- phenixbb - phenix-online.org

helix deformed during refinement in phenix
by Raja Dey 14 Oct '08

14 Oct '08

Dear All, I am using phenix to refine a long helix of about 120 residues in a complex structure, but in course of refinement the helix becoming distorted from helical geometry. As a result when I am displaying the refined structure in pymol as cartoon one long helix showed 3/4 discontinuous helices in a single chain. Is there any way to constrain or restrain the helix during refinement, so that refinement process can maintain the helical geometry? Any suggestion is well appreciated. With regards... Raja Raja Dey, Ph.D. Research Associate Molecular and Computational Biology University of Southern California

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detwin data
by HUA YUAN 13 Oct '08

13 Oct '08

Dear Phenix community, I've used the phenix.refine with its detwin function. Is there any way to have a detwinned data output so that I can use it for other things. I tried use CCP4 detwin with the same twin law and twin fraction obtained from Phenix. However, this didn't work. Another question is whether I can use "some" phase information, say from DM into Phenix? I tried to include the PHIDM but Phenix complained about it saying "wrong array". Any suggestions or comments are hightly appreciated! Thanks, Hua

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Re: [phenixbb] Files generated in Autobuild from simulated annealing runs
by Tom Terwilliger 07 Oct '08

07 Oct '08

Hi Rebecca, I'm sorry this didn't get answered on the phenix_bb! I somehow missed it too. When you run an omit map with model=mymodel.pdb omit_box_pdb=mymodel.pdb omit_res_start_list=500 omit_res_end_list=500 the autobuild wizard edits mymodel.pdb, setting the occupancies of all atoms that are within a box enclosing the atoms in residue 500 of mymodel.pdb (plus a 2 A border) to zero. Then it runs the cycles of autobuild you specify (in this case just a SA step), and produces a density-modified map (resolve_composite_map.mtz) using the resulting model to generate phase information (and keeping the occupancies of these atoms at zero). If mydata.mtz contains phase information, that is used as well. The output map is in resolve_composite_map.mtz and a pseudo-map showing where the OMIT region(s) is(are) located is in omit_region.mtz The file overall_best_denmod_map_coeff.mtz is actually not really relevant or useful when you are doing OMIT maps because it is just one of the intermediate files that are produced. In this particular example it will be identical to resolve_composite_map.mtz but if you do other types of OMIT maps it won't be the same. I changed the output of the autobuild wizard recently, so you might want to upgrade to the 1.3-final version. The end of the log file in this case should say: -------------------------------------------------- Summary of model-building for run 1 Tue Oct 7 08:17:30 2008 Files are in the directory: /net/chevy/raid1/terwill/misc/test/ AutoBuild_run_1_/ Starting mtz file: /net/chevy/raid1/terwill/misc/test/perfect.mtz Sequence file: /net/chevy/raid1/terwill/misc/test/seq.dat Composite omit map is in : /net/chevy/raid1/terwill/misc/test/ AutoBuild_run_1_/OMIT/resolve_composite_map.mtz Boundaries of omit regions are in : /net/chevy/raid1/terwill/misc/test/ AutoBuild_run_1_/OMIT/omit_region.mtz -------------------------------------------------- Which I hope is clearer than earlier output in which the overall_best_denmod_map_coeff.mtz file is mentioned but is irrelevant. I hope that helps! All the best, Tom T On Oct 7, 2008, at 7:19 AM, Page, Rebecca wrote: > Hi Tom, > I posted the question on the phenix bb and, when I got no response, > shot an email over to Frank von Delft, an old friend, to see if he > knew answer. > > He didn’t, but recommended I email you directly and to “ask him to > post the answer on the general bb :)”. He also mentioned he hadn’t > seen the post on the phenix bb and I would be interested to know if > you did not see it either (I received it). > > At any rate, here it goes: > > > I am newcomer to phenix and have a rookie question about the > generated > > files using the phenix.autobuild command. I generated an sa-omit map > > of my model, omitting the coordinates for a bound ligand (ligand is > > residue > > 500): > > > > phenix.autobuild data=mydata.mtz model=mymodel.pdb > > omit_box_pdb=mymodel.pdb omit_res_start_list=500 > omit_res_end_list=500 > > omit_chain_list=A composite_omit_type=sa_omit > > > > The output omit map (resolve_composite_map.mtz) looks great. > > > > > > My question is: > > What, exactly, is the "overall_best_denmod_map_coeff.mtz" in this > case > > and how is it related, if at all, to the > "resolve_composite_map.mtz"? > > > Thanks for your help, > Rebecca > > Rebecca Page > Brown University >

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Files generated in Autobuild from simulated annealing runs
by Page, Rebecca 06 Oct '08

