[ccp4bb] cryo-em data conversion
Dear Members, Sorry for if the question is off topic. Can someone suggest the easiest way to convert .tif file (raw data) into .mrcs format and also need to create a .star file to use Relion for the following steps? Thanks for your help. Best regards, Hena
[ccp4bb] crystallization screen for protein-protein complex
Dear Members, I am trying to crystallize a protein-protein complex. Both are soluble proteins and form complex as observed in FPLC either co-purifying or separately purifying and then mixing with equi-molar ratio. Looking for suggested screens to try for crystallization. So far tried with Qiagen - ProComplex Suite, Classics Suite and Classics II Suite No success yet. Is there any guidance which screen to try? Looking for your help... Regards, Hena.
Re: [ccp4bb] database of crystallization condition
Many thanks to all of you for useful links and suggestions. Best regards... Hena On Wed, Jul 24, 2013 at 7:51 PM, Bostjan Kobe b.k...@uq.edu.au wrote: Hena I agree with the responses so far, but I think It may not be a complete waste of time looking at the crystallization conditions for similar proteins, you may find a common additive for example and there may be a functional reason for this being required in crystallization. Bostjan --- Bostjan Kobe NHMRC Research Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. From: Segelke, Brent W. segel...@llnl.gov Reply-To: Segelke, Brent W. segel...@llnl.gov Date: Wed, 24 Jul 2013 16:52:35 + To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] database of crystallization condition Hena, ** ** I think this notion of fold families having similar crystallization conditions has been kicking around since the 80’s at least. I seem to recall Gary Gilliland presenting a fairly comprehensive and well controlled study for myoglobins and showing some correlation of crystallization conditions. However, I believe this example is an exception. ** ** Just to add to what Janet and Enrico have said: Taking the HIV integrase example from David Davies; or any of the Derewenda surface entropy reduction, protein engineering, examples; it is clear that small changes (even single point mutations) can dramatically alter the bulk properties (and crystallization behavior) of a protein. ** ** One last point, it is very hard to control for investigator preference when probing a database of successes. It may be that a review of the BMCD will reveal a correlation between crystallization conditions and fold families, but that could be due to a preference for particular crystallization conditions used in crystallization screens rather than properties of the protein family. ** ** Brent ** ** Brent W. Segelke Senior Biomedical Scientist Lawrence Livermore National Laboratory 7000 East Avenue, Livermore CA, 94550 USA segek...@llnl.gov ** ** ** ** ** ** *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKCCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Janet Newman *Sent:* Wednesday, July 24, 2013 9:23 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] database of crystallization condition ** ** Dear Hena, ** ** The BMCD might be a resource worth investigating: ** ** http://xpdb.nist.gov:8060/BMCD4/index.faces ** ** Although there are claims that structurally similar proteins may crystallise under similar conditions (the existence of directed screens -such as the Jena Biosciences 'Kinase' screen, you have to wonder (as Enrico points out) how these can work, as the bits that change the most in any protein family are the outside bits (ie, away from the active site) and thus are generally the parts going to affect crystallisation the most. ** ** ** ** Janet ** ** Janet Newman Principal Scientist / Director, Collaborative Crystallisation Centre CSIRO Material Science and Engineering 343 Royal Parade Parkville. VIC. 3052 Australia Tel +613 9662 7326 Email janet.new...@csiro.au -- *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Hena Dutta [hdutt...@gmail.com] *Sent:* 25 July 2013 00:36 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] database of crystallization condition Hi, Can anyone tell, if there is any database containing the crystallization conditions of published structures? I want to see the conditions people have used for those proteins having some structural similarity. Any suggestion would be appreciated. Regards... Hena
[ccp4bb] database of crystallization condition
Hi, Can anyone tell, if there is any database containing the crystallization conditions of published structures? I want to see the conditions people have used for those proteins having some structural similarity. Any suggestion would be appreciated. Regards... Hena
[ccp4bb] stereo set up
Hi, My apology for the off topic question. I purchased a Toshiba Qosmio laptop X875Q7390. This has inbuilt ir emiter. It came with NVIDIA 3D VISION active shutter glasses. This is a 3D vision ready laptop. I can see high quality the 3d stereo using this glass for some given still pictures. I want to set 3d stereo for PYMOL and COOT. I am currently running windows 8 (64 bit). I will install linux as well. I installed PYMOL, but can not see stereo. Could someone help me? Thanking you in advance... Regards... Hena
[ccp4bb] cloning HD
Hello, Sorry for the question if non-ccp4. I am using a HP workstation Xeon Z400. This has both windows and linux Mint. I am using crystallographic programs with stereo setup in coot, o, pymol, vmd…. I bought a new exactly same desktop with all same hardware configurations except the old one has 160 GB hard disk and new one has 500 GB. What is the best way to get all my linux set up from old machine to the new one. I tried with clonezill and it did not work. I am not sure if I selected the right package and version. Any suggestion would be very helpful. Looking forward to hearing from you… Hena
