- phenixbb - phenix-online.org

some sort of occupancy refinement
by Bryan W. Lepore 01 Jan '10

01 Jan '10

question is after the setup here : i have a ligand with multiple conformers. i gave each conformer a different chain label. refining occupancy for the overlapped parts kicks that part out of the density. i have remove_selection for the parts that are 1.0 and they seem OK. a single conformer stays in the density. i tried starting with and without site or occupancy refinement, no help. i do not want group occupancy refinement b/c some parts do not overlap - i.e. they "should" be occupancy 1.0 -- i tried it anyways with constrained_group =... to check. is the chain label an improper way to do this? -bryan p.s: Happy New Year with Blue Moon Eclipse (~10degW->180degE long. eastern HS)!

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high resolution Anomalous map
by vennila Natesan 31 Dec '09

31 Dec '09

Hello all... How do we create anomalous map using high resolution reflections? For example, if we have 2.2A resolution data (i.e 20-2.2A), i want to know how to create the anomalous map for the same dataset but from 2.4-2.2A resolution range. Vennila.

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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 19 Dec '09

19 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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refinement in low resolution
by r n 17 Dec '09

17 Dec '09

Hi I am trying to refine the model in low resolution and there are multimer in the asu. I did rigid body refinement after MR , molecule did not move much and R/Rfree stays 45 % and If I do the overlap between the monomers, rms is 0.06. If I do simulated annealing or any type of refinement (group_adp), Rfree is high and R goes down, but the if do the superposition of the monomer, rms is 1.5 to 1.8. So like to know what kind of refinement is can be done in very low resolution between 5 to 6 ang data? Is it any strict ncs could be possible in phenix that should not move the monomer too much? suggestions are appreciated rn

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B(sol) too high
by Matthew Merski 17 Dec '09

17 Dec '09

I am in the process of solving a series of protein/ligand complex structures and ran the Polygon tool on the series. I noticed that, in general, even when all the other statistics were good, the B(sol) term was a bit too high according to Polygon. (The structures with poorer statistics also had high B(sol) values as well.) Since this is a series of multiple structures of the same protein, should this be a concern for me? And if so, what are typical causes of a high B(sol) value? Matt Merski Shoichet Group UCSF

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LigPlot
by Zhou, Tongqing (NIH/VRC) [E] 16 Dec '09

16 Dec '09

Dear Phenix Users, I am trying to get Roman Laskowski's Ligplot, but could not find it on the ftp site he provided in the website below: http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html Does anyone have any information on how and where to get it? Thanks, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

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tls matrices etc.
by Bryan W. Lepore 16 Dec '09

16 Dec '09

does phenix compute the center of reaction pretty much like refmac does? i figure the matrices/center of reaction between refmac and phenix are identical - is that true? -bryan

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Rfree refmac5 issue
by anon 16 Dec '09

16 Dec '09

Hi, has anyone had any experience using phenix with refmac5? I seem to be having issues with the Rfree flag. Phenix sets aside 8.1% of the reflection for Rfree. However when i use refmac for refinement, it reports that its using 91.4% of the reflections for Rfree........? thanks

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polygon output (dev-256)
by Bryan W. Lepore 16 Dec '09

16 Dec '09

[ phenix dev 256 ] where - or should we - be looking for the polygon output .png (the one with the polygon)? its obvious in 1.5-2, so i think its dev-256 only... -bryan

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.cif use/restraints
by Bryan W. Lepore 16 Dec '09

16 Dec '09

a ligand is distorting - as if it is ignoring the .cif and i already have the angles tighted up in the .def. what else should i check? what i did : generated some elbow output. the .cif was provided to phenix.refine on cmd line. the .pdb had the H's and CONNECT's removed, but the .cif retains them. the .pdb was incorporated into a single .pdb input file. -bryan

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Firefox problem
by Phil Evans 15 Dec '09

15 Dec '09

Dear Gurus If I click the Help button on the Phenix GUI I get the following fail messages. What am I doing wrong? I'm running 64-bit Phenix on a 64-bit machine, but our Firefox (as I understand it) is 32-bit, since there is no 64-bit Java Best wishes Phil hex_pre> phenix Using browser /usr/bin/firefox (Gecko:3603): Gtk-WARNING **: /lmb/home/public/xtal/Phenix/Phenix64/phenix-dev-2 49/build/intel-linux-2.6-x86_64/base/lib/gtk-2.0/2.10.0/engines/libclearlooks.so : wrong ELF class: ELFCLASS64 (Gecko:3603): Pango-WARNING **: /lmb/home/public/xtal/Phenix/Phenix64/phenix-dev -249/build/intel-linux-2.6-x86_64/base/lib/pango/1.6.0/modules/pango-basic-fc.so : wrong ELF class: ELFCLASS64 Failed to load Pango module for id: 'BasicScriptEngineFc' (Gecko:3603): Pango-WARNING **: /lmb/home/public/xtal/Phenix/Phenix64/phenix-dev -249/build/intel-linux-2.6-x86_64/base/lib/pango/1.6.0/modules/pango-basic-fc.so : wrong ELF class: ELFCLASS64 Failed to load Pango module for id: 'BasicScriptEngineFc' (Gecko:3603): Pango-WARNING **: /lmb/home/public/xtal/Phenix/Phenix64/phenix-dev -249/build/intel-linux-2.6-x86_64/base/lib/pango/1.6.0/modules/pango-basic-fc.so : wrong ELF class: ELFCLASS64 Failed to load Pango module for id: 'BasicScriptEngineFc' (Gecko:3603): Pango-WARNING **: /lmb/home/public/xtal/Phenix/Phenix64/phenix-dev -249/build/intel-linux-2.6-x86_64/base/lib/pango/1.6.0/modules/pango-basic-fc.so : wrong ELF class: ELFCLASS64 .. snip ... Failed to load Pango module for id: 'BasicScriptEngineFc' (Gecko:3603): Pango-WARNING **: /lmb/home/public/xtal/Phenix/Phenix64/phenix-dev -249/build/intel-linux-2.6-x86_64/base/lib/pango/1.6.0/modules/pango-basic-fc.so : wrong ELF class: ELFCLASS64 Failed to load Pango module for id: 'BasicScriptEngineFc' (Gecko:3603): GLib-GObject-CRITICAL **: g_object_get_qdata: assertion `G_IS_OBJE CT (object)' failed (Gecko:3603): Pango-CRITICAL **: pango_font_describe: assertion `font != NULL' f ailed /usr/lib/firefox-3.0.15/run-mozilla.sh: line 131: 3603 Segmentation fault "$prog" ${1+"$@"}

