- phenixbb - phenix-online.org

Barely two weeks left to apply, and many seats available, for RapiData 2011, our course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 14 Jan '11

14 Jan '11

We are offering RapiData 2011, the thirteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 3-8 April 2011. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. All students are encouraged to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the ninth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 3 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sal Sclafani, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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Re: [phenixbb] Refinement Problem
by Kay Diederichs 13 Jan '11

13 Jan '11

> Date: Wed, 12 Jan 2011 17:12:04 -0500 (EST) > From: Christopher W Davies<cdavies(a)purdue.edu> > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] Refinement Problem > > > I am having an issue with refining my structure. I have a 2.36 A resolution dataset. I have found a solution by molecular replacement in the space group P3221. I have been refining the structure, however, my Rfactor/Rfree are not decreasing even though I have good density. My current Rfactor/Rfree values are .40/.43. Can anyone help me? > > > Thanks. > > Chris Chris, there is a collection of things to think about at http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement#R-fa… HTH, Kay

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Refinement Problem
by Christopher W Davies 13 Jan '11

13 Jan '11

I am having an issue with refining my structure. I have a 2.36 A resolution dataset. I have found a solution by molecular replacement in the space group P3221. I have been refining the structure, however, my Rfactor/Rfree are not decreasing even though I have good density. My current Rfactor/Rfree values are .40/.43. Can anyone help me? Thanks. Chris

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Problem with Autobuild
by Claudia Scotti 12 Jan '11

12 Jan '11

Dear List, Sorry fo r the easy question, but I have a problem with Autobuild. I'm trying to rebuild a scFv, composed of two domains linked by a linker. I've managed to find an MR solution with a polyalanine model deprived of the loops, which is my starting model for rebuilding. I've given Autobuild three input files: the mtz, the model coordinates and the sequence of the scFv, asking to model only the beta strands and helices. Problem is that in the final model Autobuild seems to guess incorrectly the density of two beta-strands, inserting the linker there instead of the expected side chains. Any suggestions on how to correct this? Shall I manually rebuild this part to avoid problems? Or is it crucial to prevent errors, for example, that the model and the sequence are numbered so that they are in register? Thanks in advance, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969

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2 quesions: 1. bond and vdw restraints; 2. cif file for BeF3-
by YoungJin 11 Jan '11

11 Jan '11

Dear Phenix users, Let me ask 2 questions and, as always, thank you whoever responses. 1. First general question is regarding bond distance or van der Waals distance in the crystal structure. As I freeze the crystals as themselves , I often see those distances are much shorter than what I normally expect in the refined structure. So how far they are acceptable or do we have any reference for bonds restraints in the crystal although ccp4 library should deal with these... 2. I was trying to model BeF3-. When I tried to get restraint file from the ReadySet, it always makes BeF3 instead of BeF3-. Is there any way I can fix the charge of the molecule? Also, I would expect it should be in the library as a kind of common inorganic molecule to mimic the phosphorus group. If so, could you let me know how I can get and use it? Thanks in advance, Young-Jin

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B-Factor issue
by Hasan Demirci 11 Jan '11

11 Jan '11

Hi, I am trying to refine a structure with a bound ligand "PAR". Unfortunately, input b-factor of the ligand and output values are matching exactly even tough I copied the ligand from a different structure. I manually changed the occupancy of the ligand to see if it changes the b-factor but again B-factor didn't change. Can someone help me to solve this issue? Below, I attached the first four lines of the pdb after occupancy change. input "HETATM51786 C11 PAR V 1 140.982 67.469 10.830 1.00 58.13 C HETATM51787 O11 PAR V 1 140.549 68.782 10.389 1.00 58.13 O HETATM51788 C21 PAR V 1 139.714 66.811 11.362 1.00 58.13 C HETATM51789 N21 PAR V 1 138.632 66.819 10.352 1.00 58.13 N " output "HETATM51828 C11 PAR V 1 157.285 114.375 -64.249 0.80 58.13 C HETATM51829 O11 PAR V 1 157.335 115.251 -65.379 0.80 58.13 O HETATM51830 C21 PAR V 1 158.559 113.509 -64.364 0.80 58.13 C HETATM51831 N21 PAR V 1 159.738 114.342 -64.677 0.80 58.13 N" Thanks. -- Hasan DeMirci, Ph.D. Postdoctoral Fellow Department of Molecular Biology, Cellular Biology & Biochemistry Brown University 185 Meeting Street Providence, RI 02912 (401) 863-3652 lab (SFH) (401) 863-6124 lab (ship st) (401) 226-7852 cell Hasan_DeMirci(a)Brown.edu demircha99(a)gmail.com

