[ccp4bb] Opening Workshop of the NMR and X-Ray facility at IECB Bordeaux France 14/04/08
There will be a workshop on NMR and X-Ray in Structural Biology to be held at IECB (Bordeaux FRANCE) on 14 April 2008. Invited Speakers : Franck Artzner (Rennes), Martin Blackledge (Grenoble), Rolf Boelens (Utrecht), Yves Bourne (Marseille), Antoinette Killian (Utrecht), Jean-Yves Lallemand (Gif-sur-Yvette), Alain Milon (Toulouse), Daniel Panne (Grenoble), Javier Perez (SOLEIL). There is no registration fee, but registration will be required. Lunch will be provided. If you are interested in participating, please email [EMAIL PROTECTED] no later than 7 April 2008. see http://www.iecb.u-bordeaux.fr for more information = Alain Dautant IBGC CNRS Bordeaux 2 University 33077 BORDEAUX FRANCE =
[ccp4bb] EMBO Course on Macromolecular Complexes: March 31 Deadline
Dear all, This is a reminder that March 31, 2008 is the deadline for applying to the EMBO Practical Course on the Structural Characterization of Macromolecular Complexes to be held in Grenoble, France during the week of June 2-7, 2008. TOPICS INCLUDE: - expression and purification of multi-subunit complexes - biophysical biochemical characterization of complexes - structural analysis of complexes by combining different methods (EM, NMR, SAXS, Crystallography) SPEAKERS: Radu Aricescu, Imre Berger, Jan Ellenberg, Anne-Claude Gavin, Christian Kambach, Chris Oubridge, Daniel Panne, Vladimir Rybin, Michael Sattler, Christiane Schaffitzel, Patrick Schultz, Bertrand Seraphin, Titia Sixma, Holger Stark, Dmitri Svergun, Song Tan, Martin Walsh, Willy Wriggers FOR MORE INFORMATION PLEASE VISIT: http://cwp.embo.org/pc08-18/ Best regards, Carlo Petosa Carlo Petosa EMBL Grenoble Outstation 6 rue Jules Horowitz B.P. 181 38042 Grenoble cedex 9 France Tel:+33 476 20 76 30 Fax:+33 476 20 71 99
[ccp4bb] Coot problems on mac...
Has anyone found a solution to the X window problem on macs running 10.5.2? Both Coot and pymol are becoming almost unusable by freezing frequently because of X11 not responding. I've upgraded my X11 to 2.1.4 from the webpage http://trac.macosforge.org/projects/xquartz/ wiki/ but the problem still persists. I know a couple others have commented on this problem, but have yet to see an answer. Simon
Re: [ccp4bb] ccp4i - Directories Project Directory Error
Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut
Re: [ccp4bb] ccp4i - Directories Project Directory Error
William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut
Re: [ccp4bb] Coot problems on mac...
