- phenixbb - phenix-online.org

difficulties with autoMR
by Feldman III, George Franklin 10 Sep '08

10 Sep '08

I am trying to run phenix.automr on what I believe is perhaps a perfectly twinned data set, at 3A resolution. It is in space group 146 and according to the matthews has 3 molecules in the asu. This is a mutant of an orriginally published structure in which only one residue has been mutated (but crystallizes in a different space group). When I give the autoMR the following input: phenix.automr coords="MR.1.pdb" data=dtscale.ref resolution=0 component_type=protein identity="95" mass=13900 build=False copies=3 seq.dat I get an LLG of 37 and the run goes quite quickly. The speed of the run itself leads me to believe that I have a correct solution regardless of the slightly low LLG, but when I open the .pdb output file there is only one molecule in the asu. Am I doing something incorrectly? Why is there only one molecule instead of 3 in the asu, and how can I go about getting the other two to appear? I did let the program go ahead run autobuild, this resulted in a structure with an r_work:.5448 and r_free:.6005. I am relatively new to crystallography, but these values seem rather high to be a good starting point for refinement. I would appreciate any advice that might help me move on with my structure. Attached is the log file from phenix.xtriage in case it may be of any help. Thank you, in advance, for all of your help and advice. Best Regards, George F. Feldman

1 0

Re: [phenixbb] cci_apps on irix
by Ralf W. Grosse-Kunstleve 07 Sep '08

07 Sep '08

On 22 Aug 2008 o.h.weiergraeber(a)fz-juelich.de wrote: > I am just compiling the latest cci_apps package for the IRIX > platform. I know this is unsupported, but since the package is very > self-contained, I would not expect major problems with the command-line > packages (who needs a gui, anyway ;)) > I'm just running into two issues with the boost package which are > obviously a matter of syntax: Our IRIX machine is up again, and - to my surprise - the current CCI Apps compiled without errors. The IRIX binary bundle is available again at the usual place: http://www.phenix-online.org/download/cci_apps/ Ralf

1 0

selection usage
by Mark Collins 05 Sep '08

05 Sep '08

Hi All, The current phenix 1.3 release automatically selects alternate conformations when refine *occupancy is selected. How do I select a loop region (in low density) to refine the loop occupancy without messing up the auto selection? Thanks in advance, Mark

2 1

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.

1 0

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

1 0

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 >

1 0

Re: [phenixbb] Real Space R value
by mathieu Coincon 02 Sep '08

02 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 > >

2 1

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 -----------------------------------------------------------------

1 0

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

2 1

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

1 0