- phenixbb - phenix-online.org

phenix and PAE kernels
by nick＠silvaggi.com 15 Jun '09

15 Jun '09

Dear List, Sorry if this is a naive question, but is there a known bug with phenix (or python?) on PAE kernels? I have looked on phenix-online.org, but did not find anything. This problem is independent of the phenix version (I have tried 1.4-92, 1.4-3, 1.3, and several releases of cci_apps) and occurs with almost all of the programs (most fail in the cci_apps test_apps script). The problem appears to be specific to the PAE kernels, since the same programs run fine in the non-PAE counterparts. I am running Fedora 10 with kernel versions 2.6.27.24-170.2.68/PAE and 2.6.27.21-170.2.56/PAE. Phenix programs fail under both PAE kernels, but are fine under the non-PAE kernels. Thanks in advance for any help you can provide. Best regards, Nick Silvaggi long int too large to convert Traceback (most recent call last): File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/builder.py", line 10, in <module> from elbow.chemistry.any_chemical_format_reader \ File "/usr/swr/cci_apps/cci_apps_sources/elbow/elbow/chemistry/any_chemical_format_reader.py", line 3, in <module> File "/usr/swr/cci_apps/cci_apps_sources/elbow/elbow/chemistry/SimpleMoleculeClass.py", line 16, in <module> File "/usr/swr/cci_apps/cci_apps_sources/elbow/elbow/utilities/monomer_utilities.py", line 2, in <module> File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 4, in <module> File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 3, in <module> File "/usr/swr/cci_apps/cci_apps_sources/mmtbx/mmtbx/refinement/print_statistics.py", line 2, in <module> File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 1, in <module> # packaging File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 518, in <module> File "/usr/swr/cci_apps/cci_apps_sources/boost_adaptbx/boost/python.py", line 68, in __init__ OverflowError: long int too large to convert

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phenix refine
by sbiswas2＠ncsu.edu 12 Jun '09

12 Jun '09

Hi all, I tried running phenix refine with a pdb file refined in cns. This has a glycerol molecule in it. I got the following message: Number of atoms with unknown nonbonded energy type symbols: 42 "ATOM 6921 OAA GLC J 1 .*.J " "ATOM 6922 CAD GLC J 1 .*.J " "ATOM 6923 CAF GLC J 1 .*.J " "ATOM 6924 OAC GLC J 1 .*.J " "ATOM 6925 CAE GLC J 1 .*.J " "ATOM 6926 OAB GLC J 1 .*.J " "ATOM 6927 OAA GLC J 2 .*.J " "ATOM 6928 CAD GLC J 2 .*.J " "ATOM 6929 CAF GLC J 2 .*.J " "ATOM 6930 OAC GLC J 2 .*.J " ... (remaining 32 not shown) Time building chain proxies: 11.79, per 1000 atoms: 1.69 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown scattering type symbols: 42 Number of atoms with unknown nonbonded energy type symbols: 42 Does anyone know how to resolve this thanks, Shya

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phasine error
by vennila Natesan 11 Jun '09

11 Jun '09

Dear members I am having solved strcutures for some five datasets of the same protein. All the cases autobuild builds ~97% of residues. I want to compare the phasing among those. Can we calculate the phasing error in the units of degrees in autosol? In all the cases, the Bayesian CC is between 45 and 56 and FOM is between 0.42 and 0.47.Is there any option in phenix to know the phasing error in degrees?

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not enough memory error in Resolve/AutobuildWizard
by Tatyana Sysoeva 10 Jun '09