HI Simon: The X11 guy at Apple is very interested in trying to help. If you could join the Apple X11 mailing list and document this as carefully as possible, it would be a real benefit. He's out of town for a few days but is interested in dealing with this as soon as he returns. There is a rc for v. 2.2.0 that I installed a couple of days ago. It isn't a magic bullet, but between that and the very latest coot from the pre-release, I was able to get a couple of hours of work done without interruption (well, from the X-server). Bill On Mar 25, 2008, at 5:35 AM, Simon Kolstoe wrote: Has anyone found a solution to the X window problem on macs running 10.5.2? Both Coot and pymol are becoming almost unusable by freezing frequently because of X11 not responding. I've upgraded my X11 to 2.1.4 from the webpage http://trac.macosforge.org/projects/xquartz/wiki/ but the problem still persists. I know a couple others have commented on this problem, but have yet to see an answer. Simon
Re: [ccp4bb] ccp4i - Directories Project Directory Error
In both cases, you have to make sure you are setting up the environment appropriately for ccp4, unique to the unix shell you are using. In the case of the ccp4 package you compile with the aid of the fink script, at the start of a shell session, you, or your dot file, needs to issue source /sw/bin/init.sh or source /sw/bin/init.csh for bash and zsh or tcsh, respectively. That in turn sources the appropriate environment setup file in $CCP4/include. On Mar 25, 2008, at 7:47 AM, Kurt Padilla wrote: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut
Re: [ccp4bb] ccp4i - Directories Project Directory Error
Hi Kurt, the CCP4 program package for Mac OS X from the CCP4 download site installs the CCP4 suite under /usr/local or any other path that you provide during installation. There is no such thing as a CCP4.app that can be started by clicking on it. Instead, you have to create in a Terminal.app a .bashrc file in your home directory (/Users/name where name is your user name) and add a line to it that calls the ccp4i setup script, like one of the following lines (check the correct path): source /usr/local/ccp4-6.0.2/bin/ccp4.setup-sh or . /usr/local/ccp4-6.0.2/bin/ccp4.setup-sh After that, this setup script is executed whenever you open a new Terminal.app. You can verify the existence of any CCP4 program by typing, for instance, which fft. The answer should give you the full path of the CCP4 fft program. If you want to use the ccp4i GUI, you should install the tcltkblt.pck for Mac OS X from the CCP4 download site under its default installation path. This is more the UNIX way of installation than the Mac way. I hope that helps, best regards, Dirk. Am 25.03.2008 um 15:47 schrieb Kurt Padilla: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: [EMAIL PROTECTED] ***
Re: [ccp4bb] ccp4i - Directories Project Directory Error
Hi - You need to add to your .chrc, or type in an ***X11*** window (and not in the Terminal). source /usr/local/ccp4-6.0.2//bin/ccp4.setup-csh then it will work. it does not really install a real application in the OSX sense. A. On Mar 25, 2008, at 15:47, Kurt Padilla wrote: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut
Re: [ccp4bb] ccp4i - Directories Project Directory Error
I also thought the problem was using the Terminal window and not the X11 window, but, interestingly, typing ccp4i in a Terminal window, not an X11 window does work. X11 does need to be installed and running, -- that could be the problem. (Caveat, this is in 10.4, not 10.5 - I have 10.5 but haven't installed it yet because of the coot discussions) Sue On Mar 25, 2008, at 8:37 AM, Anastassis Perrakis wrote: Hi - You need to add to your .chrc, or type in an ***X11*** window (and not in the Terminal). source /usr/local/ccp4-6.0.2//bin/ccp4.setup-csh then it will work. it does not really install a real application in the OSX sense. A. On Mar 25, 2008, at 15:47, Kurt Padilla wrote: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut Sue Roberts Biochemistry Biophysics University of Arizona [EMAIL PROTECTED]
Re: [ccp4bb] ccp4i - Directories Project Directory Error
Sue, Currently, when I type in ccp4i into Terminal, X11 launches and then CCP4 does too. I am running OS X 10.5 with a fink installation. Kurt On Tue, Mar 25, 2008 at 12:04 PM, Sue Roberts [EMAIL PROTECTED] wrote: I also thought the problem was using the Terminal window and not the X11 window, but, interestingly, typing ccp4i in a Terminal window, not an X11 window does work. X11 does need to be installed and running, -- that could be the problem. (Caveat, this is in 10.4, not 10.5 - I have 10.5 but haven't installed it yet because of the coot discussions) Sue On Mar 25, 2008, at 8:37 AM, Anastassis Perrakis wrote: Hi - You need to add to your .chrc, or type in an ***X11*** window (and not in the Terminal). source /usr/local/ccp4-6.0.2//bin/ccp4.setup-csh then it will work. it does not really install a real application in the OSX sense. A. On Mar 25, 2008, at 15:47, Kurt Padilla wrote: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut Sue Roberts Biochemistry Biophysics University of Arizona [EMAIL PROTECTED]
[ccp4bb] Facility manager position, University of Oregon
The Institute of Molecular Biology at the University of Oregon (www.molbio.uoregon.edu ) has an opening for a macromolecular crystallography facilities manager. The successful candidate will be responsible for maintaining a rotating anode source, area detector and computational facilities to enable structure determination by Institute researchers (4-6 laboratories). It is envisioned this could be either a part-time or full-time position depending on the level of involvement in assisting with structure determination. A Ph.D. in Biochemistry, Structural Biology or a relevant field is required, along with practical experience in macromolecular crystallographic structure solution (preferably using de novo phasing methods). Computer administration experience (linux) is also strongly preferred. Candidates with experience serving the needs of a diverse population are strongly desired. Please see the HR jobs page at: http://hr.uoregon.edu/jobs. Interested persons should send a curriculum vitae and arrange for three letters of recommendation to be sent to: Crystallography Manager Search Committee posting 8072, Institute of Molecular Biology, 1229 University of Oregon, Eugene, OR 97403-1229. To be assured of full consideration, application materials must be received by April 25, 2008, but the search will remain open until the position is filled. EO/AA/ADA institution committed to cultural diversity.