06 Oct '08

Dear Phenix users: I am newcomer to phenix and have a rookie question about the generated files using the phenix.autobuild command. I generated an sa-omit map of my model, omitting the coordinates for a bound ligand (ligand is residue 500): phenix.autobuild data=mydata.mtz model=mymodel.pdb omit_box_pdb=mymodel.pdb omit_res_start_list=500 omit_res_end_list=500 omit_chain_list=A composite_omit_type=sa_omit The output omit map (resolve_composite_map.mtz) looks great. My question is: What, exactly, is the "overall_best_denmod_map_coeff.mtz" in this case and how is it related, if at all, to the "resolve_composite_map.mtz"? Thanks in advance, Rebecca

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phenix.refine v.1.3 vs 1.24
by Leo Sazanov 06 Oct '08

06 Oct '08

When refining the same (large) molecule in several different crystal forms at about 3.1 A resolution, I noticed that in two cases when experimental phase information is available, in phenix.refine-1.3 I get worse Ramachandran compared to phenix.refine-1.24 - about 2% less residues in most favored regions. In one case when there is no experimental phase information, there is no difference between two phenix versions. What could be the reason for that? These comparisons where done for cases when final RMSDs and R-factors are similar (and all RMSDs calculated in v.1.3), so automatic weights adjustment in v.1.3 should not have played much role. Adding to other people's comments, it would be useful to be able to switch this adjustment off, as sometimes one wants full control over final RMSDs, etc. Thanks! -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-dunn.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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wxc_scale automatically doubled during the refinement
by yentingl＠gate.sinica.edu.tw 06 Oct '08

06 Oct '08

Dear phenix users, I've observed that in phenix 1.3 final if I specify wxc_scale the value is automatically doubled in every successive macrocycle. For example if I set wxc_scale=0.9 at the beginning, it becomes 1.8, 3.6, 7.2, 14.4 ... at macrocycle 2, 3, 4, 5 ... Is this normal? This was not found in phenix 1.3 rc4 on the same machine. Thanks! Yen-Ting

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library values for H in phenix.refine and MOLPROBITY
by Pavel Afonine 06 Oct '08

06 Oct '08

Hi Jianghai, > Another thing about riding H atoms. As I said before, the bond > distance between riding H and its attached atoms is different from > phenix library (ccp4 mono library) to the library MOLPROBITY uses. I > think the distance from MOLPROBITY is longer. The result is that the > structure refined by phenix.refine has a not so good clash score. Is > there a way to keep the distance from phenix.reduce in phenix.refine? Yes, I remember you mentioned this in the past (may be even several times). And this is true: the distances in Mon.Lib. and internal library in Molprobity might be different. Theoretically, longer distances are more correct since they reflect the actual nuclear position (that one can observe in neutron diffraction experiment), while the X-rays show hydrogens shifted along the bond towards the atom they are bonded to. This is why some programs (like SHELX) use shortened distances for X-H bonds and some uses those obtained from neutron scattering. Overall, I agree that the dictionaries must be made consistent within the package - this is something to fix on PHENIX end. Pavel.

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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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phenix 1.3-rc4 vs. phenix 1.3-final
by Jianghai Zhu 19 Sep '08

19 Sep '08

Hi, I have done a couple of refinements using either phenix.refine 1.3-rc4 or phenix.refine 1.3-final. And phenix.refine 1.3-rc4 always gave me a lower Rfree, about 1% lower than phenix.refine 1.3-final, which actually is pretty big. What has changed between this two versions? -- Jianghai

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Deborah Palestrant is out of the office.
by deborah.palestrant＠novartis.com 16 Sep '08

16 Sep '08

I will be out of the office starting 09/16/2008 and will not return until 09/18/2008. I will be checking email and will respond to your message at my earliest convenience.

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Anomalous difference map file
by Andrzej Lyskowski 16 Sep '08

16 Sep '08

Hi, Is it possible to write an anomalous difference map file and not just the coefficients in the mtz file? Would it be possible to get a short instructions for the operations... Regards, Andrzej Lyskwoski -- Andrzej LYSKOWSKI, Ph.D. (andrzej[.]lyskowski[(a)]helsinki[.]fi) Institute of Biotechnology - Structural Biology & Biophysics P. O. Box 65 - Viikinkaari 1 - Floor/Room: 4/4316 Mail: FIN-00014 University of HELSINKI, FINLAND Delivery: FIN-00710 University of HELSINKI, FINLAND TEL.: 358 9 191 58921 FAX : 358 9 191 59940

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phenix autobuild question
by Alex Berndt 16 Sep '08