10 Jun '09

Hello! I'm trying to run AutobuildWizard on distant computer cluster. Runs failed. In Autobuild log file there is a message: *TRIED resolve_giant ...NEED A BIGGER VERSION... TRIED resolve ...NEED A BIGGER VERSION... TRIED resolve_giant ...NEED A BIGGER VERSION... TRIED resolve_huge ...NEED A BIGGER VERSION... child process stderr output: command: 'AutoBuild_run_1_/TEMP0/temporary.com' Sorry, not enough memory for RESOLVE ---------------------------------- TRIED resolve_extra_huge ...but not OK ******************************************************************************** Failed to carry out AutoBuild_set_up_build: ******************************************************************************** * Some Autobuild runs were ok, some stopped with that error message. What am I doing wrong? I installed Phenix1.4-3, locally to my home folder, run it from script file in queue. As I found this Linux computer cluster has next parameters - 1 login node: -Sun SunFire v20z 1U Rackmount Box -Dual 2.4 GHz AMD Opteron Processors -8 GB of ECC RAM Could you advise something to start with to find a problem? Sincerely, Tanya

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Water/residue alternative conformations
by Roeland Boer 08 Jun '09

08 Jun '09

Dear all, I'm refining a 1.45 Ang structure in which I have several residues that have alternate conformations. These alternate conformations in some cases coincide with additional density that suggests the presence of a water molecule, appropriately positioned to make hydrogen bonds with near atoms. I have modeled partially occupied waters in these additional densities and linked their occupancies with the alternate conformation that is not clashing with the water in question. My problem is that these partially occupied waters are pushed away by the 'overlapping' alternate conformation of the amino acids. I guess there's an antibump restraint somewhere? How can I tell phenix that these alternate waters are not sterically clashing with the amino acid (since the sum occupancies of the water plus alternate conformation is 1)? The attached image shows one of those disordered residues after refinement. Water 1519 is pushed away from one alt conf (A) of Gln13, whereas the density suggests it should be making a hydrogen bond to OE1 of the altconf B of Gln13. I describe the occupancies of the situation in the attached image as below. refinement { refine { occupancies { constrained_group { selection = chain A and resseq 13 and altloc A selection = (chain A and resseq 13 and altloc B) or (resname HOH and resseq 1519 and altloc A) } } } } Thanks, Roeland Boer.

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Re: [phenixbb] autosol error 1.4-3 when trying to specify deriv.inano=noinano
by Thomas C. Terwilliger 07 Jun '09

07 Jun '09

Hi Francis, Thanks again for the files. They did help me debug the autosol wizard for this case. It turns out that on the command line you cannot say something like, native.data=nat.mtz native.labels="I SIGI" \ deriv.data=deriv.mtz deriv.labels="I+ SIGI+ I- SIGI-" deriv.inano=inano because only the first native.something= gets read, the others are ignored, and similarly only the first deriv.something= gets read. instead all this has to go in a parameters file, and then it all works fine. I have adjusted the wizard to catch this situation and to stop and tell the user that they need to use a parameters file to set more than one parameter in the native, deriv, or wavelength scopes. All the best, Tom T

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coordinates and map shifted after phenix.refine without simulated annealing
by hari jayaram 06 Jun '09

06 Jun '09

Hi i am using phenix version 1.4 release tag 70 hari@charlie:~$ phenix.refine --version ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.4 Release tag: 70 Platform: intel-linux-2.6-x86_64 linux User: hari ------------------------------------------------------------------------------- I am seeing a strange shifting of my coordinates "out of my experimental phases map" before and after refinement without simulated annelaing I am at the final stages of my refinement. When I refine without simulated annealing the resulting model is shifted relative to my experimental phases map into which I build my model The phenix command line strategy i am using are rigid_body+individual_sites+individual_adp+tls .or the same strategy with simulated_annealing=true The output map coefficients fortunately match my model in both cases . But I am wondering why there is a difference. I am using the mlhl target for refinement to 3.1 A , My R and rfree is 28/31 . Any ideas why my model shifts without simulated annealing . All pdbs have the same CRYST record . I am using coot version 0.61 for my building and map display using fft inside of coot . hari

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Re: [phenixbb] coordinates and map shifted after phenix.refine without simulated annealing
by Thomas C. Terwilliger 06 Jun '09

