Re: [ccp4bb] creating alternate conformations using PyMol
Dear Neeraj -- On 26 Sep 2008, at 22:48, Neeraj wrote: Is there an easy way to do this in pymol which will help me rotate only a small fragment of the protein while keeping everything else static. What you can do is to generate two coordinate files, one without your loop, one with, and more around only the one with your loop... HTH Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Marie Curie Actions Fellow Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
[ccp4bb] Call for proposals: SLS PX beamlines
Dear SLS users, Call is open for proposals for the PX (Protein Crystallography) beamlines of the Swiss Light Source, SLS. Deadline for porposal submission: Wednesday, October 15, 2008 Submission: All submissions will be handled by the SLS Digital Users Office (DUO) /contact: [EMAIL PROTECTED] Please consult the following website to obtain information about the status of the different beamlines and the procedure to set-up the proposal: http://sls.web.psi.ch/view.php/users/experiments/proposals/opencalls/PX/index .html In case of questions related to the experiments at the PX beamlines, please contact one of the beamline scientists: http://sls.web.psi.ch/view.php/beamlines/px/staff/index.html With kind regards Stefan Müller - SLS Science Coordinator Paul Scherrer Institut WSLA 116 CH-5232 Villigen PSI +41 56 310 54 27 [EMAIL PROTECTED] http://sls.web.psi.ch/
[ccp4bb] BEAMTIME AT SLS X06DA
= SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE SUPERBENDING MAGNET BEAMLINE X06DA AT SLS = Deadline: Wednesday, October 15, 2008 Periods: January 1, 2009 - April 30, 2009 ( Normal / Test proposals) January 1, 2009 - December 31, 2010 ( Long-term proposals) Beamline features: - Fully tunable from 6.0 to 17.5 keV (2.07 - 0.71 Å) - 4x10¹¹ photons/sec at sample position - 90x70 microns focused beam - MAR225 CCD detector - Mini-hutch design for fast manual mounting - Automatic sample changer (IRELEC CATS) with SPINE pucks, vials, and caps. - http://sls.web.psi.ch/view.php/beamlines/px3/index.html Proposal submission: http://sls.web.psi.ch/view.php/users/experiments/proposals/opencalls/PX/index.html Travel support: http://sls.web.psi.ch/view.php/users/experiments/eusupport/index.html Best regards, meitian __ Meitian Wang Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://sls.web.psi.ch Phone: +41 56 310 4175 Fax: +41 56 310 5292
[ccp4bb] map and model do not fit when using Turbo-Frodo
Dear All, I am refining a structure of Se-protein solved with MAD using phenix. The unit cell is P 21 21 21 with a=36.898, b=59.450, c=393.909 and alpha=beta=gamma=90. There are two molecules in A.U. The problem is that when I use Turbo-Frodo for molecular modeling, the map does not fit to the model. There is a shift (translation) between the map and the model. However, if I use coot every thing is OK. I don't know why this happens only with Turbo. Any suggestion or any trick for this problem are welcome. Thanks in advance. Youssef
[ccp4bb] program to evaluate proteins
Hi, Dear All, Does anyone have suggestions about what good programs are available that could be used to evaluate proteins?Like how good is the packing, hydrogen bonding pattern, aggregation prediction, solubility, hydrophobic surface burial etc. Thank you very much. Jenny
[ccp4bb] biotech position
Please bring the following ad to the attention of possible candidates; Best M. Schmidt Position Description: FACULTY POSITIONS IN BIOTECHNOLOGY The University of Wisconsin-Milwaukee invites applications for 2 faculty positions in biotechnology at the Assistant, Associate, or Full Professor level. Candidates conducting research in areas supporting microbial biotechnology, including biochemistry, microbial genetics, proteomics, structural biochemistry, microbial physiology or applied microbiology, are encouraged to apply. The successful candidates will be expected to develop an extramurally funded research program, teach in the departmental curriculum, and contribute to the research training of graduate and undergraduate students in areas of microbial biotechnology. Appointments can be in the Departments of Biological Sciences, Chemistry and Biochemistry, or Physics. Applicants must have a Ph.D. and postdoctoral experience. More detailed information about these positions may be found at: https://cms.uwm.edu/letsci/biologicalsciences/research/biotech/. To apply, please go to www.jobs.uwm.edu/applicants/Central?quickFind=50609 . A completed application should include: cover letter, curriculum vita, statement of research goals, statement of teaching interests, and letters of professional reference. Applicants should arrange to have three letters of reference sent as pdf attachments to the Biological Sciences departmental chair ([EMAIL PROTECTED]) or mailed to: Biotechnology Search, Department of Biological Sciences, University of Wisconsin-Milwaukee, PO Box 413, Milwaukee, WI 53201. Screening of candidates will begin October 15, 2008 and continue until the position is filled. UWM is an Equal Opportunity/Affirmative Action Employer.
[ccp4bb] cryo-protection for crystals grown in ethanol
Dear All I got crystals from 20% Ethanol with 0.1M Tris pH 8.5. This is my first time to have crystals in Ethanol and want to get some suggestions of cryo-protection from those who have done this before. I am waiting for my time on home X-ray facility, and hope I can get some suggestions before that. Thanks, Rongjin Guan
Re: [ccp4bb] cryo-protection for crystals grown in ethanol
Hi Rongjin, I had crystals that grew in 9% ethanol as a precipitant. To cryoprotect them, I first replaced the mother liquor with solution containing 10% MPD, instead of ethanol, and then briefly dunked the crystals into ~30% MPD. Hope this helps. Good luck. Katya On Mon, Sep 29, 2008 at 1:24 PM, Rongjin Guan [EMAIL PROTECTED] wrote: Dear All I got crystals from 20% Ethanol with 0.1M Tris pH 8.5. This is my first time to have crystals in Ethanol and want to get some suggestions of cryo-protection from those who have done this before. I am waiting for my time on home X-ray facility, and hope I can get some suggestions before that. Thanks, Rongjin Guan
[ccp4bb] CCP4i can NOT run
Dear friends, I have installed the latest version of CCP4i under Fedora 9 on my laptop HP Compaq 6515b (two processors). The system setup was done and the CCP4i interface can run normally. But if I submit a job, it displayes STARTING the job in the job window and will NOT actually run the job. Also I can NOT kill the job with its status as STARTING. I have checked my Tcl/tk is version 8.4 and the CCP4I_TCLTK environment variable is pointed to the right directory containing tclsh, bltwish and other files. Is there any suggestion on how to solve this problem? Thank you very much in advance. Best wishes, Yingjie Yingjie PENG, Ph.D. student Structural Biology Group Shanghai Institute of Biochemistry and Cell Biology (SIBCB) Shanghai Institute of Biological Sciences (SIBS) Chinese Academy of Sciences (CAS) 320 Yue Yang Road, Shanghai 200031 P. R. China 86-21-54921117 Email: [EMAIL PROTECTED]