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phenix and refmac5
by anon 15 Dec '09

15 Dec '09

Hi, recently i used phenix (AutoSol and AutoBuild) on a SAD dataset containing Iodine. I was wanting to do my refinement using Refmac instead of phenix.refine. I was wondering where would i be able to locate the correct .mtz file to input into Refmac5 for rounds of refinement? I was under the impression the .mtz file used for refinement was the one produced after scaling, but im not sure where phenix puts this. Also I was wondering if anyone had any issues with phenix.xtriage carrying out its Matthews coefficient calculation? When using Phenix, it gave me a solution with 3 mols/AU, despite there being 4 mols/AU according to the Matthews coeffiecient calculation in CCP4. Looking back at the xtriage log in autosol it has n_residues= 200 (despite me not specifying anywhere the number of residues, my protein has 147 residues). Realising this I re-ran Autosol, inputting my .mtz file along with my sequence this time, and specifying the number of NCS copies as 4. Looking at the phenix.xtriage log this time results in it recognising the correct number of residues, however the matthews coefficient calculation is still incorrect, claiming 1 mol/Au. Any ideas what may be the problem? ##-------------------------------------------## ## Unit cell defined manually, will ignore ## specification in reflection file: ## From file : None ## From input: (140.124, 77.954, 54.519, 90, 98.549, 90) ##-------------------------------------------## ##-------------------------------------------## ## Space group defined manually, will ignore ## specification in reflection file: ## From file : C 1 2 1 ## From input: C 1 2 1 ##-------------------------------------------## Effective parameters: #phil __ON__ scaling { input { asu_contents { n_residues = 588 n_bases = None n_copies_per_asu = 4 } Matthews coefficient and Solvent content statistics ---------------------------------------------------------------- | Copies | Solvent content | Matthews Coef. | P(solvent cont.) | |--------|-----------------|----------------|------------------| | 1 | 0.448 | 2.226 | 1.000 | ---------------------------------------------------------------- | Best guess : 1 copies in the asu | ----------------------------------------------------------------

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input/output error
by Geoffrey Feld 14 Dec '09

14 Dec '09

Greetings fellow crystallographers, This past weekend, I collected some new data on my new project, indexed, scaled it, and found a phaser solution. The resolution is 3.6 A and I need to find one of the protein components, so I'm slowly refining piece-by-piece so I don't overdo it and flatten out the missing protein. To do this, I simply do rigid body and tls refinements for decreasingly smaller pieces of the protein I've already found. This method worked for me in the past for a similar structure. However, this time, as the refinement is finishing up, I get an input/output error and the program shuts down. Sometimes I get similar errors, and I can fix them by simply running the job again, overwriting the failed job, but this time that doesn't seem to be working. Here's the output from my .log file: Traceback (most recent call last): File "/programs/phenix-1.5-2/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/programs/phenix-1.5-2/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/programs/phenix-1.5-2/phenix/phenix/refinement/driver.py", line 1121, in run call_back_handler = call_back_handler) File "/programs/phenix-1.5-2/phenix/phenix/refinement/strategies.py", line 428, in refinement_machine monitors = monitors) File "/programs/phenix-1.5-2/cctbx_project/mmtbx/refinement/rigid_body.py", line 559, in __init__ out = log) File "/programs/phenix-1.5-2/cctbx_project/mmtbx/refinement/rigid_body.py", line 619, in show translations=t_vec) File "/programs/phenix-1.5-2/cctbx_project/mmtbx/refinement/print_statistics.py", line 161, in show_rigid_body_rotations_and_translations % euler_angle_convention, suffix=frame) File "/programs/phenix-1.5-2/cctbx_project/libtbx/utils.py", line 652, in write file_object.write(str) IOError: [Errno 5] Input/output error Again, the only thing I've done is made a few rigid body and tls groups. Please advise! Thanks, Geoff -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"

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TLS-derived anisoU restraint
by Bryan W. Lepore 14 Dec '09

14 Dec '09

is wxu the easiest - perhaps indirect - way to restrain anisoU's derived from TLS? under the target_weights scope i see : wxu_scale fix_wxu optimize_wxu <-already using this .... b/c i want to pull back some anisoU deviations across C-N. -bryan

