Re: [ccp4bb] shape complementarity calculations
Hi Vaheh, Below is a reply I made to the BB in 2007 after a similar enquiry. I expect the program should still work the same, although I haven't used it in recent releases. You have to run it from line command, as there is no interface for it in CCP4i. If you are running under Windows, as I do, you have to start a DOS prompt window and run it from there. You might even need to specify the full path of the binary executable. You also need to specify the output log file, and you can either type your input directly or put it in a text file. I hope this helps. Pierre p.s. I echo Ed Berry's exhortation: If you have been running MD on your interacting molecules, the SC parameter is probably meaningless. But I am prepared for surprises. * Start of previous Reply *** The SC manual URL http://www.ccp4.ac.uk/dist/html/sc.html does contain all the information you need, but I agree it takes some deciphering. The basic parameters are the selections of two 'molecules' whose interface you want to study. For that purpose, the script or line input is really minimal, such as: molecule 1 zone C 3 C 5 molecule 2 chain D chain E end Here molecule 1 is a number of residues in chain C (zone), and molecule 2 is all of chains D and E. You can include and exclude other atoms in each 'molecule' selection. The instruction 'end' tells the program to start calculating. You can modify the program defaults by adding other instructions for 'dot density', 'probe radius' and others, but I usually run it with all the hard wired defaults. These parameters are largely equivalent to their counterparts in AREAIMOL to determine how accurately you want the interfaces to be calculated. Good Luck. ** End of previous reply *** ** Dr. Pierre Rizkallah, Senior Lecturer in Structural Biology, School of Medicine, Academic Avenue, Heath Park, Cardiff CF14 4XN email: rizkall...@cf.ac.uk phone + 44 29 2074 2248 Oganesyan, Vaheh oganesy...@medimmune.com 03/03/09 10:28 PM Colleagues, Would some one kindly suggest software that calculates shape complementarity of two interacting proteins based on co-crystal structure? I've seen number of reports with sc parameter included but none of those mention how it was done. Among non-runnable programs in CCP4 there is the sc program that indeed does not run. Thanks in advance. ___ Vaheh To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
[ccp4bb] PhD position available
Dear all, Please could you bring this advert to the attention of any potential candidates? An International PhD Program was recently created by the Doctoral School CBS2-Sciences Chimiques et Biologiques pour la Santé to attract students who wish to undertake a thesis financed by the French government. In 2009, 18 PhD grants will be attributed. General information about Program statutes, student selection, associated research groups and online application form are available on the website (http://ecole-doctorale-cbs2.igh.cnrs.fr/). The project Structural Studies of Chromatin Modifying Enzymes and their Complexes proposed by the team Regulation of Nuclear Receptors and their transcriptional cofactors at the Centre for Structural Biochemistry, Montpellier, France has been selected. Candidates interested by this offer should register at the CBS2 website and contact the laboratory (william.bourg...@cbs.cnrs.fr). The deadline for online application to the Program is March, 30th 2009. Best regards, Albane le Maire -- Albane le Maire 04 67 41 77 11 http://www.cbs.cnrs.fr
Re: [ccp4bb] Broken chain in Pymol display
Hi Joe, Do you have insertions (e.g. residues 62A, 62B, 62C) or deletions (e.g. residues 42 and 45) which are connected? These may cause broken connectivities in pymol. In this case, I would renumber the pdb file and see how it then displays. Best regards, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Joe Xtal Sent: Monday, March 02, 2009 5:08 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Broken chain in Pymol display Hi all, I tried to display a refined structure (final steps in phenix.refine) in Pymol, but several places are not connected. BTW, the structure displays normally in Coot and bond angle and length deviation are below 1.0 and 0.006, respectively. Thank you, Joe
[ccp4bb] AW: [ccp4bb] Broken chain in Pymol display
Hi Joe, check chainID and segID; there might be a break in one of them not noticed by phenix because it uses the other one, but then leading to an apparent backbone break in coot because it uses the other one ... Best Clemens -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Joe Xtal Sent: Monday, March 02, 2009 5:08 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Broken chain in Pymol display Hi all, I tried to display a refined structure (final steps in phenix.refine) in Pymol, but several places are not connected. BTW, the structure displays normally in Coot and bond angle and length deviation are below 1.0 and 0.006, respectively. Thank you, Joe
[ccp4bb] Crystallographer Position Available at Merck Research Laboratories
