Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's
It just picks the first in the list, to store in the output MTZ file, which can only handle one (92 96) Phil On 8 Nov 2007, at 22:26, Bryan W. Lepore wrote: when pointless (1.2.0) finds enantiomorphic SG's, what is the criterion for 'Selecting' one over the other? e.g. i ran pointless on some tetragonal data, and the enantiomorphs SG92/SG96 are selected as strong candidates Spacegroup TotProb SysAbsProb Reindex Conditions P 41 21 2 ( 92)0.956 0.956 00l: l=4n, h00: h=2n (zones 1,2) P 43 21 2 ( 96)0.956 0.956 00l: l=4n, h00: h=2n (zones 1,2) ... then pointless reports : Selecting space group P 41 21 2 as solutions are enantiomorphic Best Solution space group P 41 21 2 ... is that b/c pointless can only report one, and SG92 came up first? -bryan
[ccp4bb] Collaborative Crystallography Program - Advanced Light Source
The Berkeley Center for Structural Biology (BCSB) is pleased to announce the launch of a Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source in Berkeley. Through this program, scientists will be able to send protein crystals to BCSB staff researchers for data collection and analysis. The CC Pilot Program can provide an number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: == The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the regular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography. How To Apply: = To submit a proposal, go to: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/ Initialize. For question 3 select Collaborative PX 501/502. For question 9, please describe a specific research project with a clear end point. In order to request CC time for January/February, 2008, proposals must be submitted by November 15, 2007. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's
As I often say!!! The mtz format should carry point group and alternate SGs - then be upgraded when youknow the correct SG.. Eleanor Phil Evans wrote: It just picks the first in the list, to store in the output MTZ file, which can only handle one (92 96) Phil On 8 Nov 2007, at 22:26, Bryan W. Lepore wrote: when pointless (1.2.0) finds enantiomorphic SG's, what is the criterion for 'Selecting' one over the other? e.g. i ran pointless on some tetragonal data, and the enantiomorphs SG92/SG96 are selected as strong candidates Spacegroup TotProb SysAbsProb Reindex Conditions P 41 21 2 ( 92)0.956 0.956 00l: l=4n, h00: h=2n (zones 1,2) P 43 21 2 ( 96)0.956 0.956 00l: l=4n, h00: h=2n (zones 1,2) ... then pointless reports : Selecting space group P 41 21 2 as solutions are enantiomorphic Best Solution space group P 41 21 2 ... is that b/c pointless can only report one, and SG92 came up first? -bryan
Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's
I agree On 9 Nov 2007, at 13:50, Eleanor Dodson wrote: As I often say!!! The mtz format should carry point group and alternate SGs - then be upgraded when youknow the correct SG.. Eleanor Phil Evans wrote: It just picks the first in the list, to store in the output MTZ file, which can only handle one (92 96) Phil On 8 Nov 2007, at 22:26, Bryan W. Lepore wrote: when pointless (1.2.0) finds enantiomorphic SG's, what is the criterion for 'Selecting' one over the other? e.g. i ran pointless on some tetragonal data, and the enantiomorphs SG92/SG96 are selected as strong candidates Spacegroup TotProb SysAbsProb Reindex Conditions P 41 21 2 ( 92)0.956 0.956 00l: l=4n, h00: h=2n (zones 1,2) P 43 21 2 ( 96)0.956 0.956 00l: l=4n, h00: h=2n (zones 1,2) ... then pointless reports : Selecting space group P 41 21 2 as solutions are enantiomorphic Best Solution space group P 41 21 2 ... is that b/c pointless can only report one, and SG92 came up first? -bryan
Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's
I like it! -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Eleanor Dodson Sent: 09 November 2007 13:51 To: Phil Evans Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's As I often say!!! The mtz format should carry point group and alternate SGs - then be upgraded when youknow the correct SG.. Eleanor Phil Evans wrote: It just picks the first in the list, to store in the output MTZ file, which can only handle one (92 96) Phil On 8 Nov 2007, at 22:26, Bryan W. Lepore wrote: when pointless (1.2.0) finds enantiomorphic SG's, what is the criterion for 'Selecting' one over the other? e.g. i ran pointless on some tetragonal data, and the enantiomorphs SG92/SG96 are selected as strong candidates Spacegroup TotProb SysAbsProb Reindex Conditions P 41 21 2 ( 92)0.956 0.956 00l: l=4n, h00: h=2n (zones 1,2) P 43 21 2 ( 96)0.956 0.956 00l: l=4n, h00: h=2n (zones 1,2) ... then pointless reports : Selecting space group P 41 21 2 as solutions are enantiomorphic Best Solution space group P 41 21 2 ... is that b/c pointless can only report one, and SG92 came up first? -bryan Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's
