- phenixbb - phenix-online.org

Re: [phenixbb] Deposition of riding H
by Jeff Headd 15 Sep '10

15 Sep '10

Hi Mark, If hydrogens are used to arrive at a final refined model (whether riding or not) it is essential for the reproducibility of results that the H atom records be included in the deposited model. How B-factors are specified and some final atomic positions (such as rotatable methyl groups) are difficult or impossible to predict once removed, so without their deposition this information would be lost and any published statistics would not be reproducible as published. This point is illustrated in one of our recent papers: Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J. Appl. Cryst. 2010, 43, 669-67. Further, there is no universal standard currently in use that specifies H bond-lengths (some use electron cloud distances, others neutron distances, some a mixture of both), meaning that without inclusion of H atom records (or at least a reference to which library was used) it is very difficult to know where the H atoms were placed. Thanks, Jeff On Tue, Sep 14, 2010 at 10:32 AM, Dr. Mark Mayer <mayerm(a)mail.nih.gov> wrote: > Here's one for the community, which I'll post to both Phenix and CCP4 BBs. > > Where does the crystallographic community stand on deposition of coordinates > with riding hydrogens? > Explicit H are required for calculating all atom clash scores with > Molprobity, and their use frequently gives better geometry (especially at > low resolution). Phenix uses explicit riding H for refinement, and outputs > these in the refined PDB. Refmac also uses riding H but does not output H > coordinates. > > While depositing a series of structures refined at 1.4 - 2.75 A with Phenix > got the following email from the RCSB, who asked I resupply coordinates > without H for two of the structures. Since we can't see H even at 1.4 Å I > don't understand why an arbitrary cut off of 1.5 Å was chosen, and also why > explicit H atoms used in refinement and geometry validation should be > stripped from the file. > > FROM RCSB > > We encourage depositors not to use hydrogens in the final PDB file for > the low resolution structures (> 1.5 A). Please provide an updated PDB > file. We request you to use processed PDB file as a starting point for > making any corrections to the coordinates and/or re-refinement. > -- > > Mark > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

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Re: [phenixbb] autobuild : change reflection file mid-job?
by Thomas C. Terwilliger 15 Sep '10

15 Sep '10

Hi Bryan, Yes, I think to change the reflections file you will have to rerun the job as the reflections are read once in autobuild and propagated from there out. All the best, Tom T >> [it was inevitable..] >> >> if i swap the reflection file mid-job - THAT sounds like catastrophe : >> >> so does autobuild determine the format *only* from the .sca, .mtz affix? >> >> and it looks like reflections are read once at startup, and propagated >> from there out? >> >> -bryan >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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autobuild : change reflection file mid-job?
by Lepore, Bryan 15 Sep '10

15 Sep '10

[it was inevitable..] if i swap the reflection file mid-job - THAT sounds like catastrophe : so does autobuild determine the format *only* from the .sca, .mtz affix? and it looks like reflections are read once at startup, and propagated from there out? -bryan

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Palestrant, Deborah is out of the office.
by deborah.palestrant＠novartis.com 14 Sep '10

14 Sep '10

I will be out of the office starting 09/13/2010 and will not return until 09/15/2010. I have limited access to email and will respond to your message when I return.

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Re: [phenixbb] autobuild : change .seq mid-job?
by Thomas C. Terwilliger 14 Sep '10

14 Sep '10

Hi Bryan, I think that you can do this, though I have not tried it. You need to replace two files: 1. your original sequence file wherever it is "/wherever/.../myseq.dat 2 a file with the same name "myseq.dat" or whatever, in the directory AutoBuild_run_1_/TEMP0 I would expect all model-building after that to have the new sequence. (Note that runs that are already going as sub-processes will keep their sequences). Now if this is rebuild_in_place, this would not be a good idea. I am assuming it is rebuild_in_place=False, and so it should work... Let me know how it turns out, -Tom T >> i have a long autobuild job going. i'd like to change the .seq files as >> its going - if i keep residue 1 numbered, could this still be a >> catastrophe? >> >> -bryan >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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autobuild : change .seq mid-job?
by Lepore, Bryan 14 Sep '10

14 Sep '10

i have a long autobuild job going. i'd like to change the .seq files as its going - if i keep residue 1 numbered, could this still be a catastrophe? -bryan

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debugger pdb
by Krista Joosten 10 Sep '10

10 Sep '10

Hi all, I'm working with Tom Burnley on the development of time_averaging.py. I would like to use the debugger pdb, but am not sure how to do this and whether it's possible. After some googling, I tried to hack into phenix.time_averaging adding -m pdb when the variable DEBUG==1, but I got the error message 'no module called pdb'. Bye Krista

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Beamtime at the ALS-BCSB beamlines
by Peter Zwart 10 Sep '10

