- phenixbb - phenix-online.org

RuntimeError: Not enough memory for cubicles:
by Gino Cingolani 09 Mar '09

09 Mar '09

Dear Phenix community, I am still having problems to refine a large unit cell (~13,500 residues/asymmetric unit). The refinement goes well but at the very last cycle, immediately prior to outputting the refined model, phenix stops with the following error message: $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ ========== residual map mFobs-DFmodel: highest peaks and deepst holes ========= ----------peaks---------- Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py", line 9, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py", line 1098, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/strategies.py", line 710, in refinement_machine fmodels=fmodels, model=model, log=log) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/strategies.py", line 738, in highest_peaks_and_deepest_holes_in_residual_map log = log) File "/usr/local/phenix-1.4-3/mmtbx/find_peaks.py", line 212, in show_highest_peaks_and_deepest_holes log = log) File "/usr/local/phenix-1.4-3/mmtbx/find_peaks.py", line 117, in __init__ map = fft_map_data).all(max_clusters = max_number_of_peaks) File "/usr/local/phenix-1.4-3/cctbx/maptbx/__init__.py", line 196, in peak_search max_clusters=parameters.max_clusters()) File "/usr/local/phenix-1.4-3/cctbx/maptbx/__init__.py", line 303, in __init__ general_positions_only=self._general_positions_only) File "/usr/local/phenix-1.4-3/cctbx/crystal/__init__.py", line 479, in site_cluster_analysis cubicle_epsilon=cubicle_epsilon) RuntimeError: Not enough memory for cubicles: This may be due to unreasonable parameters: cubicle_edge=0.7 space_span=(293.298,92.903,214.527) n_cubicles=(419,133,307) max_number_of_bytes=1724676096 Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py", line 9, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py", line 1098, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/strategies.py", line 710, in refinement_machine fmodels=fmodels, model=model, log=log) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/strategies.py", line 738, in highest_peaks_and_deepest_holes_in_residual_map log = log) File "/usr/local/phenix-1.4-3/mmtbx/find_peaks.py", line 212, in show_highest_peaks_and_deepest_holes log = log) File "/usr/local/phenix-1.4-3/mmtbx/find_peaks.py", line 117, in __init__ map = fft_map_data).all(max_clusters = max_number_of_peaks) File "/usr/local/phenix-1.4-3/cctbx/maptbx/__init__.py", line 196, in peak_search max_clusters=parameters.max_clusters()) File "/usr/local/phenix-1.4-3/cctbx/maptbx/__init__.py", line 303, in __init__ general_positions_only=self._general_positions_only) File "/usr/local/phenix-1.4-3/cctbx/crystal/__init__.py", line 479, in site_cluster_analysis cubicle_epsilon=cubicle_epsilon) RuntimeError: Not enough memory for cubicles: This may be due to unreasonable parameters: cubicle_edge=0.7 space_span=(293.298,92.903,214.527) n_cubicles=(419,133,307) max_number_of_bytes=1724676096 $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ Following the various suggestions received after my previous email (~2 weeks ago), I have tried the following: --> Using phenix 1.4-3, which gave exactly the same problem as phenix 1.3 --> Using MACRO_CYCLE=0 before refinement to see if phenix can write out such a large asymmetric unit, and that works. Phenix does write out the model at a starting Rfree ~35.5%. --> Removing ordered_solvent=true Right now the refinement scheme I am using is as follows: phenix.refine XX.mtz model.pdb simulated_annealing=true elbow.XX_pdb.cif strategy=individual_sites+group_adp+tls tls_group_selections.params main.number_of_macro_cycles=5 main.ncs=true refinement.ncs.excessive_distance_limit=None refinement.pdb_interpretation.clash_guard.nonbonded_distance_threshold=No Once again, the refinement proceeds smoothly for 2-3 days; the Rfree drops nearly 3 points, and right at the very end, the programs stops without outputting a refined model. Does anybody have any idea what's going on? 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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installation : cctbx or cci apps
by Bryan W. Lepore 09 Mar '09

09 Mar '09

i hope this is a "yes" or "no" question : i just got the latest phenix and the latest cci_apps running together. is the latest cctbx necessary? -bryan

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Restraints on water molecules
by Engin Ozkan 08 Mar '09

08 Mar '09

Are restraints on water molecules overwritten on successive cycles of refinement where ordered solvent is on? I seem to lose my distance restraints between specific waters and metal, unless I name my water molecules something else (and supply phenix with a cif for that name which is identical to water inside). The distance restraints also seem to be in effect for all cycles if ordered_solvent is off. I am also trying to make sure water numbers don't change during solvent picking/deleting. Engin

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PDF slides: introduction to refinement, phenix.refine and why automation is important (PHENIX)
by Pavel Afonine 08 Mar '09