16 Sep '08

Dear phenix community, I started an AutoBuild run using the phenix GUI (ver 1.3 rc4) on a linux cluster. It worked okay and all the refinement looked pretty decent. However, after quite a while I obtained the following error message (see below). Would anyone please tell me what to do to prevent this error and get phenix get its job finished? Also, I don't understand why phenix AutoBuild creates 5 (or whatever number) AutoBuild_run_x in the AutoBuild-run_1/TEMP0 directory and not two dirs up in the tree. In other words in my /someplace/home/someuser/ work/someproject/phenix2/AutoBuild_run_1_/TEMP0 directory are more AutoBuild_run_x_ directories (with x=1 to 5). It is a bit confusing to me. A final question: I realised that the phenix.refine drastically increases the number of outliers. I know that thare is a weighting term someplace ... but what was it again? Many thanks in advance, Alex warnings Failed to carry out AutoBuild_multiple_models: Sorry, subprocess failed...message is: ******************************************************************************** phenix.autobuild \ write_run_directory_to_file=/someplace/home/someuser/work/someproject/ phenix2/AutoBuild_run_1_/TEMP0/INFO_FILE_1 Reading effective parameters from /someplace/home/someuser/work/ someproject/phenix2/AutoBuild_run_1_/TEMP0/PARAMS_1.eff Sending output to AutoBuild_run_1_/AutoBuild_run_1_1.log ******************************************************************************** Failed to carry out AutoBuild_build_cycle: failure ******************************************************************************** ******************************************************************************** work_pdb_file "AutoBuild_run_1_/edited_pdb.pdb" working_directory "/someplace/home/someuser/work/someproject/phenix2" worst_percent_res_rebuild 2.0 --------------------------------------------------- Alex Berndt MRC-Laboratory of Molecular Biology Hills Road Cambridge, CB2 0QH U.K. phone: +44 (0)1223 402113 ---------------------------------------------------

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BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALOGRAPHY
by Cyndi Salbego 15 Sep '08

15 Sep '08

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. Beamline 24ID-C: Variable energy between 6-18keV, ADSC Q315 Detector, MAD Capable. 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. See http://necat.chem.cornell.edu for information on our beamlines and a calendar of available days.

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link in a double conformation residue
by mvliberato＠ursa.ifsc.usp.br 12 Sep '08

12 Sep '08

Dear all, I'm refining a protein structure with a cysteine covalently bonded with a fatty acid. However, this cysteine has a double conformation. I try to make a link with "cif_link.params", but I don't know how to describe the double conformation. How can I make this link between the fatty acid oxigen and the sulfur of the cysteine in one of the conformations? Any help would be much appreciated! Thanks Marcelo Marcelo Vizoná Liberato, Ms Physics Institute of São Carlos - USP São Carlos, Brazil ---------------------------------------------------------------- WEBMAIL - IFSC - Instituto de FÃsica de SÃ£o Carlos

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Odd twinning issue (or maybe all twinning issues are odd by default)
by Francis E Reyes 11 Sep '08

11 Sep '08

All I had a structure that seemed perfectly twinned in P41 21 2, completely built to the observable density (no peaks in 2Fo-Fc map over 2sigma) and refined to 33/35 (R/Rfree). I indexed, scaled, and merged the original unmerged data to P41, molecular replaced using the above model. Three rounds of rigid body refinement of the MR solution with group adp's dropped R/Rfree to 28/30 (while generating new free R flags based on the P41 data). The resolution was to 2.5 so I skipped the NCS. Now I try to do a second round of refinement with this time individual_sites and individual_adps with no change to the input model. The final R/Rfree's are now in the 50's? Am I missing something (fundamental) ? 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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difficulties with autoMR
by Feldman III, George Franklin 10 Sep '08

10 Sep '08

I am trying to run phenix.automr on what I believe is perhaps a perfectly twinned data set, at 3A resolution. It is in space group 146 and according to the matthews has 3 molecules in the asu. This is a mutant of an orriginally published structure in which only one residue has been mutated (but crystallizes in a different space group). When I give the autoMR the following input: phenix.automr coords="MR.1.pdb" data=dtscale.ref resolution=0 component_type=protein identity="95" mass=13900 build=False copies=3 seq.dat I get an LLG of 37 and the run goes quite quickly. The speed of the run itself leads me to believe that I have a correct solution regardless of the slightly low LLG, but when I open the .pdb output file there is only one molecule in the asu. Am I doing something incorrectly? Why is there only one molecule instead of 3 in the asu, and how can I go about getting the other two to appear? I did let the program go ahead run autobuild, this resulted in a structure with an r_work:.5448 and r_free:.6005. I am relatively new to crystallography, but these values seem rather high to be a good starting point for refinement. I would appreciate any advice that might help me move on with my structure. Attached is the log file from phenix.xtriage in case it may be of any help. Thank you, in advance, for all of your help and advice. Best Regards, George F. Feldman

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Re: [phenixbb] cci_apps on irix
by Ralf W. Grosse-Kunstleve 07 Sep '08

07 Sep '08

On 22 Aug 2008 o.h.weiergraeber(a)fz-juelich.de wrote: > I am just compiling the latest cci_apps package for the IRIX > platform. I know this is unsupported, but since the package is very > self-contained, I would not expect major problems with the command-line > packages (who needs a gui, anyway ;)) > I'm just running into two issues with the boost package which are > obviously a matter of syntax: Our IRIX machine is up again, and - to my surprise - the current CCI Apps compiled without errors. The IRIX binary bundle is available again at the usual place: http://www.phenix-online.org/download/cci_apps/ Ralf

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selection usage
by Mark Collins 05 Sep '08

05 Sep '08

Hi All, The current phenix 1.3 release automatically selects alternate conformations when refine *occupancy is selected. How do I select a loop region (in low density) to refine the loop occupancy without messing up the auto selection? Thanks in advance, Mark

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Deborah Palestrant is out of the office.
by deborah.palestrant＠novartis.com 04 Sep '08

04 Sep '08

I will be out of the office starting 09/04/2008 and will not return until 09/08/2008.