I agree too! Martyn On Fri, 2007-11-09 at 13:54 +, Phil Evans wrote: I agree On 9 Nov 2007, at 13:50, Eleanor Dodson wrote: As I often say!!! The mtz format should carry point group and alternate SGs - then be upgraded when youknow the correct SG.. Eleanor Phil Evans wrote: It just picks the first in the list, to store in the output MTZ file, which can only handle one (92 96) Phil On 8 Nov 2007, at 22:26, Bryan W. Lepore wrote: when pointless (1.2.0) finds enantiomorphic SG's, what is the criterion for 'Selecting' one over the other? e.g. i ran pointless on some tetragonal data, and the enantiomorphs SG92/SG96 are selected as strong candidates Spacegroup TotProb SysAbsProb Reindex Conditions P 41 21 2 ( 92)0.956 0.956 00l: l=4n, h00: h=2n (zones 1,2) P 43 21 2 ( 96)0.956 0.956 00l: l=4n, h00: h=2n (zones 1,2) ... then pointless reports : Selecting space group P 41 21 2 as solutions are enantiomorphic Best Solution space group P 41 21 2 ... is that b/c pointless can only report one, and SG92 came up first? -bryan -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED] * * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's
Hi Kevin, I would say that the most useful place for this token will be in reduced-data land prior to getting phases - so for instance going into Phaser it could make a sensible choice about what spacegroups to test based on the accuracy information, likewise experimental phasing / dm programs. Once these programs have computed phases they will (most likely) be in a position to decide the correct spacegroup and write this out with some authority along with the phases. So what I am getting at is that you are unlikely to have phases without knowing what the right spacegroup is. Certainly, you are unlikely to have correct phases ;o) This cannot possibly cure the spacegroup naming problem, but it could certainly allow people to say what they mean when assigning some spacegroup information to a reflection file... Cheers, Graeme -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Kevin Cowtan Sent: 09 November 2007 14:12 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's This is great! But before we all get carried away, a quick reality check is in order. This isn't an area I've thought about, but my limited understanding raises the following issues Given that an MTZ file contains a cell, an indexing of the data, and possibly phases involving a choice of origin, the use of an MTZ file immediately implies that some decision has been made about the spacegroup. Selecting a different spacegroup from a list of possibilities may involve reindexing, and/or changing origin/enantiomorph dependent properties such as phases and HLs. It would be possible for an MTZ file to say something like this: 'This file is generated assuming spacegroup X. Spacegroups X1, X2, X3, X4, X5 are also possible.'. It should also be possible to compute on the fly whether a particular column type needs to be modified for a different spacegroup. How will we present this in user interfaces? As a starting point, until a spacegroup has been settled upon, the user will need the option of picking the spacegroup after having selected the MTZ. This means potentially a reindexing step added to every single task - messy. As an intermediate, being able to change the 'currently selected' spacegroup as a separate task would be an improvement. Phil Evans wrote: I agree On 9 Nov 2007, at 13:50, Eleanor Dodson wrote: As I often say!!! The mtz format should carry point group and alternate SGs - then be upgraded when youknow the correct SG.. Eleanor Phil Evans wrote: It just picks the first in the list, to store in the output MTZ file, which can only handle one (92 96) Phil On 8 Nov 2007, at 22:26, Bryan W. Lepore wrote: when pointless (1.2.0) finds enantiomorphic SG's, what is the criterion for 'Selecting' one over the other? e.g. i ran pointless on some tetragonal data, and the enantiomorphs SG92/SG96 are selected as strong candidates Spacegroup TotProb SysAbsProb Reindex Conditions P 41 21 2 ( 92)0.956 0.956 00l: l=4n, h00: h=2n (zones 1,2) P 43 21 2 ( 96)0.956 0.956 00l: l=4n, h00: h=2n (zones 1,2) ... then pointless reports : Selecting space group P 41 21 2 as solutions are enantiomorphic Best Solution space group P 41 21 2 ... is that b/c pointless can only report one, and SG92 came up first? -bryan
Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's
