onward transmission or
use of emails and attachments having left the Astex Therapeutics
domain.
Unless expressly stated, opinions in this message are those of the
individual sender and not of Astex Therapeutics Ltd. The recipient
should check this email and any attachments for the presence of
computer
viruses. Astex Therapeutics Ltd accepts no liability for damage caused
by any virus transmitted by this email. E-mail is susceptible to data
corruption, interception, unauthorized amendment, and tampering, Astex
Therapeutics Ltd only send and receive e-mails on the basis that the
Company is not liable for any such alteration or any consequences
thereof.
Astex Therapeutics Ltd., Registered in England at 436 Cambridge
Science
Park, Cambridge CB4 0QA under number 3751674
This transmission may be confidential or
Re: [ccp4bb] Problem sourcing resolved
Dear Jason: Glad to hear it is working now. If you really want to have a fun weekend, try the z-shell: zsh. zsh combines the user-friendliness of tcsh with the power of bash and ksh. It can do all sorts of cool stuff, like user and host completions, remote file name completion (with scp), and much more. You can learn more about it here: http://zsh.sourceforge.net/FAQ/ We have some crystallography-friendly initialization scripts here that work on linux and OS X: http://code.google.com/p/zsh-templates-osx/ Have fun. Bill On Mar 27, 2009, at 5:55 PM, Phan, Jason wrote: Thank you, Ian, Ben and Bill. My apology for the S in setenv, a typo. I expanded the variables in $PATH and found the culprit: set PATH = (/usr/lib /usr/lib64 /usr/local/lib /usr/local/lib64) in my /etc/cshrc file. I have the line source /etc/cshrc at the top of my ~/.cshrc file. After commenting it out, voila!!! Thank you, Gentlemen. It'll be a good weekend. One less thing to think about. fewer? Jason