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Re: [phenixbb] sugar links
by Ralf W. Grosse-Kunstleve 03 Sep '08

03 Sep '08

Hi Morten, > Why isn't it included in the standard set btw? Sorry, too many bigger things to take care off right now. But Garib told me he'll move the monomer library to a Google source server, which should make it much more practical to collectively work on changes like the one you're requesting. Ralf

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Re: [phenixbb] Real Space R value
by Thomas C. Terwilliger 03 Sep '08

03 Sep '08

Hi Matthew, You can also use phenix.get_cc_mtz_pdb with a ligand...it should treat the ligand as a single residue. Mark also asked offline about alternate conformations...here is my answer to that: If there is only on N for each residue, it will average over all atoms in all conformations. If there are multiple N atoms, and all atoms for each conformer are grouped, it will write out the residue twice. If there are multiple N atoms and they are interspersed, it will give an incorrect answer (it will write out the residue twice but the cc values will not be for the two conformers). All the best, Tom T > Hi, > Yes, you can use phenix.get_cc_mtz_pdb (see phenix.doc) > > But I wonder if there is a way to get CC value for a ligand or a metal > ion too ?? > > Nigel ??? > >> Date: Tue, 2 Sep 2008 13:18:59 -0400 >> From: "nih\mayerm" <mayerm(a)mail.nih.gov> >> Subject: [phenixbb] Real Space R value >> To: phenixbb(a)phenix-online.org >> Message-ID: <FEAAD2DC-1906-4194-881B-CA83B48E8043(a)mail.nih.gov> >> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed >> >> >> Is it possible to calculate a list of Real Space R values for >> structures refined with phenix.refine ? >> If so advice on how to do this would be greatly appreciated. >> >> Thanks - Mark Mayer >> >> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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Re: [phenixbb] Real Space R value
by mathieu Coincon 03 Sep '08

03 Sep '08

Hi, Yes, you can use phenix.get_cc_mtz_pdb (see phenix.doc) But I wonder if there is a way to get CC value for a ligand or a metal ion too ?? Nigel ??? > Date: Tue, 2 Sep 2008 13:18:59 -0400 > From: "nih\mayerm" <mayerm(a)mail.nih.gov> > Subject: [phenixbb] Real Space R value > To: phenixbb(a)phenix-online.org > Message-ID: <FEAAD2DC-1906-4194-881B-CA83B48E8043(a)mail.nih.gov> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > Is it possible to calculate a list of Real Space R values for > structures refined with phenix.refine ? > If so advice on how to do this would be greatly appreciated. > > Thanks - Mark Mayer > >

2 1

PX beamtime application deadline Sept 3rd!
by Peter Zwart 02 Sep '08

02 Sep '08

Dear All, The deadline for user proposals for PX beamtime at the ALS has been extended to September 3, 5pm pacific time. See my previous email for details. Thanks Peter 2008/8/29 Peter Zwart <PHZwart(a)lbl.gov>: > Dear All, > > The deadline for general user proposals for PX beamtime at the ALS is > comming up soon! At the BCSB, we have 5 beamlines for which you can > apply for beamtime. At the Berkeley Center for Structural Biology > (BCSB) we have recently completed a number of upgrades: > > Sector 8: Recent improvements include: > > * A high-accuracy microdiffractometer on BL 8.2.1, allowing for > centering and viewing of very small crystals > * Robot automounters which can increase the screening throughput > at the beamlines, and will allow for the implementation of remote data > collection > * A new large format (315mm active surface area) CCD detector on > BL 8.2.1, facilitating data collection on large unit cell crystals > > Sector 5: Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 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 (the tunable beamline) generates a peak flux of 8x10^11 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. > > Please visit http://bcsb.lbl.gov/ for more details about the Center > and its beamlines. > > If you'd like to apply for Oct/Nov/Dec beamtime at the Advanced Light > Source, please submit a General User proposal by September 1, 2008. > > To find out more, click on: > > http://www-als.lbl.gov/als/quickguide/independinvest.html > > We invite you to submit a proposal at: > > http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize. > > 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.) > > > -- > ----------------------------------------------------------------- > 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 > ----------------------------------------------------------------- > -- ----------------------------------------------------------------- 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 -----------------------------------------------------------------

1 0

Real Space R value
by nihmayerm 02 Sep '08

02 Sep '08

Is it possible to calculate a list of Real Space R values for structures refined with phenix.refine ? If so advice on how to do this would be greatly appreciated. Thanks - Mark Mayer

