- phenixbb - phenix-online.org

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 >>

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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

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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

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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.

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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

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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.

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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.

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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

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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

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Problem using MOSFLM-integrated MAD data
by Yu Wai Chen 04 Dec '09

04 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.

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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

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(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.

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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 02 Dec '09

02 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 30 Nov '09

30 Nov '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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Age Concern edition of the Computing Commission and Teaching Commission newsletter
by Ralf W. Grosse-Kunstleve 24 Nov '09

24 Nov '09

Posted on behalf of Lachlan Cranswick: The Computing Commission and Teaching Commission has produced a joint November 2009 newsletter on the theme of "Age Concern", which deals with issue concerning "the slow march towards retirement of the major generation of crystallographic programmers", as further explained by David Watkin within the newsletter. http://www.iucr.org/resources/commissions/crystallographic-computing/newsle… or via http://www.iucr.org/resources/commissions/crystallographic-teaching/newslet… --------------------------- This issue's articles include : - the latest background and information from the UK based EPSRC funded Age Concern Project. - history and science within the Caltech based CRYRM single crystal suite; DIMS - Direct methods In Multidimensional Space software; Crunch 1.5 Direct Methods Software; the Glasgow based GX single crystal suite; the Italian based CAOS structure refinement software; Ton Spek's Platon; and a list of programs archived at Armel Le Bail's Crystallography Source Code Museum. - experience in conversion of large crystallographic Fortran-77 to C++; as well as the place of the Quick and Dirty Crystallographic Computer Program - Historical group photographs from some of the Crystallographic Computing and Teaching School of the 1970's. - Archived manuals and source code from the above mentioned software. - Teaching material of Isabella L. Karle, as she presented at the 1978 Erice School on Direct Methods for Solving Crystal Structures - A reprint of the The Analytical Theory of Point Systems (1923) by J. D. Bernal (1901-1971) Further Computing Commission newsletters are intended on theme of Age Concern : capturing the history and the crystallographic science behind past and present Small Molecule, Powder Diffraction, Protein and other crystallographic software. Submissions on this topic are welcome and encouraged. - Lachlan Cranswick ( lachlan.cranswick(a)nrc.gc.ca )

1 0

Confused by the output from Phenix autobuild jobs
by Serah Wangari 24 Nov '09

24 Nov '09

Dear Phenix users, I have run a number of Autobuild jobs using the Phenix GUI and in all cases, I'm not sure what output I should proceed with to the next step. - The first job was for rebuilding a loop section in the model (rebuild-in-place) - As far as I can remember, there was no mtz generated from this job, I had to generate map coefficients with the overall_best pdb and an old mtz using another refinement program. Did I miss something during the job input step, so that no mtz was generated, or how would I proceed in such a case? - The next job involved rebuilding the whole model (rebuild-in-place) - in this case, I took the overall_best pdb, but when I tried to open the overall_best_refine_map_coeffs.mtz in coot, I got this error that coot failed to find F/Phi columns in the mtz file. Then I checked in the TEMPO directory, and I managed to open a random mtz from one of the refinement cycles with coot, but I wasn't confident building into that, so again I had to generate map coefficients using overall_best pdb and an old mtz in another program. - The other job was rebuilding (rebuild-in-place) another model with composite maps generation - Here, in addition to the 12 mtz and pdb files from the 12 omit regions, I got resolve_composite_map.mtz I should assume as the only final output; and no final pdb. Again, this mtz file doesn't have the F/Phi columns as I got the same error as above in coot. I'm not sure how to proceed with this mtz...... I would really appreciate if someone could point me to the right direction or at least direct me to some literature where the output from Phenix autobuild jobs is explained - as I haven't come across such info yet. Thank you in advance, Serah --

3 2

Clean Jobs
by tea.pavkov＠uni-graz.at 23 Nov '09

23 Nov '09

Dear all, I would have a general question - how can I clean the Jobs (in the Job history list and all corresponding directories) in the new GUI? Thank you in advance! Best regards, Tea ----------------------- Dr. Tea Pavkov-Keller KF Uni Graz, ZMB Structural Biology Group Humboldtstr. 50/III 8010 Graz Austria

