- phenixbb - phenix-online.org

Int'l Workshop on Macromolecular Crystallography - South America
by Alejandro Buschiazzo 26 Feb '10

26 Feb '10

Dear colleagues, just a reminder, we're close to the deadline for applications. Details below. Thank you! ----------------------------------------------------------------------------------------------------------------------- *International Workshop “Macromolecular Crystallography : Introduction and Applications"* *April 26 - May 7, 2010* *Institut Pasteur de Montevideo* *Uruguay* The principal aim of this course, is to give intense hands-on training in all main aspects of macromolecular 3D structure determination by X ray diffraction. The course will include lectures delivered by a number of international experts in the discipline, linked to hands-on experimental work and demonstrations. Special emphasis will be given to : * Experiment design : manual and robotic crystallogenesis of macromolecules, X ray diffraction of single crystals, data collection * Diffraction data processing * Model refinement and structural analysis *ACTIVITY INTENDED FOR* * Graduate Students (MSc and PhD) * Postdocs * Young Research Scientists *APPLICATION REQUIREMENTS* Candidates should send the following information : 1. -Short CV (including age, current position, scientific interests, publications) 2. -Letter of motivation (the applicant should stress how Macromolecular Crystallography is included in her/his ongoing scientific project) 3. -Reference letter from the apllicant's supervisor *SCHOLARSHIPS* Inscription fees are fully covered for all accepted students. Applicants from abroad with no financial support, are welcome to apply for a lodging and per diem expenses scholarship. This should be inlcuded as a separate document at the time of application. A limited number of traveling aids will be available: arguments backing this request should be duly explained, to be evaluated on a case by case basis. *APPLICATION DEADLINE* All applications should be received until March 7 2010. They should be sent as a single pdf document to : crystallography(a)pasteur.edu.uy *ORGANIZERS* Dr. Alejandro Buschiazzo Unidad de Cristalografía de Proteínas Institut Pasteur de Montevideo Dr. Pedro Alzari Departamento de Biología Estructural y Química Institut Pasteur de Paris Dr. William Shepard Proxima 2 Synchrotron Soleil For further information, please E-mail to crystallography(a)pasteur.edu.uy The official language of the course will be english. Detailed information is available at: http://www.pasteur.edu.uy/mxcourse Please check for regular updates of the program. *FUNDING* RIIP, AMSUD/PASTEUR, IP MONTEVIDEO (URUGUAY INNOVA), CeBEM This International Workshop is part of the activities of the Center of Structural Biology of Mercosur (Centro de Biología Estructural del Mercosur - CeBEM) -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5224185

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Which is the website to check if we have a good r free value?
by Sam Stampfer 26 Feb '10

26 Feb '10

Hi, Does anyone know which website is the one where you can compare your pdb file to others of similar resolution to see whether your file has a good r free value for its resolution? Specifically, I have a 2.8 Angstrom resolution structure with an rfree of 24. Thanks, -Sam

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Re: [phenixbb] refinement of N-glycosylation
by Nathaniel Echols 25 Feb '10

25 Feb '10

On Feb 25, 2010, at 1:35 PM, Georg Mlynek wrote: > 2) From the command line everything is perfect now, but as I also want to know how to do this with the gui (version 1.6-289), I added the files BMA.cif file and the apply_cif_link.params together with my coordinates and the mtz in the Input files. But I get following error message: > > <image001.png> > > Is this a Bug? Probably. Could you please send me (not the list) the final configuration files created by phenix.refine from both the command-line and the GUI? thanks, Nat ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 NEchols(a)lbl.gov

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Re: [phenixbb] refinement of N-glycosylation
by Ling Qin 25 Feb '10