2 1

LABIN and BLUR like options in phenix refine?
by Partha Chakrabarti 01 Sep '08

01 Sep '08

Hiya, If we use sharp for phasing, the eden_flat file has multiple columns at the end. I was wondering if it is possible to tell the program which ones to use other than having to use CAD.. and, if the FOM is suspected to be too high, Blur it.. Cheers, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra(a)nimr.mrc.ac.uk Phone: + 44 208 816 2515

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PX beamtime application deadline Sept 1st!
by Peter Zwart 29 Aug '08

29 Aug '08

Dear All, The deadline for general user proposals for PX beamtime at the ALS is comming up soon! At the BCSB, we have 5 beamlines for which you can apply for beamtime. At the Berkeley Center for Structural Biology (BCSB) we have recently completed a number of upgrades: Sector 8: Recent improvements include: * A high-accuracy microdiffractometer on BL 8.2.1, allowing for centering and viewing of very small crystals * Robot automounters which can increase the screening throughput at the beamlines, and will allow for the implementation of remote data collection * A new large format (315mm active surface area) CCD detector on BL 8.2.1, facilitating data collection on large unit cell crystals Sector 5: Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 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 (the tunable beamline) generates a peak flux of 8x10^11 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. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to apply for Oct/Nov/Dec beamtime at the Advanced Light Source, please submit a General User proposal by September 1, 2008. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize. 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.) -- ----------------------------------------------------------------- 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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User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 28 Aug '08

28 Aug '08

Dear Users, The Berkeley Center for Structural Biology (BCSB) is pleased to announce the launch of a Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source in Berkeley. Through this program, scientists will be able to send protein crystals to BCSB staff researchers for data collection and analysis. The CC Pilot Program can provide an number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: ====================== The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the regular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects 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 Click on "protein crystallography" to begin proposal. For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for October/November/December 2008 allocation period, proposals must be submitted by Sept 1, 2008. The deadline for CC proposals for the time period January/February 2009 will be November 15, 2008. Regards, Banumathi Sankaran

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map calculation
by Chen Chen 27 Aug '08

27 Aug '08

Dear all, I am having a question about map calcultation. I want to calculate a 2mFo-DFc map and a mFo-DFc map to 2.0 angstrom from xxx.pdb and yyy.mtz, and zzz.cif should be supplied. Unit cell dimension and symmetry information is in the mtz file. It seems that phenix.maps can do the job, but I did not find a good document on how to run it. In its help information, a parameter file is needed. I tried do use parameter file for refinement, which has been successfully used for phenix.refine, and I ran the command phenix.maps --unused_ok yyy.mtz xxx.pdb refine.param but phenix.maps report the error Traceback (most recent call last): File "/home/chene/phenix-1.3b-rc6/mmtbx/mmtbx/command_line/maps.py", line 7, in <module> maps.run(args=sys.argv[1:]) File "/home/chene/phenix-1.3b-rc6/mmtbx/mmtbx/maps.py", line 173, in run log = log) File "/home/chene/phenix-1.3b-rc6/mmtbx/mmtbx/maps.py", line 214, in __init__ self.data = utils.determine_data( AttributeError: 'module' object has no attribute 'determine_data' Does anyonw know what I should do to get the maps? Thanks Chen -- Chen Chen, Ph. D., Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 Office Phone: 240-314-6122

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MTZ file
by YS. Chung 27 Aug '08

27 Aug '08

Hi all, I have a simple question about the output mtz file from phenix.refine. When I look at the mtz file, it says *********************************************************** DO NOT USE THIS FILE AS INPUT FOR REFINEMENT! Resolution and sigma cutoffs may have been applied to FOBS. *********************************************************** If I have not applied either resolution or sigma cutoffs to FOBS, does that mean that this mtz file is ok to be used for the next round of refinement? Thank you, Yu Seon Chung

3 2

Dry shippers
by Peter Zwart 26 Aug '08

26 Aug '08

Dear all, Due to the presence of residual liquid nitrogen in dry shippers 'steaming' out of a tipped-over dewar on a Fedex dock, we (PX-ers in the ALS) have been placed under some scrutiny with regards to dry-shipping dewars. In particular, I am interested in how people empty their dewars/pucks/vials and prepare them for dry-shipment and how they and/or their shipping department checks if the dewars are empty indeed. 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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Refining with NCS
by Francis E Reyes 25 Aug '08

25 Aug '08

All I have 4 molecules in my ASU and I had phenix pick out my NCS operators automatically. Do a round of refinement, load 2fofc maps into coot and ask to calculate NCS Maps (Calculate -> NCS Maps). I have three new maps mapping a single chain onto the other chains (3) and an NCS average map. I look at some of the NCS maps and the question is should the model (all the chains) match to every NCS map? In my set of 3 maps, the model fits one map (independent of chain) but seems offset in the other two maps. Also if anyone has a paper/protocol for NCS refinement, I'd love to check it out (to figure out which map to fit to). 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