10 Sep '10

Dear All, July 15, 2010 is the deadline for the March/April 2010 Rapid Access Proposal cycle. All Berkeley Center for Structural Biology(BCSB) beamlines are equipped with ADSC Q315/Q315R detectors, automated sample changers and data collection software enabling high-throughput crystal screening and data collection. Remote data collection is available on all BCSB beamlines, providing the user with the full complement of sample visualization, sample manipulation, beamline control, data acquisition and data analysis tools exactly as they would see them if they were stationed at the beamline. The main difference between local operation and remote operation, is the length of the network cable! This enhanced remote operation capability is coupled with 22hr onsite support by BCSB staff who are able to assist immediately with loading additional samples for remote users or troubleshoot any issues that might arise. Remote users can furthermore be kept up-to-date on changes in ring status via an SMS service ( http://bcsb.als.lbl.gov/wiki/index.php/Ring_Status_Notifications_to_Cell_Ph…) or via twitter (@AlsRingStatus). Specific features are summarized below. Beamlines 5.0.1, 5.0.2, 5.0.3: -------------------------------------- Beamline 5.0.2 is equipped with a novel variable collimator allowing users to adjust the beamsize continuously and on the fly between 25 and 100 micron, both horizontally and vertically. With a collimator setting of 30x30 micron, typical exposures are around 1 to 2 second. The Berkeley Automounter sample handling system has a routine capacity of 96 samples (6 pucks). In a typical high-throughput screening mode, the mount-to-mount time is around 2.5 minutes per sample, allowing users to screen a full puck within 45 minutes. The sector 5 beamline user stations are equipped with fully high-adjustable, ergonomically friendly work stations. Beamlines 8.2.1 and 8.2.2: ----------------------------------- To facilitate studies on small crystals, a microdiffractometer was installed in the beamline 8.2.1 endstation. The new equipment allows precise sample positioning to within 2 microns, excellent sample viewing of very small crystals, and an off-axis crystal positioningstage. Both beamlines 8.2.1 and 8.2.2 feature a Rigaku sample changer (Actor), allowing remote operations to now be a routine mode of access for these beamlines. Data analyses in the BCSB is facilitated by software maintained by sbgrid ( http://www.sbgrid.org). A 16 core linux machine is available for our users to process their data and solve/refine their structure. An additional mode of access to the BCSB beamlines is through the Collaborative Crystallography (CC) Program. Users apply for beamtime via the general user program, and collaborate with an expert crystallographer who will conduct the experiments and data reduction on behalf of the researchers. Depending on the users, structure solution, model building and refinement can be carried out as well. Please contact BCSBBeamtime(a)lbl.govfor more information. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. To find out more, click on: http://www.als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/ Scroll down to "Structural Biology beamines (includes protein SAXS)." Click on "New Proposal." If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime. -- ----------------------------------------------------------------- P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

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Help on multi-start-simulated-annealing sigmaA-weighted 2fofc map
by fn1＠rice.edu 10 Sep '10

10 Sep '10

Hi everyone, I read on the paper that they use CNS (model_map.inp) to calculate the avarage sigmaA-weighted 2fofc map. Right now I have set up the simulated annealing with different random seeds. I wonder whether phenix could calculate the average map with the multiple coordinates from different starts? Thanks! Fengyun

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Can phenix calculate R factor based on the only given mtz file containing Fo and Fc?
by zhangh1＠umbc.edu 08 Sep '10

08 Sep '10

Hi, I am wondering whether phenix can calculate R factor based on the only given mtz file containing Fo and Fc? Thanks! Hailiang

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will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb?
by zhangh1＠umbc.edu 08 Sep '10

08 Sep '10

Hi, For the pdb file generated by refmac which contains only the residual-B, will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb? Thanks a lot! Best Regards, Hailiang

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constrained occupancy groups in phenix.refine
by Lionel Costenaro 04 Sep '10

04 Sep '10

Hello, A portion of my structure have two conformations at an interface between two (NCS) protein chains -in addition to other alternates conformations elsewhere. In both chains, I defined alt_A as one conformation and alt_B as the second conformation, and also for the waters in this region. I would like to constrained the occupancy of these conformations. I though that the following selections would do the job: occupancies { constrained_group { selection = "(chain A or chain B) and (resseq 105 or resseq 110:112 or resseq 140:143) and altid A" After refinement, all alt_A selected residues do have the same occupancy, but not the same occupancies for alt_B and the sum for one residue (occu alt_A +occu alt_B) is not 1. Adding a second group with the same selection but "altid B", constrains also the alt_B occupancies but the sum is still not 1. How should I defined my group(s)? Is it possible to select several non continuous residues from one chain (that's for the waters) without repeating each time "or resseq" ? Best regards, Lionel

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Re: [phenixbb] Can we untoggle molecular weight mean deviation check on ensembles in autoMR?
by James Thompson 04 Sep '10

04 Sep '10

A postdoc in my lab with many more files inside his Phenix build directory just showed me that the Mwt mean deviation check on input ensembles is hard-coded in Phaser. A seemingly arbitrary value of 20% is set within the file emsembles.cc. So, the answer to my previous question is presently NO. We users cannot untoggle or alter this mean deviation value without some recompile of Phaser. I will play with my Sculpt'ed output from the Mustang server to reduce the Mwt deviations within the ensemble of coordinates that I want to feed to Phaser-MP to get by. James R. Thompson <thompson.james at mayo.edu> > Can folks untoggle the molecular weight mean deviation check in > phenix.autoMR on the ensembles input? > > I want to use an ensemble of coordinates generated by the Mustangs > server from a SSM alignment. Therefore, by design the 10 PDBs input to > phenix.autoMR vary greatly in molecular weight from their mean value, > but the whole is likely an excellent probe for molecular replacement. > However, I am stymied by phenix.autoMR: > > ------------------------------------------------------------------------------------- > FATAL RUNTIME ERROR: Molecular weight of > /home/jrt04/Desktop/GB1STAS/MUSTANGServer_10_1.6_0_sculpt-coot-0.pdb > (6610.56) deviates more than 20% from the mean (3977.08). This pdb file > may contain domains or water not present in the other files. > ------------------------------------------------------------------------------------- > > I understand why this check might be of utility to the unobservant. How > can I disable this test? > > Many thanks, > Jim > > -- > James R. Thompson <thompson.james at mayo.edu>

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can phenix.refine output mtz with structure factors not just coeficients?
by amadrona＠uci.edu 03 Sep '10

03 Sep '10

Hi, I am going to deposit a structurein the pdb but noticed that all of the mtz files from phenix.refine only contain coeficients and not reflection info. Is it as simple as running another refinement with write_maps = true instead of false? Will this right out an mtz with structure factors instead of just coeficients. I am a newbie at crystalagraphy so I appolgize if this obvious. Ideally, I would like to create an mtz with structure factors as well as a map for CNS. Is there a way to do this without runing another refinment maybe using "maps.params". Thank you very much for the help! -Yarrow output { prefix = "CIN4_refine" serial = 12 serial_format = "%03d" title = None write_eff_file = True write_geo_file = True write_final_geo_file = False write_def_file = True export_final_f_model = mtz cns write_maps = false write_map_coefficients = True pickle_fmodel = False

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atom selection in phenix.pdbtools
by Michael Hothorn 02 Sep '10

