[ccp4bb] Beamtime at SLS X06SA
= SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE UNDULATOR BEAMLINE X06SA AT SLS FROM SEPTEMBER- DEC 2008 = - PILATUS 6M pixel detector available for user operation at High Resolution Diffractometer. Continuous data acquisition (12.5 frames per second) with 20 bit dynamic range, see http://pilatus.web.psi.ch/ or www.dectris.com as well as http://www.nature.com/nature/journal/v452/n7185/full/nature06717.html for further information - CATS sample changer available at the High Resolution Diffractometer, cf. http://www.irelec.fr/en/produit.asp?idproduit=38 - Detector upgrade to mar225 CCD on Micro-Diffractometer MD2. This MAD-compatible diffractometer allows for data collection with a beam size of 15 x 5 micrometers. ACTOR sample changer available at the MD2. - SLS is able to provide support for travel and accomodation for two users per trip: http://sls.web.psi.ch/view.php/users/experiments/eusupport/index.html - For recent highlights: http://sls.web.psi.ch/view.php/beamlines/px/research/index.html PROPOSAL SUBMISSION DEADLINE: Sunday, June 15th 2008. For further information and / or proposal submission: http://sls.web.psi.ch/view.php/users/experiments/proposals/opencalls/PX/index.html Looking forward to seeing you at SLS, Clemens Schulze-Briese -- Dr. Clemens Schulze-Briese - [EMAIL PROTECTED] --- Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://sls.web.psi.ch Phone +41 56 310 4533 - Fax -5292 - Secretary -3178
[ccp4bb] Phaser error
I am attempting to solve a 28kDa protein structure by sulfur anomalous scattering in Phaser for EP (2.1.2). Phaser crashes immediately and I get the following error in the log file. Thanks in advance for your input. Sarah Wisecarver EXIT STATUS: SUCCESS CPU Time: 0 days 0 hrs 0 mins 0.01 secs (0.01 secs) Finished: Fri Jun 6 15:15:02 2008 /pre /html *** * Information from CCP4Interface script *** The program run with command: phaser has failed with error message child killed: segmentation violation *** #CCP4I TERMINATION STATUS 0 child killed: segmentation violation #CCP4I TERMINATION TIME 06 Jun 2008 15:15:02 #CCP4I MESSAGE Task failed
Re: [ccp4bb] 3D model building without CRT monitor
Just a couple of days ago I received e-mail from a French company with the following content: we offer professional stereo glasses, fully compatible with all the the stereo capable software (O, Coot, Xfit, Molmol, Accelrys, Tripos.). we can provide you with a demo unit for testing purposes if need be. And we would like to take the opportunity of this mail, to introduce the brand new LCD product from Nuvision the Perceiva DSD190. This 19'' stereo monitor is delivered with Lightweight passive glasses and is fully compatible with all stereo ready software. *Hervé SCHWERTZ* ZA Les Priaux 07430 VERNOSC Tel: 04 75 69 00 40 Fax: 04 75 69 00 48 Web : http://www.pixeltech.fr I hope you find this useful, we will try the glasses to start with, Salam Al-Karadaghi -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of PhilEvans Sent: den 5 juni 2008 23:17 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 3D model building without CRT monitor We now have a Planar system, which works very nicely with coot, O , ccp4mg etc. Rather expensive though Phil Evans On 2 Jun 2008, at 17:06, Mike Latchem wrote: These new TFT monitors do seem like a really good idea, but, it is well worth doing in depth research as most of the accessible (Cheap) ones designed for gaming currently only operate with directX. As I understand it there are plans to make these work with openGL as well as directX so they should work with programs like coot etc. Just be careful and confirm with the people supplying the TFT that it will work with your software package of choice. P.S. a colleague of mine who is interested in tomography suggested the planar TFTs work well (they are also very expensive and bulky) - but be sure to confirm they work with your software of choice before paying for one http://www.planar3d.com/ Regards Mike On Mon, 2008-06-02 at 11:51 -0400, Jim Fairman wrote: Hello all, There is a new company around that makes a 3D capable 22 inch flat screen LCD monitor (http://www.iz3d.com) capable of a maximum resolution of 1680x1050. It is originally designed for the purpose of playing video games in 3D, but looks promising for ridding ourselves of the huge bulky CRTs. Cheers On Mon, Jun 2, 2008 at 11:08 AM, Warren DeLano [EMAIL PROTECTED] wrote: For used-stereo-3D-capable-CRT seekers, our stereo 3D page may be of some use. A number of target monitors are listed. http://pymol.sourceforge.net/stereo3d.html -Original Message- From: CCP4 bulletin board on behalf of Krojer,Tobias Sent: Mon 6/2/2008 5:24 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] 3D model building without CRT monitor Dear all, recently some of our CRT monitors broke down and we realized that these