[ccp4bb] stereo
Hello, Is anyone using nvidia quadro 4000 graphics card for linux environment to see stereo in pymol, coot, O or similar programs? If yes, I like to buy that. Thanks... Hena
[ccp4bb] O in windows
Hi, Is there anyone using O in windows environment with stereo setup? Could you please tell how to setup? I have quadro fx 3700 and able to set up stereo in coot, pymol, vmd in windows env. Thanks... Hena
[ccp4bb] stereo
Dear Members, Is any one using NVidia NVision 3D Setup with active stereo in linux distribution for crystallographic work? Which one would be the best choice to set up, an active stereo or a passive stereo for crystallographic work? Can anyone shade some details on this? I am planning to buy or build a new workstation with stereo set up. It would be great if someone can give some estimate on this. Many thanks, Hena
[ccp4bb] Protein expression, purification and crystallization
Dear Members of CCP4BB and PHENIXBB, Can you suggest a reliable website where I can get basic and advanced information on protein expression, purification and crystallization. I like to read on the monitor. Thanking you in advance... Hena
[ccp4bb] PYMOL installation in openSUSE 11.3 (64 bit)
Hello, I was trying to install PYMOL in my openSUSE 11.3 as follows: cd /usr/local hena@a:/usr/local sudo svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymolpymol cd pymol hena@a:/usr/local/pymol sudo python setup.py install And I got the following error at the end: package init file 'modules/web/javascript/__init__.py' not found (or not a regular file) package init file 'modules/web/javascript/__init__.py' not found (or not a regular file) running build_ext building 'pymol._cmd' extension creating build/temp.linux-x86_64-2.6 creating build/temp.linux-x86_64-2.6/modules creating build/temp.linux-x86_64-2.6/modules/cealign creating build/temp.linux-x86_64-2.6/modules/cealign/src creating build/temp.linux-x86_64-2.6/ov creating build/temp.linux-x86_64-2.6/ov/src creating build/temp.linux-x86_64-2.6/layer0 creating build/temp.linux-x86_64-2.6/layer1 creating build/temp.linux-x86_64-2.6/layer2 creating build/temp.linux-x86_64-2.6/layer3 creating build/temp.linux-x86_64-2.6/layer4 creating build/temp.linux-x86_64-2.6/layer5 gcc -pthread -fno-strict-aliasing -DNDEBUG -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c modules/cealign/src/ccealignmodule.cpp -o build/temp.linux-x86_64-2.6/modules/cealign/src/ccealignmodule.o -ffast-math -funroll-loops -O3 In file included from modules/cealign/src/ccealignmodule.H:57:0, from modules/cealign/src/ccealignmodule.cpp:32: layer0/os_python.h:30:19: fatal error: Python.h: No such file or directory compilation terminated. error: command 'gcc' failed with exit status 1 Can someone advise me at this point or suggest the right pakage of PYMOL that I can install in open SUSE 11.3 Thanks... Hena
Re: [ccp4bb] PYMOL installation in openSUSE 11.3 (64 bit)
Sorry for my earlier non CCP4 posting in CCP4BB. hena On Mon, Mar 7, 2011 at 9:30 AM, Ben Eisenbraun b...@hkl.hms.harvard.eduwrote: Hello Hena, I was trying to install PYMOL in my openSUSE 11.3 as follows: ... In file included from modules/cealign/src/ccealignmodule.H:57:0, from modules/cealign/src/ccealignmodule.cpp:32: layer0/os_python.h:30:19: fatal error: Python.h: No such file or directory You're missing the Python header files. There should be an OS package that provides this. You should really post your PyMOL questions to the PyMOL mailing list though. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |
[ccp4bb] stuck with COOT installation in openSUSE 11.3
Hello, I could not open the COOT GUI after installing either from 'coot-0.6.1-binary-Linux-x86_64-centos-5-gtk2.tar.gz' or from 'coot-0.6.2-pre-1-revision-3205-binary-Linux-x86_64-centos-5-gtk2.tar.gz' I used the following commands: 1. from /usr/loca/src sudo tar xvzf *.gz as suggested in http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installing_Coot_on_Linux 2. I created the following link by typing sudo ln -s /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot /usr/local/bin/coot After I run the command 'coot' I got the following error: hena@dl403a-2:~ coot COOT_PREFIX is /usr/local /usr/local/bin/coot-real /usr/local/bin/coot: line 247: /usr/local/bin/coot-real: No such file or directory /usr/local/bin/coot: line 253: /usr/local/bin/guile: No such file or directory hena@dl403a-2:~ Then I link the whole 'bin' directory as follows: sudo ln -s /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/ /usr/local/bin/ and I got the following error after running 'coot': hena@dl403a-2:~ coot COOT_PREFIX is /usr/local/src/coot-Linux-x86_64-centos-5-gtk2 /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot-real /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot-real: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory coot-exe: /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot-real coot-version: /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot-real /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot-real: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory platform: /bin/uname core: #f No core file found. No debugging This is not helpful. Please turn on core dumps before sending a crash report hena@dl403a-2:~ I checked that I have 'libpng12.so.0' file in different 'lib' folders. I successfully installed other programs like CCP4, CNS and PHENIX in my openSUSE 11.3 Can someone advise what's wrong I am doing? Many thanks... hena