2 1

Re: [phenixbb] How to extend R-free set to higher resolution by new phenix-1.5.2
by Thomas C. Terwilliger 14 Dec '09

14 Dec '09

Hi PC, >> >> Hi, >> >> I know this topic was discussed before, but I am still confused and still >> unable to refine my map merged from hires data because phenix.refine >> complains "No array of R-free flags found" >> >> The command was used to generate a hires map. >> phenix.autobuild data=resolve_1.mtz hires_file=hires.sca >> \seq_file=sequence.dat maps_only=True >> >> So, now I have "exptl_fobs_phases_freeR_flags.mtz", "cycle_best_1.mtz", >> "overall_best_denmod_map_coeffs.mtz"...several files in my autobuild >> folder, What this command has done is to take the phases in resolve_1.mtz and combined them with amplitudes from hires.sca and added free R flags to generate exptl_fobs_phases_freeR_flags.mtz . Additionally the file overall_best_denmod_map_coeffs.mtz now contains the above amplitudes along with some kind of density-modified phases. I would caution that this is probably not what you really wanted to do. Instead: Almost always you should use for "data=" a file that contains experimental phases only (not density-modified phases). So it would be better to use the command: phenix.autobuild data=phaser_1.mtz hires_file=hires.sca \ eq_file=sequence.dat maps_only=True which would instead density modify using hl coeffs from modify phaser_1.mtz, extending phase information to the data in hires.sca . Now you will have exptl_fobs_phases_freeR_flags.mtz with (a) experimental amplitudes from hires.sca (b) experimental phases and hl coefficients (where available) from phaser_1.mtz (c) free R flags to the full resolution of hires.sca and overall_best_denmod_map_coeffs.mtz with coefficients for a density-modified map at the resolution of hires.sca. >> >> How do I merge low and high resolution data by >> "phenix.reflection_file_editor"? What files (input and output arrays) >> should I choose? I think reflection_file_editor will only copy arrays (or columns) of data, and not merge several columns of data into one. Note that merging high and low resolution data requires (1) a scale factor between the datasets and (2) possibly a b-factor or anisotropic b-factor relating the two datasets. It cannot be properly done simply by merging reflection files. The reflection_flle_editor will add free R flags if they are missing or extend them for you if they are present only to low resolution, however. This allows you to take a low-res dataset with free R flags and a high-res dataset with no free R and to transfer the existing low-res free R flags to the high-res dataset and to extend them to full resolution. If you want, you can use phenix.solve to scale low and high resolution data by pretending that they are part of a mad dataset: make a file "scale.csh" like this, after editing to match your case: #!/bin/csh -f cp $PHENIX/solve_resolve/ext_ref_files/c2.sym . phenix.solve<<EOD resolution 20 3.0 cell 76 28 42 90 103 90 symfile c2.sym readdenzo ! readformatted/readdenzo/readtrek/readccp4_unmerged premerged ! premerged/ unmerged read_intensities ! read_intensities/read_amplitudes lambda 1 mad_atom c fprprv_mad 1. fprimv_mad 1. rawmadfile low.sca rawmadfile high.sca skip_solve sad EOD Then run with chmod +x scale.csh ./scale.csh Now solve_1.sca should have your scaled, merged data. I hope that helps! -Tom T

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How to extend R-free set to higher resolution by new phenix-1.5.2
by Pei-Chun Lin 12 Dec '09

12 Dec '09

Hi, I know this topic was discussed before, but I am still confused and still unable to refine my map merged from hires data because phenix.refine complains "No array of R-free flags found" The command was used to generate a hires map. phenix.autobuild data=resolve_1.mtz hires_file=hires.sca \seq_file=sequence.dat maps_only=True So, now I have "exptl_fobs_phases_freeR_flags.mtz", "cycle_best_1.mtz", "overall_best_denmod_map_coeffs.mtz"...several files in my autobuild folder, How do I merge low and high resolution data by "phenix.reflection_file_editor"? What files (input and output arrays) should I choose? Detail description will be very appreciate. Thanks for answer my question. PC _________________________________________________________________ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/so…

1 0

Side chain at special position
by Nate Nicely 11 Dec '09

11 Dec '09

I have a structure wherein the data show alternate conformations for a particular Trp side chain. The problem is that each of these conformations also occupies a special position: rotamer A clashes with rotamer A of the symmetry object, and similar for rotamer B. I'm attaching a screenshot wherein I tried to capture what's going on. The prerefined structure has a yellow carbon backbone, and you can see how refinement pushes rotamer A out of its rightful place in the map. I readjusted it and added the alternate conformation as seen in the green carbon backbone, but refinement after that just pushes apart both rotamers (not shown). I'd appreciate advice how to handle refining this structure in phenix. Thanks, Nate N

4 3

Re: [phenixbb] structural validation and deposit format
by Pavel Afonine 11 Dec '09

11 Dec '09

On 12/11/09 12:55 PM, rui wrote: > SO in the output pdb file, there are another set of lines start with > ANISOU, what are those, should I keep those? These are ADPs - Atomic Displacement Parameters, or B-factors. They are as important as atomic coordinates (almost) stored in ATOM records -:) > I turned on the optimze_wxc and optimize_wxu flags in the GUI, it does > give better R/Rfree. Do I need to turn on every time or just use the > optimized weights, where I can find those optimized weight? In log file? Optimization of weights is usually time consuming and the default weights are just good most of the time. So I usually recommend running weights optimization as the last step to tune up your model. Of course there might be exceptions. Since optimal weight may be different from run to run, they are not stored in .def file for the next runs. Pavel.