25 Feb '10

Dear Georg, Maybe you need to use quotation marks? I also have n-glycosylation and I in my .eff file there is: } apply_cif_link { data_link = "NAG-ASN" residue_selection_1 = "chain A and resname NAG and resid XXX" residue_selection_2 = "chain A and resname ASN and resid XXX" } Hope this is useful. Please correct me if I am wrong. Ling On Wed, Feb 24, 2010 at 1:13 PM, Georg Mlynek <georg.mlynek(a)univie.ac.at>wrote: > Dear All, > > > > I´m quite new to crystallography and I´m refining a structure with > ASN-NAG-NAG-BMA attached and already got help from Blaine who told me how to > do it, but I´m making a small mistake somewhere and can´t figure out what > I´m doing wrong. Must be just one paranthesis or so, I guess. > > In command line just for testing I put: > > phenix.refine refine_data.mtz refine_1-coot-1FrenumberedGlu.pdb > cif_link.params BMA.cif strategy=individual_sites+individual_adp > main.number_of_macro_cycles=2 --overwrite > > > > where I put in cif_link.params as suggested in the mailing list > http://www.phenix-online.org/pipermail/phenixbb/2009-November/002837.htmlwi… and without paranthesis at the beginning > > > > } > > apply_cif_link { > > data_link = NAG-ASN > > residue_selection_1 = chain A and resname NAG and resid 500 > > residue_selection_2 = chain A and resname ASN and resid 297 > > } > > apply_cif_link { > > data_link = BETA1-4 > > residue_selection_1 = chain A and resname NAG and resid 500 > > residue_selection_2 = chain A and resname NAG and resid 501 > > } > > apply_cif_link { > > data_link = BETA1-4 > > residue_selection_1 = chain A and resname NAG and resid 501 > > residue_selection_2 = chain A and resname BMA and resid 502 > > } > > apply_cif_link { > > data_link = ALPHA1-3 > > residue_selection_1 = chain A and resname BMA and resid 502 > > residue_selection_2 = chain A and resname MAN and resid 503 > > > > and suggested by Blaine with and without paranthesis at the beginning > > > > refinement.pdb_interpretation.apply_cif_link { > > data_link = NAG-ASN > > residue_selection_1 = chain A and resname NAG and resid 500 > > residue_selection_2 = chain A and resname ASN and resid 297 > > } > > refinement.pdb_interpretation.apply_cif_link { > > data_link = BETA1-4 > > residue_selection_1 = chain A and resname NAG and resid 500 > > residue_selection_2 = chain A and resname NAG and resid 501 > > } > > refinement.pdb_interpretation.apply_cif_link { > > data_link = BETA1-4 > > residue_selection_1 = chain A and resname NAG and resid 501 > > residue_selection_2 = chain A and resname BMA and resid 502 > > } > > refinement.pdb_interpretation.apply_cif_link { > > data_link = ALPHA1-3 > > residue_selection_1 = chain A and resname BMA and resid 502 > > residue_selection_2 = chain A and resname MAN and resid 503 > > > > I see in the .geo file that the residues are not bonded, and also in the > .eff file that these lines are not added there, which should be done I > guess, I put the info also direct into the .def file but I get the same > problem? > > > > By the way it shouldn´t matter which name I give to this file as long as > the extension is correct? > > > > Thank you very much and all the best, Georg. > > > > > > > > -----Ursprüngliche Nachricht----- > Von: phenixbb-bounces(a)phenix-online.org [mailto: > phenixbb-bounces(a)phenix-online.org] Im Auftrag von Ursula Schulze-Gahmen > Gesendet: Dienstag, 23. Februar 2010 19:20 > An: phenixbb(a)phenix-online.org > Betreff: [phenixbb] weights optimization, add hydrogens > > > > I am refining a 2.0 A structure in Phenix using mostly the graphical > > interface. The maps are very good and the R factors are low > > (0.208/0.173). But the geometry is not so great with bond deviations of > > 0.208 and Angle deviations of 1.85. What is the best thing to do to try > > to improve the geometry. Should I try to optimize the weights? > > > > The other question is about adding hydrogens to the model. I did add > > them in a previous refinement cycle. After rebuilding the model in coot, > > most of the model still has the hydrogens in the input file for the next > > refinement cycle, but some residues and waters don't have hydrogens. > > When I tried to add hydrogens again to the model, I got an error message > > about atoms being to close. Does Phenix know where to add hydrogens if > > the input model has already hydroegns on many residues? > > > > > > Thanks > > > > Ursula > > > > -- > > Ursula Schulze-Gahmen, PhD. > > QB3, Tjian Lab > > MCB, 16 Barker Hall #3204 > > University of California Berkeley > > Berkeley, CA 94720-3204 > > Phone: (510) 642 8258 > > uschulze-gahmen(a)lbl.gov > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > >

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Re: [phenixbb] refinement of N-glycosylation
by Ralf W. Grosse-Kunstleve 24 Feb '10

24 Feb '10

> I?m quite new to crystallography and I?m refining a structure with > ASN-NAG-NAG-BMA attached and already got help from Blaine who told me how to > do it, but I?m making a small mistake somewhere and can?t figure out what > I?m doing wrong. Must be just one paranthesis or so, I guess. > > In command line just for testing I put: > > phenix.refine refine_data.mtz refine_1-coot-1FrenumberedGlu.pdb > cif_link.params BMA.cif strategy=individual_sites+individual_adp > main.number_of_macro_cycles=2 --overwrite Did you get an error message? If not, look in the .eff file for your "apply_cif" definitions. If they don't appear there something went wrong. The file name doesn't matter at all, not even the extension, but it is important that the syntax is correct. To run the syntax check only: iotbx.phil cif_link.params Ralf

