- phenixbb - phenix-online.org

Ligand building/refinement woes
by Machius, Mischa Christian 14 Jan '13

14 Jan '13

I seem to be having the hardest time building/refining NADPH (PDB code NAP). When fetching this common ligand from within coot, Phenix (1.81-1168) subsequently does not seem to accept it and bombs noting all kinds of violations. When I have Phenix automatically build NAP into the density, it does place NAP (albeit completely out of otherwise quite nice density). When I then take the coordinates, read them into coot together with the CIF that Phenix writes into the ligand_build directory, placing and refinement in coot works well, but subsequent refinement in Phenix, using the very same CIF, again bombs. Since hydrogens are often an issue when going from coot to Phenix I remove them before running Refine. I have also tried just refining the coordinates as they came out of ligand_build. But Phenix still bombs and doesn't seem to accept its own CIF. I would have thought that a ligand as common as NAP wouldn't require a lot of gymnastics, perhaps not even reading CIF information, and that it would go all automatically.That's probably too optimistic on my part. It's probably something silly, but I can't figure out what it is. Any ideas? Many thanks in advance, MM

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Fwd: WCPCW21
by Nathaniel Echols 14 Jan '13

14 Jan '13

---------- Forwarded message ---------- From: "Williams, John Charles" <jwilliams(a)coh.org> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Cc: Date: Mon, 14 Jan 2013 10:29:12 -0800 Subject: WCPCW21 Dear All, The West Coast Protein Crystallography Workshop is rapidly approaching. The standard rates close Jan 21st. Also, we are now able to accept credit cards. Due to IT security issues, the CC number needs to be called in to Ariadna Bello, senior secretary in Dept of Molecular Medicine, City of Hope. Finally, please submit your abstracts as soon as possible as we will start to select oral presentations. Best, John

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Electron Density
by CPMAS Chen 14 Jan '13

14 Jan '13

Thanks, Nat, If the density level(map or coefficient) of phenix is not an absolute level, then I really do not need to worry what shows up by coot. I used the Fourier map generated by phenix, .mtz file. Thanks! 6. density level (CPMAS Chen) > 7. Re: density level (Nathaniel Echols) > 9. Re: density level (Pavel Afonine) > > > > ------------------------------ > > > Message: 7 > Date: Sun, 13 Jan 2013 12:21:00 -0800 > From: Nathaniel Echols <nechols(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] density level > Message-ID: > <CALeAa1Mty9= > U-CFcmhJ1ZRWAiuXMeOS0RHVT4YtXpOVBO0EDyQ(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Sun, Jan 13, 2013 at 11:38 AM, CPMAS Chen <cpmasmit(a)gmail.com> wrote: > > I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To my > > surprise, the absolute electron density on the 2Fo-Fc map is quite > > different. > > The electron density maps (or coefficients) generated by Phenix are > not on an absolute scale, and the values displayed by Coot are more or > less irrelevant. The scaling method changed significantly between > 1.6.4 and 1.8, so I'm not surprised that the map levels did too. > > > By the way, is there a simple way to keep only F and SIGF column of the > > autoxds generated truncate.mtz via phenix? the GUI does not allow to > reduce > > columns. I normally use IMEAN and SIGIMEAN to do refinement, but this may > > not be necessary as it is pointed in the maillist, since the intensity is > > already transformed to amplitude after truncation in autoxds. > > > > I can specify labels by xray_data.labels = "F, SIGF", but apparently > phenix > > treats it as containing anomalous data. the following is extracted from > the > > refine pdb file > > > > MIN(FOBS/SIGMA_FOBS) : 1.16 > > REMARK 3 COMPLETENESS FOR RANGE (%) : 97.11 > > REMARK 3 NUMBER OF REFLECTIONS : 143207 > > REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247 > > > > Also, in the auto generated def file, > > xray_data.labels = "F, SIGF, DANO, SIGDANO" > > This is intentional - why would you want to throw out information? > However, you can always use either the reflection file editor (in the > latest builds) or the French & Wilson GUI to convert IMEAN to F. > > > -Nat > > > > > ------------------------------ > > Message: 9 > Date: Sun, 13 Jan 2013 21:19:17 -0800 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] density level > Message-ID: <50F39555.8000000(a)lbl.gov> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi, > > what kind of file you use to see the map in Coot: Fourier map > coefficients (MTZ file) or actual map (CCP4 binary formatted file with > the map)? I need to know this before offering a first guess on what may > be the reason for this. > > Pavel > > On 1/13/13 11:38 AM, CPMAS Chen wrote: > > Dear PhenixBBer, > > > > I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To > > my surprise, the absolute electron density on the 2Fo-Fc map is quite > > different. > > > > https://www.dropbox.com/s/prs0z8ayb73kg9k/Screenshot_sigma.png > > > > At the same sigma level(1.5), the absolute density of the violet map > > is 0.32e/A^3 (phenix-dev-1266), while that of the blue map is > > 0.01e/A^3(phenix-1.6.4-486). Besides the different phenix used, there > > is no other difference on the data and model used. > > > > Sam encountered a similar problem on the density. > > > > http://phenix-online.org/pipermail/phenixbb/2012-December/019226.html > > > > By the way, is there a simple way to keep only F and SIGF column of > > the autoxds generated truncate.mtz via phenix? the GUI does not allow > > to reduce columns. I normally use IMEAN and SIGIMEAN to do refinement, > > but this may not be necessary as it is pointed in the maillist, since > > the intensity is already transformed to amplitude after truncation in > > autoxds. > > > > I can specify labels by xray_data.labels = "F, SIGF", but apparently > > phenix treats it as containing anomalous data. the following is > > extracted from the refine pdb file > > > > MIN(FOBS/SIGMA_FOBS) : 1.16 > > REMARK 3 COMPLETENESS FOR RANGE (%) : 97.11 > > REMARK 3 NUMBER OF REFLECTIONS : 143207 > > REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247 > > > > Also, in the auto generated def file, > > xray_data.labels = "F, SIGF, DANO, SIGDANO" > > > > Or there is a work round for this issue? > > > > Thanks! > > > > -- > > > > *************************************************** > > > > Charles Chen > > > > Research Associate > > > > University of Pittsburgh School of Medicine > > > > Department of Anesthesiology > > > > ****************************************************** > > > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > >

