- phenixbb - phenix-online.org

phenix.refine change: support for residues on symmetry elements
by Ralf W. Grosse-Kunstleve 28 Dec '09

28 Dec '09

The current development version of phenix.refine (dev-268 or later) supports residues located on symmetry elements, e.g. SO4 on a three-fold axis. phenix.refine now computes structure factors slightly differently compared to older versions. The new rules are: - Atoms with occupancy == 1 are subject to automatic handling of the symmetry. Example: An atom near a three-fold axis (distance to symmetry copy <= 0.5 A) is moved onto the axis and constrained in refinement to stay on the axis. The "special position factor" (1/3 is this case) is taken into account internally. The factor does not appear in the occupancy. - Atoms with occupancy != 1 are assumed to take the special position factor into account in the occupancy. Automatic handling of the symmetry is turned off. Example: A disordered SO4 molecule near a three-fold axis should have occupancies of 0.33 for all atoms. - If all atoms in a residue have occupancies != 1, all nonbonded symmetry interactions between the atoms in the residue are disabled. These three rules are meant - to bring phenix.refine in line with other programs and the PDB. - "to do the right thing" in most cases without manual intervention. Please let me know if you see problems with the new way phenix.refine uses occupancies to determine special position constraints and exclusions for nonbonded symmetry interactions. Does anyone need atoms with partial occupancies but constrained to stay on a symmetry axis during refinement? Ralf

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Re: [phenixbb] Phaser SAD question
by Kitty Pattridge 24 Dec '09

24 Dec '09

"Randy J. Read" <rjr27(a)cam.ac.uk> wrote: >Dear Peter, > >I'm interested in your observation that you get better signal from an >anomalous difference map computed with density-modified phases than you get >with an LLG map using the MR model. Presumably the density modification >just started from the model phases as well? We've never tried that, so >we'll have to look into that. Unfortunately, you can't at the moment start >the LLG completion with a "model" specified through structure factors, >though this is on our to-do list. > >With the MR+SAD option, because it is iterative, there are sites found in >subsequent cycles (where the information from some of the anomalous >scatterers has become available) and you end up with a set of reliable >sites that can be significantly larger than the set obtained from the first >LLG map. Does your anomalous difference Fourier with density modified >phases give you a larger apparently reliable substructure than the >iterative completion? You could use phenix.emma to compare the two >substructures and see how much they have in common. > >You can indeed give Phaser the set of sites that you got from the anomalous >difference map. One way to choose the cutoff would be to see how deep the >deepest hole is (i.e. how many standard deviations the map goes in the >negative direction), and choose a larger number in the positive direction. >Or you could just use the peaks above 6-7 sigma. > >I'd be interested in hearing how you get on with this approach, off-line if >you prefer. > >Good luck and Happy Christmas! > >Randy Read > >On Dec 24 2009, Peter Grey wrote: > >>Dear Phenix Experts, >> >>I use the SAD+MR option in Phenix. The ASU is huge and the number of >>scatterres is in the few hundreds range. I try to minimize the number of >>runs of Phaser SAD+MR since they take long time on my computer and would >>appreciate your insight regarding the following : >> >> - I noticed that I get much higher signal and much larger number of sites >> if I use density modified phases to calculate the anomalous difference >> map. Is it possible to input these phases instead of the model to Phaser >> ? >> >> - If not, do you recommend providing Phaser with the list of sites found >> in this difference anomalous map. Should such a list include only the >> sites you can be sure of (say above 7 sigma) or all possible sites (say >> above 5 sigma) ? >> >> - Should I use the (peak height)/(sigma of map) as the first estimate of >> occupancy ? if so do I have to normalize it (strongest site has occupancy >> of 1) or can I leave the height/sigma values as they are ? >> >> >>Many thanks, >> >>Peter. >> > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb > >

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Re: [phenixbb] Phaser SAD question
by Kitty Pattridge 24 Dec '09

