- phenixbb - phenix-online.org

Re: [phenixbb] Very very small Phaser Bug
by Tom Terwilliger 12 Dec '07

12 Dec '07

Hi James, Yes this sounds like a bug to me. I think it is a mis-communication between the automr wizard and phaser. We'll check it out. Thank you! -Tom T At 10:05 PM 12/10/2007, you wrote: >This is a fairly trivial bug, but I thought I'd report it anyway (I'm >not sure whether the problem is with the phenix.automr (rc6 build) or >with all phaser implementations (the one included is: 2.1.1 so I've >emailed both lists): > >when running phaser in data that was scaled in P 31 2 1, I used >phenix.automr to automate MR searches in all spacegroups that are >indistinguishable by systematic absences with: > >phenix.automr template.pdb final_P3121.sca RMS=1 mass=17000 >rebuild_after_mr=False copies=1 use_all_plausible_sg=True > >The program correctly finds the solution in P3221 with a log >likelihood gain of 1000 vs 20 for P3121, everything is fine in the >outputted PDB CRYST1 line and MTZ; however the log file annoyingly >mentions the spacegroup for the last time with "Final space group:P 31 >2 1" even though elsewhere in the log file it correctly lists >"SpaceGroup of Solution: P 32 2 1". I've excerpted the log file >below. If this is the intended behaviour and not a bug, then I >apologize but find it quite counterintuitive. > >Just a small bug, haven't seen if this behaviour occurs in other >systematic absence-equivalent space groups. > >Best, > >jf > >**BEGIN LOG > > SpaceGroup of Solution: P 32 2 1 > > SINGLE solution > > Solution written to PDB file: /Users/jfraser/data/AutoMR_run_7_/MR.1.pd >b > Solution written to MTZ file: /Users/jfraser/data/AutoMR_run_7_/MR.1.mt >z > Solution log-likelihood gain: 1056.73 > Solution annotation (history): RFZ=11.9 TFZ=27.5 PAK=0 LLG=850 LLG=1057 > > > >AUTOMR RUN: 7 > >Files in directory : AutoMR_run_7_ > > > >CRITERIA FOR PHASER MR RUN: >selection_criteria_rot : Percent_of_best >selection_criteria_rot_value : 75 >use_all_plausible_sg : Yes >overlap_allowed : > >List of space groups tested: >['P 3 2 1', 'P 31 2 1', 'P 32 2 1'] > >Final space group:P 31 2 1 > >CURRENT ENSEMBLES: > >ENSEMBLE ID: ensemble_1 >FILE: template.pdb RMS = 1.0 >ENSEMBLES USED IN SEARCH: ensemble_1 > >**************** SOLUTION MR ******* > > Log likelihood gain for solution MR: 1056.7344 > Output PDB files for solution MR: MR.1.pdb > Output MTZ files for solution MR: MR.1.mtz > >**END LOG > > >-- >James Fraser >jamesfraser(a)berkeley.edu >Alber Lab >356 Stanley Hall, QB3 >UC Berkeley >Berkeley, CA 94720 >http://ucxray.berkeley.edu/~jfraser/ >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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Very very small Phaser Bug
by James Fraser 11 Dec '07

11 Dec '07

This is a fairly trivial bug, but I thought I'd report it anyway (I'm not sure whether the problem is with the phenix.automr (rc6 build) or with all phaser implementations (the one included is: 2.1.1 so I've emailed both lists): when running phaser in data that was scaled in P 31 2 1, I used phenix.automr to automate MR searches in all spacegroups that are indistinguishable by systematic absences with: phenix.automr template.pdb final_P3121.sca RMS=1 mass=17000 rebuild_after_mr=False copies=1 use_all_plausible_sg=True The program correctly finds the solution in P3221 with a log likelihood gain of 1000 vs 20 for P3121, everything is fine in the outputted PDB CRYST1 line and MTZ; however the log file annoyingly mentions the spacegroup for the last time with "Final space group:P 31 2 1" even though elsewhere in the log file it correctly lists "SpaceGroup of Solution: P 32 2 1". I've excerpted the log file below. If this is the intended behaviour and not a bug, then I apologize but find it quite counterintuitive. Just a small bug, haven't seen if this behaviour occurs in other systematic absence-equivalent space groups. Best, jf **BEGIN LOG SpaceGroup of Solution: P 32 2 1 SINGLE solution Solution written to PDB file: /Users/jfraser/data/AutoMR_run_7_/MR.1.pd b Solution written to MTZ file: /Users/jfraser/data/AutoMR_run_7_/MR.1.mt z Solution log-likelihood gain: 1056.73 Solution annotation (history): RFZ=11.9 TFZ=27.5 PAK=0 LLG=850 LLG=1057 AUTOMR RUN: 7 Files in directory : AutoMR_run_7_ CRITERIA FOR PHASER MR RUN: selection_criteria_rot : Percent_of_best selection_criteria_rot_value : 75 use_all_plausible_sg : Yes overlap_allowed : List of space groups tested: ['P 3 2 1', 'P 31 2 1', 'P 32 2 1'] Final space group:P 31 2 1 CURRENT ENSEMBLES: ENSEMBLE ID: ensemble_1 FILE: template.pdb RMS = 1.0 ENSEMBLES USED IN SEARCH: ensemble_1 **************** SOLUTION MR ******* Log likelihood gain for solution MR: 1056.7344 Output PDB files for solution MR: MR.1.pdb Output MTZ files for solution MR: MR.1.mtz **END LOG -- James Fraser jamesfraser(a)berkeley.edu Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/