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weights optimization, add hydrogens
by Ursula Schulze-Gahmen 24 Feb '10

24 Feb '10

I am refining a 2.0 A structure in Phenix using mostly the graphical interface. The maps are very good and the R factors are low (0.208/0.173). But the geometry is not so great with bond deviations of 0.208 and Angle deviations of 1.85. What is the best thing to do to try to improve the geometry. Should I try to optimize the weights? The other question is about adding hydrogens to the model. I did add them in a previous refinement cycle. After rebuilding the model in coot, most of the model still has the hydrogens in the input file for the next refinement cycle, but some residues and waters don't have hydrogens. When I tried to add hydrogens again to the model, I got an error message about atoms being to close. Does Phenix know where to add hydrogens if the input model has already hydroegns on many residues? Thanks Ursula -- Ursula Schulze-Gahmen, PhD. QB3, Tjian Lab MCB, 16 Barker Hall #3204 University of California Berkeley Berkeley, CA 94720-3204 Phone: (510) 642 8258 uschulze-gahmen(a)lbl.gov

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Phenix.ligandfit is not happy with my labels
by ucbccka 24 Feb '10

24 Feb '10

I am getting an error when trying to run phenix.ligandfit in the version phenix-1.6-289. I am trying to get it to use an mtz generated via refmac <recoils at the chorus of booooo's> and fit the ligand into the difference map. If I run phenix.ligandfit data=phaser_1.1_refmac1.mtz model=phaser_1.1_refmac1.pdb ligand=ATP.pdb It complains about my labels, saying.. ********************************* Sorry, input labels or map type unclear for phaser_1.1_refmac1.mtz For lig_map_type=pre_calculated_map_coeffs supply F and PHI (optionally FOM) (or 2FOFCWT and PH2FOFCWT) For lig_map_type=fo-fc_difference_map supply one column label for FP For lig_map_type=fobs_map supply one column label for FP Please specify which lig_map_type above you would like and also specify the necessary input column labels for your map like one of these samples: input_labels="FP" input_labels="2FOFCWT PH2FOFCWT" input_labels="FP PHIB FOM" ************************************* Looking at the documentation I tried getting PHENIX to tell me what labels it could see by running that autosol query and it kindly told me that my mtz file contained ************************ 'FreeR_flag' 'F_New' 'SIGF_New' 'FC' 'PHIC' 'FC_ALL' 'PHIC_ALL' 'FWT' 'PHWT' 'DELFWT' 'PHDELWT' 'FOM' ************************** so, I ran phenix.ligandfit data=phaser_1.1_refmac1.mtz model=phaser_1.1_refmac1.pdb ligand=ATP.pdb input_labels="DELFWT PHDELWT" and got the original message complaining that my labels are unclear. I even used the GUI, it recognises all the pairs of labels giving me the options to look at each map if I want and then..... complains that my labels are unclear. Clearly my labels are unclear, but I am now unclear how to proceed. If anyone could suggest something please then I would be most appreciative. Clearly. cheers

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Technology Specialist Position, Lawrence Berkeley National Laboratory
by Paul Adams 23 Feb '10

23 Feb '10

We are seeking a structural biologist technology specialist to research, document, and communicate new technologies to the scientific community. This project is part of the NIH-funded Protein Structure Initiative (PSI) Knowledgebase. The position requires interactions with other groups in the Knowledgebase, members of the Protein Data Bank, researchers at NIH-funded PSI centers, scientific journals, and the broader biological research community. The successful candidate will work under the direction of the Principal Investigator for this project. Primary duties and responsibilities are promoting new PSI- developed technologies to the broader scientific community, and maintaining and further developing a web portal describing these technologies. The successful candidate will need to be able to produce attractive online content, and have good scientific writing /proof reading skills. There is also a large community outreach element to the role, including presentations at meetings, the answering of questions via email, and the possibility of establishing an online forum. Additional tasks may include setting up a SVN software repository, and other online tools which will be of assistance to the structural biology community. Qualifications: B.S., M.S., Ph.D. or equivalent in a scientific discipline, preferably structural biology, biology, or chemistry. Demonstrated experience of scientific research using either computation or instrumentation. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Excellent spoken and written English skills are essential. Familiarity with scripting languages such as Python. Experience with maintaining web sites. To apply: visit http://cjo.lbl.gov/ and search for the keyword PSI or the job number 24114. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. -- Paul Adams Acting Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Patty Jimenez [ PAJimenez(a)lbl.gov ] [ 1-510-486-7963 ] --

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metal ion
by chene＠umbi.umd.edu 19 Feb '10