24 Dec '09

"Randy J. Read" <rjr27(a)cam.ac.uk> wrote: >Dear Peter, > >I'm interested in your observation that you get better signal from an >anomalous difference map computed with density-modified phases than you get >with an LLG map using the MR model. Presumably the density modification >just started from the model phases as well? We've never tried that, so >we'll have to look into that. Unfortunately, you can't at the moment start >the LLG completion with a "model" specified through structure factors, >though this is on our to-do list. > >With the MR+SAD option, because it is iterative, there are sites found in >subsequent cycles (where the information from some of the anomalous >scatterers has become available) and you end up with a set of reliable >sites that can be significantly larger than the set obtained from the first >LLG map. Does your anomalous difference Fourier with density modified >phases give you a larger apparently reliable substructure than the >iterative completion? You could use phenix.emma to compare the two >substructures and see how much they have in common. > >You can indeed give Phaser the set of sites that you got from the anomalous >difference map. One way to choose the cutoff would be to see how deep the >deepest hole is (i.e. how many standard deviations the map goes in the >negative direction), and choose a larger number in the positive direction. >Or you could just use the peaks above 6-7 sigma. > >I'd be interested in hearing how you get on with this approach, off-line if >you prefer. > >Good luck and Happy Christmas! > >Randy Read > >On Dec 24 2009, Peter Grey wrote: > >>Dear Phenix Experts, >> >>I use the SAD+MR option in Phenix. The ASU is huge and the number of >>scatterres is in the few hundreds range. I try to minimize the number of >>runs of Phaser SAD+MR since they take long time on my computer and would >>appreciate your insight regarding the following : >> >> - I noticed that I get much higher signal and much larger number of sites >> if I use density modified phases to calculate the anomalous difference >> map. Is it possible to input these phases instead of the model to Phaser >> ? >> >> - If not, do you recommend providing Phaser with the list of sites found >> in this difference anomalous map. Should such a list include only the >> sites you can be sure of (say above 7 sigma) or all possible sites (say >> above 5 sigma) ? >> >> - Should I use the (peak height)/(sigma of map) as the first estimate of >> occupancy ? if so do I have to normalize it (strongest site has occupancy >> of 1) or can I leave the height/sigma values as they are ? >> >> >>Many thanks, >> >>Peter. >> > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb > >

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Phaser SAD question
by Peter Grey 24 Dec '09

24 Dec '09

Dear Phenix Experts, I use the SAD+MR option in Phenix. The ASU is huge and the number of scatterres is in the few hundreds range. I try to minimize the number of runs of Phaser SAD+MR since they take long time on my computer and would appreciate your insight regarding the following : - I noticed that I get much higher signal and much larger number of sites if I use density modified phases to calculate the anomalous difference map. Is it possible to input these phases instead of the model to Phaser ? - If not, do you recommend providing Phaser with the list of sites found in this difference anomalous map. Should such a list include only the sites you can be sure of (say above 7 sigma) or all possible sites (say above 5 sigma) ? - Should I use the (peak height)/(sigma of map) as the first estimate of occupancy ? if so do I have to normalize it (strongest site has occupancy of 1) or can I leave the height/sigma values as they are ? Many thanks, Peter.

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Re: [phenixbb] phenix GUI freezing during refinement and file naming issues
by John Berrisford 23 Dec '09

23 Dec '09

Dear all. When the GUI freezes on me its a complete freeze with no pop up dialog boxes. This means the job history is not recorded and no results are recorded in the GUI. I'm not sure if this is screensaver or desktop switching related - it only seems to happen randomly - mostly when running long jobs where nothing much happens on the screen, in my experience. I'm also using an nVidia card and an upto date version of the X-server (on my ubuntu 9.10 box). I agree this is a minor issue compared to having a great program which works well. But it does mean that if its easier to use a command line all your hard work with the GUI (and its enhancements) will go to waste... John -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk TEL: +44 (01223) 252918

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rotational pseudosymmetry in P61?
by Gabriela Guédez R. 23 Dec '09

23 Dec '09

Hi all, how could i determine the r.m.s.d. and matrix of the NCS operator that relates two molecules in the asymmetric unit in P61? i would like to know whether there is rotational pseudosymmetry in the crystal because i see peaks for two molecules in the kappa=180º SR map. Thanks a lot!