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density level
by CPMAS Chen 14 Jan '13

14 Jan '13

Dear PhenixBBer, I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To my surprise, the absolute electron density on the 2Fo-Fc map is quite different. https://www.dropbox.com/s/prs0z8ayb73kg9k/Screenshot_sigma.png At the same sigma level(1.5), the absolute density of the violet map is 0.32e/A^3 (phenix-dev-1266), while that of the blue map is 0.01e/A^3(phenix-1.6.4-486). Besides the different phenix used, there is no other difference on the data and model used. Sam encountered a similar problem on the density. http://phenix-online.org/pipermail/phenixbb/2012-December/019226.html By the way, is there a simple way to keep only F and SIGF column of the autoxds generated truncate.mtz via phenix? the GUI does not allow to reduce columns. I normally use IMEAN and SIGIMEAN to do refinement, but this may not be necessary as it is pointed in the maillist, since the intensity is already transformed to amplitude after truncation in autoxds. I can specify labels by xray_data.labels = "F, SIGF", but apparently phenix treats it as containing anomalous data. the following is extracted from the refine pdb file MIN(FOBS/SIGMA_FOBS) : 1.16 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.11 REMARK 3 NUMBER OF REFLECTIONS : 143207 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247 Also, in the auto generated def file, xray_data.labels = "F, SIGF, DANO, SIGDANO" Or there is a work round for this issue? Thanks! -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Refining anomalous groups
by Brennan Bonnet 13 Jan '13

13 Jan '13

Hi All, I hope everyone had relaxing holidays to begin the new year. I am back to work trying to refine anomalous groups using phenix.refine. I have managed to merge my files so that my exptl_fobs_phases_flags_1_with_hl_anom.mtz now contains F(+), SIGF(+), F(-), SIGF(-). Now I have a new problem which was not occurring before the break. Usually I check the box for "Anomalous groups", then select "Modify selections for: Anomalous groups" which brings up a screen for atom selection and definition of f' and f''. In the past, clicking on the View/pick button launches Coot for selection of the atoms. Sadly, now clicking on the View/pick doesn't launch Coot and instead crashes Phenix. Does anyone else have this problem or know how to fix it? Please help! Thanks, ~Brennan~