19 Feb '10

Dear Phenix users, My question may have been asked before. I am refining a structure containing calcium ions. I am wondering if the program considers it to be divalent Ca++ or neutral calcium atom. It seems that the ion and neutral atom have different atomic scattering factors. Thanks Chen 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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Re: [phenixbb] riding model and deposition
by Alex Theodossis 18 Feb '10

18 Feb '10

Dear Pavel, thank you for your comments. Alex

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omit map with twinning?
by Kelly Daughtry 18 Feb '10

18 Feb '10

Hello all, The omit_map in the new gui (version 1.5) is great, but I can not include a twin law when calculating the omit map, thus the result is very messy unclear maps. I do not know if 1.6 has the solution or not, I am still lobbying our computer guy to upgrade to it... Is there a way from the command line i can include the twin law in autobuild so I can calculate the omit map, or can I just add it into the eff file? My other solution has been to use the create maps function with my data and pdb with ligand removed. This works, giving me a nice Fo-DFc map, but it would be nice to be able to show a true omit map for the ligand, as is customary in most structure papers I have run across. Thanks in advance for any help you can provide! Kelly ******************************************************* Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 617-358-5548 *******************************************************

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riding model and deposition
by Alex Theodossis 18 Feb '10

18 Feb '10

Dear phenixbb, I have refined a 1.3A structure using individual anisotropic B-factors (Rfactor, 15.5%; Rfree, 17.7%). Additional use of the riding model during refinement has improvement the R values (Rf, 14.5%; Rfree, 16.6%), although bond length and angle outliers did increase (anyone know why that would be?). I have decided to deposit the model obtained using the riding model, but am unsure whether to include the hydrogen coordinates in the deposition. The Phenix.refine documentation advises that they are left in, as they are needed to reproduce the refinement statistics. However, reviewing the high resolution structures in the PDB I found that: 1. In the case of structures refined using REFMAC or SHELX, the riding model does not seem to be included, although its use during refinement is mentioned in the pdb header. 2. In the case of structures refined using PHENIX, use of the riding model is sometimes indicated in the header, but hydrogen coordinates only appear to be included in the pdb in the case of structures refined to a resolution better than 1.3A. As far as I can understand the purpose of the riding model is to provide additional restraints for refinement, so as long as its use is made evident in the pdb header (and maybe the methods section of the publication) that should be enough. Inclusion of hydrogens in the model, when you can't see them seems inappropriate. Nevertheless, I would appreciate a more authoritative perspective on this issue. Thank you in advance, Alex Theodossis

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refinement error with ligand
by Christian Roth 17 Feb '10

17 Feb '10

Dear all, I started a refinement of one of my structures using the GUI of phenix (Version 1.6). I used the options of adding hydrogens and dis a suimulated annealing. I used the output file and corrected it manually using Coot. I incorporated a few Ethylenglycol Monomers which might have bound. I merged everything wrote the file out and loaded this pdb in the GUI. I got an error which might be du to the fact that I didnt specify a CIF file for the ligand. I started ready set from the GUI to check the pdb and used REEL to create a CIF File. I added the CIF-File to the File list and tried to start again phenix.refine using the hydrogen option but no sim. annealing. However I got always the following error log: # Date 2010-02-17 Time 12:00:35 CET +0100 (1266404435.31 s) #phil __OFF__ Command line arguments: "/homes/roth/clcf/049b32mlsyncref/phenix/phenix/project_data/refine_15.eff" "-- overwrite" HOST = bbzws339 HOSTTYPE = i486-linux VENDOR = intel USER = roth PID = 29983 ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.6 Release tag: 289 Platform: intel-linux-2.6 linux User: roth ------------------------------------------------------------------------------- phenix.refine: Macromolecular Structure Refinement Monomer Library directory: "/software/linuxsoft/phenix-1.6-289/chem_data/mon_lib" Total number of atoms: 16881 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1575 Classifications: {'peptide': 94} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 87} and so on for other chains Chain: "R" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'EDO': 1} Unexpected atoms: {'EDO,HO1': 1, 'EDO,HO2': 1} Classifications: {'undetermined': 1} Number of atoms with unknown nonbonded energy type symbols: 16 "HETATM16821 HO2 EDO K 1 .*. H " "HETATM16826 HO1 EDO K 1 .*. H " "HETATM16828 HO2 EDO L 1 .*. H " "HETATM16834 HO1 EDO L 1 .*. H " "HETATM16836 HO2 EDO M 1 .*. H " "HETATM16840 HO1 EDO M 1 .*. H " "HETATM16842 HO2 EDO N 1 .*. H " "HETATM16848 HO1 EDO N 1 .*. H " "HETATM16850 HO2 EDO O 1 .*. H " "HETATM16857 HO1 EDO O 1 .*. H " ... (remaining 6 not shown) I looked in the pdb for this atoms, but I cannot find them. When I use a cif file created directly by phenix elbow using command line and when I did not use the update hydrogen button the refinement works. But the new residues as well as the EDO molecules have no hydrogens in riding positions. Do I have to remove all hydrogens and attach them again for every cycle? One Refinement runs for more then 5 hours regardless I use sim annealing or not. This seems to be very long for me. Maybe I want too many optimization steps? Could anyone explain me what goes wrong here. I am no so much experienced with phenix and now I run out of ideas. Thanks in advance Christian