4 5

anisotropic refinement and hydrogens in coot.
by Mark Collins 25 Aug '08

25 Aug '08

Two hopefully quick questions; 1) The phenix.refine documentation has a section 'Refinement at "higher than medium" resolution - getting anisotropic'. I have a 1.4A structure that clearly falls into this category, I've added riding hydrogens and now I'd like to try anisotropic ADPs. Is there a way, to list all residues (preferably in phenix selection format) that have "relatively small isotropic B-factors ~5-20A**2 of so."? 2) The output.pdb file from phenix.refine is I think the pdb v3.0 format. Is there an option or apps to convert to v2.3, within phenix rather using remediator (duke)? Coot still uses v2.3 files, which is fine until hydrogens are added to a pdb, because the nomenclature has changed. RSR in coot causes these 3.0 named hydrogens to fly off the residue into surrounding density. Thanks in advance, Mark

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Re: [phenixbb] cci_apps on irix
by o.h.weiergraeber＠fz-juelich.de 25 Aug '08

25 Aug '08

Hello Ralf, I have now tried to compile the cctbx version of May 25th (which was the latest version with an official IRIX build). It gives me the very same type of error which I have seen with the latest cci_apps: -------- Declaration is incompatible with function template "boost::basic_format<Ch, Tr, Alloc> &boost::io::detail::feed(boost::basic_format<Ch, Tr, Alloc> &, T)" (declared at line 52 of "/usr/local/archive/cctbx/2008_05_25/cctbx_sources/boost/boost/format /internals_fwd.hpp"). io::detail::feed (basic_format<Ch2, Tr2, Alloc2>&, T); --------- This means that probably there always have been certain changes to be made for the code to compile under IRIX/Mipspro. Could somebody maybe tell me the email address of the person who actually did the last IRIX build, or just forward my message accordingly? Thanks a lot! Oliver ------------------------------- Dr. Oliver H. Weiergraeber Institute of Neurosciences and Biophysics Molecular Biophysics Research Centre Juelich D-52425 Juelich Germany Phone: +49-2461-612028 Fax: +49-2461-612020 ------------------------------- ----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" <rwgk(a)cci.lbl.gov> Date: Sunday, August 24, 2008 12:41 pm Subject: Re: [phenixbb] cci_apps on irix > Hi Oliver, > > You can get the boost directory via these cctbx bundles: > http://cci.lbl.gov/cctbx_build/ > Click on the date/time tag for the cci apps version you had > previously, or if you don't know, go back one by one. > BTW: there is no need to delete cci apps or phenix versions. > Simply don't source the old setpaths or phenix_env and the > old version is "virtually not there (tm)". > > Ralf > ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

2 1

Re: [phenixbb] cci_apps on irix
by o.h.weiergraeber＠fz-juelich.de 24 Aug '08

24 Aug '08

Hello Ralf, thanks a lot for Your suggestions. Yes, I have thought about that, comparing with the older version to fix the differences. Unfortunately, I was brave enough to delete my previous (precompiled) version before I realized that IRIX support has been dropped in the meantime !!! The cci_apps download area does not provide an obvious possibility to download an older version (the cci_apps packages don't have version numbers anyway). But maybe somebody could provide a link to the latest sgi-compatible version (sources and binary package, if possible)?? That would be great! If these minor problems can be solved, it should be no problem to compile the main phenix package ;)) Cheers Oliver ------------------------------- Dr. Oliver H. Weiergraeber Institute of Neurosciences and Biophysics Molecular Biophysics Research Centre Juelich D-52425 Juelich Germany Phone: +49-2461-612028 Fax: +49-2461-612020 ------------------------------- ----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" <rwgk(a)cci.lbl.gov> Date: Sunday, August 24, 2008 3:48 am Subject: Re: [phenixbb] cci_apps on irix > > I am just compiling the latest cci_apps package for the IRIX > > platform. I know this is unsupported, but since the package is very > > self-contained, I would not expect major problems with the > command-line > > packages (who needs a gui, anyway ;)) > > I'm just running into two issues with the boost package which are > > obviously a matter of syntax: > > The first one is a typical MIPSpro quirk and would be easy to fix > (add inline to the prototype), but I'm not sure about the second one. > Unfortunately we don't currently have a MIPSpro machine I could use > to figure this out (not enough power in the room to keep that old > amp-eater running!). > Do you still have an older CCI Apps that worked on your machine? > Then you could try to replace the newer boost sources with the > older version. E.g. something like > > cd /usr/local/archive/phenix/cci_apps-1.3/cci_apps_sources > mkdir incompatible > mv boost incompatible > cp -r /usr/local/archive/phenix/cci_apps-that- > worked/cci_apps_sources/boost . > cd .. > rm cci_apps_build/.sconsign.dblite # like make clean; could be > important ./cci_apps_install_script.csh > > Ralf > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