08 Mar '09

Dear PHENIX community: I would like to draw your attention to these two PDF files with the slides that I recently made for a PHENIX workshop (workshop on Neutron crystallography, March 5-6, Japan). The first file (69 of very dense slides) makes a general introduction to crystallographic structure refinement (certainly biased towards how things are done in phenix.refine), plus some introduction to phenix.refine functionality. The second PDF file talks about PHENIX and "quick validation" with the strong accent of why automation is important. In general, I don't like and normally don't do such advertisements, but in this case I believe I can make an exception since I spent too much "of my software development" time on making these slides and they might be instructive for (new) PHENIX users. The links are (the first two!): http://www.phenix-online.org/presentations/neutron_japan_2009/ Thanks, Pavel. PS> Two slides in the first file are borrowed from Sasha Urzhumtsev, and 2-3 slides are borrowed from Paul Adams (second file).

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Re: [phenixbb] phenixbb Digest, Vol 40, Issue 7
by Pascal Egea 08 Mar '09

08 Mar '09

Pavel and Paul, this is really awesome.Thanks a lot. Pascal Egea UCSF Department of Biochemistry and Biophysics Laboratory of Robert Stroud On Sun, Mar 8, 2009 at 1:00 PM, <phenixbb-request(a)phenix-online.org> wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. PDF slides: introduction to refinement, phenix.refine and why > automation is important (PHENIX) (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 07 Mar 2009 23:41:35 -0800 > From: Pavel Afonine <PAfonine(a)lbl.gov> > Subject: [phenixbb] PDF slides: introduction to refinement, > phenix.refine and why automation is important (PHENIX) > To: phenixbb(a)phenix-online.org > Message-ID: <49B376AF.1020803(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear PHENIX community: > > I would like to draw your attention to these two PDF files with the > slides that I recently made for a PHENIX workshop (workshop on Neutron > crystallography, March 5-6, Japan). > > The first file (69 of very dense slides) makes a general introduction to > crystallographic structure refinement (certainly biased towards how > things are done in phenix.refine), plus some introduction to > phenix.refine functionality. > > The second PDF file talks about PHENIX and "quick validation" with the > strong accent of why automation is important. > > In general, I don't like and normally don't do such advertisements, but > in this case I believe I can make an exception since I spent too much > "of my software development" time on making these slides and they might > be instructive for (new) PHENIX users. > > The links are (the first two!): > > http://www.phenix-online.org/presentations/neutron_japan_2009/ > > Thanks, > Pavel. > > PS> Two slides in the first file are borrowed from Sasha Urzhumtsev, and > 2-3 slides are borrowed from Paul Adams (second file). > > > > > ------------------------------ > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > End of phenixbb Digest, Vol 40, Issue 7 > *************************************** >

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Re: [phenixbb] refinement using a multiprocessor machine or on a cluster
by Pavel Afonine 06 Mar '09

06 Mar '09

Hi Gino, phenix.refine does not use any advantage of multiple available CPUs. Sorry. Pavel. On 3/4/09 11:26 AM, Gino Cingolani wrote: > Dear Phenix community, > > I was wondering if it is possible to run a refinement job on multiple > processor. The refinement of my 13,000 asymmetric unit takes about 2 > days. It could be greatly speeded up by taking advantage of the 4 CPUs > in my PC. The phenix manual suggest to use > nproc=3 > to run using a multiprocessor machine or on a cluster. > But this applies only to LigandFit and AutoBuild Wizards. > What about simple refinement? > > Thanks in advance, > > Gino > >

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fwd: TLS without isotropic adp refinement
by Nathaniel Echols 06 Mar '09