3 3

Problem installing on Leopard PowerPC G5
by Satpal Virdee 23 Nov '09

23 Nov '09

Hi, I am trying to install the latest 1.5-2 official release on an iMac PowerPC G5 running OSX 10.5.8. During installation I get the error: " Relocating Python framework. . . /usr/bin/install_name_tool: object: libwx_mac-2.8.0.5.0.dylib malformed object (unknown load command 20) Error: see /Users/Sat/Downloads/phenix-installer-1.5-2/build-binary/ mac-ppc-osx/cpemac406-18/log/binary.log for details " Inspection of the binary.log files reveals this: " libfreetype.6.3.10.dylib: /usr/local/phenix-1.5-2/build/mac-ppc-osx/ base/lib/libfreetype.6.3.10.dylib --> /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/libfreetype. 6.3.10.dylib libfreetype.6.dylib libfreetype.6.dylib: /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/ lib/libfreetype.6.dylib --> /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/libfreetype. 6.dylib libfreetype.dylib libfreetype.dylib: /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/ libfreetype.dylib --> /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/libfreetype.dylib libwx_mac-2.8.0.5.0.dylib fix_mac_python: caught error - exiting. " Any help would be most appreciated. Regards, Satpal

2 1

baton build in coot
by Raja Dey 22 Nov '09

22 Nov '09

Dear Friends, How does CA ZONE > MAIN CHAIN under 'other modeling tools' in coot work? I was trying to rebuild main chain atoms for 3 residues(8,9,10) using CA ZONE > MAIN CHAIN. when I click on one atom in residue 8 and then one atom in residue 10, it failed with a message that says the zone is too short. I increased the zone to 5 residues, still same failed message. Also, is it possible to move an atom in coot? Thanking you in advance for your reply. Raja

2 1

phasing power value in Autosol/Autobuild
by vennila Natesan 19 Nov '09

19 Nov '09

Dear all... I need toknow the phasing power value for my solved structure. Where can i find it out in the output files of autosol and autobuild? I am using phenix1.14.4b and also i need to know the weighted mean phase errors vs resolution. Thanking you.

3 2

I vs F data input
by gerwald jogl 18 Nov '09

18 Nov '09

Hi All, A quick question about diffraction data input. I just noticed that phenix.refine uses Imean/SIGImean and converts these by default in my refinements. Is this the preferred way or would it be better to use F/SIGF (after CCP4)? Thanks, Gerwald

2 1

external ncs reference structures?
by Cathy Lawson 18 Nov '09

18 Nov '09

Dear Phenix developers, We are finishing up refinement of some multiprotein-DNA complex structures at 3-3.5 A resolution and I am wondering if it would be possible with phenix.refine to supply one or more external sets of coordinates from higher-resolution determinations to serve as the ncs references. If so what would be the best way to set this up? thanks, Cathy ********************************** Catherine Lawson, Ph.D. Rutgers University Chemistry & Chemical Biology 610 Taylor Rd Piscataway, NJ 08854 732 445 5494 cathy.lawson(a)rutgers.edu http://roma.rutgers.edu **********************************

2 1

Mac OSX Phenix GUI
by Miguel Ortiz Lombardia 18 Nov '09

18 Nov '09

Hi, This is a question/request to the phenix developers. Are there any plans to make the new phenix GUI to use an X11 python interface instead of the Aqua one? The reason I ask is that we use Mac OSX servers for calculations here and an X11 interface would be a lot more appropriate for this configuration. That way users could export the GUI to their local workstations. As it is implemented now this use of the GUI is impossible on Mac OSX. Before someone makes the suggestion: Remote Desktop simply allows to share the only Aqua desktop that the server can produce, that is, only one user can access the Aqua desktop, whether remotely or locally. We would be happy to test any X11 version you might be willing to develop. Thanks for your great software, which we can use anyway from the command line :-) Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2

