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refinement of a ligand with alternate conformations in one region but not the other.
by Pascal Egea 26 May '09

26 May '09

Dear All, I am refinining a protein-NAD complex structure at ~1.9A resolution. I have included a main conformation for my NAD ligand but while I see clearly the position for the nicotinamide- first ribose part, my density bifurcates when it comes to the second ribose-adenine. It seems that I have two (at least) conformations for this part of the ligand molecule. Can I refine these two alternate conformations in Phenix knowing that a part of the ligand will be common (have an occupancy of one) while the two other ones will be separate? Do I need to enter two ligand molecules or do I have to do more elaborate things? Last question is it possible that for the variable regions I may end up with a sum of occupancies that is not 1 while for the fixed region it might end up being one? That's three questions for the wizards. Thanks in advance. Pascal Egea UCSF

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Attaching H onto phosphate group and ATP
by Young-Jin Cho 26 May '09

26 May '09

Hello phenix users, I am wondering if phenix.elbow can attach H onto phosphate group for refinement. The reason for that, based on different pH environment, phosphate group should have different charges with respect to how many protons attached. In addition, how can I know normal distance restraints such as ATP? What I only know from the coot is that it shows P-O bond length is 1.61A and P-O bond (delocalized double bond) is 1.5A. The reason for this is, I heard about phosphate ion, if it is protonated, then the bond length of HO-P is longer than that of non-protonated O-P. I want to try if is true for ATP as well. Is there anyone who knows practically testing this fact by using phenix? Thanks in advance, YoungJin

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turbo frodo
by Zhongli Cui 22 May '09

22 May '09

Dear all, I think turbo frodo is a very good software for modelling. I tried to get a licence key from turbo(a)afmb.cnrs-mrs.fr, but got no reply. I would like to know if this software is still in support. Thank you. ---------------- Cui Zhongli Professor, Ph.D Dept. of Microbiology College of Life Sciences Nanjing Agricultural University 1 Weigang, Nanjing, 210095 Jiangsu Province P.R. China. Mail: czl(a)njau.edu.cn Tel: 86-25-84396753 Mob: (0)13951080529

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Autobuild error (ligands)
by Katya Heldwein 21 May '09

21 May '09

Hi, I'm using autobuild in phenix-1.4-59 to rebuild the structure. Autobuild throws the error: **************************************** AutoBuild Input failed Sorry, the generation of cif files from AutoBuild_run_2_/TEMP0/LIGANDS.pdb did not work. Error message was: 'NoneType' object has no attribute 'id' **************************************** I think this may have to do with carbohydrates that I have in the structure. I provided the .eff and the .cif files for the carbohydrates but something must be going wrong. Could you, please, let me know how to troubleshoot this error? Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

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Occupancies
by AMIT 20 May '09

20 May '09

Hello I am new to phenix. I am tring to refine the occupancies using the phenix.refine gui. In the refinement settings- refinement strategy : occupancies , when I define the groups for individual atoms as chain A and resseq 1:200 (for protein atoms) and a ligand group in constrained as chain B and resseq 1:10 and chain C and resseq 1:10, the refinement fails with several errors. The refinement runs fine when I do not touch the "occupancies" panel on the gui. How do I refine in Phenix the occupancies defining as well as partitioning the molecule as individual, groups and coupled groups? Thanks in advance, Amit -- AMIT DAS, PROTEIN CRYSTALLOGRAPHY SECTION, SOLID STATE PHYSICS DIVISION, BARC, TROMBAY, MUMBAI-400085. INDIA. Alt E-mail:[email protected] <E-mail%3Aamitdas(a)barc.gov.in> PHONE:+91-22-25594688/4063 FAX:+91-22-25505151

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Autobuild error
by Katya Heldwein 20 May '09

