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TLS refinement
by HUA YUAN 05 Oct '08

05 Oct '08

Dear Phenix community members, I have a molecular replacement solution refined agains a twinned 2.7 angstrom data to Rfree as 33%, with TLS and twin-law and others as default. The map looks good and shows extra map for my flavin ligand. Then I manually rebuild the model, fixing some obvious off-map residues and put a flavin molecule into the model. After this, I used the *def file from previous run to do another round of refinement. This time the Rfree increased to 36%. I realized that it has something to do with the TLS, isotropic and aniostropic B factor. However, I don't know exactly what's the reason and what to do at this stage. Any comments or suggestions? Should I do TLS refinement at the last step? Thanks and Best Wishes for all, Hua

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AssertionError in refinement
by Raja Dey 05 Oct '08

05 Oct '08

Dear PhenixBB Members, I am getting the following error while I am running the refinement given below: It stopped after a while. I enclosed the last part of the log file. phenix.refine gat.mtz gat-tlsmd.pdb simulated_annealing=true strategy=rigid_body+individual_sites+group_adp+individual_adp+tls tls.params output.prefix=final_1 --overwrite ================================ ADP refinement =============================== ----------TLS refinement---------- |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2491 r_free = 0.3251 target = 3.621992 convergence test = off | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 15)----------------| | r_work = 0.2437 r_free = 0.3120 target = 3.588460 convergence test = off | |-----------------------------------------------------------------------------| |-Information about rigid groups----------------------------------------------| | Total number of atoms = 1591 Number of rigid groups = 3 | | group: start point: end point: | | x B atom residue <> x B atom residue | | 1: -3.758 92.66 N MET 259 <> 10.389 94.12 CD2 LEU 300 | | 2: 14.264 58.92 N ILE 301 <> 1.800 100.80 O THR 315 | | 3: 1.098 66.36 N SER 316 <> -10.129 70.49 CE MET 368 | |-----------------------------------------------------------------------------| Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 549, in refinement_machine h_params = h_params) File "/usr/local/phenix-1.3b-rc6/mmtbx/mmtbx/refinement/adp_refinement.py", line 153, in __init__ tools.split_u(fmodels.fmodel_xray().xray_structure, tls_selections, offset) File "/usr/local/phenix-1.3b-rc6/mmtbx/mmtbx/tls/tools.py", line 498, in split_u assert (u_iso < 0.0).count(True) == 0 AssertionError While I can successfully run similar refinement on another project. I have another question. Inclusion of individual_adp in strategy increases R and R(free) in one case(2.8 A data), while decreases in another case (3.6 A data). Both are at the final stage of refinement. Is there any explanation? Looking forward to hearing from you... Thanking you in advance... Raja

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sfcheck & Phenix
by john kryst 04 Oct '08

04 Oct '08

Hi all, I have a little problem... R and R-free from phenix.refine are 22.9 and 30.6 respectively.... when i validated in the rcsb server... sfcheck gave me a R and Rfree of 30.8 and 37.8. I am aware that sfcheck never reproduces the result. but i am worried that the difference is quite large... indeed i have used TLS NCS and bulk solvent correction... Did i do anything wrong... please help me Thanks for your help regards John

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mmCIF format
by Simon Kolstoe 30 Sep '08

30 Sep '08

Is there a simple way of creating an mmCIF formatted structure factor file for pdb deposition from the outputs of a phenix.refine run? Thanks, Simon

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Deborah Palestrant is out of the office.
by deborah.palestrant＠novartis.com 30 Sep '08

30 Sep '08

I will be out of the office starting 09/30/2008 and will not return until 10/02/2008.

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error
by Jianghai Zhu 25 Sep '08

25 Sep '08

Hi, I got the following error from phenix.refine version 1.3-rc4. iotbx.reflection_file_utils.Sorry_Not_a_suitable_array: Not a suitable array of experimental phases: refineme nt.input.experimental_phases.labels=HLAM,HLBM,HLCM,HLDM What is the problem? -- Jianghai

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Post-doctoral position available with Phaser team
by Randy J. Read 24 Sep '08

24 Sep '08

We are looking to expand the team developing our program Phaser, for use within both the CCP4 and Phenix packages. Our goals include expanding the functionality to new phasing experiments (in addition to the options for molecular replacement and SAD that exist in the current version), and enhancing the automation of Phaser runs. The ideal applicant would be someone with experience solving macromolecular crystal structures and programming in both C++ and Python. However, if you only have experience in one of those areas, but a strong desire to expand your skills, then you might be the right person. If you're interested, please look at the formal advertisement (http://www.admin.cam.ac.uk/offices/hr/jobs/vacancies.cgi?job=4017), and submit an application as described there. I'm also happy to answer any informal enquiries. The position is funded by a grant from the Wellcome Trust, which extends to May 2013. Please note that the closing date for applications is 2 October 2008. Regards, Randy Read

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chainid and segid?
by deborah.palestrant＠novartis.com 23 Sep '08

23 Sep '08

Hi Phenix Community- A very basic question.. Is there an option to have a "segid" automatically generated? (For example, in CNS generate.inp, it was possible to "convert chainid to segid if chainid is non-blank"). Unless I strip out the segid completely, I am running into problems when I add residues using Coot (which adds chainid, but not segid) and then follow up with refinement in Phenix. Thanks for your input, Deb Deborah Palestrant, PhD Novartis Institutes for BioMedical Research CPC, Protein Structure Unit USCA, 600-6C343 Novartis Institutes for BioMedical Research, Inc. 250 Massachusetts Avenue Cambridge, MA 02139 USA Phone: +1 617 8713565 Email : deborah.palestrant(a)novartis.com _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by e-mail and delete the material from any computer. Thank you.

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Simon Holton ist außer Haus.
by simon.holton＠bayerhealthcare.com 23 Sep '08

23 Sep '08

Ich werde ab 23.09.2008 nicht im Büro sein. Ich kehre zurück am 24.09.2008. Ich werde Ihre Nachricht nach meiner Rückkehr beantworten.

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memory error
by Anastasia A Aksyuk 22 Sep '08

22 Sep '08

Hello everyone! I have the following error when using phenix-1.3-final: /========================== Target weights: x-ray data ========================= Traceback (most recent call last): File "/usr/local/rossmann/phenix/phenix-1.3-final/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line 89, in run File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/driver.py", line 1081, in run File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/strategies.py", line 472, in refinement_machine File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/weight_xray_chem.py", line 264, in __init__ File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/weight_xray_chem.py", line 307, in xyz_weights File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/weight_xray_chem.py", line 196, in __init__ File "/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/__init__.py", line 72, in update_xray_structure force_update_f_mask = force_update_f_mask) File "/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/f_model.py", line 675, in update_xray_structure force_update = force_update_f_mask) File "/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/masks.py", line 207, in f_mask return self.compute_f_mask() File "/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/masks.py", line 222, in compute_f_mask miller_set = self.miller_array) File "/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/masks.py", line 138, in structure_factors flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real())) MemoryError /I am running with defaults, i.e. the following command: phenix.refine se.water2.noano_001-2acetate-noH-coot-0.pdb cr2remote.cr3.1.8-2_scaleit1.mtz ray_data.r_free_flags.test_flag_value=1 output.prefix=se.noano2.acetate refinement.input.xray_data.labels="F_peak(+),SIGF_peak(+),F_peak(-),SIGF_peak(-),merged" I would greatly appreciate your help to resolve this issue and I can provide any additional information needed. Thank you, Anastasia

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