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Problem rebuilding ligand structure
by bsubedi＠btk.fi 11 Jan '13

11 Jan '13

Hi, I am using Phenix 1.0-1069 for refinement and coot 0.7-pre-1 for visualization and rebuilding. I used SMILES in coot to build the ligand and then merged them with PDB.I had to do this as a separate step for both chains and the .cif file so produced was not accepted for refinement. I used readyset to obtain the restrains for refinement using .pdb file, even though my refinement works, when i try to run real build refine in coot I get this error message: Failed to match (to the dictionary) the following model atom names: HB3 O6 C10 C11 C12 O7 C13 O5 C8 C9 ...... That would cause exploding atoms, so the refinement didn't start. Could someone help me with fixing this problem. Best regards, Bishwa

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symmetry related bond restraint in R3 space group
by Xiang Li 11 Jan '13

11 Jan '13

I am trying to add some restraints between symmetric molecule with symmetry operation. However, I found it is not correct to use the operation information directly provided in Coot. The crystal I worked on has R3 symmetry. The symmetry operation in Coot shows to be -x+y,-x,z+ (1,1,0) and it did not work in Phenix refine. I read one previous email on this topic about the difference of symmetry operation in Coot and Phenix. However, I do not know how to do the conversion between the two when the numbers changed. Could you help me to work out on correct the symmetry operation in Phenix and talk some more on how to do the conversion please? I really appreciate your help! Sincerely, Xiang

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AutoSol error
by Luca Pellegrini 10 Jan '13

10 Jan '13

AutoSol (phenix 1.8.1-1168) stops at the build stage with the following message: *** ERROR MESSAGE: The cell appears to have changed during the run Original cell: [49.22, 91.325, 103.285, 113.16, 97.64000000000001, 76.74] New cell : [49.173301696777344, 92.32479858398438, 103.37100219726562, 66.54070281982422, 82.29070281982422, 76.58550262451172] If running from a script, please specify the space group in the input file. The incorrect space group may be coming from another wizard... *** Can you please advice as to what might be wrong? I am running AutoSol from the GUI and it did pick up the space group from the mtz file. What AutoSol refers to as the 'new cell' is actually my original cell. I was running two AutoSol jobs simultaneously from two mtz files with the same cell dimensions, and they both failed with the same message. Thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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DEN refinement and reference model
by Luca Pellegrini 08 Jan '13

08 Jan '13

Phenix.den_refine (1.8.1-1168) stops and complains that: "Sorry: Reference model contains SEGIDs that do not match the working model." I have four chains in both working and reference model, ordered in the same way (A to D). Chains A and C are the same molecule, and chains B and D are also the same. Can you please advice? Some of the chains in the reference model contain more residues, is this a problem? Thanks for your help. Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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dev-1261 wizard.test fail
by Morten Groftehauge 08 Jan '13

08 Jan '13

Hi guys, I just updated Rosetta to 3.4 and it seems to have compiled correctly (at least no error interruptions). I've done this enough to not be satisfied by that and ran > phenix_regression.wizards.test_command_line_rosetta_quick which goes past the Rosetta tests correctly but fails at ================================================================= Running test_prerefine ------------------------------------------------------------ Numbers do not match: 0.47825 0.53601 r {{ 0.87799 0.06946 -0.47362} {-0.02049 0.99396 0.10779} { 0.47825 -0.08494 0.87411}} --- r {{ 0.84375 0.06393 -0.53291} {-0.02789 0.99676 0.07541} { 0.53601 -0.04877 0.84280}} ------------------------------------------------------------ FAILED See log files test_prerefine/test_prerefine.log test_prerefine/test_prerefine_current.log ================================================================= Running test_prerefine_double OK ================================================================= Running test_prerefine_no_data ------------------------------------------------------------ Numbers do not match: 0.47825 0.53601 r {{ 0.87799 0.06946 -0.47362} {-0.02049 0.99396 0.10779} { 0.47825 -0.08494 0.87411}} --- r {{ 0.84375 0.06393 -0.53291} {-0.02789 0.99676 0.07541} { 0.53601 -0.04877 0.84280}} ------------------------------------------------------------ FAILED See log files test_prerefine_no_data/test_prerefine_no_data.log test_prerefine_no_data/test_prerefine_no_data_current.log ================================================================= When I look in the log there are no error messages. I don't need to prerefine so I'm good but I still find it weird. I tried again with Rosetta 3.3 and got no error flags. Is it because the quick tests are checking the result against the results that you got earlier and the algorithm has been changed between 3.3 and 3.4? Cheers, Morten PS Really enjoyed the talks at the CCP4 study weekend. -- Morten K Grøftehauge, PhD Pohl Group Durham University