All- We currently have one open position for an x-ray crystallographer at Merck Research Labs in Pennsylvania. The official job posting is pasted below, and if you are interested in applying, please apply formally through the Merck Website (www.merck.com/careers) with Job ID BIO001940. Best Wishes, Steve Sr. Research Biochemist/Research Fellow Merck Co. Inc., established in 1891, is a global research-driven pharmaceutical company dedicated to putting patients first. Join us and experience our culture first-hand - one of strong ethics integrity, diversified experiences and a resounding passion for improving human health. As part of our global team, you'll have the opportunity to collaborate with talented and dedicated colleagues while developing and expanding your career. X-Ray Crystallographer This exciting position within Merck Global Structural Biology at West Point, PA will support drug lead discovery and optimization through the determination of X-ray structures of proteins. The successful candidate will perform crystallization, crystal optimization, and structure determination of protein-ligand complexes and will work in collaboration with medicinal and computational chemists. The successful candidate will also work closely with molecular biologists and protein biochemists in a center with automated cloning, expression, and crystallization technologies. Collaborative and productive interactions with other members of the cross-functional department is a must. The position involves active interaction with the internal and external scientific community to continually improve scientific understanding, including presentations at national or international meetings. Required 1. PhD degree with at least 3 years postdoctoral training in protein crystallography (Senior Research Biochemist) or Ph.D. degree with postdoctoral training and at least 3-6 years of industry experience in protein crystallography (Research Fellow) are required. 2. Excellent communication (written, presentation, and oral), collaboration and scientific skills are required. 3. Ability to work effectively within timelines is required. 4. Experience with project management and demonstrated ability to manage a portfolio of projects is a plus at the Research Fellow level. 5. Experience with molecular biology and protein biochemistry is preferred. 6. Experience in the application of biophysical characterization methods (e.g., protein NMR, Biacore, Thermoflor) or functional properties (e.g., enzyme kinetics) is a plus. 7. Previous industrial experience is a plus. 8. Ability to prepare peer-reviewed publications. 9. Demonstrated potential to develop project management skills and identify/develop new areas of scientific expertise in protein crystallography. Education Requirement - PhD degree with at least 3 years postdoctoral training in protein crystallography (Senior Research Biochemist) or Ph.D. degree with postdoctoral training and at least 3-6 years of industry experience in protein crystallography (Research Fellow) are required. Consistently cited as a great place to work, we discover, develop, manufacture and market a wide range of vaccines and medicines to address unmet medical needs. Each of our employees is joined by an extraordinary sense of purpose - bringing Merck's finest achievements to people around the world. We offer an excellent salary and an industry-ranked benefits program, including tuition reimbursement, work-life balance initiatives and developmental programs at all levels. Merck's retirement package includes a pension plan and one of the best 401(k) plans in the nation. To be considered for this position, please visit our career site at www.merck.com/careers to create a profile and submit your resume for requisition # BIO001876. Merck is an equal opportunity employer, M/F/D/V - proudly embracing diversity in all of its manifestations. Our work is someone's hope. Join us. Where patients come first - Merck -- Stephen M. Soisson, Ph.D. Global Structural Biology Merck Research Laboratories 770 Sumneytown Pike, WP14-1101 West Point, PA 19486 Phone: (215) 652-6185 Fax:(215) 652-9051 stephen_sois...@merck.com Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it
Re: [ccp4bb] Problem with setting up ccp4 gui
Hi Jan
If they exist, could you please send me any of the .log files in the
following directory:
~/.CCP4/
In particular the file dbhandler.log. These should help to fix the
problem.
Thanks
Norman Stein
CCP4
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Jan Jensen
Sent: 03 March 2009 17:43
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Problem with setting up ccp4 gui
Hi all,
I have been struggling with installing the new CCP4 package. I run
RedHat Enterprise 4 and have previously used older packages with
success. After I untar and run ./install as root everything seems to
install just fine. When I run ccp4i -c to configure I think something
goes wrong or extensions get misdirected. If I try to run all the
scripts to test, they all seem to execute fine.
I have had luck starting the GUI as root or user but when you get to the
part where projekt directories are setup the GUI stops working and
cannot be restarted (showing the message below)
Error in startup script: wrong # args: should be dbccp4i_open_project
project args
while executing
dbccp4i_open_project
(eval body line 1)
invoked from within
eval dbccp4i_open_project $project $args
(procedure DbLoadFile line 12)
invoked from within
DbLoadFile $project
(procedure DbOpenDatabase line 13)
invoked from within
DbOpenDatabase $project
(procedure DbOpen line 30)
invoked from within
DbOpen -init
(procedure DbInitialise line 19)
invoked from within
DbInitialise
(procedure task line 14)
invoked from within
task
(configure arm line 6)
invoked from within
switch $system(RUN_MODE) \
script {
# Run a script ($CCP4I/scripts/project.script) with parameters from def
file
source [file join $env(CCP4I_...