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The phenix autobuilder does not find buccaneer
by Pietro Roversi 10 Jan '11

10 Jan '11

Dear all, I have Buccaneer 1.5.0: partyring:~/Projects/Japanin/autoBUSTER> $CBIN/cbuccaneer <B><FONT COLOR='#FF0000'> <html>  <hr> <pre> ############################################################### ############################################################### ############################################################### ### CCP4 6.1: cbuccaneer version 1.5.0 : 28/05/10## ############################################################### User: pietro Run date: 10/ 1/2011 Run time: 17:18:57 and yet the phenix autobuilder fails - saying I need 1.3.0 or higher (see below) What environment variable is being checked and what should I set for the phenix autobuilder to be able to detect buccaneer? Thanks Regards Pietro **************************************** AutoBuild Input failed Sorry, the necessary version of BUCCANEER does not seem to be available.. For BUCCANEER model building you need CCP4 version 6.1.2 or higher and BUCCANEER version 1.3.0 or higher **************************************** ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] On Behalf Of Pavel Afonine [pafonine(a)lbl.gov] Sent: 07 September 2010 17:56 To: PHENIX user mailing list Subject: Re: [phenixbb] will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb? Hi Hailiang, > For the pdb file generated by refmac which contains only the residual-B, > will phenix.fmodel automatically generates and takes into account the TLS > B by reading the TLS REMARK from pdb? Thanks a lot! phenix.tls is the tool to convert between total and residual ADPs. It can recognize Refmac and phenix.refine formats of TLS records. phenix.model_vs_data does this internally to compute correct R-factors and ADP statistics. phenix.fmodel takes the PDB file as is, so it is your responsibility to provide the correct input B-factors. Pavel. _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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Displaying electron density in PyMol
by Michael Thompson 10 Jan '11

10 Jan '11

Hi All, Does phenix have a utility that will allow me to produce an electron density map that can be opened in PyMol, similar to the "FFT" utility in ccp4? Thanks for the help, Mike Thompson -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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autobuild
by Page, Rebecca 09 Jan '11

09 Jan '11

Dear phenix community. We would like to 'fix' the residues of our current protein model, and use Autobuild (perhaps via rebuild-in-place=false, which is what we've been trying) to add missing residues to our current model . However, our efforts thus far have only resulted in models that get rebuilt from scratch. Is it possible to just 'add' residues to a current structure using Autobuild? If so, is someone could share the correct command with us, we'd be very appreciative. We can't seem to find it. Thanks in advance, Rebecca

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Accessing the CCP4 monomer library in Coot opened from Phenix
by Joseph Noel 09 Jan '11

09 Jan '11

Hi All, Having trouble getting Coot loaded by Phenix to access monomers such as DTT, glycerol, etc I assume through the CCP4 monomer library. If I insert the following in the phenix file, start_coot.sh: DYLD_LIBRARY_PATH=/Applications/ccp4-6.1.13/lib:$DYLD_LIBRARY_PATH export DYLD_LIBRARY_PATH will Coot now access the monomer library? Thanks! Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Postdoctoral position at the University of Toronto
by Jinrong Min 08 Jan '11