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mr_rosetta and disulphide bonds
by Morten Groftehauge 07 Jan '13

07 Jan '13

Hello again, I forgot my important question in all my "this seems to be working but the test says it doesn't"-drama: How do I specify disulphide bonds for MR_rosetta? I know it keeps them if they are in the input model but disulphides are generally poorly conserved, especially in the %identity range where mr_rosetta is the most useful. According to the changelog this feature should be available in the latest dev. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Ph.D. position at Lund University
by Derek Logan 07 Jan '13

07 Jan '13

A 4-year PhD position is available in the groups of Dr. Derek Logan and Prof. Ulf Ryde at the Dept. of Biochemistry and Structural Biology and the Dept. of Theoretical Chemistry at Lund University, Sweden. The project is sponsored by the European Spallation Source and will also involve the participation of ESS scientists. The PhD student will work on structural and theoretical studies of protein-ligand interactions, using the carbohydrate binding protein galectin-3 as a model system. Structural studies will be conducted principally using neutron crystallography in combination with X-ray crystallography at very high resolution (< 0.9 Å). The work will include production of crystals of suitable size for neutron diffraction, data collection at various neutron sources around the world, data processing and modelling. The theoretical studies will be conducted in Ulf Ryde's group at Theoretical Chemistry. We will develop methods to combine crystallographic refinement and quantum mechanical calculations. In addition, we perform molecular dynamic simulations and estimates of binding affinities using free-energy perturbation. The project is part of a larger network at Lund University including organic chemists, medical scientists and NMR experts, dedicated to a fundamental understanding of protein-ligand interactions in general and galectin inhibition in particular. The candidate must have bachelor's degree in an appropriate subject (preferably chemistry) and should ideally have previous experience in structural biology, both theoretical and practical. The candidate should also have good knowledge of theoretical chemistry. Experience of quantum chemistry, statistical mechanics and simulations is an advantage. The deadline for application is 31st January 2013. For more information on the eligibility requirements, please see: http://admin.lu.se/o.o.i.s?id=22598&Dnr=511988&Type=E Application should be made using the link in the right hand column of this web page. For informal enquiries on the project contact: Derek Logan, Associate professor +46 46-2221443 derek.logan(a)biochemistry.lu.se Ulf Ryde, Professor +46-2224502 ulf.ryde(a)teokem.lu.se http://www.cmps.lu.se/ http://www.teokem.lu.se/ http://www.chem.lu.se/People/galectins_in_Lund/ http://www.esss.se

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Deadline: 4 February -- Please apply for RapiData 2013, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 04 Jan '13

04 Jan '13

We are offering RapiData 2013, the fifteenth 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 21-26 April 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students 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 eleventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 21 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, Sonya Kiss, 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/ Photon Sciences and Biology Dept Mail Stop, Bldg 463 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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Fwd: WCPCW 21
by Nathaniel Echols 03 Jan '13

03 Jan '13

---------- Forwarded message ---------- From: "Williams, John Charles" <jwilliams(a)coh.org> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Date: Thu, 3 Jan 2013 10:42:14 -0800 Subject: WCPCW 21 Dear All, Happy New Year! The West Coast Protein Crystallography Workshop is fast approaching (March 17th). The site (wcpcw.org) is up, registration is open and the option to pay by credit card is now available. The conference has a long tradition of methods development and organized as such to facilitate discussion and colloboration. We are especially interested in having speakers that are doing the ‘real’ work - graduate students, postdocs and staff scientists! We are also honored having Prof. Wayne Hendrickson as our keynote speaker. Prof. Hendrickson has made seminal contributions to the field including efforts in phase combination (Hendrickson-Lattman coefficients), incorporation of stereochemical constraints in protein refinement (e.g., PROLSQ – the predecessor to many of the refinement programs we now use), and the development of MAD phasing (including the development of selenomethionine incorporation). In addition, Prof. Hendrickson’s lab has produced a large number of biologically important structures including the HIV caspid GP120 bound to CD4, the first tyrosine kinase structure (Lck), and many, many others. We look forward to seeing you in Monterey! Best, John