1 0

structural validation and deposit format
by rui 11 Dec '09

11 Dec '09

Hi, All, Sorry for this stupid question. When I tried to use phenix to validate the structure, it generate geometry outliers, model validation, real-space correlations and a phenix_map_coeffs.mtz file which I assume could be open in coot. How should I use this generated mtz file? When I open in coot, it tellls me core dump. I'm wondering if phenix will automatically do the corrections or should I look one by one in the log file and modify? It also generate a test_reduced.pdb, should I use this reduced pdb ( H added) for next round of refinement? Thanks. Is the format from phenix.refine ready for deposit?

3 2

refinement
by r n 11 Dec '09

11 Dec '09

Hi all I do have very low resolution data (around 4 ang), what are the efficient way of doing refinement, either rigid body alone or rigidbody and tls or individual with group_adp. I did both, but not much significant changes in Rfree stays around 48/50%. Also I do have other questions 1. While doing rigid body refinement, phenix complaint about the special position and could not perform rigid body refinement, whereas individual site refinement is working fine. I do have to delete the atom in special position for rigid body refinement? Thanks

8 20

How to reload a project into the gui
by Dirk 11 Dec '09

11 Dec '09

Hi, during a phenix refinement the gui froze and I had to kill the process. After restarting the gui the project I was working with was disappeared - all other projects are still there. Is there a way to reload the project into the gui? All files including the project folder still exists but are somehow not recognized by the gui. I'm using dev-249 64bit. Greetings Dirk

2 1

Re: [phenixbb] How to reload a project into the gui
by Thomas C. Terwilliger 10 Dec '09

10 Dec '09

Hi Dirk, Try phenix.refine --gui Refine_xx/refine_xx.eff where xx is the run number of your refinement. That should preload all the parameters you had set at least. All the best, Tom T >> Hi, >> >> during a phenix refinement the gui froze and I had to kill the >> process. After restarting the gui the project I was working with was >> disappeared - all other projects are still there. Is there a way to >> reload the project into the gui? All files including the project folder >> still exists but are somehow not recognized by the gui. >> I'm using dev-249 64bit. >> >> Greetings >> >> Dirk >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

1 0

Are sigma cutoffs for R-free reflections cheating?
by Joe Krahn 10 Dec '09

10 Dec '09

Using a sigma cutoff in refinement is almost always a bad idea. It appears that some people still use them. The problem is that sigma cutoffs almost always improve R-factors, because it increases the denominator in the error/average equation. Some people incorrectly think that the reduced R-factor means that the cutoff was an improvement in the structure quality. The result of a sigma cutoff is that the R-factor can be made to look better than it really is. I think that this should be prevented by never excluding any R-free reflections by any sort of cutoff criteria. That keeps the R-free value unbiased. If culling R-free is required for proper error analysis, or just because the culled data are almost certainly bogus values, then the un-culled R-free could be a separate value. Now days, most people use a sigma cutoff of zero, so it is normally not a big problem. However, it appears that PHENIX still throws out many reflections where Fobs==0, which can be a significant fraction in the last shell with anisotropic data. Unfortunately, the exclusion of weak reflections depends on how amplitudes were derived. If using CCP4 Truncate, those weak reflections will be inflated a bit to a non-zero value, and a zero-sigma cutoff will have a significantly different affect. Therefore, I think that the default should be to use reflections with Fobs==0, with SigFobs > 0 as the criterion for non-absent reflections in reflection files without a missing number flag (i.e. CNS format). Joe Krahn

6 12

cif_as_mtz : column labels
by Bryan W. Lepore 10 Dec '09

10 Dec '09

a .cif has a bunch of labels (see below). the output .mtz has three: FOBS, SIGFOBS, R-free-flags ... without getting anyones' hands dirty, are the F's merged from the four correct columns, viz. F_plus, F_minus, (and sigmas)? -bryan (for pdb code, pls. off-list) labels in .cif : _refln.F_meas_au _refln.F_meas_sigma_au _refln.F_calc _refln.phase_calc _refln.pdbx_F_plus _refln.pdbx_F_plus_sigma _refln.pdbx_F_minus _refln.pdbx_F_minus_sigma _refln.pdbx_HL_A_iso _refln.pdbx_HL_B_iso _refln.pdbx_HL_C_iso _refln.pdbx_HL_D_iso

2 1

Clearing old NCS group definitions
by John Pascal 09 Dec '09

09 Dec '09

Hello, I am using NCS restraints in phenix.refine, and I am defining the restraints in a parameter file that I read into the GUI interface. After modifying the ncs parameters file, I see in the log file that phenix.refine has used the updated NCS groups, but also retains the old restraints settings. Therefore, the number of NCS groups doubles each time I make an edit. Is there a way to erase the previous NCS restraints? I see that the restraints are accumulating in the project_data/*.eff files. Are those read in by default on consecutive runs? I am probably missing something obvious, but I would appreciate any advice. Thanks. Best, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

2 1

Is it possible to do Molecular Replacement for synthesized "small" molecule X-ray data?
by Yves Wang 08 Dec '09