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automr with muti components (NMR models)
by ming lu 10 Dec '07

10 Dec '07

Hi everyones I am trying automr to solve the structure of my protein. It has three domains, each domain has NMR structure available. So the sequence identity of my search model is 100%. I tried use mutiple components as search models, but I had a hard time to obtain a interpretable solution. Any suggestions on the use of mutiple components as search models? or suggestions on how to use NMR structure as search models? Thanks for your help. Ming

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Can geometry restraints include non-ideal target values?
by Joe Krahn 08 Dec '07

08 Dec '07

I see that phenix is using the same kind of simplistic statistical restraints as CCP4. Are there plans to improve the geometry restraints once the rest of phenix is stable? The problem with simple statistical restraints as used by CCP4 is that they completely ignore correlations due to interactions of multiple restraints. This is particularly bad for puckered rings like proline and nucleic acids. Nucleic acids get around this by using a fixed sugar pucker, which results in a lot of bad geometries for non-helical nucleic acids (many of which make it in to the PDB). However, if you consider the geometries "ideal value" and "ideal value esd" as just another way to write a harmonic restraint, then it is possible to make an improved restraint library. In this case, some individual geometry restraints will have target values that restrain towards non-ideal values in order to produce the correct result when all terms are combined. The problem is that these terms will give higher RMSD values, which would probably confuse software like REFMAC, which is designed to tweak restraint weights based on RMSDs. So, does phenix have any built-in restraint adjustments that is based on current rmsds? If so, is there a way to disable it? Joe Krahn

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Hydrogens of ligands generated in elbow explode in coot realspace refinement
by Schubert, Carsten [PRDUS] 07 Dec '07

07 Dec '07

Hi, when I refine a ligand with hydrogens in coot using realspace refinement, the hydrogens explode into the surrounding density. This only happens with ligand/cif files generated in elbow and not libcheck. Coot apparently needs and additional loop in the .cif file: _chem_comp_tree.xxxx, which is missing from the elbow output. Unfortunately the geometry generated by libcheck is pretty dismal, so I can probably get around this by running libcheck on the refined coords from elbow ... Nigel, is it possible to fix elbow for the next rc? PS I am running the latest phenix (rc6) and coot 0.33 if that helps. Cheers Carsten

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Question about adding hydrogrens with reduce -- parameters for phenix.refine
by Schubert, Carsten [PRDUS] 07 Dec '07

07 Dec '07

Hi I am trying to generate a model with all hydrogens placed using reduce. To my surprise it only applies hydrogens to a selected few residues. How do I coax reduce to add ALL hydrogens to my model, according to the Richardson Lab paper this should be possible? The help from reduce was not helpful in that regard. Or is adding all hydrogens a bad idea? Along those lines. If I would use another tool to generate the hydrogens, like CNS(X) or Maeastro, how compatible are the parameter files? Thanks for any input Carsten

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Re: [phenixbb] Forcing autobuild wizard to do a complete rebuild
by Tom Terwilliger 04 Dec '07

04 Dec '07

Hi Carsten, Yes, I see this is unclear. All commands listed at the end of the documentation for each wizard can be applied at the command line. (Not just the ones labelled command-line only). All the best, Tom T At 11:15 AM 12/3/2007, you wrote: >Thanks Tom, Peter > >As a follow-up question, which may have been addressed in the >manual, but I don't recall seeing it: Does the (wizard) command line >accept ALL keywords under the autobuild/autosol scope or ONLY the >ones listed as "command-line-only"? I assumed (wrongfully?) that the >command line only accepts the keywords explicitely listed under >"command-line-only", and the rest is reserved for scripts/input files. > >I know, I could test this out, but a general clarification by the >experts and an addition to the manual, if necessary, would be great. > >Cheers, > > Carsten > > > > > -----Original Message----- > > From: phenixbb-bounces(a)phenix-online.org > > [mailto:[email protected]]On Behalf Of Tom > > Terwilliger > > Sent: Monday, December 03, 2007 12:59 PM > > To: PHENIX user mailing list > > Subject: Re: [phenixbb] Forcing autobuild wizard to do a complete > > rebuild > > > > > > Hi Carsten, > > > > You can tell the autobuild wizard from the command line: > > > > rebuild_in_place=False > > > > You can also set this in the GUI on the 2nd input screen at the top > > of the screen. > > > > I hope that helps! > > -Tom T > > > > At 10:17 AM 12/3/2007, you wrote: > > >Content-class: urn:content-classes:message > > >Content-Type: multipart/alternative; > > > boundary="----_=_NextPart_001_01C835D0.68A40BB9" > > > > > >Hi, > > > > > >I am using the autobuild wizard in the latest phenix release to > > >rebuild a model from a MR solution. Since the MR-template I used > > >has been modified with chainsaw, its sequence identity to the target > > >sequence is fairly high. The autobuild wizard therefore uses the > > >rebuilt-in-place mode to rebuild the model. How can I force the > > >wizard to do a complete rebuild? > > > > > >Thanks > > > > > > Carsten > > >_______________________________________________ > > >phenixbb mailing list > > >phenixbb(a)phenix-online.org > > >http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > > > > > > > Thomas C. Terwilliger > > Mail Stop M888 > > Los Alamos National Laboratory > > Los Alamos, NM 87545 > > > > Tel: 505-667-0072 email: terwilliger(a)LANL.gov > > Fax: 505-665-3024 SOLVE web site: >http://solve.lanl.gov >PHENIX web site: http:www.phenix-online.org >ISFI Integrated Center for Structure and Function Innovation web >site: http://techcenter.mbi.ucla.edu >TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB > > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb > > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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Re: [phenixbb] Forcing autobuild wizard to do a complete rebuild
by Tom Terwilliger 04 Dec '07