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phenix.elbow and compound refinement
by YS. Chung 16 Feb '10

16 Feb '10

Dear all, I am having some difficulties in refining my compound within my structure. I was able to create the compound and the cif file using PRODRG and was able to fit it in coot perfectly fine. However, as pointed out by many users of phenix.refine, the cif file from PRODRG does not work well with phenix.refine. I have created a cif file using phenix.elbow and the refinement itself works fine. However, when I try to use the cif file from phenix elbow in coot, it pulls apart my compound and it's extremely difficult to work with. This still happens when I create the cif file using the --final_geometry option. Is there a way around this or is there something I can do? Any help will be much appreciated. Thank you, Yu Seon Chung

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refinement at 4.4 A => side chains or not
by jonathan elegheert 12 Feb '10

12 Feb '10

Dear bb, could anyone please share his/her opinion on following matter; I am refining a 4.4 A protein complex structure which I could solve using MR with the high resolution models of the separate components. I also have another 3.5 A crystal form of the complex. My question is whether or not to rebuild/leave "positionally known" side chains in the 4.4 A structure, because of course 2/3 of the time there is of course no density for it. However, a review of the PDB learnes that almost all models deposited between 4 and 5 A contain full side chains! Personally my opinion is not to include them because a model should be a representation of the information content of the experiment and thus density, but maybe that deviates from the consensus. On a more technical note: until now the trimming procedure has only sporadically led to Fo-Fc 'blobs' in the hydrophobic protein interior; are there proven modifications one has to apply to the bulk solvent model mask to avoid these even more? Thanks a lot for your insights, Jonathan -- Jonathan Elegheert Ph.D. Student Unit for Structural Biology& Biophysics http://www.lprobe.ugent.be/xray.html Lab for Protein Biochemistry and Biomolecular Engineering Department of Biochemistry& Microbiology Ghent University, Belgium e-mail: jonathan.elegheert(a)ugent.be

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multiple model refinement
by chene＠umbi.umd.edu 12 Feb '10

12 Feb '10

Hi, PHENIX users, Does anyone know if multiple model refinement is implemented in the latest version? I am using version 1.3. It was not implemented yet in that version. Thanks Chen 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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iMosflm .mtz
by anon 11 Feb '10

11 Feb '10

Hi, i was under the impression Phenix (AutoSol) could handle .mtz files from iMosflm, however when i input the .mtz file into AutoSol, no labels appears in the pull-down menu, and pressing Run results in a dialogue box appearing stating you must select a column label for the reflection file, if no labels are present it may not be a valid format. If i input the iMosflm .mtz file into phenix.reflection_file_editor, and copy over the I, SIGI, M_ISYM columns, i get the following error; A Python error was detected. This is probably a bug; click "OK" to send a bug report to the PHENIX developers. TypeError : not all arguments converted during string formatting Traceback (most recent call last): File "/usr/local/phenix-1.6-289/phenix/wxGUI2/MainWindow.py", line 880, in OnRun self.run() File "/usr/local/phenix-1.6-289/phenix/wxGUI2/Programs/ HKLTools.py", line 81, in run symmetry_callback=None) # TODO File "/usr/local/phenix-1.6-289/cctbx_project/iotbx/ reflection_file_editor.py", line 358, in __init__ "related reflections are not identical.)" % array_name) TypeError: not all arguments converted during string formatting When i use the scaled .mtz file produced by scala, AutoSol works fine. Just wondering what's going on! Also, how do you delete individual Jobs in the Job History window (ie jobs that have failed or you no longer want to keep etc) Thanks for the help

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phenix.refine frozen
by Roberto Steiner 11 Feb '10