(file /opt/ccp4/ccp4-6.1.0/ccp4i/bin/ccp4i.tcl line 163)
invoked from within
source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
(file /opt/ccp4/ccp4-6.1.0/ccp4i/bin/ccp4i line 5)
Can anyone help me?
Thanks,
Jan K Jensen, Pl-R, Ph.D.
Post doctoral fellow at University of Illinois at Chicago (UIC)
Laboratory of Peter GW Gettins Department of Biochemistry and Molecular
Genetics MBRB Room 1260 900 S Ashland Chicago Il, 60607
Phone: 312 996 7664 or 773 574 9276 (mobile)
Email: j...@uic.edu
Homepage: http://www.epernicus.com/jkj
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Nadir T. Mrabet
Sent: Monday, February 16, 2009 12:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB protein strucutrues as screen saver
Hi,
You may want to have a look at
http://www.luminorum.com/html/luminorum_ltd___extras.html.
hth
Nadir
--
Pr. Nadir T. Mrabet
Cellular Molecular Biochemistry
INSERM U-724
Nancy University, School of Medicine
9, Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy Cedex
France
Phone: +33 (0)3.83.68.32.73
Fax: +33 (0)3.83.68.32.79
E-mail: nadir.mra...@medecine.uhp-nancy.fr
Jayashankar wrote:
Dear Scientists,
It may be too much...
But as a biophysics student I would like to appreciate and feel happy
to have pdb structures as my computers screen savers than to have some
funny and fancy stuffs.
And it may help me as a motivator to solve my own structures in
future
I want to ask is there any existing script that grep strucutres one by
one with one line definition of that structure.
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
[ccp4bb] Rigaku RUH3R Generator for Free
Hello, We are upgrading our x-ray crystallography system. The old equipment includes Rigaku RUH3R generator and RAXIS-IIc detector is available for FREE. You are responsible for shipping. If you are interested, please contact Ming Wang at wa...@cshl.edu. Below is list of component of the equipment. 1) Rigaku RUH3R 18 KW rotating anode x-ray generator 2) Cu anode (belt-drive) 3) Haskris WW2 (water to Water) water chiller 4) Yale mirror system 5) Raxis IIc detector with a SCSI interface to an SGI Indigo Elan R4000 computer
[ccp4bb] .phs file conversion
Hi, I have a .phs file with map coefficients that I would like to open in pymol. So, I would like to convert the file to either a ccp4 or cns map file, or a file format that pymol will recognize. I do not have an .mtz file with the same map coefficients included. Can anyone help me? Thanks, John
Re: [ccp4bb] .phs file conversion
Hi, Not the quickest way, but you can easily convert PHS files to MTZ files using CCP4i (Convert to/modify/extend MTZ - via the f2mtz programme). Then generate the map as you would a normal MTZ file. Since PHS files come in 2 flavours, check the following web site to see which format your's is in ( http://www.sdsc.edu/CCMS/Packages/XTALVIEW/XV5.docmod2_2.html#xfit). You need to input the Fortran format of the PHS file; for H, K, L, Fobs, FOM, and PHI it's 3f4.0,f8.2,2f10.2. Other useful tools for PHS/FIN/FSFOUR maps can be found at: http://www.scripps.edu/~cdputnam/software/software.html Cheers! On Wed, Mar 4, 2009 at 2:48 PM, John Bruning jbrun...@gmail.com wrote: Hi, I have a .phs file with map coefficients that I would like to open in pymol. So, I would like to convert the file to either a ccp4 or cns map file, or a file format that pymol will recognize. I do not have an .mtz file with the same map coefficients included. Can anyone help me? Thanks, John
Re: [ccp4bb] .phs file conversion
SFTOOLS should read the phs file and allow you to write it out in a number of different formats, including MTZ. From the command line type: sftools read yourfile.phs write yourfile.mtz quit The program will ask a bunch of questions to get space group, unit cell etc. Bart John Bruning wrote: Hi, I have a .phs file with map coefficients that I would like to open in pymol. So, I would like to convert the file to either a ccp4 or cns map file, or a file format that pymol will recognize. I do not have an .mtz file with the same map coefficients included. Can anyone help me? Thanks, John
Re: [ccp4bb] .phs file conversion