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Anomalous group refinement question
by Pawel Grochulski 03 Jan '13

03 Jan '13

Dear all, Instruction says: Anomalous groups refines the anomalous coefficients f' and f'' for anomalously scattering atoms such as Se or heavy metals; it is only appropriate if you have anomalous data (I+/I- or F+/F-). How do I indicate which atoms to be considered? Thank you for your help. Happy New Year. Pawel ____________________ Dr. Pawel Grochulski, D.Sc. Canadian Macromolecular Crystallography Facility (cmcf.lightsource.ca<http://cmcf.lightsource.ca/>), Canadian Light Source Inc., 44 Innovation Boulevard, Saskatoon, SK S7N 2V3, Canada. Phone: +1 (306) 657-3538, Fax: +1 (306) 657-3535. Adjunct Professor of Pharmacy, College of Pharmacy and Nutrition, University of Saskatchewan (www.grochulski.com<http://www.grochulski.com/>) __________________________________________________________________________________________

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Problem with anomalous scattering factor refinement
by Subhani Bandara 27 Dec '12

27 Dec '12

Hi all, I've been trying to refine a structure with anomalous data with anomalous scattering factors. After some refinements without anomalous scattering factor refinement, I used the data.mtz file and original reflection file in reflection file editor to get the anomalous data merged with Rfree flags. When I tried to use this file with a pdb file (deleted hexadigest remark) and a cif file for ligands, the refinement ends with the following error at the end of the 3rd refinement cycle (I have only 3 cycles for a refinement). I was able to run a similar refinement with anomalous scattering factors for another structure without a problem. One difference in this structure is that this has NCS and the previous one didn't. I am using dev-1243 GUI. RuntimeError : scitbx array_family range error Traceback: File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/libtbx/thread_utils.py", line 234, in run return_value = self._target(self._args, self._kwargs, self._c) File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/libtbx/runtime_utils.py", line 87, in __call__ result = self.target() File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/libtbx/runtime_utils.py", line 66, in __call__ result = self.run() File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/runtime.py", line 69, in run refine_object = self._run(args, callback) File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/runtime.py", line 85, in _run call_back_handler=callback) File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/command_line.py", line 169, in run map_manger.write_files() File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/driver.py", line 1735, in write_files map_coeff_dataset=self.write_mtz_file(), File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/driver.py", line 1724, in write_mtz_file pdb_hierarchy=self.refine_object.model.pdb_hierarchy()) File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/mmtbx/maps/__init__.py", line 500, in __init__ pdb_hierarchy = pdb_hierarchy) File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/mmtbx/maps/__init__.py", line 428, in map_coefficients_from_fmodel sharp = params.sharpening).map_coeffs File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/mmtbx/map_tools.py", line 55, in __init__ data = self.map_coeffs.data()*scale) Thanks in advance for any help Subhani

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Re: [phenixbb] problems with Rosetta_mr
by Yoni - UW 22 Dec '12

22 Dec '12

Thank you For you suggestions, Tom! Unfortunately I already ran the phenix.regression.wizard a few time, and actually also for the rebuild module only. This module seems to cause me all the troubles. It goes to the wrong .map file (compared with the provided log files of the tutorial) and have trouble reading the edited alignment file. I also tried to use the .eff files to run the failed steps only, with similar results. Another thing i think is worth mentioning is that I have a suspicion something is wrong with my installation of Phenix, because when I try to run "autobuild.creat 20 very good models" from the GUI it fails with an autobuild error, while working well with the command line. Thanks again, Yoni

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Excluding atoms from coordinate refinement ignored
by Engin Özkan 22 Dec '12

