- phenixbb - phenix-online.org

Deborah Palestrant is out of the office.
by deborah.palestrant＠novartis.com 04 Sep '08

04 Sep '08

I will be out of the office starting 09/04/2008 and will not return until 09/08/2008.

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Re: [phenixbb] sugar links
by Ralf W. Grosse-Kunstleve 03 Sep '08

03 Sep '08

Hi Morten, > Why isn't it included in the standard set btw? Sorry, too many bigger things to take care off right now. But Garib told me he'll move the monomer library to a Google source server, which should make it much more practical to collectively work on changes like the one you're requesting. Ralf

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Re: [phenixbb] Real Space R value
by Thomas C. Terwilliger 03 Sep '08

03 Sep '08

Hi Matthew, You can also use phenix.get_cc_mtz_pdb with a ligand...it should treat the ligand as a single residue. Mark also asked offline about alternate conformations...here is my answer to that: If there is only on N for each residue, it will average over all atoms in all conformations. If there are multiple N atoms, and all atoms for each conformer are grouped, it will write out the residue twice. If there are multiple N atoms and they are interspersed, it will give an incorrect answer (it will write out the residue twice but the cc values will not be for the two conformers). All the best, Tom T > Hi, > Yes, you can use phenix.get_cc_mtz_pdb (see phenix.doc) > > But I wonder if there is a way to get CC value for a ligand or a metal > ion too ?? > > Nigel ??? > >> Date: Tue, 2 Sep 2008 13:18:59 -0400 >> From: "nih\mayerm" <mayerm(a)mail.nih.gov> >> Subject: [phenixbb] Real Space R value >> To: phenixbb(a)phenix-online.org >> Message-ID: <FEAAD2DC-1906-4194-881B-CA83B48E8043(a)mail.nih.gov> >> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed >> >> >> Is it possible to calculate a list of Real Space R values for >> structures refined with phenix.refine ? >> If so advice on how to do this would be greatly appreciated. >> >> Thanks - Mark Mayer >> >> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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Re: [phenixbb] Real Space R value
by mathieu Coincon 03 Sep '08

03 Sep '08

Hi, Yes, you can use phenix.get_cc_mtz_pdb (see phenix.doc) But I wonder if there is a way to get CC value for a ligand or a metal ion too ?? Nigel ??? > Date: Tue, 2 Sep 2008 13:18:59 -0400 > From: "nih\mayerm" <mayerm(a)mail.nih.gov> > Subject: [phenixbb] Real Space R value > To: phenixbb(a)phenix-online.org > Message-ID: <FEAAD2DC-1906-4194-881B-CA83B48E8043(a)mail.nih.gov> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > Is it possible to calculate a list of Real Space R values for > structures refined with phenix.refine ? > If so advice on how to do this would be greatly appreciated. > > Thanks - Mark Mayer > >

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PX beamtime application deadline Sept 3rd!
by Peter Zwart 02 Sep '08

02 Sep '08

Dear All, The deadline for user proposals for PX beamtime at the ALS has been extended to September 3, 5pm pacific time. See my previous email for details. Thanks Peter 2008/8/29 Peter Zwart <PHZwart(a)lbl.gov>: > Dear All, > > The deadline for general user proposals for PX beamtime at the ALS is > comming up soon! At the BCSB, we have 5 beamlines for which you can > apply for beamtime. At the Berkeley Center for Structural Biology > (BCSB) we have recently completed a number of upgrades: > > Sector 8: Recent improvements include: > > * A high-accuracy microdiffractometer on BL 8.2.1, allowing for > centering and viewing of very small crystals > * Robot automounters which can increase the screening throughput > at the beamlines, and will allow for the implementation of remote data > collection > * A new large format (315mm active surface area) CCD detector on > BL 8.2.1, facilitating data collection on large unit cell crystals > > Sector 5: Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 photons > per second at 0.97 Angstrom. This wavelength is slightly above the Se > K edge making them ideal for performing Se SAD experiments. Beamline > 5.0.2 (the tunable beamline) generates a peak flux of 8x10^11 photons > per second, and the energy range of 5.0.2 has been extended to 17 keV, > enabling the routine use of shorter wavelengths and anomalously > scattering elements such as bromine. > > Please visit http://bcsb.lbl.gov/ for more details about the Center > and its beamlines. > > If you'd like to apply for Oct/Nov/Dec beamtime at the Advanced Light > Source, please submit a General User proposal by September 1, 2008. > > To find out more, click on: > > http://www-als.lbl.gov/als/quickguide/independinvest.html > > We invite you to submit a proposal at: > > http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize. > > If you have any questions or would like to request open beamtime, > please e-mail BCSBBeamtime(a)lbl.gov. > > (Please note that executed user agreements must be received by LBNL > prior to beamtime. Proprietary fees, if applicable, must be received > by LBNL at least five working days prior to scheduled beamtime.) > > > -- > ----------------------------------------------------------------- > P.H. Zwart > Beamline Scientist > Berkeley Center for Structural Biology > Lawrence Berkeley National Laboratories > 1 Cyclotron Road, Berkeley, CA-94703, USA > Cell: 510 289 9246 > BCSB: http://bcsb.als.lbl.gov > PHENIX: http://www.phenix-online.org > CCTBX: http://cctbx.sf.net > ----------------------------------------------------------------- > -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Real Space R value
by nihmayerm 02 Sep '08

