Re: [ccp4bb] Server or software for B factor analysis
MOLEMAN2 is your friend. Stats: http://xray.bmc.uu.se/usf/moleman2_man.html#S50 Plots: http://xray.bmc.uu.se/usf/moleman2_man.html#S57 --dvd Will you please tell me a server of software which can draw a curve for the B factor of the atoms in a protein PDB file from the first residue to the residue?Or a server or software by which we can easily order the B factors of the atoms in the PDB file according to the B factor in decrease or in increase? Or to get the residues with the highest B factor and the lowest B factor? ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
[ccp4bb] Molrep - Fortran runtime errors
When using a multi-copy search/fitting two models in Molrep, I encounter a fortran runtime error. This happens at the stage where the second model is being read in. I see that there are some previous posts concerning this. I did try using a different version (as previous posters reported working) of molrep, but this is not working either. Here are two log outputs concerning the error: 1.) Fortran runtime error: Attempt to allocate negative amount of memory. 2.) Possible integer overflow/usr/lab/people/jcp/xlinksc/trimmed.pdb has failed with error message At line 1064 of file molrep_keywords.fh Fortran runtime error: Bad real number in item 3 of list input I am using Molrep version 11.0.02. All other modules work except for the multi-copy search. Any help and/or suggestions are appreciated, Best regards, Jason P
[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] LCP Tools Technologies Workshop, August 2nd, 2012, Boston, MA
The Joint Center for Innovative Membrane Protein Technologies (JCIMPT), operated at The Scripps Research Institute (TSRI) and funded by the NIH Common Fund's Structural Biology program, is teaming up with Formulatrix to host a workshop on Lipidic Cubic Phase (LCP) Tools Technologies following the ACA 2012 Annual Meeting in Boston, MA. Participants will get involved in comprehensive hands-on and demonstration sessions and will have an opportunity to setup LCP crystallization trials using their own samples. Registration is limited to 32 people on a first come, first served basis. Follow this link (http://www.formulatrix.com/workshophttp://www.formulatrix.com/workshop) for more information. Vadim Cherezov, TSRI. Workshop organizer.
Re: [ccp4bb] stereo
On 02/23/12 14:16, Hena Dutta wrote: 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 Yes, we have a Quadro 4000. It seems to work on both Fedora 15 and Scientific Linux 6.1. I do recall a bit of grief in that the default nouveau driver did not properly recognize the Q4000, possibly because it is a new model; so you will have to know what to do in text console mode to get the proprietary driver working. This should do it for SL6.1: # first, enable the elrepo repository: rpm --import http://elrepo.org/RPM-GPG-KEY-elrepo.org rpm -Uvh http://elrepo.org/elrepo-release-6-4.el6.elrepo.noarch.rpm # then you can install the driver. This automatically takes care of blacklisting the nouveau driver. yum -y --enablerepo=elrepo install kmod-nvidia You will need to tweak the xorg.conf file to add the stereo line and disable composite. A /etc/X11/xorg.conf file for SL6.1 attached. Detailed instructions will vary with your Linux distribution, of course. Cheers, -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu # nvidia-xconfig: X configuration file generated by nvidia-xconfig # nvidia-xconfig: version 290.10 (buildmeis...@swio-display-x86-rhel47-07.nvidia.com) Wed Nov 16 18:47:40 PST 2011 Section ServerLayout Identifier Layout0 Screen 0 Screen0 0 0 InputDeviceKeyboard0 CoreKeyboard InputDeviceMouse0 CorePointer EndSection Section Files ModulePath /usr/lib64/xorg/modules/extensions/nvidia ModulePath /usr/lib64/xorg/modules FontPath /usr/share/fonts/default/Type1 EndSection Section InputDevice # generated from default Identifier Mouse0 Driver mouse Option Protocol auto Option Device /dev/input/mice Option Emulate3Buttons no Option ZAxisMapping 4 5 EndSection Section InputDevice # generated from data in /etc/sysconfig/keyboard Identifier Keyboard0 Driver kbd Option XkbLayout us Option XkbModel pc105 EndSection Section Monitor Identifier Monitor0 VendorName Planar ModelNameSA2311W HorizSync30.0 - 140.0 VertRefresh 56.0 - 120.0 Option DPMS EndSection Section Device Identifier Device0 Driver nvidia VendorName NVIDIA Corporation EndSection Section Screen Identifier Screen0 Device Device0 MonitorMonitor0 Option Stereo 10 DefaultDepth 24 SubSection Display Depth 24 Modes 1920x1080 1920x1080_120 EndSubSection EndSection Section Extensions Option Composite Disable EndSection
[ccp4bb] Problem running imosflm
I installed CCP4 6.2.0 on Scientific Linux 6.1 (x86_64) on Feb 9, including the versions of tcl tk offered by CCP4. When I try to run imosflm, I get the following: MOSFLM_EXEC set to /usr/local/xtal/ccp4_master/ccp4-6.2.0/bin/ipmosflm testing MOSFLM_WISH (/usr/local/xtal/ccp4_master/tcltkplusplus/bin/wish) Error in startup script: invalid command name iwidgets::tabnotebook while executing iwidgets::tabnotebook $itk_interior.f.tabs -tabpos n -background #dcdcdc -tabbackground #a9a9a9 -foreground black -tabforeground black ... ... On the problems web page I find the following: CCP4i ... 8. imosflm exits with invalid command iwidgets::tabnotebook Date : 24/04/2009 CCP4 Version: 6.1.1 using tcltk++ This is due to /tclIndex/ not being copied from /tcltk++/iwidgets4.0.1/generic/ to the /install loc/lib/iwidgets4.0.1/scripts/ during the /build-tcl-tk++.sh/ process. The solution is to manually copy the file. But in my installation I find this: # find . -name tclIndex | grep iwid ./tcltkplusplus/iwidgets4.0.1/generic/tclIndex ./tcltkplusplus/lib/iwidgets4.0.1/scripts/tclIndex # diff tcltkplusplus/iwidgets4.0.1/generic/tclIndex tcltkplusplus/lib/iwidgets4.0.1/scripts/tclIndex (No output returned; i.e. files are identical) I have version 6.2.0, so that fix should have been incorporated in the distribution. Also, the file is present where it is supposed to be. So that does not seem to be the cause of my problem. Did I miss something? Is there another fix? -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] molrep question - how get our ducks in a row?
