June 2013 - phenixbb - phenix-online.org

possible Xtriage bug??
by Michael Thompson 25 Jun '13

25 Jun '13

Hello Developers, I would like to report a possible bug in newer versions of phenix.xtriage. I have noticed recently that I am getting some strange results for the results of the L-test when I run xtriage, as described below: My data show a strong non-crystallographic translation, described by the vector <uvw>=(1/3, 2/3, 1/2). This NCS translation is readily identified by xtriage. When Xtriage performs the L-test, the output states: L test for acentric data using difference vectors (dh,dk,dl) of the form: (2hp,2kp,2lp) where hp, kp, and lp are random signed integers such that 2 <= |dh| + |dk| + |dl| <= 8 Mean |L| :0.504 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.340 (untwinned: 0.333; perfect twin: 0.200) These results don't make sense, as the statistics show an "anti-twinned" effect, which should not happen with the L-test. It appears that xtriage is using reflections that do not have the same expected intensity values due to the NCS translation. The strange thing is that I have another xtriage logfile, which I produced in September of 2012 using the same input data, that indicates the reflections used for the L-test were chosen "using difference vectors (dh,dk,dl) of the form: (3hp,3kp,2lp)." This choice of reflections does account for proper parity, and I get results that are much more sensible (Mean |L|=0.394; Mean L^2=0.221). I am wondering why I am getting different results now than I did last September? Has something changed in the underlying code, or am I missing something silly? I do not have an easy way of determining which version of phenix I used when the L-test was conducted using sensible reflections (the xtriage logfile doesn't contain this info as far as I can tell), but the version that seems to choose reflections inappropriately is 1.8.2-1334. Thanks a lot for the help, and for phenix being awesome in general! Mike -- 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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How to treat EDTA on a special position
by Jan Gebauer 25 Jun '13

25 Jun '13

Dear all, I recently solved a structure in R32/H (155). Interestingly some crystal contacts are mediated by an Metal/EDTA complex. The metal -presumably a magnesium- sits on a special position (x,0, 1/2) in the middle of a twofold axis with the EDTA molecule coordinating it. (See "top" view in dropbox image below) If I fit the EDTA/Mg complex in the density, the symmetry will of course generate a symmetry mate on the same spot. (see "side" view in dropbox image below). In phenix.refine, both entities are refined, which of course gives wrongs results. My question is, how to best define the Ligand to be compatible with phenix.refine and -later- with pdb submission. Should I just set occupancy to 0.5 for the whole EDTA molecule? - But then I would still get two molecules at this site... Or split it somehow half and let the second half be generated by symmetry? In that case, I would need to define bonds over the asymmetric unit to prevent "dissociation" of my ligand halves, wouldn't I? Or is there a third way? I already searched the phenixBB, but only found some "old" threads discussing vaguely similar problems. Unfortunately, they didn't help me to answer which way is better... (or right...) Regards, Jan DROPBOX IMAGE: https://dl.dropboxusercontent.com/u/29745394/R32%20-%20EDTA.jpg -- Dr. Jan Gebauer AG Prof. Baumann Institut für Biochemie / Uni-Köln Otto-Fischer-Str. 12-14 / 50674 Köln Fon: +49 (221) 470 3212 Fax: +49 (221) 470 5066 http://px.uni-koeln.de/

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completeness in table1
by Alexander Batyuk 24 Jun '13

24 Jun '13

Dear developers, What could be the reason for discrepancy in completeness reported in XSCALE.LP (94.5% - 100.0%) vs from Table1: 89.57% (37.49%)? Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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Re: [phenixbb] How to export difference patterson map in PHENIX
by Ulrich Baumann 20 Jun '13