08 Dec '09

Hi PHENIX users, We've got a synthesized molecule, called Cucurbit[7]uril, molecular weight 1163 Da. We were able to grow crystals of cucurbit[7]uril with one of its ligand. This crystal diffracted to 1.5A at our X-ray machine. The dilemma is that, at this resolution, we can't use small molecule crystallography softwares to solve the structure (correct me if I'm wrong, we need at least 1A resolution?), while macromolecular X-ray softwares are really not designed for synthesized molecules. We have collected diffraction data of this crystal with decent quality. So I'm wondering if there's any way we can put a known crystal structure of cucurbit[7]uril and solve the structure of the complex. We have tried AutoMR but the solution is not very encouraging. Any suggestion will be gratefully appreciated. Best, -- Yi(Yves) Wang Department of Biochemistry Structural Biology & Biophysics Program Duke University BS: University of Science and Technology of China School of Life Sciences, National Laboratory for Physical Sciences at Microscale Tel: +1-919-236-3307 (Cell) +1-919-684-0235 (Lab 1) +1-919-660-1634 (Lab 2) Office: A20 LSRC / 5301 FFSC E-Mail: yves.wang(a)duke.edu Mail: Box 90317, Chemistry Department

3 2

Re: [phenixbb] Problem using MOSFLM-integrated MAD data
by Chen, Yu Wai 08 Dec '09

08 Dec '09

Dear All, Thanks to all those who have responded to my previous query. The problem was due to I used MOSFLM raw data without scaling or sorting. I put the MOSFLM data through SORTMTZ and SCALA and output as "unmerged intensities in SCALEPACK format" and that error I mentioned earlier in the BB has gone. SOLVE completed successfully with some possible solutions. But now I have another problem. When RESOLVE tries to run DM, it reported another problem which seems to indicate it cannot read the scala-produced file correctly. The last bit of the log file before AutoSol stopped is as follows. I also print out the first few lines of the scala-produced SCALEPACK-format data file at the bottom for your diagnosis. Can you advise me what went wrong (and how to fix it)? Thanks a lot. Regards. Wai ##################### AutoSol_build AutoSol Run 22 Mon Dec 7 17:07:41 2009 SOLUTION FOR MODEL-BUILDING: Solution 2 using HYSS on /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl_ano_1.sca and taking inverse. Dataset #1 SG="P 21 21 21" SOLUTION FOR MODEL-BUILDING: Solution 1 using HYSS on /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl_ano_1.sca. Dataset #1 SG="P 21 21 21" DM SOLUTION USED FOR MODEL-BUILDING 1:Solution 2 using HYSS on /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl_ano_1.sca and taking inverse. Dataset #1 SG="P 21 21 21" WARNING: As the experimental data have been corrected for anisotropy and no input_refinement_file is available, no refinement will be carried out. Model-building will continue without refinement. Trying to guess refinement file for later use from ['/home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl'] Choosing guess of refinement file for later use from all files: ['/home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl'] FILE TYPE scalepack_no_merge_original_index GUESS FILE TYPE MERGE TYPE sca unmerged TARGET LABELS ['I', 'SIGI'] CONTENTS: ['/home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl', 'sca', 'unmerged', 'P 2 2 2', None, None, ['I', 'SIGI']] File /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.hkl ******************************************************************************** Failed to carry out AutoSol_build: float argument required, not NoneType ******************************************************************************** ########################### SeM8/phnx> more sem8_peak.hkl 4 P222 1 0 0 0 1 0 0 0 1 0 0 0 -1 0 0 0 -1 0 0 0 1 0 0 0 1 0 0 0 -1 0 0 0 -1 0 0 0 -1 0 0 0 1 0 0 0 -1 0 0 0 0 -1 -2 0 1 2 2 0 0 1 608.6 133.4 0 -1 -2 0 1 2 179 0 0 1 660.0 138.4 0 1 -2 0 1 2 176 0 0 2 519.0 130.9 0 -1 -3 0 1 3 4 0 0 1 1409.6 239.7 0 -1 -3 0 1 3 179 0 0 1 1525.0 251.0 -- Yu Wai Chen, PhD........................................Lecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.

2 1

Problem using MOSFLM-integrated MAD data
by Yu Wai Chen 07 Dec '09

07 Dec '09

> > Message: 3 > Date: Fri, 4 Dec 2009 15:54:13 -0800 > From: Nathaniel Echols <NEchols(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Problem using MOSFLM-integrated MAD data > Message-ID: <7B4AA329-8759-4603-BC26-9FD0A9120FC2(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii > > On Dec 4, 2009, at 3:44 PM, Yu Wai Chen wrote: > >> > .... >> > Unable to analyze /home/wai/dbe15_sh/SeM8/phnx/sem8_remo.mtz with xtriage >> > (a total of 3 instances of this) >> > . . . >> > Testing anisotropy in /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.mtz ... >> > Applying overall anisotropic B correction to /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.mtz to yield AutoSol_run_8_/TEMP0/ANISO_sem8_peak.mtz.sca >> > Overall B set to minimum of the trace of B values >> > Unable to get range of aniso B from xtriage output >> > Multiple equally suitable arrays of observed xray data found. >> > >> > wavelength { >> > data = sem8_peak.mtz >> > labels = "I, SIGI, M_ISYM" >> > } >> > > What happens when you specify the labels as simply "I SIGI"? > > The same errors resulted. Any advise please? Wai -- Yu Wai Chen, PhD........................................Lecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.