2 1

cci_apps on irix
by o.h.weiergraeber＠fz-juelich.de 24 Aug '08

24 Aug '08

Hello, I am just compiling the latest cci_apps package for the IRIX platform. I know this is unsupported, but since the package is very self-contained, I would not expect major problems with the command-line packages (who needs a gui, anyway ;)) I'm just running into two issues with the boost package which are obviously a matter of syntax: 1st: ----- Function function "boost::python::api::object_base::~object_base" is redeclared "inline" after being called. inline api::object_base::~object_base() ^ ----- 2nd: ----- Declaration is incompatible with function template "boost::basic_format<Ch, Tr, Alloc> &boost::io::detail::feed(boost::basic_format<Ch, Tr, Alloc> &, T)" (declared at line 52 of "/usr/local/archive/phenix/cci_apps-1.3/cci_apps_sources/boost/boost/ format/internals_fwd.hpp"). io::detail::feed (basic_format<Ch2, Tr2, Alloc2>&, T); ^ ----- I have attached the complete output for your reference. Maybe these problems can be corrected easily. In fact, all this may be a matter of the mipspro compilers being more strict about syntax than gcc. But how to tell the install script to use gcc??? There doesn't seem to be a standard way to provide general compilation options... Just renaming the cc binaries makes the python configure script to switch to gcc without complaints, but other packages (scons if I remember correctly) still explicitly check for mipspro ?! Any ideas how to resolve this? Oliver ------------------------------- Dr. Oliver H. Weiergraeber Institute of Neurosciences and Biophysics Molecular Biophysics Research Centre Juelich D-52425 Juelich Germany Phone: +49-2461-612028 Fax: +49-2461-612020 ------------------------------- ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

2 1

'ordered solvent' switch error (AssertionError)
by Jonathan Elegheert 23 Aug '08

23 Aug '08

Dear Phenix developers, since downloading the latest CCI Apps software release version (2008_08_09_0053), I keep running into this same error (AssertionError) when turning on the 'ordered solvent' switch in phenix.refine. I did not encounter this error with the 'release candidate 2' version I was running previously. Platform: RHEL4 with the Red Hat 8.0 or the Red Hat WS 3 (x86_64) binary bundles. Many thanks in advance for your help. Jonathan Elegheert, PhD student Ghent University ================== ordered solvent: location/analysis/update ================== Start model: number = 359 b_iso_min = 7.13 (limit = 1.00) b_iso_max = 56.80 (limit = 50.00) b_iso_mean = 27.85 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 1.00) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = 1.92 (limit = 1.80) dist_sol_mol_max = 4.46 (limit = 6.00) Filtered: number = 324 b_iso_min = 7.13 (limit = 1.00) b_iso_max = 49.84 (limit = 50.00) b_iso_mean = 26.59 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 1.00) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = 2.05 (limit = 1.80) dist_sol_mol_max = 4.18 (limit = 6.00) Traceback (most recent call last): File "/usr/local/PHENIX/cci_apps_sources/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/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/PHENIX/cci_apps_sources/phenix/phenix/refinement/driver.py", line 1081, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/PHENIX/cci_apps_sources/phenix/phenix/refinement/strategies.py", line 364, in refinement_machine log = log) File "/usr/local/PHENIX/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 159, in __init__ use_kick_map = self.params.use_kick_maps).peaks_mapped() File "/usr/local/PHENIX/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 332, in find_peaks log = self.log) File "/usr/local/PHENIX/cci_apps_sources/mmtbx/mmtbx/find_peaks.py", line 85, in __init__ symmetry_flags = maptbx.use_space_group_symmetry) File "/usr/local/PHENIX/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", line 2244, in electron_density_map "m_gradient") AssertionError

2 1

phenix.refine writing maps error
by Francis E Reyes 22 Aug '08

22 Aug '08

Writing refined structure to PDB file: /Users/francisreyes/Desktop/No_Sync/RBD_MOSFLM_P4_processing/ cns_P41_solution_18/RBD_P4PROCESS_18.1_refine_001.pdb n_use = 1586 n_use_u_iso = 1586 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 n_anisotropic_flag = 0 total number of scatterers = 1586 Traceback (most recent call last): File "/usr/local/phenix-1.3-rc2/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-1.3-rc2/phenix/phenix/refinement/ command_line.py", line 99, in run map_manger.write_files() File "/usr/local/phenix-1.3-rc2/phenix/phenix/refinement/ driver.py", line 1170, in write_files coeffs = self.refine_object.fmodel.map_coefficients(map_type=map_type) File "/usr/local/phenix-1.3-rc2/mmtbx/mmtbx/twinning/ twin_f_model.py", line 2205, in map_coefficients result = result.customized_copy( data = result.data()*aniso_scale ) RuntimeError: scitbx array_family range error Using version ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.3 Release tag: rc2 cctbx tag: 2008_05_25_1144 Platform: mac-ppc-osx osx-10.5.3 User: francisreyes ------------------------------------------------------------------------------- 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