04 Dec '07

Hi Carsten, You can tell the autobuild wizard from the command line: rebuild_in_place=False You can also set this in the GUI on the 2nd input screen at the top of the screen. I hope that helps! -Tom T At 10:17 AM 12/3/2007, you wrote: >Content-class: urn:content-classes:message >Content-Type: multipart/alternative; > boundary="----_=_NextPart_001_01C835D0.68A40BB9" > >Hi, > >I am using the autobuild wizard in the latest phenix release to >rebuild a model from a MR solution. Since the MR-template I used >has been modified with chainsaw, its sequence identity to the target >sequence is fairly high. The autobuild wizard therefore uses the >rebuilt-in-place mode to rebuild the model. How can I force the >wizard to do a complete rebuild? > >Thanks > > Carsten >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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Forcing autobuild wizard to do a complete rebuild
by Schubert, Carsten [PRDUS] 04 Dec '07

04 Dec '07

Hi, I am using the autobuild wizard in the latest phenix release to rebuild a model from a MR solution. Since the MR-template I used has been modified with chainsaw, its sequence identity to the target sequence is fairly high. The autobuild wizard therefore uses the rebuilt-in-place mode to rebuild the model. How can I force the wizard to do a complete rebuild? Thanks Carsten

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phenix gui startup problem
by david albesa-jove 01 Dec '07

01 Dec '07

Dear phenix users, After installation of phenix using phenix-installer-1.3b-rc6-intel-linux-2.6-x86_64.tar and setting up the environmental variables, phenix gui fails to startup giving the following error: (99, 'Cannot assign requested address'). See bellow for further details. Thanks for your help, David ************************************************************8 [root@bio-daj2 phenix2]# phenix +++++++++++++++++++++++++++++++++++ Warning +++++++++++++++++++++++++++++++++++ Hostname is bio-daj2.cmmi.ic.ac.uk but fully qualified domain is bio-daj2 +++++++++++++++++++++++++++++++++++ Warning +++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++ Warning +++++++++++++++++++++++++++++++++++ IP nslookup is ls-saf-g34b.saf.ic.ac.uk but FQDN is bio-daj2 +++++++++++++++++++++++++++++++++++ Warning +++++++++++++++++++++++++++++++++++ Running the PHENIX GUI with /usr/local/phenix-1.3b-rc6/build/intel- linux-2.6-x86_64/base/bin/python PHENIX distribution located in /usr/local/phenix-1.3b-rc6/phenix Exception in thread Thread-1: Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc6/build/intel- linux-2.6-x86_64/base/lib/python2.5/threading.py", line 460, in __bootstrap self.run() File "/usr/local/phenix-1.3b-rc6/build/intel- linux-2.6-x86_64/base/lib/python2.5/threading.py", line 440, in run self.__target(*self.__args, **self.__kwargs) File "/usr/local/phenix-1.3b-rc6/phenix/wxGUI/GUIServer.py", line 14, in __init__ PhenixServer.PhenixServer.__init__(self, port, GUIRequestHandler) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/server/PhenixServer.py", line 50, in __init__ ddbs = apply(func, (server_address, handler),{}) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/server/SocketServer.py", line 333, in __init__ self.server_bind() File "/usr/local/phenix-1.3b-rc6/phenix/phenix/server/PhenixServer.py", line 65, in server_bind SocketServer.ThreadingTCPServer.server_bind(self) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/server/SocketServer.py", line 344, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind error: (99, 'Cannot assign requested address') ======================================================= David Albesa-Jove PhD Centre for Molecular Microbiology and Infection Division of Cell and Molecular Biology Flowers Building, Level 1 South Kensington Campus Imperial College London London. SW7 2AZ. Tel: 020.7594.3070 e-mail: d.albesa-jove(a)imperial.ac.uk

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