1 0

Re: [phenixbb] P32 twin or p3221?
by lauren 05 Dec '09

05 Dec '09

Hi Peter, Thanks for your reply. >This data can be processed to P3 or P321 with the R-fac almost the same >After that, I used Bales to do the MR, two solutions were found in P32 >(dimmer) and one in P32 21 (monomer) >Then, I refine the structure using phenix.refine in both P32 and P32 21 sets, but the R/Rfree stopped at 0.19/0.25 and never goes down. >However, if I treat the P32 data as a twin (with twin law h,-h-k,-l ), the R/Rfree can down to 0.12/0.18. >Do an R vs R analysis by loading up a model as well in xtriage to get a clue about the extend of the pseudo symmetry. I do the R vs R analysis with P32 in xtriage, but the R value seems very close to zero. And the D_ncs is high (0.95) in resolution range 9.9841-4.2623, which may indicate an incorrect point group? The results are as follow. --------------------------------------------- Analysing possible twin law : h,-h-k,-l --------------------------------------------- mean |H| : 0.018 (0.50: untwinned; 0.0: 50% twinned) mean H^2 : 0.001 (0.33: untwinned; 0.0: 50% twinned) Estimation of twin fraction via mean |H|: 0.482 Estimation of twin fraction via cum. dist. of H: 0.487 Britton analyses Extrapolation performed on 0.47 < alpha < 0.495 Estimated twin fraction: 0.455 Correlation: 0.9777 R vs R statistic: R_abs_twin = <|I1-I2|>/<|I1+I2|> Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 R_abs_twin observed data : 0.022 R_abs_twin calculated data : 0.090 R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> R_sq_twin observed data : 0.001 R_sq_twin calculated data : 0.006 Perfoming correlation analyses The supplied calculated data are normalized and artificially twinned Subsequently a correlation with the observed data is computed. Results: Correlation : 0.832594802609 Estimated twin fraction : 0.49 Maximum Likelihood twin fraction determination Zwart, Read, Grosse-Kunstleve & Adams, to be published. The estimated twin fraction is equal to 0.478 Log[likelihood]: 78991.418 twin fraction: 0.443 D_ncs in resolution ranges: 9.9841 -- 4.2623 :: 0.950 4.2623 -- 3.4280 :: 0.694 3.4280 -- 3.0083 :: 0.655 3.0083 -- 2.7394 :: 0.885 2.7394 -- 2.5466 :: 0.853 2.5466 -- 2.3986 :: 0.824 2.3986 -- 2.2800 :: 0.817 The correlation of the calculated F^2 should be similar to the estimated values. Observed correlation between twin related, untwinned calculated F^2 in resolutiuon ranges, as well as ewstimates D_ncs^2 values: Bin d_max d_min CC_obs D_ncs^2 1) 9.9841 -- 4.2623 :: 0.981 0.902 2) 4.2623 -- 3.4280 :: 0.970 0.482 3) 3.4280 -- 3.0083 :: 0.958 0.429 4) 3.0083 -- 2.7394 :: 0.954 0.783 5) 2.7394 -- 2.5466 :: 0.964 0.728 6) 2.5466 -- 2.3986 :: 0.953 0.679 7) 2.3986 -- 2.2800 :: 0.963 0.667 Best Regards, Lauren

1 0

Re: [phenixbb] Phenix installation issue
by smoniot＠chemie.fu-berlin.de 05 Dec '09

05 Dec '09

Well, I've dowloaded the installer again and changed my use of tar from -xvf to -xf option. Then reran the installation It went through and everything seems to work now. The only thing is that i'm normally running bash shell and that phenix doesn't work so. sourcing the phenix_env does not work under bash (setenv) Did I miss something or switching to tcsh is necessary ? Thanks for your help installing Seb > just a thought: > > if /net/anaconda is an nfs-shared drive, and you are trying to sudo > something on it from another workstation, it will fail because sudo > grants administrative privileges on the workstation, not on the server > where drive is housed. > > On Fri, 2009-12-04 at 04:59 +0100, smoniot at chemie.fu-berlin.de wrote: > Hi, > > I'm trying to install phenix on my computer (Linux distribution Kubuntu 64 > bits (virtual machine but it should not be an issue)) but the installation > failed after some minutes ... > the last lines on the installation log file are : > > /bin/tar: ./build/intel-linux-2.6-x86_64/base/bin/wx-config : un lien > symbolique ne peut pas être créé vers > «/net/anaconda/scratch1/phenix/phenix-1.5-2/build/intel-linux-2.6-x86_64/base/lib/wx/config/gtk2-ansi-release-2.8»: > Opération non permise > > It's in french but basiccaly it can't create a symbolic link to > /net/anaconda.... not allowed. > > I don't get it since I did try both the sudo ./install command and the su > - root. > > If anyone experienced this and get to fix it I would be glad to know :) > > Thanks in advance > > Sebastien > _______________________________________________ > phenixbb mailing list > phenixbb at phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