06 Jun '09

Hi Hari, What is your space group? I am guessing that the shift is along an axis where the origin is not fixed, for example the b axis in P21. This could happen with rigid-body refinement where a molecule can move as a whole so that the center of mass could move along that axis. Perhaps someone else can comment as to whether there is or could be an optional term in phenix.refine to maintain the center of mass at the same coordinate in such cases. All the best, Tom T >> Hi i am using phenix version 1.4 release tag 70 >> >> hari@charlie:~$ phenix.refine --version >> ------------------------------------------------------------------------------- >> PHENIX: Python-based Hierarchical ENvironment for Integrated >> Xtallography >> Version: 1.4 >> Release tag: 70 >> Platform: intel-linux-2.6-x86_64 linux >> User: hari >> ------------------------------------------------------------------------------- >> >> >> I am seeing a strange shifting of my coordinates "out of my experimental >> phases map" before and after refinement without simulated annelaing >> >> I am at the final stages of my refinement. When I refine without simulated >> annealing the resulting model is shifted relative to my experimental >> phases >> map into which I build my model >> The phenix command line strategy i am using are >> rigid_body+individual_sites+individual_adp+tls .or the same strategy with >> simulated_annealing=true >> >> The output map coefficients fortunately match my model in both cases . But >> I >> am wondering why there is a difference. >> I am using the mlhl target for refinement to 3.1 A , My R and rfree is >> 28/31 >> . >> >> Any ideas why my model shifts without simulated annealing . All pdbs have >> the same CRYST record . >> I am using coot version 0.61 for my building and map display using fft >> inside of coot . >> >> >> hari >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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autosol error 1.4-3 when trying to specify deriv.inano=noinano
by Francis E Reyes 05 Jun '09

05 Jun '09

------------------------------------------------------------ Starting AutoSol with the command: phenix.autosol Reading effective parameters from autosol.eff The key inano is not in var_type_dict...this means the command-line Wizard needs a conversion in the autosol.py script under 'Translating inputs' or else in excluded_inputs(['write_run_directory_to_file', 'carry_on', 'run', 'copy_run', 'delete_runs', 'display_runs', 'display_facts', 'display_summary', 'display_labels', 'coot', 'dry_run', 'stop', 'params_only', 'sites', 'atom_type', 'sites_file', 'seq_file', 'quick', 'data', 'f_prime', 'f_double_prime', 'labels', 'sites', 'atom_type', 'peak', 'infl', 'high', 'low', 'remote', 'native', 'deriv']) Any ideas? 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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Parallel Version of Phenix?
by Angelo Rossi 03 Jun '09

03 Jun '09

Hello Phenix Users and Developers: I am new to Phenix and am trying to help a colleague move his project using Phenix from a single workstation to a Linux cluster. My background is chemistry and high performance computing, but I am not intimately knowledgeable about the workings of Phenix. Are there parts of Phenix that can run on a Linux cluster in parallel. I understand that a good part of Phenix is written in python, but there are certainly numerically intensive aspects of structure refinement that could be amenable to parallelization. It would really help if you could provide an overview of those components that are now running in parallel. A search on the net did not reveal information about a parallel version of Phenix. Thank you for your attention and any possible help. Kind regards, A. R. Rossi

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Fixing coordinates in phenix.refine_gui
by AMIT 02 Jun '09

02 Jun '09

Hi All Is it possible to fix only the coordinates(xyz's) of residues or individual atoms in phenix.refine_gui while refining it for rest of the atoms? Any suggestions will be helpful. 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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mutate to polyAla in phenix.automr?
by Francis E Reyes 28 May '09

28 May '09

Is there an option or a phenix.* utility to mutate a MR model to poly ALA before the MR is done? 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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Failed to carry out AutoBuild_build_cycle: Word too long.
by Gino Cingolani 28 May '09

28 May '09

Hi Folks, does anybody know what this means? My AutoBuild dies off in the middle with this error message ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /home/gino/XTAL/SYN/V1/DASETs/Se3/SAD/REF/AutoBuild_run_2_/TEMP0/RUN_FILE_1' Word too long. ******************************************************************************** Thanks, Gino *********************************************************** Gino Cingolani, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology SUNY Upstate Medical University 750 E. Adams Street, Syracuse, NY, 13210 Tel. (315) 464 8744 Fax. (315) 464 8750 Email: cingolag(a)upstate.edu *********************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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covalently linked ligand
by Joerg Standfuss 27 May '09