08 Jan '11

A Post-doctoral position in chromatin structural biology is available in my group. My lab aims to characterize proteins and protein/DNA or RNA complexes by X-ray crystallography in combination with other biochemical and biophysical techniques. Applicants should have a Ph.D. in structural biology, biochemistry, molecular/cell biology with 0-4 years postdoctoral research experience. Interested candidates are invited to send their CV with 3 references to: Jinrong Min by email: jr.min(a)utoronto.ca Jinrong Min Principal Investigator, Chromatin Biology and Epigenetics Structural Genomics Consortium Assistant Professor, Department of Physiology University of Toronto 101 College St., Toronto On M5G 1L7, Canada http://www.sgc.utoronto.ca/Chromatin

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error on Autobuild GUI on new version (1.7.629)
by Young-Jin Cho 08 Jan '11

08 Jan '11

Hi Phenix developers, I recently installed new version of phenix(phenix-1.7-629) FYI. I chose this installer version phenix-installer-1.7-629-intel-linux-2.6-x86_64-fc3.tar as my computer indicates 2.6.18-194.17.4.el5 x86_64 after uname -rm command. Everything was ok until I started AutoBuild program. Somehow it keeps giving me following error messages on my GUI window: ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /amnt/datnew/yjcho/RUN_FILE_2.log : ImportError: numpy.core.multiarray failed to import Possibly this subprocess is run on a machine with different architecture than the main process? ******************************************************************************** *************ERROR ENDING ******************* I would thank if you can help me out from this problem. Thanks in advance, Young-Jin

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anisotropic refinement gui more than one chain
by Christian Roth 06 Jan '11

06 Jan '11

Dear all, I want refine a structure with several chlorides and want refine these chlorides anisotropic. I use the GUI for the setup and manipulate the eff file just before it starts. To my surprise my constrained group definitions are used, but my anistropic refinement definitions are removed I incorporated it as followed: adp { individual { isotropic = None anisotropic = "chain a" anisotropic = "chain f" anisotropic = "chain Y" anisotropic = "chain T" anisotropic = "chain U" anisotropic = "chain z" anisotropic = "chain d" anisotropic = "chain g" anisotropic = "chain e" anisotropic = "chain V" anisotropic = "chain X" anisotropic = "chain n" } but in the log the following is stated: adp { individual { anisotropic = "chain a" } Why are all the other definitions gone? And if I defined it wrong, how I have to define it correctly? The current version I use is 1.6.4-486 Thanks Christian

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CCP4 SW Web Broadcast
by ronan.keegan＠stfc.ac.uk 06 Jan '11

06 Jan '11

Dear All, For those of you hoping to view the CCP4 Study Weekend online, we're experiencing some technical difficulties with the webcast equipment. Unfortunately the live stream won't be available for the first part of the meeting. We're hoping to fix it as soon as possible and we'll send an update as soon as it's available. Our apologies for the inconvenience. Best wishes, Ronan Ronan Keegan CCP4 Group -- Scanned by iCritical.

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Questions about phenix.refine with twin_law
by Keitaro Yamashita 06 Jan '11

06 Jan '11

Dear Phenix developers, I'm working with pseudo-merohedrally twinned data (fraction 45%), using Phenix-dev-616. I have three questions about phenix.refine with twin_law. (running on the command line) During refinement with twin_law, the log file says x-ray target function is set to "twin_lsq_f". Does it mean, we cannot use maximum likelihood target for twinned data? If so, is it recommended to refine without twin_law at first several cycles? When I tried to refine using the model refined without twin_law, the target function was still ml, not twin_lsq_f although I specified twin_law. Is this a bug? When I used twin_law option, in the table "R-free likelihood based estimates", "Scale factor" were None in all resolution bins. Cannot scale factor be calculated during twin refinement? Thanks in advance and Wishing you the best holidays, Keitaro

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How to get a statistics of sidechain&mainchain Bfactors?
by 商元 06 Jan '11

06 Jan '11

Dear all, I used TLS+ADP refinement to get the final structure model, after that I used phenix.model_vs_data to get the statistics for table1. However there is no B factor statistics in the output. Can I get the overall B factor by just simply averaging the B factors of each residue in the output text? Then how can I get the B factor value of the sidechains and that of the mainchain? Thanks and regards, Yuan SHANG Hong Kong