11 Feb '10

Hi there, I would appreciate some feedback on the following: I am playing around with phenix.refine which comes with Phenix distro 1.6-289 for Mac-Intel. When running a normal refinement job (ind site + grouped ADPs + ncs+TorsionSimulatedAnnealing) phenix.refine gets stuck after bulk solvent modelling and scaling. The last things I see in the log page are: ====================== bulk solvent modeling and scaling ====================== |--(resolution: 3.50 - 58.55 A; n_refl. = 55140)------------------------------| | | | r_work= 0.2687 r_free= 0.2800 ksol= 0.38 Bsol= 10.09 scale= 1.148 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (-2.67,-2.67,5.34,0.00,0.00,-0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.41 A | | x-ray target function (ml) for work reflections: 7.216427 | | -----------------------------------------------------------------------------| ========================== Target weights: x-ray data ========================= and that's it. For completeness, I must report that I changed the defaults of wxc_scale and wxu_scale (but surely that cannot be the problem...). Switching off the TorsionSimAnnealing does not help. Additionally, if I click on the abort button on the bottom-left of the page nothing happens. On the other hand if I click on the abort icon at the top of the page I get the message "You are not currently running any calculations. Do you want to close this window?" If I say Ok the following message appears: "There is at least one process running; are you sure you want to exit before it is finished" Other tasks (phenix.xtriage for example) seem to run fine. Any suggestion? Best Roberto

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phenix.model_vs_data or something else for 'most disagreeable reflections' ?
by Francis E Reyes 10 Feb '10

10 Feb '10

Hi phenixer's I'm looking for a utility that'll calculate Fc given a refined model and compare it to Fo not on a global scale, but on an individual reflection scale. ShelX does this a reflection list of 'most disagreeable reflections'. Is this possible in phenix? Or another utility (besides shelx)? thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Re: [phenixbb] Omit map Problem
by Carruthers, Carl W. 09 Feb '10

09 Feb '10

Coot works fine. When I click the GUI button after the run, it loads the pdb file that I used as a start model and nothing else. When I try opening the composite map manually (using coot: "open mtz", "auto open mtz" or even "open map" ) it says at the bottom "read map /file path/ resolve_composite_map.mtz failed." Thanks again! Carl Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp and www.facebook.com/methodisthospital ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Omit map Problem
by Carruthers, Carl W. 09 Feb '10

09 Feb '10

When making an composite omit map in Phenix 1.6 GUI, the final "resolve_composite_map.mtz" file won't load in coot or pymol. When I click the little magnifying glass on the Summary page, Phenix states that it can't find the file, even though I can see it when using Finder (Mac OS). The final lines of the run status are below: Putting all omit results in AutoBuild_run_61_/OMIT OMIT results in AutoBuild_run_61_/OMIT : ['overall_best.pdb_OMIT_REGION_1', 'overall_best.pdb_OMIT_REGION_10', 'overall_best.pdb_OMIT_REGION_11', 'overall_best.pdb_OMIT_REGION_12', 'overall_best.pdb_OMIT_REGION_2', 'overall_best.pdb_OMIT_REGION_3', 'overall_best.pdb_OMIT_REGION_4', 'overall_best.pdb_OMIT_REGION_5', 'overall_best.pdb_OMIT_REGION_6', 'overall_best.pdb_OMIT_REGION_7', 'overall_best.pdb_OMIT_REGION_8', 'overall_best.pdb_OMIT_REGION_9', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_10', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_11', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_12', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_2', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_3', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_4', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_5', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_6', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_7', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_8', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_9', 'resolve_composite_map.mtz'] Combining all 12 omit regions in AutoBuild_run_61_/OMIT No background map in composite map Composite omit result is in /Users/carlcarruthers/Crystallography/AutoBuild_run_61_/OMIT/resolve_composite_map.mtz Possible operation: finished Required antecedents: [] Expected results: [] Application method: finished Yes, have antecedents... Resulting expectation:10000.0 Am I doing something wrong? Is it a bug? Thanks for helping a crystallogaophy newb (this is my first model!)... Carl Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp and www.facebook.com/methodisthospital ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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phenix.maps: a command line tool to compute various maps
by Pavel Afonine 04 Feb '10