22 Dec '12

Hi Phenix developers, I have an issue using 1.8.1 (1168) with excluding atoms from coordinate refinement. I have defined a certain residue to be excluded from coordinate refinement, as can be seen in the .eff file produced by this run. refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp *tls *occupancies group_anomalous sites { individual = not (resseq 60 and resname PHE) torsion_angles = not (resseq 60 and resname PHE) rigid_body = None ... However, this gets ignored, and this residue and its NCS-related brethren get moved into nondescript electron density on a symmetry axis. This residue was just fine in an earlier version of Phenix, but when I switched to 1.8.1, it started moving into this density. So, I thought excluding it from xyz refinement, which is a dirty trick in my opinion, would fix this problem. Not so. I have the feeling that this is due to rotamer corrections as part of the torsion NCS implemented in 1.8.1 now. Sticking a zero occupancy dummy atom in the density did prevent this residue from moving in. Turning off torsion NCS also fixed it. By the way, I have "fix rotamer sidechains" off, as I am yet to see it improve things (at medium or low resolution). Thanks and happy holidays! Engin

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Problems with rosetta_mr
by Yoni Haitin 21 Dec '12

21 Dec '12

Hello all, I have been trying (desperetly) to run the Rosetta_MR. I have encountered some problems with my data, so I switched to the "HNP3-mr-rosetta" tutorial dataset. I followd the debugging suggestions in the instructions webpage with no improvement. It seems that I have a problem in the rebuild stage. Attached are the RUN_FILE_1.log from REBUILD_IN_SETS_5 and ../WORK_1/rebuild.log. The edited_align.ali file cannot be opened for some reason. Another issue is that the map used is being taken from "overall_best_denmod_map_coeffs_nf.map" instead of "cycle_best" (as is in the tutorial's mr_rosetta_output log). this seems to produce an error (last log file attached). What should I do next? Thank you, Yoni Parameters taken from: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/PARAMS_1.eff # mr_rosetta_rebuild # # Run automr mr_rosetta_rebuild with rosetta # Type phenix.doc for help Values of all params: mr_rosetta_rebuild { input_files { model = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/1zmm_mr.1.pdb" map = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/overall_best_denmod_map_coeffs_nf.map" seq_file = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/EDITED_1dfn.seq" hhr_files = None alignment_files = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/edited_align.ali" model_info_file = "" fragment_files = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/phaser_rosetta/aat000_09_05.200_v1_3.gz" fragment_files = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/phaser_rosetta/aat000_03_05.200_v1_3.gz" fragment_files_chain_list = None fragment_files_9_mer_by_chain = None fragment_files_3_mer_by_chain = None use_dummy_fragment_files = False sort_fragment_files = True } output_files { log = "mr_rosetta_rebuild.log" params_out = "mr_rosetta_rebuild_params.eff" } directories { temp_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1" workdir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1" output_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1" gui_output_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta" top_output_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14" rosetta_path = "/Users/administrator/rosetta_3.4" rosetta_binary_dir = "rosetta_source/bin" rosetta_binary_name = "mr_protocols.default.macosgccrelease" rosetta_script_dir = "rosetta_source/src/apps/public/electron_density" rosetta_pilot_script_dir = "rosetta_source/src/apps/pilot/frank/" rosetta_database_dir = "rosetta_database" } rosetta_rebuild { run_rosetta_rebuild = True stage_to_rebuild = "rescored_mr_solution" max_solutions_to_rebuild = 5 min_solutions_to_rebuild = 1 llg_percent_of_max_to_keep = 50 rosetta_models = 20 chunk_size = 1 edit_model = True superpose_model = False } rosetta_modeling { map_resolution = 3 map_grid_spacing = 1.5 map_weight = 1 map_window = 5 include_solvation_energy = True weights_file = "" } crystal_info { resolution = 0 space_group = "P 21 21 2" chain_type = *PROTEIN DNA RNA ncs_copies = 1 } control { verbose = False debug = False raise_sorry = False dry_run = False nproc = 1 group_run_command = "sh " queue_commands = None condor_universe = "vanilla" add_double_quotes_in_condor = True condor = None one_subprocess_level = None single_run_command = "sh " last_process_is_local = True background = True ignore_errors_in_subprocess = True check_run_command = False max_wait_time = 100 wait_between_submit_time = 1 wizard_directory_number = 14 n_dir_max = 100000 number_to_print = 5 write_run_directory_to_file = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/INFO_FILE_1" resolve_command_list = None start_point = place_model rescore_mr rosetta_rebuild rosetta_rescore \ similarity refine_top_models average_density_top_models \ relax_top_models autobuild_top_models \ setup_repeat_mr_rosetta repeat_mr_rosetta stop_point = place_model rescore_mr rosetta_rebuild rosetta_rescore \ similarity