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DNA covalent bond angles deviate from PDB standard dictionary
by Scott Classen 05 Jan '11

05 Jan '11

Hello, I'm running into validation problems with DNA when validating on PDB website. the validation report indicates that the refined value is significantly different that the PDBs standard dictionary. Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond Dictionary Standard Name ID Number Angle Value Deviation ------------------------------------------------------------------------------------------- 2.2 DG D 6 N9 - C1' - O4' 110.5 108.3 0.3 2.6 DC D 7 N1 - C1' - O4' 110.9 108.3 0.3 2.3 DC D 8 N1 - C1' - O4' 110.6 108.3 0.3 3.0 DT D 9 N1 - C1' - O4' 111.3 108.3 0.3 I've looked through a few of these in the .geo file and it appears that phenix.refine is using different values. for example, angle pdb=" O4' DG D 6 " pdb=" C1' DG D 6 " pdb=" N9 DG D 6 " ideal model delta sigma weight residual 108.40 110.18 -1.78 3.00e+00 1.11e-01 3.52e-01 ideal is specified as 108.4º so clearly my refinement has converged, but it has NOT converged on the RCSBs accepted value of 110.5º What to do? Who is "right" phenix or RCSB? Thanks, Scott

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bugs in dev 625
by Weiergräber, Oliver H. 05 Jan '11

05 Jan '11

Hello, trying to use phenix.autobuild (command line version, didn't try the gui) in dev 625, I encountered the following error: ############################################ Build cycle 1 of 6 method:rebuild Initial rebuild cycle: just combining previous models or copying over initial PDB file Using edited_pdb.pdb for rebuild, copied to unrefined.pdb_1 Refining model: unrefined.pdb_1 No refinement carried out (may need free R flags) Error message from phenix.refine: global name 'libtbx' is not defined Refinement failed... ############################################ If invoked directly, phenix.refine seems to run fine, so there may be a problem with scripting in the autobuild wizard. Regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institut für Strukturbiologie und Biophysik ISB-3: Strukturbiochemie Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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viewing maps in xfit
by David Shin 05 Jan '11

05 Jan '11

Hi - Anyone have a script to convert phenix .mtz output so I can read in maps in xfit? I still find xfit handy for a few things. D

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errors when disabling Rfree
by chene＠umbi.umd.edu 03 Jan '11

03 Jan '11

Dear Phenixers, I have a low resolution twinned data, for which I disabled cross validation in refinement. The refinement worked and exported the refined coordinates. However, the phs files for maps are empty and there were such errors as below. It seems the free set is required for maps. I wonder how to fix this problem? Thanks Chen Traceback (most recent call last): File "/home/chene/phenix-1.6.4-486/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/home/chene/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py", line 103, in run map_manger.write_files() File "/home/chene/phenix-1.6.4-486/phenix/phenix/refinement/driver.py", line 1281, in write_files fmodel = self.refine_object.fmodels.fmodel_xray(), params = mtz_mc) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/maps/__init__.py", line 290, in map_coefficients_from_fmodel centrics_pre_scale = params.centrics_pre_scale) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py", line 1780, in map_coefficients w2 = w2) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py", line 1695, in map_coefficients sigmaa_object = self.sigmaa_object( detwinned_data=dt_f_obs,f_model_data=tmp_f_model, tmp_free=tmp_free,forced_update=True) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py", line 1504, in sigmaa_object kernel_width_free_reflections=200, File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/scaling/sigmaa_estimation.py", line 131, in __init__ raise RuntimeError("No free reflections.") RuntimeError: No free reflections. Chen Chen, PhD, Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 240-314-6122

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Automated Mg & K ions picking
by Hasan Demirci 02 Jan '11

