- phenixbb - phenix-online.org

Re: [phenixbb] Map after refinement
by Xuewu Zhang 26 Feb '10

26 Feb '10

Hi Phenix developers/gurus, I got a SAD structure, the experimental map (overall_best_denmod..mtz) from Autosol looks great. I then built the model and used phenix.refine to refine the model using the "exptl_fobs....mtz", which worked well as shown by the lowered Rfree. However, the map from the refinement makes no sense at all, totally featureless. Using the same refined model and mtz, phenix.model_vs_data did make the right map. I have tried both phenix 1.5 and 1.6. Any clue? Thanks, Xuewu Zhang UT Southwestern Medical Center

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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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