04 Feb '10

Starting PHENIX nightly build version 1.6-295 (or whatever next version), the new command line tool phenix.maps is available. As the name suggests, this is the tool for map calculation: regular (p*Fobs-q*Fcalc) or maximum-likelihood (p*mFobs-q*DFcalc), with any user-defined coefficients p and q, as many as requested. For example, 2mFo-DFc, 3Fo-2Fc, mFo-DFc, Fc, Fo, Anomalous difference maps can be all computed at once. Also, a user has a full control over various map calculation parameters, such as filling missing Fobs with DFc, computing kick maps, etc. Maps can be output in X-plor formatted files or as Fourier map coefficients in MTZ formatted file. X-plor formatted maps can be computed for the whole molecule/unit cell or any selected part of the structure. This new tool is meant to be a replacement for current practice of computing the maps using phenix.refine (although, phenix.refine still output maps as before). For more information and usage examples simply run phenix.maps . This is available from PHENIX GUI too (thanks Nathaniel Echols). For usage instructions and quick manual type phenix.maps and hit Enter. Please let me know should any questions or problems related to using this tool arise. Pavel. P.S. Below is the result of running phenix.maps: phenix.maps: a command line tool to compute various maps. How to run: 1. Run phenix.maps without any arguments: just type phenix.maps in the command line and hit Enter. This will create a parameter file called maps.params, which can be renamed if desired. 2. Edit maps.params file to specify input/output files and the desired maps. It is possible to request as many maps as desired. 3. Run this command to compute requested maps: phenix.maps maps.params Remarks: - The scope of parameters 'map_coefficients' defines the map that will be output as Fourier map coefficients. The scope of parameters 'map' defines the map that will be output as X-plor formatted map. - To create several maps: duplicate either 'map_coefficients' or 'map' or both scopes of parameters as many times as many maps is desired. Then edit each of them to define the maps. - A map is defined by specifying a map type using 'map_type' keyword available within each scope of parameters: 'map_coefficients' or 'map'. The general supported format for 'map_type' is: [p][m]Fo+[q][D]Fc[kick][filled]. For example: 2Fo-Fc, 2mFobs-DFcalc, 3Fobs-2Fmodel, Fo-Fc, mfobs-Dfcalc, anom. The 'map_type' parser will automatically recognize which map is requested. - The program creates as many files with X-plor formatted maps as many X-plor formatted maps is requested, and it creates only one MTZ formatted file with all Fourier map coefficients in it. - The X-plor formatted map can be computed in the entire unit cell or around selected atoms only. - Kick maps and missing Fobs filling is done (if requested) as described in Adams et al. (2010). Acta Cryst. D66, 213-221. - Twinning (if detected) will be accounted for automatically. - All arrays used in map calculation, for example: Fobs, Fmodel, Fcalc, Fmask, m, D, etc., can be output into a CNS or MTZ formatted reflection file.

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Completeness issue by phenix - revisited
by J. Fleming 03 Feb '10

03 Feb '10

Hi, I'm having a problem using phenix.refine with my x-ray data. My completeness is always 89% when it should be 99%. My data was originally processed with CCP4i. I found an old post (see below) with a potential fix that doesn't work for me. I've tried changing the 'Anomalous flag: True' to 'Anomalous flag: False' but my completeness is still 89%. I've clicked through a variety of other setting in the GUI that I thought would help but no luck. Does anyone have any ideas? Thanks in advance, Jon ----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov <http://www.phenix-online.org/mailman/listinfo/phenixbb>> To: phenixbb at phenix-online.org <http://www.phenix-online.org/mailman/listinfo/phenixbb> Sent: Monday, December 15, 2008 12:59:12 PM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Completeness issue by phenix Hi YoungJin, I suspect phenix.refine decided your mtz file contains anomalous data when you actually have non-anomalous data. Could you look in the phenix.refine output for something like this: ================================== X-ray data ================================= F-obs: 1yjp.mtz:FOBS_X,SIGFOBS_X R-free flags: 1yjp.mtz:R-free-flags Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X Observation type: xray.amplitude Type of data: double, size=495 Type of sigmas: double, size=495 Number of Miller indices: 495 Anomalous flag: False ^^^^^ in particular here If you see "Anomalous flag: True" try adding this to the phenix.refine command line: xray_data.force_anomalous_flag_to_be_equal_to=False Let me know if this doesn't help. If it does help, I'd be interested to know how the .mtz file was generated. Ralf

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BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY
by Cyndi Salbego 02 Feb '10

02 Feb '10

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. Beamline 24ID-C: Equipped with MD2 microdiffractometer, tunable between 6-21KeV, ADSC Q315 Detector, MAD Capable. Outfitted with ALS-style robot that can use ALS pucks or Unipucks. Beamline 24ID-E: Equipped with MD2 microdiffractometer, delivering beam as small as 5 microns. Single energy (12662eV) optimized for Se-SAD experiments, ADSC Q315 Detector. Outfitted with ALS-style robot that can use ALS pucks or Unipucks. For more information on our beamlines (beamline and robot manuals) along with updated schedule availability please see: http://necat.chem.cornell.edu or contact Cyndi Salbego (csalbego(a)anl.gov) for further information. To apply for General User Time (Rapid Access for current run cycle) please follow this link: https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page Cyndi Salbego Administrator, NECAT 630.252.0689

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AUTOSOL for MAD data with error message-'Need a symfile for solve'
by m.b.rajasekaran＠reading.ac.uk 02 Feb '10