02 Jan '11

Hi, I have a low resolution data and I am trying to place Mg++ and K+ ions. As far as I know for ligand search at least 3 atoms required. Is it possible to do an automated search of these single atom ions by using phenix similar to automated water picking protocol? Thanks. -- Hasan DeMirci, Ph.D. Postdoctoral Fellow Department of Molecular Biology, Cellular Biology & Biochemistry Brown University 185 Meeting Street Providence, RI 02912 (401) 863-3652 lab (SFH) (401) 863-6124 lab (ship st) (401) 226-7852 cell Hasan_DeMirci(a)Brown.edu demircha99(a)gmail.com

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MACOSX_DEPLOYMENT_TARGET mismatch between PHENIX and Coot
by Ben Eisenbraun 30 Dec '10

30 Dec '10

Howdy PHENIXians, One of my users reported this error: File "/programs/i386-mac/coot/coot-latest/lib/python2.7/sysconfig.py", line 300, in _init_posix raise IOError(msg) IOError: $MACOSX_DEPLOYMENT_TARGET mismatch: now "10.4" but "10.5" during configure The person is running on OS X Intel, using a PHENIX nightly and trying to call Coot. It looks like the PHENIX nightlies are built with MACOSX_DEPLOYMENT_TARGET=10.4, and the Coot I built used M_D_T=10.5 and Python is unhappy about this. It's easy to test this: $ export MACOSX_DEPLOYMENT_TARGET=10.3 $ phenix.python Traceback (most recent call last): File "/programs/i386-mac/phenix/dev-606/phenix-dev-606/build/mac-intel-osx/base/Python.framework/Versions/Current/lib/python2.7/site.py", line 553, in <module> <snip> IOError: $MACOSX_DEPLOYMENT_TARGET mismatch: now "10.3" but "10.4" during configure Or if you have access to one of our installations: $ phenix.python import os os.system('coot') Results in the original error pasted above. After playing a bit, I came up with a workaround. If you just set the M_D_T to 10.5 before starting Coot and _after_ starting PHENIX, it all seems to work. E.g. I can start Coot using this script: $ cat coot.py #!/usr/bin/env phenix.python import os os.putenv('MACOSX_DEPLOYMENT_TARGET', '10.5') os.system('coot') And since the 'coot' binary in the PATH is a wrapper script, I can just set it in the environment there. My question is: does Python actually need this? Is my workaround going to break something? I'm not enough of a Pythonista to be able to tell from looking at the sysconfig code if this will be an issue. There is a comment in the source: # On MacOSX we need to check the setting of the environment variable # MACOSX_DEPLOYMENT_TARGET: configure bases some choices on it so # it needs to be compatible. But it's not clear to me when it's going to be used. I'm almost certainly going to implement the workaround, so I'm mostly posting this for the list archives and to see if anyone has a better idea. Thanks. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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LigandFit (distorted manesium hexahydrate cluster)
by Hasan Demirci 28 Dec '10

28 Dec '10

Dear All, I am trying to run " LigandFit " with the following hydrated magnesium hexahydrate cluster (without the hydrogens) pdb. "HETATM 7 MG MG6 A 1 -53.936 117.342 91.273 1.00128.70 A MG HETATM 2 O1 MG6 A 1 -55.351 117.224 89.749 1.00128.62 A O HETATM 3 O2 MG6 A 1 -52.532 117.421 92.718 1.00127.25 A O HETATM 4 O3 MG6 A 1 -55.370 118.284 92.428 1.00127.74 A O HETATM 5 O4 MG6 A 1 -53.253 119.219 90.518 1.00128.43 A O HETATM 6 O5 MG6 A 1 -54.385 115.379 91.937 1.00127.84 A O HETATM 7 O6 MG6 A 1 -52.566 116.391 89.994 1.00128.62 A O " LigandFit automatically runs the elbow and creates a new search pdb file with hydroges and while doing this, elbow totally screws up the original starting geometry of the Oxygen atoms within the cluster after the addition of hydrogens. "HETATM 1 MG MG6 A 1 -53.913 117.323 91.231 1.00128.70 A MG HETATM 2 O1 MG6 A 1 -55.140 117.947 90.141 1.00128.62 A O HETATM 3 O2 MG6 A 1 -53.080 118.061 92.589 1.00127.25 A O HETATM 4 O3 MG6 A 1 -55.453 117.480 92.061 1.00127.74 A O HETATM 5 O4 MG6 A 1 -52.768 118.528 90.669 1.00128.43 A O HETATM 6 O5 MG6 A 1 -53.676 115.727 91.923 1.00127.84 A O HETATM 7 O6 MG6 A 1 -53.363 116.194 90.004 1.00128.62 A O HETATM 8 H11 MG6 A 1 -55.461 117.161 89.473 1.00128.62 A H HETATM 9 H21 MG6 A 1 -52.333 117.378 92.967 1.00127.25 A H HETATM 10 H31 MG6 A 1 -55.430 118.350 92.700 1.00127.74 A H HETATM 11 H41 MG6 A 1 -53.300 119.422 90.378 1.00128.43 A H HETATM 12 H51 MG6 A 1 -54.636 115.255 92.077 1.00127.84 A H HETATM 13 H61 MG6 A 1 -52.319 116.372 89.793 1.00128.62 A H " Is it a bug or am I making something wrong? Does the search pdb HAVE TO be covalently linked? or can I search for a cluster? Thanks. -- Hasan DeMirci