20 Jun '13

Hi Nat I tried to limit the resolution by either --diff_limit 4 or --high_resolution 4.0. This does not work - probably is not supposed to work in this way? Thanks, ULrich lrich-Baumanns-iMac:xds_new ubaumann$ cctbx.patterson_map au1_run1_Rfree.mtz --high_resolution 4. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !! WARNING - EXPERIMENTAL PROGRAM !! !! !! !! This program is still in development - some functionality may be !! !! missing and/or untested. Use at your own risk! For bug reports, etc. !! !! email bugs(a)phenix-online.org. !! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Traceback (most recent call last): File "/usr/local/phenix-dev-1405/build/mac-intel-osx-x86_64/../../cctbx_project/iotbx/command_line/patterson_map.py", line 176, in <module> run(sys.argv[1:]) File "/usr/local/phenix-dev-1405/build/mac-intel-osx-x86_64/../../cctbx_project/iotbx/command_line/patterson_map.py", line 136, in run params = cmdline.work.extract() File "/usr/local/phenix-dev-1405/cctbx_project/libtbx/phil/__init__.py", line 1690, in extract value = object.extract(parent=result) File "/usr/local/phenix-dev-1405/cctbx_project/libtbx/phil/__init__.py", line 1086, in extract return self._type_from_words()(self.words, master=self) File "/usr/local/phenix-dev-1405/cctbx_project/libtbx/phil/__init__.py", line 320, in from_words value = self._value_from_words(words=words, path=master.full_path()) File "/usr/local/phenix-dev-1405/cctbx_project/libtbx/phil/__init__.py", line 348, in _value_from_words return float_from_words(words=words, path=path) File "/usr/local/phenix-dev-1405/cctbx_project/libtbx/phil/__init__.py", line 274, in float_from_words result = number_from_words(words=words, path=path) File "/usr/local/phenix-dev-1405/cctbx_project/libtbx/phil/__init__.py", line 227, in number_from_words value_string=str_from_words(words), words=words, path=path) File "/usr/local/phenix-dev-1405/cctbx_project/libtbx/phil/__init__.py", line 212, in number_from_value_string path, value_string, words[0].where_str())) RuntimeError: Error interpreting high_resolution="True" as a numeric expression (command line argument, line 1) Ulrich-Baumanns-iMac:xds_new ubaumann$ cctbx.patterson_map au1_run1_Rfree.mtz --diff_limit 4 ---------------------------------------- Prof. Ulrich Baumann, PhD Institute of Biochemistry, University of Cologne Otto-Fischer-Strasse 12-14, D-50674 Cologne, Germany

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X-ray/Neutron joint refinement
by Emily Golden 19 Jun '13

19 Jun '13

Hi All, I have a couple of questions about X-ray/neutron joint refinement in phenix. Is it possible to use the neutron data only for refining hydrogen atom positions and the X-ray data for all other atoms? I used the option to add hydrogen atoms to model and refine H/D at exchangable sites and H elsewhere. This worked for many of the exchangeable hydrogen atoms. However, for some side chains, especially Lysine, the program has placed a hydrogen and deuterium atom (with refined occupancies) in the same position as the atom it is supposed to be bonded to. Does anybody know why this is happening and what I may be able to do about it. Or will I need to manually move each misplaced H/D in Coot? Thank you for your help. Emily

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Jerry Karle
by Robert Sweet 19 Jun '13

19 Jun '13

Jerry Karle died a couple of weeks ago, and one of us here learned about it by noticing his obituary in the NY Times: http://www.nytimes.com/2013/06/15/health/jerome-karle-94-dies-nobelist-for-… He's well known to those of us who started in this field when the solving of a Patterson function for a heavy atom in a structure was the only way we knew to get the structure. With Herb Hauptman, and in close teamwork with his wife Isabella who actually >did< crystallography, he played a major role in working out the sort of Direct Methods that allowed one to solve ordinary small-molecule structures before the days of high-speed computing. As the obituary points out, Jerry and Herb shared the 1985 Nobel Prize in Chemistry for this work. The obit. is worth reading. I suspect you'll see an even better one in Nature soon. My own tiny personal memory of Jerry Karle: When I was a grad student at the Univ. of Wisc. with Larry Dahl I made a pilgrimage to the NRL to visit Jerry and Isabella. I was trying to use direct methods to solve at least one cephalosporin structure, which eventually appeared in my thesis, and there was a feature of DM that I failed to understand. They were very patient with me, but couldn't understand what it was I didn't get. It turns out to have been essentially trivial, but that's the way it goes sometimes. Anyway he always recognized me afterwards, or pretended to. I was delighted on arriving at BNL to discover that his daughter Louise was here. Bob ========================================================================= 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/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 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] cv convert to mtz file
by Pavel Afonine 17 Jun '13

17 Jun '13

Hi Majid, I had no problems converting cbh1_c10a.cv into MTZ using Phenix "Reflection file editor". To convert he other one (cbh1_fg34.cv) you need to add CRYST1 record similarly to cbh1_c10a.cv. Make sure you use recent version of Phenix.. Pavel On 6/17/13 5:48 AM, Majid Haddad Momeni wrote: > Dear Sir/Madam, > > I need help to be able to convert my .cv file to mtz, I have already tried both ccp4 package and Phenix through "Convert to/modify/extend MTZ" and "Reflection file editor" > However they didn't work! > I do highly appreciated of your assistance, > > Best Regards > Majid Haddad Momeni > PhD Student > Swedish University of Agricultural Sciences, > Uppsala-Sweden

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Beamtime available at NE-CAT (APS)
by Cyndi Salbego 14 Jun '13