2 1

Problem using MOSFLM-integrated MAD data
by Yu Wai Chen 05 Dec '09

05 Dec '09

Dear All, I am trying to use a set of MAD data integrated with MOSFLM in phenix. But when I ran autosol, I've got the following error in the log file: .... Unable to analyze /home/wai/dbe15_sh/SeM8/phnx/sem8_remo.mtz with xtriage (a total of 3 instances of this) ... AutoSol_setup_for_scaling AutoSol Run 8 Fri Dec 4 23:18:59 2009 Shifting to Automatic mode.... RESOLUTION 2.5 SOLVENT_FRACTION 0.54 RESIDUES 364 MAD-N-HA 14 NCS-COPIES 2 Setting up for scaling dataset resolution: 2.5 solvent_fraction: 0.54 Scoring criteria will be: ['SKEW', 'CORR_RMS'] Scoring method will be: BAYES-CC AutoSol_scale_and_analyze_mad AutoSol Run 8 Fri Dec 4 23:18:59 2009 scale_and_analyze_mad for dataset 1 file type :ccp4_unmerged ccp4_unmerged merge type :unmerged Testing anisotropy in /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.mtz ... Applying overall anisotropic B correction to /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.mtz to yield AutoSol_run_8_/TEMP0/ANISO_sem8_peak.mtz.sca Overall B set to minimum of the trace of B values Unable to get range of aniso B from xtriage output Multiple equally suitable arrays of observed xray data found. ******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mad: Sorry, there is something wrong with the file /home/wai/dbe15_sh/SeM8/phnx/sem8_peak.mtz ... xtriage cannot analyze it? ******************************************************************************** THIS IS MY parameters input to phenix.autosol: autosol { seq_file = dbe15.seq sites = 14 atom_type = Se crystal_info { resolution = 2.5 space_group = P212121 } wavelength { data = sem8_peak.mtz labels = "I, SIGI, M_ISYM" lambda = 0.9794 f_prime = -7.83 f_double_prime = 5.97 } wavelength { data = sem8_edge.mtz labels = "I, SIGI, M_ISYM" lambda = 0.9796 f_prime = -9.72 f_double_prime = 3.08 } wavelength { data = sem8_remo.mtz labels = "I, SIGI, M_ISYM" lambda = 09719 f_prime = -4.11 f_double_prime = 3.85 } } Can some guru help me? I can send the mtz file if needed. -- Yu Wai Chen, PhD........................................Lecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.

2 1

Phenix installation issue
by smoniot＠chemie.fu-berlin.de 04 Dec '09

04 Dec '09

Hi, I'm trying to install phenix on my computer (Linux distribution Kubuntu 64 bits (virtual machine but it should not be an issue)) but the installation failed after some minutes ... the last lines on the installation log file are : /bin/tar: ./build/intel-linux-2.6-x86_64/base/bin/wx-config : un lien symbolique ne peut pas être créé vers «/net/anaconda/scratch1/phenix/phenix-1.5-2/build/intel-linux-2.6-x86_64/base/lib/wx/config/gtk2-ansi-release-2.8»: Opération non permise It's in french but basiccaly it can't create a symbolic link to /net/anaconda.... not allowed. I don't get it since I did try both the sudo ./install command and the su - root. If anyone experienced this and get to fix it I would be glad to know :) Thanks in advance Sebastien

3 3

(no subject)
by John Pascal 03 Dec '09

03 Dec '09

Hello, I am looking for advice on how to best refine the structure of a complex that has one component that can adopt two completely different conformations (a DNA duplex). I can model both conformations and set occupancies to 0.5, and try to constrain_group their occupancies, but in phenix.refine the two conformations are interpreted as major clashes. Thanks. Best, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

4 5

P32 twin or p3221?
by lauren 03 Dec '09

03 Dec '09

Hi everyone, I have a dimmer protein diffract to 1.6 A resolution. After processing the data, the Linear R-fac was 0.26/0.038 (last/all), the data quality seems good. This data can be processed to P3 or P321 with the R-fac almost the same After that, I used Bales to do the MR, two solutions were found in P32 (dimmer) and one in P32 21 (monomer) Then, I refine the structure using phenix.refine in both P32 and P32 21 sets, but the R/Rfree stopped at 0.19/0.25 and never goes down. Rfree 25% seems a little bit too high for a 1.6 resolution data. However, if I treat the P32 data as a twin (with twin law h,-h-k,-l ), the R/Rfree can down to 0.12/0.18. I use P3 to run the phenix.xtriage (see bellows), it looks like the L-test says it is not a twin data. So, I am wondering is it a twin data or not? The results are as follow. "Twinning and intensity statistics summary (acentric data): --------------------------------------------------------------------------- Statistics independent of twin laws - <I^2>/<I>^2 : 2.105 - <F>^2/<F^2> : 0.773 - <|E^2-1|> : 0.757 - <|L|>, <L^2>: 0.508, 0.344 Multivariate Z score L-test: 2.013 Statistics depending on twin laws ------------------------------------------------------------------ | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ------------------------------------------------------------------ | -h,-k,l | M | 0.484 | -0.003 | 0.022 | 0.022 | | h,-h-k,-l | M | 0.026 | 0.454 | 0.479 | 0.478 | | -k,-h,-l | M | 0.507 | -0.004 | 0.026 | 0.022 | ------------------------------------------------------------------ Patterson analyses - Largest peak height : 8.386 (corresponding p value : 0.29163) The largest off-origin peak in the Patterson function is 8.39% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected. Even though no twinning is suspected, it might be worthwhile carrying out a refinement using a dedicated twin target anyway, as twinned structures with low twin fractions are difficult to distinguish from non-twinned structures. The correlation between the intensities related by the twin law h,-h-k,-l with an estimated twin fraction of 0.45 % is most likely due to an NCS axis parallel to the twin axis. This can be verified by supplying calculated data as well." Thanks! Lauren