monitors are no longer produced. However, we would still like to continue model building in 3D which is apparently not possible with current TFT displays. Beside the possibility of getting old CRT monitors at ebay, I was wondering how other groups solved this problem. Thank you very much for suggestions! best wishes, Tobias Tobias Krojer, PhD IMP (Research Institute of Molecular Pathology) Dr. Bohr-Gasse 7 1030 Vienna Austria Tel.: +43-1-797303358 Fax.: +43-1-7987153 -- Jim Fairman Graduate Research Assistant Department of Biochemistry, Cellular, and Molecular Biology (BCMB) University of Tennessee -- Knoxville 216-368-3337 [EMAIL PROTECTED] [EMAIL PROTECTED] DIVFONT size=1 color=grayThis e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom /FONT/DIV
Re: [ccp4bb] Phaser error
Could you add information about - operating system - computer platform - version of phaser - how ccp4 was installed (binary or from source)? Maybe you are trying to run a Mac binary on the wrong platform? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Mon, 9 Jun 2008, Wisecarver, Sarah N wrote: I am attempting to solve a 28kDa protein structure by sulfur anomalous scattering in Phaser for EP (2.1.2). Phaser crashes immediately and I get the following error in the log file. Thanks in advance for your input. Sarah Wisecarver EXIT STATUS: SUCCESS CPU Time: 0 days 0 hrs 0 mins 0.01 secs (0.01 secs) Finished: Fri Jun 6 15:15:02 2008 /pre /html *** * Information from CCP4Interface script *** The program run with command: phaser has failed with error message child killed: segmentation violation *** #CCP4I TERMINATION STATUS 0 child killed: segmentation violation #CCP4I TERMINATION TIME 06 Jun 2008 15:15:02 #CCP4I MESSAGE Task failed
[ccp4bb] Position Available
A postdoctoral position is available in the Protein Structure Section of the Macromolecular Crystallography Laboratory (MCL), National Cancer Institute (NCI), Frederick, MD, USA. The main area of interest of PSS covers structure-function relationship of helical cytokines and their receptors. PSS also has an extensive program of investigating proteolytic enzymes such as HIV and HTLV proteases, Lon, sedolisin, and VirA, as well as antiviral lectins and proteins involved in tumor suppression and translation regulation. MCL is fully equipped with all tools for protein _expression_, purification, crystallization, and data collection, with assured access to the SER-CAT sector (22) at the Advanced Photon Source, Argonne National Laboratory. The position is open to a recent Ph. D. (less than 5 years since the award of doctorate) with strong background in molecular biology, protein _expression_ and purification, and protein crystallography. The minimum annual starting stipend at NCI is $46,200 for new graduates, with additional increases based on previous postdoctoral experience. NCI provides full health insurance, as well as relocation benefits. Interested candidates should apply to Dr. Alexander Wlodawer, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA; Phone +1-301-846-5036; e-mail [EMAIL PROTECTED].
[ccp4bb] Refinement in half occupancy
Dear All, Can anyone teach me how to refine a ligand in a protein structure with half occupancy in refmac? I have tried to combine the coordinates of the two different conformations of that particular ligand in one pdb, after modeling in Coot individually, and then changed the occupancy to 0.5 for each of the conformation. However, I couldn't manage to refine this pdb in Refmac. Thanks in advance! Best regards, Matt Matthew LH Chu PhD Student School of Pharmacy and Pharmaceutical Sciences University of Manchester
Re: [ccp4bb] Refinement in half occupancy
It should be straight forward. A good example you can use is to make an alternate conformation of a residue in coot. Then you can follow the generated pdb to modify your ligand. Are you sure refmac won't run? What is the error message from refmac? Nian Huang, Ph.D. Dept. of Biochemistry UT Southwestern Medical Center On Mon, Jun 9, 2008 at 5:21 PM, Matthew Chu [EMAIL PROTECTED] wrote: Dear All, Can anyone teach me how to refine a ligand in a protein structure with half occupancy in refmac? I have tried to combine the coordinates of the two different conformations of that particular ligand in one pdb, after modeling in Coot individually, and then changed the occupancy to 0.5 for each of the conformation. However, I couldn't manage to refine this pdb in Refmac. Thanks in advance! Best regards, Matt Matthew LH Chu PhD Student School of Pharmacy and Pharmaceutical Sciences University of Manchester
[ccp4bb] Michele Cianci is out of office.
I will be out of the office starting 03.06.2008 and will not return until 23.06.2008. I maybe able to reply to your message from the 03/06 till the 11/06. There will be no replies from the 12/06 till the 23rd/06. Apologies for any inconvenience.