Of course, you may need to re-index even if you have the right space group... Offering a selection of space groups compatible with a point group will not require reindexing. Some point groups of course permit reindexing, but one hope you have chosen a consistent set as you combine data sets into an MTZ file - pointless and the GUI both offer ways to check this. Phasing cannot be carried out till you have chosen a spacegroup, and any existing phase associated data should probably be weeded out as part of a Assign Spacegroup function. Eleanor Kevin Cowtan wrote: This is great! But before we all get carried away, a quick reality check is in order. This isn't an area I've thought about, but my limited understanding raises the following issues Given that an MTZ file contains a cell, an indexing of the data, and possibly phases involving a choice of origin, the use of an MTZ file immediately implies that some decision has been made about the spacegroup. Selecting a different spacegroup from a list of possibilities may involve reindexing, and/or changing origin/enantiomorph dependent properties such as phases and HLs. It would be possible for an MTZ file to say something like this: 'This file is generated assuming spacegroup X. Spacegroups X1, X2, X3, X4, X5 are also possible.'. It should also be possible to compute on the fly whether a particular column type needs to be modified for a different spacegroup. How will we present this in user interfaces? As a starting point, until a spacegroup has been settled upon, the user will need the option of picking the spacegroup after having selected the MTZ. This means potentially a reindexing step added to every single task - messy. As an intermediate, being able to change the 'currently selected' spacegroup as a separate task would be an improvement. Phil Evans wrote: I agree On 9 Nov 2007, at 13:50, Eleanor Dodson wrote: As I often say!!! The mtz format should carry point group and alternate SGs - then be upgraded when youknow the correct SG.. Eleanor Phil Evans wrote: It just picks the first in the list, to store in the output MTZ file, which can only handle one (92 96) Phil On 8 Nov 2007, at 22:26, Bryan W. Lepore wrote: when pointless (1.2.0) finds enantiomorphic SG's, what is the criterion for 'Selecting' one over the other? e.g. i ran pointless on some tetragonal data, and the enantiomorphs SG92/SG96 are selected as strong candidates Spacegroup TotProb SysAbsProb Reindex Conditions P 41 21 2 ( 92)0.956 0.956 00l: l=4n, h00: h=2n (zones 1,2) P 43 21 2 ( 96)0.956 0.956 00l: l=4n, h00: h=2n (zones 1,2) ... then pointless reports : Selecting space group P 41 21 2 as solutions are enantiomorphic Best Solution space group P 41 21 2 ... is that b/c pointless can only report one, and SG92 came up first? -bryan
[ccp4bb] POSTDOCTORAL POSITIONS
POSTDOCTORAL POSITIONS Department of Pharmaceutical Sciences University of Pittsburgh Postdoctoral positions are available to study structural and molecular biology of nuclear hormone receptors in human diseases and drug discovery http://www.pharmacy.pitt.edu/directory/dir_grad.lasso?Last=LiY. Preferred experience: X-ray crystallography, protein purification and/or nuclear receptor biology like adipocyte differentiation. Send curriculum vitae and names of three references to Dr. Yong Li at email: [EMAIL PROTECTED] Yong Li, Ph.D. Assistant professor Department of Pharmaceutical Sciences and Center for Pharmacogenetics University of Pittsburgh 709 Salk Hall, Pittsburgh, PA 15261 Email: [EMAIL PROTECTED]https://webmail.pitt.edu/webmail/src/compose.php?send_to=yol21%40pitt.edu Phone: 412- 648-1982
[ccp4bb] SGI monitor on Mac Pro
Hi folks, I just got a new Mac Pro (NVIDIA Quadro FX 4500 graphics card; Apple Cinema LCD display primary) and wonder if I can hook up the big ol' CRT monitor from a now-defunct SGI as my 2nd display. The monitor in question is a 21 SGI/Sony GDM-5411. I have to use two adaptors to attach it (Sun to VGA and VGA to DVI), but that's fine. When I attach and power up, the monitor is black except for this information: Monitor is working Input 1: 37.7 kHz/300 Hz Out of scan range Change signal timing Has anyone been able to make this work? Can't find any mention of how to proceed, but that could just be Friday afternoon stupidity... Cheers, Pat Loll --- Patrick J. Loll, Ph. D. (215) 762-7706 Associate Professor FAX: (215) 762-4452 Department of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA [EMAIL PROTECTED]
[ccp4bb] MacPro Xeon NVIDIA Quadro FX4500 Stereo Nuvision problem
MacPro Xeon NVIDIA Quadro FX 4500 Stereo Nuvision problem We just bought a Mac Pro Intel Xeon (2x 2.66 GHz) computer with an NVIDIA Quadro FX 4500 graphics card, connected to a flat screen SGI monitor, and a Viewsonic G225fB CRT monitor.The Nuvision IR emitter which we connected to the Mac Pro does not work, yet. The emitter works on a linux system, so we know the emitter is o.k. I also made sure that the displays are arranged in the Mac System Preferences so that the CRT display is No. 1 and the flat screen is No. 2., but that made no difference. So does anyone have a straightforward solution to this problem? Is it a Mac issue? A monitor issue? I just want to see that little red LED light up on top of the monitor, HELP! Thanks!