02 Sep '10

Hi, I want to calculate the mean b-value for all atoms of a specific ligand in my structure. I tried: phenix.pdbtools --show-adp-statistic model.pdb keep="chain A and residue 400" , but it still prints out all b-values including solvent etc. any ideas? thanks Michael

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Re: [phenixbb] question on bad geometry
by Thomas C. Terwilliger 02 Sep '10

02 Sep '10

Hi Fengyun, Just to emphasize what Ed points out here, an essential step in completing a structure is to compare it, one residue, solvent molecule, or ligand at a time, with your electron density map, fixing any inconsistencies between the model and the map. There are many wonderful tools in all the crystallographic graphics programs to help you do this. All the best, Tom T >> On Tue, 2010-08-31 at 20:37 -0500, fn1(a)rice.edu wrote: >>> Does >>> that mean I need to manually adjust the model? >> >> Autobuilder is a fantastic tool which greatly simplifies the model >> building process, but you always must validate your structure by >> inspecting the electron density. I fully understand that (hopefully) it >> is what you plan to do and this is more of a reaction to the alarming >> number of obvious and easily correctable systematic errors one finds in >> structures deposited in the PDB these days. >> >> Thanks to Pavel for providing an excellent example to illustrate the >> point. One only needs to take a look at the model in context of >> electron density maps to confirm that autobuilder will fix some errors >> but also sometimes introduce some that require manual correction. >> >> Cheers, >> >> Ed. >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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question on bad geometry
by fn1＠rice.edu 01 Sep '10

01 Sep '10

Hi everyone, I have a structure at 2.3 A refined in phenix to R/Rfree=0.23/0.28. However, the geometry is not that good, the followings are the output from phenix.model_vs_data, Stereochemistry statistics (mean, max, count): bonds : 0.0080 0.0547 3244 angles : 1.1669 12.1085 4374 dihedrals : 15.7241 85.6280 1202 chirality : 0.0706 0.2831 536 planarity : 0.0036 0.0246 573 non-bonded (min) : 2.1217 Ramachandran plot, number of: outliers : 17 (4.02 %) allowed : 37 (8.75 %) favored : 369 (87.23 %) Rotamer outliers : 30 (8.62 %) goal: < 1% Cbeta deviations >0.25A : 0 All-atom clashscore : 40.51 (steric overlaps >0.4A per 1000 atoms) I tried to use fix_rotamer=True, but it doesn't help at all. As to the rotamer outliers, the value is far higher than the ideal one. Does that mean I need to manually adjust the model? Or will autobuild help improve the geometry? Thanks! Fengyun

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How to do a phenix.fmodel calculation incorporating the exponential scaling model only?
by zhangh1＠umbc.edu 01 Sep '10

01 Sep '10

Hi, I want to use phenix.fmodel to do a calculation incorporating the exponential scaling model only (Not the flat model). I am not sure whether I just need simply specify: mask { use_asu_masks = False } since the output maps are just identical no matter use_asu_masks = True or False. Should I do something else to enable exponential scaling model only? Thanks! Best Regards, Hailiang

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0.00 Refined Isotropic ADPs
by Joseph Noel 01 Sep '10

01 Sep '10

Hi All. Me again! LOL I am sure this has come up and related to how the "B-factor" in the refined PDB's ADP column is calculated including the overall anisotropic B-factor, etc but is it unusual to have isotropic ADPs refine to 0.00? I have several nice structures with 0.00 isotropic ADPs. I am not refining TLS or anisotropic ADPs at all. Just the normal course of refinement. These are regions of a high degree of order and the maps are beautiful but just wandering what the 0.00 ultimately means particularly when I eventually submit to the Protein Data Bank. Joe P.S. Nat's tips on COOT and Phenix are working beautifully now! Thanks Nat! ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Re: [phenixbb] Phenix and COOT Together on a Mac (and Probe too?)
by Joseph Noel 01 Sep '10

01 Sep '10

Nat, One thing that seemed to solve all the problems at once was to completely remove any reference to the COOT path in the Phenix preferences! Is that weird? When I removed it completely only leaving the path to PYMOL then COOT is working just fine in conjunction with Phenix and even the Probe issues have disappeared. Prior to this, I was tried two different paths to COOT. 1. /sw64/bin/coot 2. /Applications/coot.app/Contents/MacOS/coot Neither behaved but if I don't specify anything it works. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Problem with low figure of merit
by sankaranarayanan srinivasan 01 Sep '10

01 Sep '10

Hi all, I am new to structure solving. I have a 2.9A dataset for a Seleno crystal of which i am trying to use Autosol to build an initial map. I used the settings for a thorough solution, instead of quick. All the other parameters were set to default settings. The solution that i got from autosol, gave me the following result Solution # 1 BAYES-CC: 23.7 +/- 30.9 Dataset #1 FOM: 0.27 Residues built: 238 Side-chains built: 139 Chains: 15 Overall model-map correlation: 0.65 R/R-free: 0.38/0.42. Score type: SKEW CORR_RMS Raw scores: 0.02 0.77 100x EST OF CC: 16.86 32.11 The density modification map matches, quite well with many of my side chains fitted. My question here is , IS THERE A WAY I CAN IMPROVE THE Figure Of Merit , BY CHANGING ANY PARAMETERS IN PHENIX-AUTOSOL. I HAVE A HIGH SOLVENT CONTENT IN MY CRYSTAL AND I DID NOT INPUT THAT IN MY INITIAL PARAMETERS. DOES PHENIX AUTOSOL CONSIDER SOLVENT FLATTENING FOR SUCH CRYSTALS? I would appreciate someone's help in this regard Thanks Shankar

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Phenix and COOT Together on a Mac (and Probe too?)
by Joseph Noel 31 Aug '10