refine_top_models average_density_top_models \ relax_top_models autobuild_top_models \ setup_repeat_mr_rosetta repeat_mr_rosetta clean_up = False } non_user_params { file_base = "1zmm_mr.1" print_citations = False highest_id = 10 is_sub_process = True dummy_autobuild = False dummy_refinement = False dummy_rosetta = False prerefine_only = False skip_clash_guard = True correct_special_position_tolerance = None comparison_mtz = "" labin_comparison_mtz = None write_local_files = False rosetta_fixed_seed = None } } Starting mr_rosetta_rebuild Date: Thu Dec 20 14:44:49 2012 Directory: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5 HOST = ZagottasMacPro.local HOSTTYPE = intel-mac MACHTYPE = x86_64 OSTYPE = darwin VENDOR = apple USER = administrator PID = 36828 Checking rosetta paths: rosetta binary: /Users/administrator/rosetta_3.4/rosetta_source/bin/mr_protocols.default.macosgccrelease database_dir: /Users/administrator/rosetta_3.4/rosetta_database script_dir: /Users/administrator/rosetta_3.4/rosetta_source/src/apps/public/electron_density pilot_script_dir: /Users/administrator/rosetta_3.4/rosetta_source/src/apps/pilot/frank/ Changing to work directory: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1 Rebuilding the model /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/1zmm_mr.1.pdb with rosetta Rebuilding model using map at resolution of 3.0 A Generating 20 rebuilt models ================================================================================ Reading model from /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/1zmm_mr.1.pdb ================================================================================ ALIGNMENT LINES: ## TARGET 1zmm_ # hhsearch scores_from_program: 0 1.00 0 DCYCRIPACIAGERRYGTCIYQGRLWAFCC 1 -CYCRIPACIAGERRYGTCIYQGRLWAFCC -- Trying to adjust the PDB sequence from alignment file: -CYCRIPACIAGERRYGTCIYQGRLWAFCC to match the actual PDB sequence: YCRIPACIAGERRYGTCIYQGRLWAFCC New alignment line 4 for PDB: 1 --YCRIPACIAGERRYGTCIYQGRLWAFCC Start position of target sequence in sequence file: 0 Aligned model for comparison: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1/WORK_1/aligned_model.pdb Log for rebuilding: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1/WORK_1/rebuild.log **************ERROR ENDING********************** Failed to run REBUILD...see log file in /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1/WORK_1/rebuild.log **************ERROR ENDING********************** --- Here is ../WORK_1/rebuild.log: core.init: Mini-Rosetta version unknown from unknown core.init: command: /Users/administrator/rosetta_3.4/rosetta_source/bin/mr_protocols.default.macosgccrelease @rebuild.flags core.init: 'RNG device' seed mode, using '/dev/urandom', seed=345021854 seed_offset=0 real_seed=345021854 core.init.random: RandomGenerator:init: Normal mode, seed=345021854 RG_type=mt19937 ERROR: Warning: can't open file /Users/administrator/Yoni/Rosettal/ tutorial/ data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/edited_align.ali! ERROR:: Exit from: src/core/sequence/util.cc line: 380 --- core.init: Mini-Rosetta version exported from unknown core.init: command: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_source/bin/mr_protocols.default.macosgccrelease @rebuild.flags core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-340184367 seed_offset=0 real_seed=-340184367 core.init.random: RandomGenerator:init: Normal mode, seed=-340184367 RG_type=mt19937 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/pdb_pair_stats_fine core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/scoring/score_functions/hbonds/standard_params/HBPoly1D.csv core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/scoring/score_functions/hbonds/standard_params/HBEval.csv core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/P_AA core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/P_AA_n core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/P_AA_pp core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/Rama_smooth_dyn.dat_ss_6.4 core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/env_log.txt core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/cbeta_den.txt core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/pair_log.txt core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/cenpack_log.txt core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12 core.scoring.electron_density.ElectronDensity: Loading Density Map core.scoring.electron_density.ElectronDensity: [ ERROR ] Error opening MRC map /Users/administrator/Yoni/Rosettal\ tutorial\ data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_5/WORK_1/junk/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/overall_best_denmod_map_coeffs_nf.map. Not loading map. core.scoring.electron_density.ElectronDensity: [ ERROR ] Error loading density map named '/Users/administrator/Yoni/Rosettal\ tutorial\ data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_5/WORK_1/junk/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/overall_best_denmod_map_coeffs_nf.map' -- Yoni Haitin, Ph.D. Department of Physiology and Biophysics University of Washington Seattle, WA 98195-7290 Email: yonihaitin(a)gmail.com Email(2): haitinyo(a)uw.edu