27 May '09

Dear phenix users, I am currently building a model where the ligand is linked via schiff base to a lysine residue. To let phenix know about the link I provide the ligand.cif file and created the link parameter file as described in the manual. The type of link I defined with Jligand as it does not appear in the standard ccp4 library. Unfortunately phenix.refine stops with the error message below when I provide the so created files. It seems phenix has problems to apply the needed ligand modifications ie removing hydrogens and oxygens and stops with the refinement. I have no idea why this doesn't work and am getting a little desperate so any suggestions how to do this properly would be greatly appreciated. Could I use for example elBOW to create the link description? many thanks, Joerg File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/pdb_interpretation.py", line 499, in __init__ mod_mod_id=self.mon_lib_srv.mod_mod_id_dict[apply_data_mod]) File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/pdb_interpretation.py", line 771, in apply_mod mod_mon = self.monomer.apply_mod(mod_mod_id) File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/cif_types.py", line 339, in apply_mod result.delete_atom_in_place(mod_atom.atom_id) File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/cif_types.py", line 244, in delete_atom_in_place raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" % atom_id) RuntimeError: delete_atom_in_place: unknown atom_id: H151

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AutoBuild can't align sequence file
by Moritz.Metlitzky＠sbg.ac.at 27 May '09

27 May '09

Hi all, i'm currently trying to solve my structure with phenix and i tried to do it via AutoMR. At first everything works fine, it finds a MR solution, but then i get this error: Chain too short or poor match to sequence: MYIQVLGSAAGGGFPQWNCNCVNCKGYRDGTLKATARTQSSIALSDDGVHWILCNASPDIRAQLQAFAPMQPARALRDTGINAIVLLDSQIDHTTGLLSLREGCPHQVWCTDMVHQDLTTGFPLFNMLSHWNGGLQWNRIELEGSFVIDACPNLKFTPFPLRSAAPPYSPHRFDPHPGDNLGLMVEDTRTGGKLFYAPGLGQVDEKLLAMMHGADCLLVDGTLWEDDEMQRRGVGTRTGREMGHLAQNGPGGTLEVLDGFPRQRKVLIHINNTNPILDENSPERAEVLRRGVEVAFDGMSIELL NOTE: chain A (residues 1-304) MYIQVLGSAAGGGFPQWNCNCVNCKGYRDGTLKATARTQSSIALSDDGVHWILCNASPDIRAQLQAFAPMQPARALRDTGINAIVLLDSQIDHTTGLLSLREGCPHQVWCTDMVHQDLTTGFPLFNMLSHWNGGLQWNRIELEGSFVIDACPNLKFTPFPLRSAAPPYSPHRFDPHPGDNLGLMVEDTRTGGKLFYAPGLGQVDEKLLAMMHGADCLLVDGTLWEDDEMQRRGVGTRTGREMGHLAQNGPGGTLEVLDGFPRQRKVLIHINNTNPILDENSPERAEVLRRGVEVAFDGMSIELL did not match the input sequence... ignoring alignment and rebuilding segment without sequence information. *************************************** AutoBuild Input failed Sorry, the PDB file and sequence file could not be aligned (with no gaps and >50.0% identity) Please restart the wizard... You have several possibilities to try .... You can set rebuild_in_place=No You can set input_sequence_file=None You can set min_seq_identity_percent to a lower value You can set highest_resno to a higher value You can specify start_chains_list if your PDB file sequence starts with a residue number greater than the number of residues in the sequence. what can i do now? the pdb file has nearly the same sequence (2 mutations) but he says that he can't align them, i use a .dat file for this is this correct? i also have a fasta line in it >... but it doesn't work without this line either. i tried with different phenix versions and have always the same problem Any suggestions would be appreciated.

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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 25 May '09

25 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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