31 Aug '10

Hi All, I am having trouble getting COOT to link up with Phenix. I know that Bill Scott's fink version of COOT breaks the link but I have also tried the stand alone latest version for Mac OSX without success. I suspect there may be something additional I need to set up to get the two programs to talk to one and other. I can open COOT with the GUI link in Phenix but that's it. The two do not communicate and the "Phenix button" does not appear. I am running everything on a Mac laptop with an Intel chip and the latest snow leopard operating system. I can also run probe independently in COOT using the script suggestion for the .coot file from the MOLPROBITY web site. However, after several checks of bad contacts the system freezes at the level of XQuartz and I have to kill X-Windows to start over. I don't know if this is in someway linked to the problem getting COOT and Phenix to talk to one and other but I thought I would throw it out there. Finally, if I do run COOT by starting it from the Phenix GUI it also freezes after several rounds of building, etc just like the probes to check for clashes. If anyone has observed this behavior and has some suggestions I would much appreciate it! Its not a big deal as I can run things separately and work from a print out of Molprobity outliers but it would be sure nice to just click and correct. Sorry to keep going but I should say I have Bill Scott's fink'ed version of coot installed in as directed in /sw64 and the stand alone version installed along with CCP4 and Phenix in my Mac's /Applications directory where all my standard Mac apps appear. Thanks! Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Can we untoggle molecular weight mean deviation check on ensembles in autoMR?
by James R. Thompson 30 Aug '10

30 Aug '10

Can folks untoggle the molecular weight mean deviation check in phenix.autoMR on the ensembles input? I want to use an ensemble of coordinates generated by the Mustangs server from a SSM alignment. Therefore, by design the 10 PDBs input to phenix.autoMR vary greatly in molecular weight from their mean value, but the whole is likely an excellent probe for molecular replacement. However, I am stymied by phenix.autoMR: ------------------------------------------------------------------------------------- FATAL RUNTIME ERROR: Molecular weight of /home/jrt04/Desktop/GB1STAS/MUSTANGServer_10_1.6_0_sculpt-coot-0.pdb (6610.56) deviates more than 20% from the mean (3977.08). This pdb file may contain domains or water not present in the other files. ------------------------------------------------------------------------------------- I understand why this check might be of utility to the unobservant. How can I disable this test? Many thanks, Jim -- James R. Thompson <thompson.james(a)mayo.edu>

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stuck with phenix refine
by intekhab alam 30 Aug '10

30 Aug '10

Hi I am working with a twinned data set having R32 space group. when i tried to refine with phenix refine using the twin option it got stuck after some time. There is no error message showing up and the refinemnet donot progresses further. I have used the twin law suggested by Xtriage program in Phenix. Kindly help me out. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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Re: [phenixbb] phenix.automr questions
by Kay Diederichs 30 Aug '10

30 Aug '10

Dear Randy, Nat, Tom, thank you for pointing out the existence of phenix.phaser to me, and sketching its usage. I think I'll make my way with that information; nevertheless it would be great if it were officially documented (Google returned nothing to me about phenix.phaser). BTW, I'm trying to put together some orthogonal Phenix documentation at http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Phenix . I take the opportunity to state that although the URL refers to the CCP4 users' wiki, and obviously Phenix is not part of CCP4, the wiki covers a broad range of crystallographic information. Thus, I do think it is appropriate to collect Phenix-related information (from a user perspective) there, and would like to invite everybody to contribute to the Phenix entry (and others!). thanks, Kay

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Re: [phenixbb] phenix.automr questions
by Kay Diederichs 30 Aug '10