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problem about phase caculate
by yzhao 19 Dec '12

19 Dec '12

Hi everyone, I have came into a problem recently. My structure was solved by MAD and a crude model was built manually. Several peak data sets were collected, resolution is about 4A-4.2A. The heavy atom can be located by anomalous difference fourier. I feed the initial phase or heavy atom sites, and the peak data set to phenix. However the map after DM is too bad. The density is very strange. I don't know what's the problem? In addition, how to define protein mask at phenix autosol for density modification? Thanks in advance. -- Yan Zhao, M.Phil. National Laboratory of Protein Sciences Institute of Biophysics Chinese Academy of Sciences 15 Datun Rd. Beijing, 100101 China

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composite simulated annealing omit map.
by Appu kumar 18 Dec '12

18 Dec '12

Dear members, please guide me which mtz. file i should use to make composite SA omit map. Out of two mtz file which one should i consider, Initial mtz file which is an output of scalepacktomtz programme or the recent mtz file which is an output of phenix/refmac after refinement. What is the sigma level at which these map should be made.? Thanks in advance Appu

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fwd: WPCPW 21
by Nathaniel Echols 14 Dec '12

14 Dec '12

---------- Forwarded message ---------- From: "Williams, John Charles" <jwilliams(a)coh.org> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Cc: Date: Fri, 14 Dec 2012 13:03:49 -0800 Subject: WCPCW 21 All, Just wanted to inform you that registration for the West Coast Protein Crystallography Conference is now open. Wayne Hendrickson will be the keynote speaker! The meeting, March 17th to the 21st at the Monterey Plaza and Spa, emphasizes all aspects of protein/macromolecular methods and developments. The fees are all inclusive - registration, room, food and social hours. Please see www.wcpcw.org. Happy Holidays. Best, John

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PDB header
by Eric Girard 13 Dec '12

13 Dec '12

Dear phenix users, I currently try to deposit a structure within PDBe. I discovered that the pdb header has missing information, in particular K_sol, B_sol, Wilson B, Estimate_errors, overall anisotropic B value . Is it linked to the TWIN_LSQ_F target used (Phenix version 1.8.1_1168) or to something wrong I did? How can I recover these information? Thanks for your help. Best regards. Eric. -- *************************************************************** Eric Girard Extremophiles and Large Macromolecular Assemblies (ELMA) group Institut de Biologie Structurale J.-P. Ebel UMR 5075 CEA-CNRS-UJF-PSB 41, Rue Jules Horowitz 38027 Grenoble Cedex 1, France Phone: +33 (0)4 38 78 96 45 Fax: +33 (0)4 38 78 54 94 Web site: http://www.ibs.fr/ ***************************************************************

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Refinement and glycosylation.
by Jan van Agthoven 12 Dec '12

12 Dec '12

Hi everyone, I refined my structure using phenix.refine and used the following parameters to define the ASN-NAG link: refinement.pdb_interpretation.apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resseq x residue_selection_2 = chain A and resname ASN and resseq y } However I would like the glycosylation to be Beta (NAG in Beta configuration). How can I define this in the parameter file? Thanks,

2 3

pathological case with soaking
by Appu kumar 12 Dec '12

12 Dec '12

Respected members,, I have one question regarding soaking. Binding of the substrate to enzyme leads to active site closure. So if we are soaking the enzyme crystal with the substrate, and collecting the data and solving the structure, then how would one distinguish the existence of apo and substrate bound form of enzyme in same crystal. I meant to say, soaking may cause the crystal to have quasi-apo-enzyme and quasi-substrate-enzyme complex existing together. Is there any way to take care of such pathological condition during data processing, or structure solving? . I would highly appreciate your help and looking forward to get valuable advices. Please graduate me in this kind of weired situation. Thank you Appu

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