02 Sep '08

Is it possible to calculate a list of Real Space R values for structures refined with phenix.refine ? If so advice on how to do this would be greatly appreciated. Thanks - Mark Mayer

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LABIN and BLUR like options in phenix refine?
by Partha Chakrabarti 01 Sep '08

01 Sep '08

Hiya, If we use sharp for phasing, the eden_flat file has multiple columns at the end. I was wondering if it is possible to tell the program which ones to use other than having to use CAD.. and, if the FOM is suspected to be too high, Blur it.. Cheers, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra(a)nimr.mrc.ac.uk Phone: + 44 208 816 2515

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PX beamtime application deadline Sept 1st!
by Peter Zwart 29 Aug '08

29 Aug '08

Dear All, The deadline for general user proposals for PX beamtime at the ALS is comming up soon! At the BCSB, we have 5 beamlines for which you can apply for beamtime. At the Berkeley Center for Structural Biology (BCSB) we have recently completed a number of upgrades: Sector 8: Recent improvements include: * A high-accuracy microdiffractometer on BL 8.2.1, allowing for centering and viewing of very small crystals * Robot automounters which can increase the screening throughput at the beamlines, and will allow for the implementation of remote data collection * A new large format (315mm active surface area) CCD detector on BL 8.2.1, facilitating data collection on large unit cell crystals Sector 5: Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 photons per second at 0.97 Angstrom. This wavelength is slightly above the Se K edge making them ideal for performing Se SAD experiments. Beamline 5.0.2 (the tunable beamline) generates a peak flux of 8x10^11 photons per second, and the energy range of 5.0.2 has been extended to 17 keV, enabling the routine use of shorter wavelengths and anomalously scattering elements such as bromine. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to apply for Oct/Nov/Dec beamtime at the Advanced Light Source, please submit a General User proposal by September 1, 2008. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize. If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. (Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime.) -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 28 Aug '08

28 Aug '08

Dear Users, 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://www-als.lbl.gov/als/quickguide/independinvest.html Click on "protein crystallography" to begin proposal. 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 October/November/December 2008 allocation period, proposals must be submitted by Sept 1, 2008. The deadline for CC proposals for the time period January/February 2009 will be November 15, 2008. Regards, Banumathi Sankaran

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map calculation
by Chen Chen 27 Aug '08

27 Aug '08

Dear all, I am having a question about map calcultation. I want to calculate a 2mFo-DFc map and a mFo-DFc map to 2.0 angstrom from xxx.pdb and yyy.mtz, and zzz.cif should be supplied. Unit cell dimension and symmetry information is in the mtz file. It seems that phenix.maps can do the job, but I did not find a good document on how to run it. In its help information, a parameter file is needed. I tried do use parameter file for refinement, which has been successfully used for phenix.refine, and I ran the command phenix.maps --unused_ok yyy.mtz xxx.pdb refine.param but phenix.maps report the error Traceback (most recent call last): File "/home/chene/phenix-1.3b-rc6/mmtbx/mmtbx/command_line/maps.py", line 7, in <module> maps.run(args=sys.argv[1:]) File "/home/chene/phenix-1.3b-rc6/mmtbx/mmtbx/maps.py", line 173, in run log = log) File "/home/chene/phenix-1.3b-rc6/mmtbx/mmtbx/maps.py", line 214, in __init__ self.data = utils.determine_data( AttributeError: 'module' object has no attribute 'determine_data' Does anyonw know what I should do to get the maps? Thanks Chen -- Chen Chen, Ph. D., Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 Office Phone: 240-314-6122

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