30 Aug '10

Hi Tom, thanks for answering my questions! Yes, it would be good to have a flag to turn off the inverse hand because a) having the possibility to look at each spacegroup offers a very effective way of parallelization b) if I "grep" the spacegroup name in the logfile I find: dikay@turn10:-2010/phenix.automr% grep "P 4" mf92.log Space group: P 41 21 2 (No. 92) LIST OF ALL PLAUSIBLE SG: ['P 4 2 2', 'P 4 21 2', 'P 41 2 2', 'P 41 21 2', 'P 42 2 2', 'P 42 21 2', 'P 43 2 2', 'P 43 21 2'] Space group: P 41 21 2 (No. 92) NEW dictDATA {'raw_data': [' P 4abw 2nw', (101.71700286865234, 101.71700286865234, 344.74798583984375, 90.0, 90.0, 90.0), <scitbx_array_family_flex_ext.double object at 0xe554a10>, <scitbx_array_family_flex_ext.double object at 0xe554bd0>, <cctbx_array_family_flex_ext.miller_index object at 0xe4716c0>]} space_group : P 41 21 2 all_plausible_sg_list : ['P 4 2 2', 'P 4 21 2', 'P 41 2 2', 'P 41 21 2', 'P 42 2 2', 'P 42 21 2', 'P 43 2 2', 'P 43 21 2'] dictDATA: {'raw_data': [' P 4abw 2nw', (101.71700286865234, 101.71700286865234, 344.74798583984375, 90.0, 90.0, 90.0), <scitbx_array_family_flex_ext.double object at 0xe554a10>, <scitbx_array_family_flex_ext.double object at 0xe554bd0>, <cctbx_array_family_flex_ext.miller_index object at 0xe4716c0>]} HALL: P 4abw 2nw P 43 21 2 P 41 21 2 Space-Group Name (Number): P 41 21 2 (92) Space-Group Name: P 41 21 2 Space-Group Name (Number): P 41 21 2 (92) P 43 21 2 * P 41 21 2 Space-Group Name (Number): P 43 21 2 (96) Fast Translation Function Table: Space Group P 43 21 2 Space Group Name (Number): P 43 21 2 (96) Packing Table: Space Group P 43 21 2 Space-Group Name (Number): P 43 21 2 (96) Refinement Table (Unsorted): Space Group P 43 21 2 Refinement Table (Sorted): Space Group P 43 21 2 Best Space Group: P 43 21 2 P 43 21 2 P 41 21 2 * Space-Group Name (Number): P 41 21 2 (92) Fast Translation Function Table: Space Group P 41 21 2 Best Space Group so far: P 43 21 2 Space Group Name (Number): P 41 21 2 (92) Packing Table: Space Group P 41 21 2 Space-Group Name (Number): P 41 21 2 (92) Refinement Table (Unsorted): Space Group P 41 21 2 Refinement Table (Sorted): Space Group P 41 21 2 Space-Group Name (Number): P 43 21 2 (96) Best spacegroup from search with first component in permutation: P 43 21 2 Space-Group Name (Number): P 43 21 2 (96) Fast Translation Function Table: Space Group P 43 21 2 Space Group Name (Number): P 43 21 2 (96) Packing Table: Space Group P 43 21 2 Space-Group Name (Number): P 43 21 2 (96) Refinement Table (Unsorted): Space Group P 43 21 2 Refinement Table (Sorted): Space Group P 43 21 2 Best Space Group: P 43 21 2 Space-Group Name (Number): P 43 21 2 (96) Best spacegroup from search with first component in permutation: P 43 21 2 Space-Group Name (Number): P 43 21 2 (96) Fast Translation Function Table: Space Group P 43 21 2 Space Group Name (Number): P 43 21 2 (96) Packing Table: Space Group P 43 21 2 Space-Group Name (Number): P 43 21 2 (96) Refinement Table (Unsorted): Space Group P 43 21 2 Refinement Table (Sorted): Space Group P 43 21 2 Best Space Group: P 43 21 2 Space-Group Name (Number): P 43 21 2 (96) which shows that at a certain point the MTZ file's spacegroup is abandoned and the calculation finishes in the enantiomorph spacegroup, which has the drawback that I cannot really compare the best (complete) results of both enantiomorphs. And with one good and three bad search models I don't know if abandoning the given spacegroup early is definitively the right decision (but it's hard for me to tell exactly what criterion the decision was based upon - it may have been after an exhaustive search in #92 in which case my worry would not be justified). thanks, Kay > Message: 2 > Date: Sat, 28 Aug 2010 09:07:08 -0600 (MDT) > From: "Thomas C. Terwilliger"<terwilliger(a)lanl.gov> > To: "PHENIX user mailing list"<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] phenix.automr questions > Message-ID:<14563.128.165.0.81.1283008028.squirrel(a)webmail.lanl.gov> > Content-Type: text/plain;charset=iso-8859-1 > > Hi Kay, > > I'll answer what I can; perhaps Randy the others may have more comments. > >>> Dear developers, >>> >>> I have four questions concerning phenix.automr (I'm using version 1.6.4): >>> >>> a) is there a way to make the program try all permutations for the >>> search order of my four search molecules, or do I have to write a script ? > > It would be a good idea for me to put that in. For now, yes, you have to > make a script to do that. > >>> >>> b) how can I completely switch off the search in the alternative >>> spacegroups - I am under the impression that although the "effective >>> parameters" are >>> all_plausible_sg_list = None >>> use_all_plausible_sg = False >>> the search is not only done in the spacegroup I specified (#92=P41212) >>> but also in #96=P43212 . I believe so because the output says: >>> ... >>> 2 alternative spacegroups >>> SpaceGroup will be determined by highest LLG in search for FIRST >>> ensemble >>> Search order: >>> P 43 21 2 >>> P 41 21 2 >>> ... >>> (I would rather run a second search "manually" in the other spacegroup!) > > Yes, it runs the inverse hand even if you say > "use_all_plausible_sg=False". However it should not run all the other > space groups (all_plausible_sg_list : ['P 4 2 2', 'P 4 21 2', 'P 41 2 2', > 'P 41 21 2', 'P 42 2 2', 'P 42 21 2', 'P 43 2 2', 'P 43 21 2']). I'll see > if we can put in a flag so it doesn't run the inverse hand if you don't > want it to. > > >>> >>> c) I have two occurrences of seq_file ("all.seq" and "all.dat"; the >>> latter is symlinked to the former). Am I right that I could just leave >>> out one of them? I did this after looking at >>> http://www.phenix-online.org/documentation/automr.htm#anch70 but I >>> wonder which of the specifications of sequences and masses overrides the >>> other one? or is the first specification used for editing the search >>> models, and the second for getting the likelihood terms right? > > Looking at your parameters file, I see what you mean. If you supply two > different files, then yes, the one you specified at the top of your file > with "seq_file=all.dat" is going to be used for editing the file for > autobuild, and the one you specified in the scope "component" is going to > be used for getting the likelihood terms right. > > Normally (always?) these should be the same. So normally, just supply the > first one "input_seq_file=seq.dat") and it will be used for both purposes. > > Or if you have several components, only specify them in the "component" > scopes, and all of them will be put together into a single file and used > as the input to autobuild. > > >>> >>> d) what kind of editing is done? Is phenix.sculptor run internally? I >>> find {a,b,c,d}_edited.pdb but are they actually used? > > Only basic editing to make the model compatible with autobuild is done. No > sculpting is done inside automr for now. > > All the best, > Tom T

1 0

phenix.automr questions
by Kay Diederichs 30 Aug '10

30 Aug '10

Dear developers, I have four questions concerning phenix.automr (I'm using version 1.6.4): a) is there a way to make the program try all permutations for the search order of my four search molecules, or do I have to write a script ? b) how can I completely switch off the search in the alternative spacegroups - I am under the impression that although the "effective parameters" are all_plausible_sg_list = None use_all_plausible_sg = False the search is not only done in the spacegroup I specified (#92=P41212) but also in #96=P43212 . I believe so because the output says: ... 2 alternative spacegroups SpaceGroup will be determined by highest LLG in search for FIRST ensemble Search order: P 43 21 2 P 41 21 2 ... (I would rather run a second search "manually" in the other spacegroup!) c) I have two occurrences of seq_file ("all.seq" and "all.dat"; the latter is symlinked to the former). Am I right that I could just leave out one of them? I did this after looking at http://www.phenix-online.org/documentation/automr.htm#anch70 but I wonder which of the specifications of sequences and masses overrides the other one? or is the first specification used for editing the search models, and the second for getting the likelihood terms right? d) what kind of editing is done? Is phenix.sculptor run internally? I find {a,b,c,d}_edited.pdb but are they actually used? thank you, Kay P.S. I run with "phenix.automr mr.eff" where mr.eff is automr { data = "m879_2_rg92.mtz" seq_file = all.dat ensemble { ensembleID = "mol1" copies_to_find = 1 coords = a.pdb identity = 80 } ensemble { ensembleID = "mol2" copies_to_find = 1 coords = b.pdb identity = 45 } ensemble { ensembleID = "mol3" copies_to_find = 1 coords = c.pdb identity = 45 } ensemble { ensembleID = "mol4" copies_to_find = 1 coords = d.pdb identity = 45 } component { component_type = *protein nucleic_acid seq_file = all.seq component_copies = 1 } autobuild_variables{ n_cycle_rebuild_max = 1 } }