Hello all, We are solving a superstructure of a protein complex with 2 parts. Built 6 of the first part and they are all sensibly stacked next to each other. Then we read this into molrep as the fixed model and solved for the second part. The solution was found but the 6 for the second model are in different ASU's and unit cells. What is the easiest way to get everyone together in one asu? We can think of hard ways to do it, but any advice? Thanks, Gloria
[ccp4bb] Postdoc position
There is an immediate opening for a Post Doctoral Research Associate in the group of Dr. Lan Guan, Department of Cell Physiology and Molecular Biophysics at Texas Tech University Health Science Center, Lubbock, TX, focuses on the structure determination of a sugar transport protein by 3-D X-ray crystallography. This position requires a strong background in membrane protein purification, crystallization, and crystal structure determination. Experience in molecular biology or membrane protein biochemistry will be an advantage. Highly motivated candidates with two-year successful postdoc experience in protein crystallography are encouraged to apply. Interested candidates should submit an application, a CV and the names of three references through TTUHSC’s website (http://jobs.texastech.edu/postings/43152). TTUHSC is an EEO/AA employer.
Re: [ccp4bb] Aggregated protein for crystallization
I should have been more clear. If your protein is insoluble aggregate, you can use crystal screen results to get an idea of what buffer conditions favor solubility (and hopefully monodispersity). An example is described nicely in Collins et al, Acta Cryst F 61:1035. Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry h...@hawaii.edu On Wed, Feb 22, 2012 at 5:54 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: You might get lucky by setting up crystallization plates, but chances are you won't get very useful information from them, especially if your aggregated protein is soluble. I seem to fail to understand how crystallization plates would give information in the not-special case of protein aggregates NOT being soluble? BR Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry h...@hawaii.edu
Re: [ccp4bb] molrep question - how get our ducks in a row?
Hi Gloria, It depends on if you mean hard as in thinking up a slick trick, or hard as in maybe 20-30 mins of tedious work. I had the same problem with 18 in the ASM, where the solution had scattered models, but didn't want to think about it, so just used pymol. 1) open the first model with the original 6 models 2) then make separate files with each of the other subunits (with the CRYST line) - with short names like m1.pdb, m2.pdb, m3.pdb etc. (this is so you can read easily in the gui later for saving) 3) then open m1.pdb 4) on the left, go to the A or action menu for m1 .pdb generate symmetry mates within 100 Angstroms (this can be smaller or larger, just need to see them) 5) then you'll have the symmates on the screen and the list of each right listed as m1_100-1-100 etc. So you can just click them on and off to see which one you like, then save that molecule. 6) Then delete the symmates delete m1_* so you can check 7) Open the saved symmate to check 8) go to step 3 for the next model, ie. m2.pdb not a slick answer, but can be done when tired with minimal error. On Thu, Feb 23, 2012 at 4:07 PM, Gloria Borgstahl gborgst...@gmail.comwrote: Hello all, We are solving a superstructure of a protein complex with 2 parts. Built 6 of the first part and they are all sensibly stacked next to each other. Then we read this into molrep as the fixed model and solved for the second part. The solution was found but the 6 for the second model are in different ASU's and unit cells. What is the easiest way to get everyone together in one asu? We can think of hard ways to do it, but any advice? Thanks, Gloria -- David Shin, Ph.D Lawrence Berkeley National Labs 1 Cyclotron Road MS 83-R0101 Berkeley, CA 94720 USA
Re: [ccp4bb] molrep question - how get our ducks in a row?
Hi, There is an option in the molrep interface (in the search parameters tab) to output all models closest to the input coordinate file With a bit of luck, that should do it. Johan On 24 February 2012 00:07, Gloria Borgstahl gborgst...@gmail.com wrote: Hello all, We are solving a superstructure of a protein complex with 2 parts. Built 6 of the first part and they are all sensibly stacked next to each other. Then we read this into molrep as the fixed model and solved for the second part. The solution was found but the 6 for the second model are in different ASU's and unit cells. What is the easiest way to get everyone together in one asu? We can think of hard ways to do it, but any advice? Thanks, Gloria -- Dr. Johan P. Turkenburg X-ray facilities manager York Structural Biology Laboratory University of York Phone (+) 44 1904 328251 York YO10 5DD UK Fax (+) 44 1904 328266 Note new email address johan.turkenb...@york.ac.uk