06 Mar '09

(I think the server must have a lag time between adding a new email address and accepting posts from it. . .) > From: Roeland Boer <rbocri(a)ibmb.csic.es> > Date: March 5, 2009 5:29:19 AM PST > To: phenixbb(a)phenix-online.org > Subject: TLS without isotropic adp refinement > > Dear all, > > I'm trying to refine a structure using TLS on some of the domains > without refining the isotropic B factors of the atoms of the full > structure. I haven't been able to do this: the isotropic B factors > seem to be refined per residue when I include TLS. If I don't use > TLS, the B factors are not refined. I've looked around in the > archives and browsed the manual without luck. Any suggestions would > be highly appreciated. I include the parameter file I've used. Quoting Pavel (since he's teaching a workshop): "phenix.refine always writes out the total B-factors and not split them. The total B-factor in phenix.refine is defined as: Utotal = Utls + Ulocal + Ucryst." So the atomic B-factors in your structure are not being refined individually, but they change anyway because the contribution of the TLS refinement is included. -Nat > > Kind regards, > Roeland Boer. > > > ++++++++++++++ Parameters ++++++++++++++++ > > refinement.main.number_of_macro_cycles=4 > refinement.main.ncs = True > refinement.input.xray_data { > labels=F > low_resolution=20.0 > high_resolution=3.6 > } > refinement.refine { > strategy=tls+individual_sites > adp { > tls="chain A and (resid 4:132 or resid 301)" > tls="chain B and (resid 4:132 or resid 301)" > tls="chain C and (resid 4:132 or resid 301)" > tls="chain X and (resid 4:132 or resid 301)" > tls="chain Y and (resid 4:132 or resid 301)" > tls="chain Z and (resid 4:132 or resid 301)" > } > } > refinement.ncs { > find_automatically = False > restraint_group { > reference = chain A and resid 133:203 > selection = chain B and resid 133:203 > selection = chain C and resid 133:203 > selection = chain X and resid 133:203 > selection = chain Y and resid 133:203 > selection = chain Z and resid 133:203 > } > restraint_group { > reference = chain B and (resid 4:132 or resid 301) > selection = chain A and (resid 4:132 or resid 301) > selection = chain C and (resid 4:132 or resid 301) > selection = chain X and (resid 4:132 or resid 301) > selection = chain Y and (resid 4:132 or resid 301) > selection = chain Z and (resid 4:132 or resid 301) > } > } > refinement.output.prefix=3.6-tlsnter-indsite-inputb-autowght-ncs > -------------------- Parameters -------------------------- > > ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 NEchols(a)lbl.gov

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Re: [phenixbb] fwd: kicked maps
by Pavel Afonine 06 Mar '09

06 Mar '09

Hi Maia, I think it's easier to try out and have an answer right away rather than speculate. Why don't you just try and see if it helps? I can't tell in advance if it will help or not. Again, a "average kick map" (AKM) is computed as following: we create a large ensemble of structures (~500 structures) that are all randomly shaken. The shake amount (rmsd distortion introduced to coordinates) varies from 0 to 1.0A. Then for each structure the map is computed (mFo-DFc or 2mFo-DFc or any other requested by the user). And finally, all maps are averaged out to produce one "averaged kick map". Obviously, just from general considerations, such map is supposed to have less or no bias, less noise and enhanced signal, and potentially can clear up some initially bad densities. I would also try an "omit AKM", where you remove some model parts in questions and compute mFo-DF and 2mFo-DFc AK maps. Please use the latests CCI Apps for this since we recently fixed a number of problems with this. Pavel. >> Hi Pavel, I have a problem with long linkers between domains in a >> protein structure that is a biological hexamer. >> I don't have much density for the linkers. Should "kicked maps" help >> me to see the density? The resolution of the X-ray data is 2.3A. >> >> Maia >

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default bondlengths - metal
by Engin Ozkan 06 Mar '09

06 Mar '09

Hi, all, Recently following the phenixbb, I was made aware of phenix.metal_coordination. So I just gave it a try for a structure of mine with sodium in it. Specifically, I decided to turn the use-default-bondlengths option on. The result was surprising, because the output file thinks that sodum to oxygen distances are supposed to be 1.9 Angstroms. Work done by Marjorie Harding and others have shown that this distance should be about 2.4 (Acta Cryst. D62 (2006), 678-682; for a summary of their numbers, http://tanna.bch.ed.ac.uk/newtargs_06.html). I wonder why phenix.metal_coordination chose 1.9 A as the default Na-O distance, or is the default option a different type of bond distance, I am not sure. Any clarification from the authors would be appreciated. Below is part of the output, showing the distance: refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name NA and chain N and resname NA and resseq 1 atom_selection_2 = name O and chain A and resname PHE and resseq 76 distance_ideal = 1.920420 sigma = 0.01 } } Engin

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fwd: phenix.autobuild- multiple models.
by Nathaniel Echols 04 Mar '09

04 Mar '09

> (The server bounced this message for some reason.) > From: Michael Karl Uhl <michael.uhl(a)uni-graz.at> > Date: March 3, 2009 11:55:16 PM PST > To: phenixbb(a)phenix-online.org > Subject: phenix.autobuild- multiple models > Reply-To: michael.uhl(a)a-b.at > > > Hello, > > I have not registered for this list until now, but have a very > urgent question concerning phenix.autobuild and multiple models as > input. Is there a possibility to merge models generated by different > phenix.autobuild runs. I have several overall_best-structure and > want to merge them into one single overall_best structure. I have > found the keyword "merge_models= True" but it does not really work > (Sorry, unknown file or keyword: merge_models=True). How should I > make the input in this case? > > > Thanks a lot, > > > Michael Uhl. > > ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 NEchols(a)lbl.gov

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