4 3

Phenix error running MIR-example
by Shankar Prasad Kanaujia 30 Aug '10

30 Aug '10

Dear Developers/Users, I am getting an error while running "rh-dehalogenase-mir" example provided in the phenix example. I am using phenix 1.6.4 version. It runs properly using the command "phenix.run_example rh-dehalogenase-mir", whereas, it gives error in GUI mode. I am attaching the picture of my input and error (in the right-top corner). Please let me know the reason of this error. -- Yours Sincerely, Shankar Prasad Kanaujia Research Student C/O - Dr. K. Sekar Bioinformatics Centre, SERC Indian Institute of Science, Bangalore-12 Phone - 9480258032 Office - 080-2293-3059

2 1

Postdoctoral position in Protein X-ray Crystallography
by cdas＠purdue.edu 29 Aug '10

29 Aug '10

Applications are invited for a postdoctoral research position in the Das Lab, Department of Chemistry, Purdue University, West Lafayette, IN, USA. The position requires the applicant to work on structural and biochemical characterization of ubiquitin hydrolases (deubiquitinases) and their complexes with substrates, cofactors and inhibitors (see Boudreaux et al, PNAS, 107, 9117 (2010)). The applicant is also expected to work on an ongoing collaborative project on method development related to imaging of protein crystals (of ubiquitin hydrolases and others) using second order non-linear optical methods. We are looking for highly motivated candidates with extensive experience in biochemical studies, crystallization and structure determination of proteins by x-ray crystallography. Specifically, the candidate is required to have hands-on experience with protein purification, crystallization, X-ray data collection, structure determination and structural analysis. Applicants should send their CV and the names and contact information of at least three references via email to: Chitta Das Assistant Professor Department of Chemistry Purdue University 560 Oval Drive West Lafayette IN, 47907 Email address: cdas(a)purdue.edu

1 0

Can Phenix refine B factors for several residues only?
by zhangh1＠umbc.edu 29 Aug '10

29 Aug '10

Hi, I want to refine B factors for several residues only (all the other B factors and all coordinates fixed, I know it sounds weird but there is a reason to try that). Is there anyway Phenix can do this? Thanks for any suggestions! Best Regards, Hailiang

4 11

Re: [phenixbb] advice for refinement with anomalous information
by John Rose 28 Aug '10

28 Aug '10

Hi, I am refining my first structure (Cd-SAD) with the Phenix (GUI) and would like to refine anomalous f' and f". When i check the box, a menu appears and I have no idea of how to define the Cd atoms. I looked at the help and FAQ and found this: refinement.refine.anomalous_scatterers { group { selection = name BR f_prime = 0 f_double_prime = 0 refine = *f_prime *f_double_prime So I thought the name should be input as CD in the gui but when I submitted the refinement I got an error. Any help here would be appreciated? Thanks, John Rose

4 3

file type not supported???
by Joseph Noel 25 Aug '10

25 Aug '10

Hi All, I am having a problem that should be totally simple but I am stuck trying to find out what is happening. I use Text Wrangler on my Mac as a text editor of files. I have used it many many times to edit PDB files. It seems now that some PDB files that I have opened and removed a few lines now show up as an unrecognized file type when trying to read them into Phenix or into COOT. However, when I upload them on the Molprobity site they are read fine and processed. However, even the downloaded file from Molprobity gives the same error. I know it must be something simple but stumped and hoping someone else has experienced the same problem and has a quick fix. Thanks! Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

2 1

Re: [phenixbb] phenix.ready_set hydrogens not compatable with coot library
by Joseph Noel 25 Aug '10

25 Aug '10

Hi All, Indeed even the latest COOT still relies on the old PDB format and hydrogens fly. Its probably not prudent to use hydrogens in refinement then remove them and add back each time. Kind of defeats the purpose of using them in the first place. Until COOT is updated I found a pretty easy way around things as long as you have access to the internet. Just use the MOLPROBITY site (http://molprobity.biochem.duke.edu/). In addition to it being a fantastic tool for really cleaning up structures, you can quickly upload your refined file from Phenix with hydrogens, then hit the button to downgrade to PDB v23. It creates the appropriate file with renamed hydrogens that work great in COOT. You can then re-upload the COOT rebuilt model and it will "upgrade" naming to the latest PDB version. Download that file and there you go for Phenix refinement. Sounds like a bit but very fast and easy to implement until COOT is upgraded. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

5 4

Phenix Structure Soluiton & Refinement webinar
by Angela Criswell 24 Aug '10

24 Aug '10

Dear colleagues, I would like to draw your attention to an upcoming educational webinar to be presented by Paul Adams titled "Structure Solution and Refinement with Phenix" which is scheduled to occur Thursday, August 26th at 10:00 PDT (13:00 PM EST /17:00 UTC/GMT). You can find more information including a registration link at the following site: http://www.rigaku.com/protein/webinars.html Best regards, Angela

2 1

Palestrant, Deborah is out of the office.
by deborah.palestrant＠novartis.com 24 Aug '10

24 Aug '10

I will be out of the office starting 08/23/2010 and will not return until 08/27/2010. I will respond to your message when I return.