20 May '09

Hi, I am trying to run Autobuild to generate a very good rebuilt model using phenix.autobuild data=data.mtz model=coords.pdb multiple_models=True \ include_input_model=True \ multiple_models_number=1 n_cycle_rebuild_max=5 with some modifications. When I run it, I get the following error: ******************************************************************************** Failed to carry out AutoBuild_multiple_models: [Errno 2] No such file or directory: 'AutoBuild_run_1_/TEMP0/temporary.com' ******************************************************************************** How can I troubleshoot this problem? Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

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BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY
by Cyndi Salbego 20 May '09

20 May '09

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. Beamline 24ID-C: Equipped with MD2 microdiffractometer. Variable energy between 6-18keV, ADSC Q315 Detector, MADCapable. Sample Robot. Beamline 24ID-E: Equipped with MD2 microdiffractometer, delivering beam as small as 5 microns. Single energy (12662eV), ADSC Q315 Detector. Contact csalbego(a)anl.gov for further details.

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creating map file only
by Raja Dey 15 May '09

15 May '09

Dear Friends, I was trying to create map file only as follows: phenix.refine 1205A-p21212.mtz may15_1_001.pdb map.params strategy=none output.prefix=may15_2 , map.params is as follows refinement { electron_density_maps { map { mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT likelihood_weighted = True obs_factor = 2 calc_factor = 1 } map { mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT likelihood_weighted = True obs_factor = 1 calc_factor = 1 } map { mtz_label_amplitudes = 3FO2FCWT mtz_label_phases = PH3FO2FCWT likelihood_weighted = False obs_factor = 3 calc_factor = 2 } grid_resolution_factor = 1/4. region = *selection cell atom_selection = name CA or name N or name C apply_sigma_scaling = False apply_volume_scaling = True } } But, still I am getting only the map_coeffs.mtz file in the output. I am expecting 3 map files in the output. Could you please tell what's wrong I am doing. I want to create only the map file without any refinement. Looking forward to hearing from you... Regards... Raja

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Beamtime proposal deadline for ALS GU time
by Peter Zwart 15 May '09

15 May '09

May 15, 2009 is the deadline for the July-August Rapid Access Proposal cycle. Please note that the ALS will be shut down in September, 2009. The deadline for applications of beamtime on the BCSB beamlines in the ALS is today! Other notable features include: * A high-accuracy microdiffractometer on BL 8.2.1 allows for centering and viewing of very small crystals; * Robot automounters on BL8.2.1 and 8.2.2 are now fully commissioned. * A new large format (315mm active surface area) CCD detector on BL 8.2.1 facilitates data collection on large unit cell crystals. * Beamlines 5.0.1 and 5.0.3 now generate 1.5x1011 photons per second at 0.97 Angstrom. This wavelength is slightly above the Se K edge making them ideal for performing Se SAD experiments. * Beamline 5.0.2 (a tunable beamline) generates a peak flux of 8x1011 photons per second, and the energy range of 5.0.2 has been extended to 17 keV, enabling the routine use of shorter wavelengths and anomalously scattering elements such as bromine. All beamlines of the BCSB (5.0.1, 5.0.2, 5.0.3, 8.2.1 and 8.2.2) can all be operated remotely. Please contact Peter Zwart (sector 5 beamlines) or Corie Ralston (sector 8 beamlines) for more information. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. To find out more, click on: http://www.als.lbl.gov/als/quickguide/independinvest.html Scroll down to "Structural Biology and SAXS." We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize If you'd like to apply for October-November-December beamtime at the Advanced Light Source, please submit a General User proposal by August 15, 2009. If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime. Cheers, Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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March 15, 2009 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 14 May '09

14 May '09

Dear Users, The deadline for July/August 2009 Collaborative Crystallography proposals will be May 15, 2009. ============= Thumbnail Description: Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ============= How To Apply: To submit a proposal, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html Scroll down to "Structural Biology and SAXS" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only ?) * In question 9, please describe a specific research project with a clear end point. In order to request CC time for July/August 2009allocation period, proposals must be submitted by *May 15, 2009*. Please note that the ALS will be shut down in September, 2009. The deadline for CC proposals for the time period October/November/December 2009 will be August 15, 2009. Regards, Banumathi Sankaran

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