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Autosol problem: Failed to carry out Autosol_scale_and_analyze_mad
by Zheng Zhou 23 Dec '09

23 Dec '09

Dear all I installed phenix nightly builds, dev-256. I have solved structures using molecular replacement. Phenix.refine runs smoothly. Thanks for your great work. When I run some test data using autosol, I met the following error message: ******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked See overall log file and also solve log file (in AutoSol_run_1_/LAST.LOG) ******************************************************************************** The LAST.LOG appears to be empty. I also run the phenix.solve command. Here is the output: ********************************************************************************************* $ phenix.solve binary=/usr/local/phenix-dev-254/build/intel-linux-2.6/solve_resolve/exe/solve SOLVEDIR=/usr/local/phenix-dev-254/solve_resolve/ext_ref_files SYMOP=/usr/local/phenix-dev-254/solve_resolve/ext_ref_files/symop.lib SYMINFO=/usr/local/phenix-dev-254/solve_resolve/ext_ref_files/syminfo.lib CCP4_OPEN=UNKNOWN SOLVE_RESOLVE_MALLOC_MAX=7.48024e+09 /usr/local/phenix-dev-254/build/intel-linux-2.6/solve_resolve/exe/solve: error while loading shared libraries: /usr/local/phenix-dev-254/build/intel-linux-2.6/lib/libimf.so: cannot restore segment prot after reloc: Permission denied ***************************************************************************************************** The libimf.so file is there. I run phenix.solve as superuser, but I still have the same problem. Thanks for your help. Best, Joe

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phenix GUI freezing during refinement and file naming issues
by John Berrisford 22 Dec '09

22 Dec '09

Dear all I've recently been having a few problems with the new phenix GUI freezing during refinement runs on several different systems, most often when I try and do something different on the computer which puts the GUI in the background or on a different desktop. I've seen this problem when running a local copy of phenix on a ubuntu 9.10 system or when running the GUI remotely on a mac connected to our Centos linux cluster. When I switch to a different desktop to get on with doing something else (refine jobs can take a long time) the GUI freezes - although the underlying task runs correctly. The only way out of this problem is to force quit the GUI and then restart it. However, this means that the task isn't recorded in my history and all settings used to run the job are lost from the GUI - the parameter file to run the job does exist though. This also means I lose all the nice molprobibity connections to coot which are really useful. Also if I try to run phenix on the Centos linux cluster when running a local windows system the GUI is so sllloooowwww whenever the GUI tries to open a new window that its unsuable. Has anyone else seen these problems and know a cure? If I run phenix locally on a mac I don't seem to have this problem, but it is nice to run the refine job on our linux cluster so that I can get on with doing something else without it slowing down my mac. On another note, when running phenix refine from the GUI it nicely puts all the files in a folder called "Refine_1" etc... with the number incrementing with each run. So, why are the pdb and mtz file always called "refine_1..." not "refine_2 etc... to match the folder name? This would help with keeping track of files during itterative refinement and model building. It would also stop the problem of having lots of files called "refine_1" loaded into coot when I try to compare models from different refine runs. It would also be useful to be able to be able to add a prefix to the file name / folder name / job name in the GUI so that I could distinguish between different refinement experiments. This is easy to do on the command line.... Thanks and merry christmas John -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk TEL: +44 (01223) 252918

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Re: [phenixbb] ncs resolve
by Thomas C. Terwilliger 19 Dec '09