From: Mark A. White mawh...@utmb.edu To: John Bruning jbrun...@gmail.com Cc: CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] .phs file conversion Date: Wed, 4 Mar 2009 14:16:47 -0600 John, The PHS file has the coefficients to make a map, along with the cell parameters, but is not itself a map. There are a few choices. 1) View the PHS file in XtalView (xfit) or MIFit, which is where it was meant to be viewed. COOT will also display maps from PHS files. The PDB file must have the correct CRYST1 entry. Xfit has an output option to save the map coefficients as an MTZ file. This requires a working CCP4 installation. 2) Use CCP4 to convert the PHS file into an MTZ and then to a CCP4 MAP, using FFT. This can then be viewed in PYMOL. ## # Convert LSCALE.PHS file to MTZ ## f2mtz HKLIN pmb_lscale.phs HKLOUT pmb_lscale.mtz f2mtz_eof f2mtz.html TITLE MTZ from PHSS From FoFc_calc.inp - pmb_cns2phs.pl PNAME D999 DNAME D999 CELL86.15 72.65 25.89 90.00 90.00 90.00 LABOUT H K L FOFC PHIC CTYPout H H H F F P FORMAT '(2X,3F5.0,3F10.3)' SYMM18 f2mtz_eof # Note that the format of the PHS file is not standardized, but that F2MTZ requires a well defined fixed format. Good luck, Mark On Wed, 2009-03-04 at 13:48 -0600, John Bruning wrote: Hi, I have a .phs file with map coefficients that I would like to open in pymol. So, I would like to convert the file to either a ccp4 or cns map file, or a file format that pymol will recognize. I do not have an .mtz file with the same map coefficients included. Can anyone help me? Thanks, John Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://wh...@xray.utmb.edu http://xray.utmb.edu http://xray.utmb.edu/~white Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://wh...@xray.utmb.edu http://xray.utmb.edu http://xray.utmb.edu/~white
[ccp4bb] MAX-lab beamtime Deadline March 20th 2009
CALL FOR PROPOSALS for beam time at MAX-lab, Lund, Sweden. Researchers using synchrotron radiation are invited to submit proposals for beam time for experiments to be carried out during the time period July 2009 to June 2010. The available facilities include beamlines for MX and SAXS, see below. Information on how to prepare and submit proposals as well as descriptions of the other experimental facilities available at MAX-lab can be found at http://www.maxlab.lu.se It is also possible to apply for Fast Access MX beam time at any time though it is recommended to submit normal proposals if possible. *** The proposal deadline is March 20th, 2009 *** ___ MACROMOLECULAR CRYSTALLOGRAPHY Beam time for macromolecular crystallography is available at: * Beamline I911-2: Fixed-wavelength (1.04 Å): 165mm marccd, mardtb, marccs sample changer * Beamline I911-3: Tunable 0.7-2.0 Å, suitable for MAD/SAD: 225mm marmosaic, kappa goniostat, semi-automatic crystal centering, Roentec fluorescence detector * Beamline I911-5: Fixed-wavelength (0.91 Å): 165mm marccd, mardtb All beamlines are equipped with user-friendly data collection software. For more information, see the beamline web site: http://www.maxlab.lu.se/beamlines/bli911 ___ SAXS Beam time is also available at the SAXS station at beamline I711. This recently developed low background set-up offers the possibility to measure in a q range down to 0.007 Å-1 depending on the chosen sample to detector distance. The set-up is further described at: http://www.maxlab.lu.se/beamlines/bli711 ___ ACCESSIBILITY AND SUPPORT MAX-lab is situated in Lund, 50 km or 30 minutes by car from Copenhagen airport (with less than 2 hour flights from e.g. London, Paris, Strasbourg, Munich, Budapest, Helsinki,...). Trains leave the airport every 20 to 40 minutes (44 minutes to Lund). Users from EU countries and associated states can apply for financial support through the project Integrating Activity on Synchrotron and Free Electron Laser Science (IA-SFS) within the Sixth Framework Programme (more information can be found in the beam time application instructions). ___ -- ___ Thomas Ursby, PhD Beamline manager, Cassiopeia (Beamline I911) MAX-lab, Lund University, P.O.B. 118, S-221 00 Lund, Sweden thomas.ur...@maxlab.lu.se http://www.maxlab.lu.se Phone +46-(0)733 439551, Fax +46-(0)46 2224710 Cassiopeia: MAD and Fixed-Wavelength Stations for Macromolecular Crystallography __ http://www.maxlab.lu.se/beamlines/bli911/ __