1 0

labelit.version bug?
by Ben Eisenbraun 24 Aug '10

24 Aug '10

labelit seems to be working fine, but one of my users pointed this out to me: $ which labelit.version /programs/i386-linux/phenix/1.6.4-486/phenix-1.6.4-486/build/intel-linux-2.6-x86_64/bin/labelit.version $ labelit.version Traceback (most recent call last): File "/programs/i386-linux/phenix/1.6.4-486/phenix-1.6.4-486/labelit/command_line/version.py", line 18, in <module> run() File "/programs/i386-linux/phenix/1.6.4-486/phenix-1.6.4-486/labelit/command_line/version.py", line 7, in run assert (os.path.dirname(build) == os.path.dirname(repos)) AssertionError -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

2 1

phenix.ready_set hydrogens not compatable with coot library
by amadrona＠uci.edu 24 Aug '10

24 Aug '10

hello, After reading many posts on the phenix and coot boards I realize that the hydrogens produced by phenix.ready_set are not compatable with coot. Specifically, coot does not recognize HB3 and HD3 hydrogens. When I do realspace refinement they fly off into space. I have edited HB3 to read HB2 and HB2 to read HB1 and everything works well. I was wondering if there is a fix for this besides editing the pdb each time you run phenix.ready_set. Is there a way to add HB3 hydrogens to the phenix library (CCP4 library)? Thank you -Yarrow

6 10

MD with phenix.refine?
by Ed Pozharski 21 Aug '10

21 Aug '10

Silly question: is there some way to run what would essentially be an MD simulation with phenix.refine? I mean, turn off X-ray-term by setting tardy.target_weights.fix_wxc=0, and then run cartesian dynamics? Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs

2 1

Ringer: A program to detect molecular motions by systematic X-ray electron-density sampling
by Terry Lang 21 Aug '10

21 Aug '10

The Alber lab at UC Berkeley is pleased to release of the code for Ringer version 1.0 (http://ucxray.berkeley.edu/ringer.htm). Ringer is a program to detect molecular motions by systematic X-ray electron-density sampling. The aim of Ringer is to go beyond static structural snapshots of proteins by uncovering structural ensembles in X-ray electron density. This information can reveal not only which parts of proteins are flexible and which parts are rigid, but it also can define alternate conformations that may be important for function. Alternate conformations of binding sites also may afford additional targets for drug design. The Ringer method is described in Lang et al. /Protein Sci/. 2010 Jul; 19(7):1420-31 <http://www.ncbi.nlm.nih.gov/pubmed/20499387>. An application of Ringer, determining the structural underpinnings of the side chain dynamics critical for the function of the enzyme proline isomerase, was published in Fraser JS et al. /Nature/. 2009 Dec 3;462(7273):669-73 <http://www.ncbi.nlm.nih.gov/pubmed/19956261>. Ringer is freely available to academics. -- PaulaTherese Lang Postdoctoral Scholar Alber Lab, UC Berkeley http://ucxray.berkeley.edu/ringer.htm

1 0

hydrogens in riding model create steric clashes after refinement
by amadrona＠uci.edu 21 Aug '10

21 Aug '10

Hi, I am having a problem with hydrogens causing steric clashes after refinement. I added hydrogens to my pdb using: "phenix.ready_set model.pdb". I was given two sets of coordinates (my model and a pdb for Iron atoms) I included this new model in the next round of refinement but I did not include the pdb for the Iron atoms. I ran refinement with the folowing parmeter file: refinement.main.ordered_solvent = true #refinement.main.ordered_solvent.mode=filter_only refinement.refine.strategy = individual_sites+individual_adp #refinement.refine.adp.individual.isotropic = "chain W" refinement.output.prefix = CIN4_refine refinement.output.serial = 18 refinement.output.write_def_file = True resolution is 1.37A with close to 400,000 unique observations (obs/param is still about 4) Stats: Rwork Rfree bonds angles start: .1444 .1723 .016 1.617 end: .1371 .1657 .010 1.301 I also ran wxu and wxc optimization from the command line. I know that the defualt is "riding-model" so that the hydrogen atoms are not refined. However, I thought that the program would be able to avoid steric clashes. Is there an aditional command I need to turn on to account for this? I am currently fixing every hydrogen that clashes on an individual basis in coot. There are also a handfull of hydrogens that exist out in space that I decided to delete. Thank you very much for your help. -Yarrow

4 11

altloc non-bonded interactions
by Paul Smith 20 Aug '10

20 Aug '10

Is it possible to tell phenix.refine to ignore certain non-bonded interactions? I have a structure at 1.1A with some interesting sulfate molecules that refuse to refine well. I suspect two positions are alternately occupied by sulfate in some cases and two water molecules in others. I would like to refine with both (a sulfate and two waters) with each component at 1/2 occupancy. With alternate conformations of a given sidechain, the two alternate locations automatically ignore one another w.r.t. non-bonded interactions. However, different residues, it would seem, do not. Has anyone encountered a similar situation or do the phenix gurus have any input? As an alternative, can I define an alternate sulfate residue with several missing atoms? Thanks in advance, --Paul

3 2

Re: [phenixbb] stuck with phenix refine
by Ian Munro Slaymaker 20 Aug '10

20 Aug '10

I also have been having a problem with phenix.refine freezing with no error message from the GUI. It usually freezes at the first macro cycle. I am using version 1.6.4-486. -Ian

3 4

Constraining carbohydrate conformation
by Kenneth Verstraete 20 Aug '10

20 Aug '10

Dear phenixbb users, I wonder how I can constrain the conformation of a NAG-residue during refinement. I have a dataset to 4.2 Angstrom. After refinement some sugars end up in the boat conformation. I would like to run the refinement so that the Asn side chain and the Asn-NAG linkage is refined (using xyz or torsion angle dynamics) but that the NAG-residue itself is considered as a rigid group. Maybe one way of doing this is constraining the bonds and angles of the NAG residue by the defining them as "custom bonds and angles" with sigma=0? Is there a possibility in phenix to generate these constraints from an ideal NAG-residue automatically? Thank you very much for you advice, Kenneth Verstraete

3 2

clean up temporary files
by Jianghai Zhu 18 Aug '10

18 Aug '10

Hi, I realize that after a phenix run, especially autobuild and autosol, there are a lot of temporary files. Is there a way to clean up the disk? Even the .geo file can be removed after some time, because it is huge and can be easily regenerated. -- Jianghai