3 2

ICSG 2008 Announcement Oxford Sept 20-24
by Thomas C. Terwilliger 22 Aug '08

22 Aug '08

Dear Colleagues, The ICSG 2008 International Conference On Structural Genomics is coming up Sept 20-24 in Oxford, UK. We have a terrific program lined up and I hope that you'll register now if you haven't already! I've copied the latest announcement of the meeting below. All the best, Tom Terwilliger ISGO International Conference On Structural Genomics, Oxford 2008 Web site: http://www.spine2.eu/ISGO The 5th International Conference on Structural Genomics (ICSG 2008) will be held in Oxford, UK on September 20-24th. The biennial Conference is the premier meeting for the Structural Genomics scientific community world-wide and is hosted on behalf of the International Structural Genomics Organization (ISGO) by Professor David Stuart at the University of Oxford, Division of Structural Biology. Keynote Speakers: Ian Wilson Dino Moras Chas Bountra Peter Donnelly Session Topics - ( See http://www.spine2.eu/SPINE2/ISGO/ for details) Structural genomics, systems biology and complexes Generating insight into protein function with structural genomics SG technologies: methodologies and dissemination The impact of structural genomics on treating diseases Structural determination, methods and computational tools International funding, co-operation and visions for the future Maximising impact on and integration with biology HTP methods for membrane proteins Hybrid/multidisciplinary approaches Strategies for intrinsically unfolded proteins Should we expand the protein universe or concentrate on biology? New Technologies Social program reservations closing date: August 31st (Blenheim Palace Dinner) Registration form: http://www.spine2.eu/SPINE2/ISGO/register The venue will be in the UK at the University of Oxford Examination Schools, High Street, Oxford. The Schools are in the heart of Oxford, central to all colleges, the main Oxford cultural and shopping areas and close to hotel and college accommodation. Registration is now open

1 0

(no subject)
by Thomas C. Terwilliger 22 Aug '08

22 Aug '08

Dear Colleagues, The ICSG 2008 International Conference On Structural Genomics is coming up Sept 20-24 in Oxford, UK. We have a terrific program lined up and I hope that you'll register now if you haven't already! I've copied the latest announcement of the meeting below. All the best, Tom Terwilliger ISGO International Conference On Structural Genomics, Oxford 2008 Web site: http://www.spine2.eu/ISGO The 5th International Conference on Structural Genomics (ICSG 2008) will be held in Oxford, UK on September 20-24th. The biennial Conference is the premier meeting for the Structural Genomics scientific community world-wide and is hosted on behalf of the International Structural Genomics Organization (ISGO) by Professor David Stuart at the University of Oxford, Division of Structural Biology. Keynote Speakers: Ian Wilson Dino Moras Chas Bountra Peter Donnelly Session Topics - ( See http://www.spine2.eu/SPINE2/ISGO/ for details) Structural genomics, systems biology and complexes Generating insight into protein function with structural genomics SG technologies: methodologies and dissemination The impact of structural genomics on treating diseases Structural determination, methods and computational tools International funding, co-operation and visions for the future Maximising impact on and integration with biology HTP methods for membrane proteins Hybrid/multidisciplinary approaches Strategies for intrinsically unfolded proteins Should we expand the protein universe or concentrate on biology? New Technologies Social program reservations closing date: August 31st (Blenheim Palace Dinner) Registration form: http://www.spine2.eu/SPINE2/ISGO/register The venue will be in the UK at the University of Oxford Examination Schools, High Street, Oxford. The Schools are in the heart of Oxford, central to all colleges, the main Oxford cultural and shopping areas and close to hotel and college accommodation. Registration is now open

1 0

Re: [phenixbb] cci_apps on irix
by o.h.weiergraeber＠fz-juelich.de 22 Aug '08

22 Aug '08

Hello Nat, thanks for your suggestions. Yes, I have used these tricks before, but sadly, the cci_apps build system ignores them completely. As far as I can see, there is no "central" place to set these variables, and the component packages behave differently. The cleanest way to go would be to just correct the syntax problems. Until recently, cci_apps was available as a precompiled irix package (and I think it was mipspro), so maybe one of the developers could comment on the specifics of this compilation. Thanks Oliver ------------------------------- Dr. Oliver H. Weiergraeber Institute of Neurosciences and Biophysics Molecular Biophysics Research Centre Juelich D-52425 Juelich Germany Phone: +49-2461-612028 Fax: +49-2461-612020 ------------------------------- ----- Original Message ----- From: Nat Echols <NEchols(a)lbl.gov> Date: Friday, August 22, 2008 4:57 pm Subject: Re: [phenixbb] cci_apps on irix ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

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phenix.pdbtools
by Jianghai Zhu 21 Aug '08

21 Aug '08

Hi, I am trying to use phenix.pdbtools to calculate the geometry statistics for a model from Rosetta. "phenix.pdbtools --show-geometry- statistics foo.pdb" stopped with a message "Sorry: Number of bonds with excessive lengths: 707". Anybody know what happened there? Thanks. -- Jianghai

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