19 Dec '09

Hi Georg, I think that if phenix.find_ncs says No NCS found...you might try ncs_in_type=sites then it is interpreting the sites as parts of chains and is trying to find NCS in those chains, while what you want is for it to interpret these as sites and to find ncs in the sites. So I wonder if you did try adding the keyword ncs_in_type as in: phenix.find_ncs my_sites.pdb my_map_coeffs.mtz ncs_in_type=sites If that failed, then I would suggest trying fewer sites that are more separated: perhaps 3 or 4 sites per monomer, as far apart as possible. If that fails (or maybe as your first try actually), take the entire helix, and make 2 copies A and B, placing them in their appropriate places, and then feed these to phenix with: phenix.simple_ncs_from_pdb my_two_copies.pdb and that may do it for you. All the best, Tom T >> Dear phenix users, >> >> luckily autobuild could solve my SAD problem, but didn´t find any NCS. >> Although the protein is a dimer. I analysed the structure in coot now and >> SSM superposed a homolog protein (just one chain) which (fits quite good) >> on >> chain A and B. I then could find a helix which was built in chain A and B, >> I >> took the 8 corresponding aminoacids from A and B and run: phenix.find_ncs >> overall_best_denmod_map_coeffs.mtz overall_best198206ca155163b.pdb with >> and >> without ncs_parameters.force_ncs=True and didn´t get any solution. >> >> The program gives me an output saying: No NCS found...you might try >> ncs_in_type=sites >> >> Any suggestions whats wrong and a smarter way to do this. >> >> Thanks in advance Georg. >> >> -----Ursprüngliche Nachricht----- >> Von: phenixbb-bounces(a)phenix-online.org >> [mailto:[email protected]] Im Auftrag von Thomas Stout >> Gesendet: Freitag, 18. Dezember 2009 23:56 >> An: PHENIX user mailing list >> Betreff: Re: [phenixbb] queueing systems >> >> >> >> We don't use PHENIX, but we do use several queueing systems on three >> different clusters. >> >> SGE is bulletproof and highly recommended. >> >> Condor has some degree of "evilness" -- especially under Windows. I have >> found it prone to grabbing resources indiscriminately and also being very, >> very resistant to uninstallation. Your mileage may vary. >> >> Certain implementations of "torque" are broken - stay away, or at least be >> very cautious and enter with your eyes open. >> >> Cheers, >> Tom >> >> >> -----Original Message----- >> From: phenixbb-bounces(a)phenix-online.org on behalf of Phil Evans >> Sent: Fri 12/18/2009 2:47 PM >> To: PHENIX user mailing list >> Subject: Re: [phenixbb] queueing systems >> >> >> Dear Nat >> >> We use Sun grid engine >> >> Phil >> >> On 18 Dec 2009, at 18:47, Nathaniel Echols wrote: >> >>> Hi all-- >>> >>> I'd like to hear what kinds of queueing systems people are using for >>> running Phenix on managed clusters. The eventual goal - if feasible - >>> is to add support for submitting jobs directly from the Phenix GUI. >>> Anyone who is interested, please send me (not the list) a brief email >>> describing a) the OS, b) the queueing software, and c) the submission >>> method (i.e. shell script, configuration file, simple command). >>> (Also, anyone who is willing to help test this if and when it becomes >>> available, let me know - I have access to Sun Grid Engine and Condor >>> already, but it's probably going to be difficult to test anything else >>> personally.) >>> >>> thanks, >>> Nat >>> >>> -------------------- >>> Nathaniel Echols >>> Lawrence Berkeley Lab >>> 510-486-5136 >>> NEchols(a)lbl.gov >>> >>> >>> >>> >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> This email (including any attachments) may contain material that is >> confidential and privileged and is for the sole use of the intended >> recipient. Any review, reliance or distribution by others or forwarding >> without express permission is strictly prohibited. If you are not the >> intended recipient, please contact the sender and delete all copies. >> Exelixis, Inc. reserves the right, to the extent and under circumstances >> permitted by applicable law, to retain, monitor and intercept e-mail >> messages to and from its systems. >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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queueing systems
by Nathaniel Echols 18 Dec '09

18 Dec '09

Hi all-- I'd like to hear what kinds of queueing systems people are using for running Phenix on managed clusters. The eventual goal - if feasible - is to add support for submitting jobs directly from the Phenix GUI. Anyone who is interested, please send me (not the list) a brief email describing a) the OS, b) the queueing software, and c) the submission method (i.e. shell script, configuration file, simple command). (Also, anyone who is willing to help test this if and when it becomes available, let me know - I have access to Sun Grid Engine and Condor already, but it's probably going to be difficult to test anything else personally.) thanks, Nat -------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 NEchols(a)lbl.gov

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