4 3

ubuntu 10.04 phenix installation
by vincent rao 18 Aug '10

18 Aug '10

Dear Phenix bb user, i'm trying to install the latest version of phenix (1.6.4-486) on my pc with Ubuntu 10.04 installed. I'm using the*phenix-installer-1.6.4-486-intel-linux-2.6-x86_64-fc13.tar * installer. The installer complains that the * bundle-1.6.4-486-intel-linux-2.6-x86_64.tar.gz* is missing in the phenix-installer-1.6.4-486/bundles folder, and requires *bundle-1.6.4-486-intel-linux-2.6.tar.gz *to be present in this folder. So i simply renamed *bundle-1.6.4-486-intel-linux-2.6-x86_64.tar.gz *to *bundle-1.6.4-486-intel-linux-2.6.tar.gz *and this allowed the installation to complete without any further errors. However, when trying to start Phenix, i get the following error: laptop:~/Documents/installers/phenix-installer-1.6.4-486> phenix Traceback (most recent call last): File "/usr/local/phenix-1.6.4-486/phenix/wxGUI2/command_line/main.py", line 13, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.6.4-486/phenix/wxGUI2/command_line/main.py", line 7, in run from wxGUI2 import App File "/usr/local/phenix-1.6.4-486/phenix/wxGUI2/App.py", line 6, in <module> import wx.lib.dialogs File "/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/site-packages/wx-2.8-gtk2-ansi/wx/__init__.py", line 45, in <module> from wx._core import * File "/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 4, in <module> import _core_ ImportError: /usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/site-packages/wx-2.8-gtk2-ansi/wx/_core_.so: wrong ELF class: ELFCLASS64 Not sure if this is of any use in solving the problem, but i typed the following command phenix.wxpython -c "import sys; print sys.path" and got the following output; ['', '/usr/local/phenix-1.6.4-486', '/usr/local/phenix-1.6.4-486/cctbx_project', '/usr/local/phenix-1.6.4-486/reel', '/usr/local/phenix-1.6.4-486/phaser', '/usr/local/phenix-1.6.4-486/tntbx', '/usr/local/phenix-1.6.4-486/phenix', '/usr/local/phenix-1.6.4-486/elbow', '/usr/local/phenix-1.6.4-486/PyQuante', '/usr/local/phenix-1.6.4-486/docutils', '/usr/local/phenix-1.6.4-486/PyCifRW', '/usr/local/phenix-1.6.4-486/cctbx_project/boost_adaptbx', '/usr/local/phenix-1.6.4-486/cctbx_project/libtbx/pythonpath', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/lib', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python26.zip', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/plat-linux2', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/lib-tk', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/lib-old', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/lib-dynload', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/site-packages', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/site-packages/Numeric', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/site-packages/PIL', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/site-packages/wx-2.8-gtk2-ansi'] thanks

4 3

geometry weight and rmsd bonds - angles
by Lionel Costenaro 18 Aug '10

18 Aug '10

Hello, I'm using phenix.refine for the first time and have some problem to get it reach reasonable rmsd bonds (0.012-0.015) and angles (1.5-1.8). I set the bonds rmsd_max and angles rmsd_max to these values and try different values for: wxc_scale (from default 0.5 downto 0.015), wxu_scale (from default 1 down to 0.03), wc (from default 1 up to 8), with and without optimising wxc wxu. Whatever the parameters, phenix never reached final rmsd better than 0.022 and 2.2. I refine the structure with refmac so far, but need to refine the occupancies (so phenix). Am I doing something wrong? Should I just use phenix to refine only the occupancy (I am actually doing it)? Any help or comment are welcome. Some information: space group: P21, 2 molecules (180 aa) / au, 510 waters, about 20% alternate conformations, ligand covalently link to the protein (correct dictionary and link parameters for refmac or phenix -add link to cif), resolution: 1.32, refine xyz for all, Baniso for all (refmac), ncs not used, R 13.6 Rfree 17.7 fom 0.913 rmsd 0.012 1.56 (last refmac) phenix version 1.6 289 (gui) Best regards, Lionel

8 20

HKL_base
by Ed Pozharski 17 Aug '10

17 Aug '10

MTZ-files generated by phenix (at least some of them) are missing the base dataset (HKL_base) which is a requirement since CCP4 5.0. Is this deliberate? Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs

3 6

AutoSol scaling error
by Yogesh Gupta 17 Aug '10

17 Aug '10

I got following error while running MIR in phenix: "Failed to carry out AutoSol_scale_and_analyze_MIR: list index out of range". Could some one tell me how to fix this? Thanks, Yogesh

2 1

Re: [phenixbb] Restraints file for a new amino acid residue
by Joseph Noel 17 Aug '10

17 Aug '10

Pavel, I sent you the associated pdb file as an attachment. The site in question is 169 in both monomer A and monomer B. I think one way around the problem for me is to create alternative conformations for the residues on either end of the modified cysteine. In that way I can refine each as a section of alternative conformations and then I think things should link up both in Phenix and COOT. COOT is particularly problematic. It only recognizes conformer A and not any additional conformers for a particular position if the name of the amino acid changes. I guess my case is not that common - ie a mixture of oxidation states of a regular amino acid. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Re: [phenixbb] Restraints file for a new amino acid residue
by Joseph Noel 14 Aug '10

14 Aug '10

Thanks all for the advice. Basically that is what I have been doing. It is actually an oxidized cysteine to sulfenic acid. I am refining the site as alternative conformers with the normal Cys, the single oxidation state to sulfenic acid (CSO) and the double to sulfinic acid (CSD). I know that CSO is in the phenix library but it adds hydrogens to the amino group every time I run elbow or ready set. I then I have to edit the PDB file to delete the hydrogen or Phenix will not refine. I also have problems in COOT. It will not let me move the residues torsional angles. I have checked other structures in the PDB and the density fits perfectly with the structures of many such oxidized systems but for some reason Phenix is giving me some problems. I was going to create a "new" residue and explicitly define the oxygen as charged rather then protonated since the pKa of sulfenic acid is quite low. Maybe the problems all stem from refining this particular position with three alternative "conformers", each conformer of which is chemically distinct. For now, I have CSO labeled as convention BCSO for conformer B. Cys is ACYS. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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