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ramachandran_restraints
by José Trincão 28 Dec '10

28 Dec '10

Dear all, I am refining a structure to 2.9 A, with pretty bad experimental data (P1, ~5400 residues in the A.U. (4 mol), anisotropic, fairly incomplete...). I have been running phenix.refine with NCS, 1 ADP per residue, lower target weights, TLS. My R/Rfree are stuck at about 2.4/3.05. I was getting around 2% ramachandran outliers at every cycle so I have been giving the nightly builds a shot. Now I get 0.2% outliers without changing any parameters for the ramachandra_restraints but it is forcing some of the peptide bonds out of the density. What can I tweak to improve the refinement? Thanks all in advance! Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr

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Re: [phenixbb] Simple Phaser Question (Ed Pozharski
by Joseph Noel 27 Dec '10

27 Dec '10

Hi Ed, Yes, that is what I generally do but it sometimes is a slightly different so I wanted a more general approach. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________ On Dec 25, 2010, at 12:00 PM, phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Simple Phaser Question (Joseph Noel) > 2. Re: Simple Phaser Question (Ed Pozharski) > 3. Questions about phenix.refine with twin_law (Keitaro Yamashita) > 4. Re: Questions about phenix.refine with twin_law (Peter Zwart) > 5. Re: Questions about phenix.refine with twin_law (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 24 Dec 2010 17:11:37 -0800 > From: Joseph Noel <noel(a)salk.edu> > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] Simple Phaser Question > Message-ID: <5E3B81ED-4C13-488E-8C28-33DB29263AEF(a)salk.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi All, > > I am working with a protein that is a physiological dimer. On occasion I obtain a unit cell with one monomer in the asymmetric unit but most often I obtain an enantiomorphic space group with an expanded C axis that contains two molecules in the asymmetric unit. Anyway, that is all moot to some extent. I am wondering if for the case of my NCS dimer, is there a way using Phaser in Phenix to ensure that when both monomers are found, they are "close together" representative of the physiological dimer? When I search with individual monomers I often obtain a solution with two monomers but in different asymmetric units. Of course, I could easily do the transformation to form the physiological NCS dimer for later refinement but just wondering if I could avoid this from the get go with the appropriate Phaser keyword input (GUI if possible). > > Thanks and Happy Holidays! > > Joe > ___________________________________________________________ > Joseph P. Noel, Ph.D. > Investigator, Howard Hughes Medical Institute > Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics > The Salk Institute for Biological Studies > 10010 North Torrey Pines Road > La Jolla, CA 92037 USA > > Phone: (858) 453-4100 extension 1442 > Cell: (858) 349-4700 > Fax: (858) 597-0855 > E-mail: noel(a)salk.edu > > Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 > Web Site (HHMI): http://hhmi.org/research/investigators/noel.html > ___________________________________________________________ > >

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