Re: [ccp4bb] ccp4i - Directories Project Directory Error
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 This is a 10.5 feature : when an application tries to connect to the X11 window server, X11 is automatically launched (unless it was already running). Hence in Leopard you can call ccp4i from within Terminal.app without much more to setup than the regualr CCP4 setup. Serge. Le 25 mars 08 à 17:32, Kurt Padilla a écrit : Sue, Currently, when I type in ccp4i into Terminal, X11 launches and then CCP4 does too. I am running OS X 10.5 with a fink installation. Kurt On Tue, Mar 25, 2008 at 12:04 PM, Sue Roberts [EMAIL PROTECTED] wrote: I also thought the problem was using the Terminal window and not the X11 window, but, interestingly, typing ccp4i in a Terminal window, not an X11 window does work. X11 does need to be installed and running, -- that could be the problem. (Caveat, this is in 10.4, not 10.5 - I have 10.5 but haven't installed it yet because of the coot discussions) Sue On Mar 25, 2008, at 8:37 AM, Anastassis Perrakis wrote: Hi - You need to add to your .chrc, or type in an ***X11*** window (and not in the Terminal). source /usr/local/ccp4-6.0.2//bin/ccp4.setup-csh then it will work. it does not really install a real application in the OSX sense. A. On Mar 25, 2008, at 15:47, Kurt Padilla wrote: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut Sue Roberts Biochemistry Biophysics University of Arizona [EMAIL PROTECTED] -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkfpLPAACgkQlz6UVQtc2uwjGgCeK+8Fb6esGzt4Qcjcv13mKeyS ZewAmgN/vIIkKY77YTTdEr3Yv3a2sC05 =Kf12 -END PGP SIGNATURE-
[ccp4bb] TopMatch protein structure alignment and superposition webservice
Dear All: I want to draw your attention to a very useful server for checking for new folds etc... Thx, br -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Markus Wiederstein Sent: Tuesday, March 25, 2008 6:56 AM To: [EMAIL PROTECTED] Subject: pdb-l: TopMatch protein structure alignment and superposition webservice We announce the release of TopMatch-web, a public web service for the alignment and superposition of protein structures and the instant visualization of structural similiarities. We believe that TopMatch is an exceptionally effective, accurate, and enjoyable program for the investigation of protein structure similarities. For further information and instructive examples see Sippl Wiederstein (2008) A Note on Difficult Structure Alignment Problems. Bioinformatics 24, pp. 426-427 TopMatch-web is available as a public web service at http://topmatch.services.came.sbg.ac.at. Enjoy! The TopMatch Team Center of Applied Molecular Engineering University of Salzburg Austria
Re: [ccp4bb] ccp4i - Directories Project Directory Error
That is exactly how it is supposed to work with 10.5. No need to use an xterm, and it sets the DISPLAY variable automatically. I assume you have write-permissions in the directory it is trying to make the .CCP4 directory? On Mar 25, 2008, at 9:32 AM, Kurt Padilla wrote: Sue, Currently, when I type in ccp4i into Terminal, X11 launches and then CCP4 does too. I am running OS X 10.5 with a fink installation. Kurt On Tue, Mar 25, 2008 at 12:04 PM, Sue Roberts [EMAIL PROTECTED] wrote: I also thought the problem was using the Terminal window and not the X11 window, but, interestingly, typing ccp4i in a Terminal window, not an X11 window does work. X11 does need to be installed and running, -- that could be the problem. (Caveat, this is in 10.4, not 10.5 - I have 10.5 but haven't installed it yet because of the coot discussions) Sue On Mar 25, 2008, at 8:37 AM, Anastassis Perrakis wrote: Hi - You need to add to your .chrc, or type in an ***X11*** window (and not in the Terminal). source /usr/local/ccp4-6.0.2//bin/ccp4.setup-csh then it will work. it does not really install a real application in the OSX sense. A. On Mar 25, 2008, at 15:47, Kurt Padilla wrote: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut Sue Roberts Biochemistry Biophysics University of Arizona [EMAIL PROTECTED]