02 Feb '10

Dear all, I have a query regarding the Autosol option in the PHENIX-1.6-289 version. We are trying to process a MAD data for a zinc bound protein crystal with AuTOSOL. We uploaded the scaled files, sequence and all other details and started running AUTOSOL. But the program stopped with the following error message pasted below mentioning some missing of symfile. We were not able to locate any parameters file on the installation directory. It would be helpful if we get some useful suggestions on this. Thanks in advance, Mohan *********************************************************** PHENIX AutoSol Tue Feb 2 12:37:41 2010 ************************************************************ Working directory: /home/sar06mbr/30JanDiamondI02/107/107_php22121 PHENIX VERSION: 1.6 of 29-01-2010 PHENIX RELEASE_TAG : 289 PHENIX MTYPE : intel-linux-2.6 PHENIX MVERSION : suse AutoSol_start AutoSol Run 2 Tue Feb 2 12:37:41 2010 INPUT FILE LIST: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] Copied /home/sar06mbr/30JanDiamondI02/107/107_php22121/result.seq to /home/sar06mbr/30JanDiamondI02/107/107_php22121/AutoSol_run_2_/sequence_autosol.dat Setting chain_type to PROTEIN Setting defaults for data_quality moderate Setting thorough_denmod to Yes Settin fix_xyz_after_denmod to False Setting max_ha_iterations to 2 Setting fixscattfactors to No Settin defaults for thoroughness quick Setting best_of_n_hyss_always to 1 Setting max_extra_unique_solutions to 0 Settin ha_iteration to No Setting max_choices to 1 Setting number_of_models to 1 Setting number_of_builds to 1 Setting test_mask_type to No Setting n_cycle_build to 0 Setting thorough_loop_fit to Setting create_scoring_table to No Not truncating ha sites at start of resolve as this is not PHASER SAD phasing Trying to guess refinement file for later use from ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] Choosing guess of refinement file for later use from all files: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re', 'SIGF_107_2re', 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)', 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', 'SIGIMEAN_107_2re', 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)'] GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space group: P 2 21 21 (No. 18) CONTENTS: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344, 108.92009735107422, 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1', 'SIGF1', 'DANO1', 'SIGDANO1']] File /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz RES: 2.5 FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_3re', 'SIGF_107_3re', 'F_107_3re(+)', 'SIGF_107_3re(+)', 'F_107_3re(-)', 'SIGF_107_3re(-)', 'DANO_107_3re', 'SIGDANO_107_3re', 'IMEAN_107_3re', 'SIGIMEAN_107_3re', 'I_107_3re(+)', 'SIGI_107_3re(+)', 'I_107_3re(-)', 'SIGI_107_3re(-)'] GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell: (34.85, 109.18, 135.27, 90, 90, 90) Space group: P 2 21 21 (No. 18) CONTENTS: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', 'mtz', 'premerged', 'P 2 21 21', [34.849998474121094, 109.18000030517578, 135.26980590820312, 90.0, 90.0, 90.0], 2.4889952912293629, ['F1', 'SIGF1', 'DANO1', 'SIGDANO1']] File /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz RES: 2.5 FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_4re', 'SIGF_107_4re', 'F_107_4re(+)', 'SIGF_107_4re(+)', 'F_107_4re(-)', 'SIGF_107_4re(-)', 'DANO_107_4re', 'SIGDANO_107_4re', 'IMEAN_107_4re', 'SIGIMEAN_107_4re', 'I_107_4re(+)', 'SIGI_107_4re(+)', 'I_107_4re(-)', 'SIGI_107_4re(-)'] GUESS FIL TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell: (34.87, 109.2, 135.33, 90, 90, 90) Space group: P 2 21 21 (No. 18) CONTENTS: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz', 'mtz', 'premerged', 'P 2 21 21', [34.869998931884766, 109.19999694824219, 135.32989501953125, 90.0, 90.0, 90.0], 2.4890134311310943, ['F1', 'SIGF1', 'DANO1', 'SIGDANO1']] File /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz RES: 2.5 Guess of datafile for refinement: /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz Using /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz for refinement Specify input_refinement_file=/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz to change this HKLIN ENTRY: /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re', 'SIGF_107_2re', 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)', 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', 'SIGIMEAN_107_2re', 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)'] GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space group: P 2 21 21 (No. 18) CONTENTS: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344, 108.92009735107422, 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1', 'SIGF1', 'DANO1', 'SIGDANO1']] Inverse hand of space group: P 2 21 21 Creating sg entry from /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space group: P 2 21 21 (No. 18) Space group name is: P 2 21 21 symbol is: p22121 **************************************** AutoSol Input failed Need a symfile for solve ****************************************

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