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High B Factors
by Miles Pufall 03 Dec '09

03 Dec '09

Hello All - I am working on a kinase:inhibitor complex with some interesting properties. First, it is a long, thin unit cell (45x45x300) that has highly anisotropic B-factors (60 in two dimensions and 35 in the other according to xtriage). We had a fair amount of trouble collecting data for these complexes due to somewhat high mosaicity (1.5) and overlap trouble, mostly due to the long unit cell. As a result, although we get diffraction out to ~2.3 A with good signal (I/sigma of 3), the completeness is only OK - dropping off from a high of 95% around 3.5 A pretty much linearly to 75% at 2.3. As a result, the maps look only OK for 2.3A data, but clearly show the interactions between the inhibitor and the kinase that we are looking to define. In that sense, the experiment worked just fine. That said, the structure looks pretty good, although about 1/3 shows poor density for sidechains, which I wouldn't expect at this resolution. But as I put the finishing touches on the structure a couple of things have worried me - first, there is consistently a larger than average gap between R and Rfree (Typically in the R~22 and Rfree~29). This, according to Polygon, is within the range of reported structures, so I think that's OK. What is odd is that despite having an average B caluclated from the reflection of ~50, the average B after refinement is ~80, which is very much on the high end of what has been reported. I have played around a lot with the wxc/wxu balance, and although this can change the Rs and tends to tighten the geometry perhaps inappropriately (rms bond ~0.003, rms angle ~0.7), the B factors stay very high. My question is, should I worry about this? And if so, what can you recommend trying. As usual, I'm happy to provide data if it help elucidate the problem. Thanks in advance - M Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480

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Atom Selection for Conformers
by John Pascal 02 Dec '09

02 Dec '09

Hello, What is the syntax for selecting one conformer of a residue? for example, if there are two arginine alternate conformations labeled A and B, how do you select just one of them. Thanks. Best Regards, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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phenix server upgrade
by Ralf W. Grosse-Kunstleve 01 Dec '09

01 Dec '09

Over the weekend we've moved the phenix web server and mailing list to new hardware. If you notice any problems with the web content, the downloads, or the mailing list, please let us know. Ralf

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Re: [phenixbb] sigma cutoff
by Kay Diederichs 30 Nov '09

30 Nov '09

> > > Hi, > > According to the Phenix manual, phenix.refine uses no sigma cutoff by > default. Since I haven't changed this manually, why do I see in my pdb > file MIN(FOBS/SIGMA_FOBS) 1.340? > > Thanks for help, > Karolina > > This one I can answer because I asked myself the same question recently. The answer is that Phenix does not impose any sigma cutoff, but rather your data are such that the minimum value of Fobs/Sigma_Fobs is 1.34 . You can verify this for yourself by going through your reflection file, line by line, and calculating Fobs/Sigma_Fobs for each reflection. You will find that all your reflections have a Fobs/Sigma_Fobs larger or equal to 1.34 . So it has nothing to with phenix; phenix just reports a property of your data. An easier way than doing it "manually" is using CCP4 sftools for calculating a new column "ratio", writing out the resulting MTZ file, and looking at this with mtzdmp. HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz

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Re: [phenixbb] Confused by the output from Phenix autobuild jobs
by Thomas C. Terwilliger 30 Nov '09

30 Nov '09

Hi Serah, You are right that the coefficients that you want for a difference map are not present in the overall_best_refine_map_coeffs.mtz file. The coefficients in that file (labelled FP PHIM) are the same as 2FOFCWT PH2FOFCWT from the refinement output, but there are no difference map coefficients. I will change this. In the meantime, I would do this after the end of autobuild: phenix.refine AutoBuild_run_1_/overall_best.pdb \ AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz and then you will have your map coefficients. >> I'm still wondering about the overall_best_*.* outputs - are these the >> really final output, or do we go for cycle_best_3.* series? The overall_best_xxx files are copied from the cycle_best_xxx files which are copied from the original files, all of which are in the TEMP0/ subdirectory. Thanks for pointing out that the difference coefficients are not present in the autobuild map file. I will fix the output to have the original refinement map file available. All the best, Tom T

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alternate conformation
by subhash bihani 25 Nov '09

25 Nov '09

Hi, I am refining a structure with ligand in alternate conformations. I tried giving them A and B, it worked. but I feel that this doesnot make interactions between alternate conformations absolutely zero. Is there any command in phenix similar to Igroup statement in CNS which can be used for such cases. Regards subhash -- Subhash Bihani Scientific Officer Solid State Physics Division Bhabha Atomic Research Centre Trombay, Mumbai-85 Ph. 25594688 (o) alternate email: subhashbihani(a)yahoo.co.in

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R-free rules
by Bryan W. Lepore 25 Nov '09

25 Nov '09

in the phenix.reflection_file_editor gui not sure i understand this: [x] Extend existing R-free array(s) ... [R-free flags generation] <--+ | | | | +-if this is checked, then do NOT check "Generate R-free flags" in here ... because "extend" is not the same as "generate", right? ... and thanks for the help before. -bryan

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