14 Jun '13

Synchrotron beam time available to general users at NE-CAT (Sector 24 of APS) during the month of July 24ID-C beamline features: - Undulator beamline fully tunable from 6 to 21 keV (2.1 to 0.6 Angstroms) - PILATUS 6M pixel array detector, allowing continuous fine phi-sliced data acquisition at up to 25 frames per second - MD2 microdiffractometer with triple aperture (70, 30, or 10 micron apertures) - MK3 mini-kappa available on the microdiffractometer allowing reorientation of crystals for better diffraction geometry. - ALS style sample mounting robot compatible with ALS pucks or Unipucks 24ID-E beamline features: - Fixed energy undulator beamline (12662 eV) optimized for Se-SAD data collection - Beam stability optimized for smaller beams (down to 5 micron) - ADSC Q315 CCD detector - MD2 microdiffractometer with triple aperture (50, 20, or 5 micron apertures) - ALS style sample mounting robot compatible with ALS pucks or Unipucks - Remote data collection available For more info on our beamlines and updated schedule availability please see necat.chem.cornell.edu or contact Cyndi Salbego (csalbego(a)anl.gov). To apply for General User Time (Rapid Access for 2013-2 run) please go to: https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page Cyndi Salbego Administrator, NE-CAT 630.252.0689

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Re: [phenixbb] elbow
by Mengbin Chen 13 Jun '13

13 Jun '13

Dear Dr. Dias, I tried the command line in Terminal, but Elbow still regularized the conformation and bonds of the ligand and the result turned out to be the same with that I ran thorough GUI. The thing is that the input pdb file has a conformation the ligand should adopt so that I do not really want energy minimization or geometry optimization to be done on it. Although I set "none" for "geometry optimization" in GUI, it unfortunately changed the ligand conformation. Thank you, Mengbin On Thu, Jun 13, 2013 at 2:52 PM, Mengbin Chen <mengbinc(a)sas.upenn.edu>wrote: > Dear Dr. Dias, > > I tried the command line in Terminal, but Elbow still regularized the > conformation and bonds of the ligand and the result turned out to be the > same with that I ran thorough GUI. The thing is that the input pdb file has > a conformation the ligand should adopt so that I do not really want energy > minimization or geometry optimization to be done on it. Although I set > "none" for "geometry optimization" in GUI, it unfortunately changed the > ligand conformation. > > Thank you, > Mengbin > > > On Thu, Jun 13, 2013 at 2:42 PM, Joao Dias <joao.dias(a)heptares.com> wrote: > >> Dear Mengbin, >> You can open a terminal window and run elbow as a command line. >> >> phenix.elbow --final_geometry input_file.pdb**** >> >> >> Do not forget to initialize the phenix environment, depending on your >> terminal shell, one example is: >> source >> /Applications/PHENIX-dev-1320/Contents/phenix-dev-1320/phenix_env.sh >> >> All the best, >> Joao >> >> Dr Joao Dias**** >> >> Principal Scientist**** >> >> ** ** >> >> Heptares Therapeutics Ltd**** >> >> BioPark, Broadwater Road,**** >> >> Welwyn Garden City,**** >> >> Herts, AL7 3AX**** >> >> UK >> >> From: Mengbin Chen <mengbinc(a)sas.upenn.edu> >> Reply-To: PHENIX user mailing list <phenixbb(a)phenix-online.org> >> Date: Thursday, 13 June 2013 19:32 >> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> >> Subject: [phenixbb] elbow >> >> Dear PHENIX Users, >> >> I have been playing around with Elbow for a while, but I kept having >> problems generating .cif file. For "Chemical file type" and "Template PDB >> file", I used the pdb file of the ligand. Since the coordinates in the pdb >> file corresponds to a conformation desired, I chose "None" for "geometry >> optimization". After running Elbow, the output pdb file was completely >> different than the input one -- even double bonds became single bonds and >> 10-membered ring conformation changed. I have tried Sketcher in CCP4 >> package, but no good results either. Could anyone tell me how to do this >> correctly? Any help is appreciated! >> >> Thank you in advance, >> Mengbin >> >> -- >> Mengbin Chen >> Department of Chemistry >> University of Pennsylvania >> >> [image: www.heptares.com] <http://www.heptares.com><http://www.heptares.com> >> >> >> The information in this e-mail is confidential and may be legally >> privileged. It is intended for the exclusive attention of the addressee >> stated above and should not be copied or disclosed to any other. If you >> have received this transmission in error, please make no use of its >> contents and contact the sender. Contact and registered office address: >> Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden >> City, Hertfordshire, AL7 3AX. Company No: 06267989 >> >> > > > -- > Mengbin Chen > Department of Chemistry > University of Pennsylvania > -- Mengbin Chen Department of Chemistry University of Pennsylvania

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elbow
by Mengbin Chen 13 Jun '13

13 Jun '13

Dear PHENIX Users, I have been playing around with Elbow for a while, but I kept having problems generating .cif file. For "Chemical file type" and "Template PDB file", I used the pdb file of the ligand. Since the coordinates in the pdb file corresponds to a conformation desired, I chose "None" for "geometry optimization". After running Elbow, the output pdb file was completely different than the input one -- even double bonds became single bonds and 10-membered ring conformation changed. I have tried Sketcher in CCP4 package, but no good results either. Could anyone tell me how to do this correctly? Any help is appreciated! Thank you in advance, Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

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