[ccp4bb] MSE and Refinement
Hi all, I have a question about registering Se. Since diffraction quality of my SeMet dataset is better than a native one, I want to use a SeMet dataset (collected at a remote wavelength) for a final model while I am trying to get a decent native dataset. I tried to put MSE in some MET positions based on Fo-Fc density, but this caused an increase in R free factor after refinement (about 2 %). I'm using a Coot for model building and Refmac for refinement. If anyone has experienced to refine SeMet data, I hope to share some tips. Thanks, Eunyoung
Re: [ccp4bb] Peltier Crystallisation Incubators
I've used cheap Peltier incubators in the past (when funds were scarse) and they were just fine - with the caveat that the incubators I used were small -- basically they were portable beer coolers with a temperature controller (made by Koolatron). First thing I did was to check the temperature and it usually returned to normal within minutes after closing the lid. Artem http://koolatrononline.stores.yahoo.net/koolatron-p75-kool-kaddy.html + PS3 temperature controller (factory installed from the same company) I clearly have no association with Koolatron, however if they want to send me free beer - that's always good! -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jan Dohnalek Sent: Tuesday, March 25, 2008 6:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Peltier Crystallisation Incubators Dear all, Has anyone got experience with Peltier Crystallisation Incubators? According to manufacturers' info they should be OK for small volumes. I have some doubts regarding their effieciency when you open one say ten times a day for one minute how quick they cope with it. Any ideas? Thanks Jan Dohnalek PS: I have found these, there might be more http://www.memmert.com/en/products/product-range/peltier-cooled-incubators/o verview/ http://www.analis.be/products/product.asp?idP=282prodCatg=1778prod=1471 -- == Mr. Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Laboratory of Structural Analysis of Molecules Heyrovskeho nam. 2 16206 Prague 6 Tel: +420 296809205 Fax: +420 296809410 ==
[ccp4bb] N-terminal cleavage after thrombin cleavage?
Dear all, Sorry for the non-CCP4 question. We recently crystallized a protein expressed from pGEX4T-1 vector. The GST tag is cleaved by thrombin before crystallization. The cleavage site of thrombin is Leu-Val-Pro-Arg || Gly-Ser, thus Gly and Ser should remain at the N-terminus of the protein. Strangely, from the 2.5A map, we observed some unexplainable electron density before the most N-terminal glycine residue (http://www.dddc.ac.cn/group/htc/NT_map.jpg). Has anyone encountered similar situation with thrombin cleavage? Could it be some kind of modification or additional residues resulted from unspecific cleavage of thrombin? The crystallization liquor contains MES, PEG6000, Tris, DTT, NaCl and EDTA. Any suggestion is highly appreciated! Thanks in advance! -- Tiancen Hu Shanghai Institute of Materia Medica Chinese Academy of Sciences Rm. 2107, #555, ZuChongzhi Rd. Shanghai 201203 P.R. China Phone: +86-21-50806600 ext. 2107