2 1

Phaser output and error messages
by Ian Stokes-Rees 17 Nov '09

17 Nov '09

I'm having some discussion with a colleague about phaser output (we're using Phaser 2.1.4). We haven't been able to find any documentation which can clarify our situation, and I'm hoping someone on the list can help answer these questions. I should mention that I am relatively new to Phaser. 1. PHASER.sol files: Which "SOLU SET" does Phaser consider to be the best? The first or the last? Or the one with the highest LLG, wherever that may be? In our experience of running Phaser over several MTZ files with a range of models the best Phaser solution has always been the first, and this has had the highest LLG. Note: this is with "untuned" Phaser settings for identity, solvent fraction, or number of search models in ASU -- our goal is to do a first run with "generic" settings for these over a larger set of models, then (from TFZ and LLG scores) select a subset for which we will tune Phaser parameters and PDB search model variations. 2. If we are right that the first "SOLU SET" entry is indicative of the potential for the search model to form a good MR candidate, then is it the case that the first entry is the first Phaser solution that is computed? Or is the PHASER.sol file a sorted list output at the end of the run? From my reading of the documentation it is output in order of computation, and *for our purposes* (if my first statement in this question is correct) Phaser can stop after it outputs this first solution. Is there some way to tell Phaser to stop after the first solution is output? I realize that this doesn't sound like it makes sense (how could Phaser know to pick the best solution first, and even if it could, why would it ever continue past this point), however I ask because we have put a 10 minute timeout into our Phaser runs and we have many situations where we get a timeout but PHASER.sol has already been generated and the best LLG solutions are output first. It leaves me wondering why it didn't just stop on its own after outputting the first result instead of being aborted by our (external) timeout that terminates the process? 3. PHASER.sol files: For single domain search models, we usually get output of the form: SOLU SET RFZ=4.5 TFZ=5.2 PAK=0 LLG=14 LLG=14 SOLU 6DIM ENSE model1 EULER 242.049 45.040 326.088 FRAC -0.09425 0.50268 0.42575 however we see three variations: i) No LLG: SOLU SET RFZ=3.1 TFZ=5.0 PAK=0 SOLU 6DIM ENSE model2 EULER 59.983 69.335 319.701 FRAC -1.17131 -0.70030 0.23150 ii) One LLG: SOLU SET RFZ=3.7 TFZ=4.6 PAK=0 LLG=25 SOLU 6DIM ENSE model3 EULER 293.943 128.068 332.147 FRAC 0.06273 0.13175 0.25054 iii) Two LLG entries, but with different values: SOLU SET RFZ=3.8 TFZ=4.1 PAK=0 LLG=21 LLG=20 SOLU 6DIM ENSE model4 EULER 278.058 129.347 33.292 FRAC 0.28446 0.29011 -0.07986 4. Occasionally we get an error that we don't understand: FATAL RUNTIME ERROR: No scattering in pdbfile model1.pdb What does this mean? Is there a problem with the PDB file? We can't see anything obvious in the ones which produce this error. Thanks, Ian -- Ian Stokes-Rees, Research Associate SBGrid, Harvard Medical School http://sbgrid.org

2 2

Request: read definitions from stdin
by Joe Krahn 15 Nov '09

15 Nov '09

I want to be able to run PHENIX in a shell script, where stdin is accepted as a definition input file. It could be simply specified as the usual POSIX syntax where "-" defines stdin in place of an input file. If the front-end is based too heavily on file suffix mappings, you could add a flag "--stdin=SUFFIX" to define reading stdin as if it had the given SUFFIX. It would also be nice to avoid the duplication of output to both stdout and the .log file. Output can always be sent to /dev/null, but it would be nicer to have either a --quiet flag to suppress stdout, or a DEF option to disable the .log output, or both options to let the user decide. Most other computational programs can be run this way, so I assume that other people would find this useful, especially for running PHENIX from scripts. Hopefully, it is also a fairly easy feature to implement. Thanks, Joe Krahn

3 2

R-free rules
by Bryan W. Lepore 13 Nov '09

13 Nov '09

[ phenix.refine v1.5 rel. tag 2 intel linux 2.6 ] if i provide the test set .mtz (flag = "1") in refinement separately from the data .mtz, it looks like reflection_file_converter.py does not flag the work set as "0", if the work set lacks such a flag -- is that right? i.e. when providing the test set, it looks like all observed data must be in the test set, however the work set has flag "0". -bryan (some error output below) Sorry: R-free flags not compatible with F-obs array: missing flag for 22206 F-obs selected for refinement:

3 4

November 15, 2009 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 12 Nov '09

12 Nov '09

Dear Users, The deadline for October/November/December 2009 Collaborative Crystallography proposals will be *November 15, 2009. * ------------------------------------------------------------------------ Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ----------------------------------------------------------------------------------------- How To Apply: To learn more, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 9, please describe a specific research project with a clear end point. In order to request CC time for October/November/December 2009 allocation period, proposals must be submitted by *November 15, 2009.* The deadline for CC proposals for the time period March/April 2010 will be January 15, 2010. Regards, Banumathi Sankaran

1 1

sulfate on a 2 fold axis
by David Cobessi 12 Nov '09

12 Nov '09

Hi, I am finishing to refine a structure using Phenix. A sulfate ion is located on a 2 fold axis. When I refine the structure with Refmac, the geometry of the ion is well conserved, while when I use Phenix the geometry is destroyed and the sulfate ion is like a cross!! Any idea to keep the good geometry of this ion in Phenix during the refinement? Thanks in advance, David -- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122

2 1

phenix.cif_as_mtz
by Bryan W. Lepore 12 Nov '09

12 Nov '09

[ v. 1.5 release tag 2 intex-linux-2.6 redhat-e4.8 ] `phenix.cif_as_mtz file.cif --symmetry=FILE.pdb --show-log --show-details-if-error` .. reports "No data extracted from input cif file.", nothing else. command works w/ other .cif/.pdb's, CRYST1 lines, etc. look comparable between them,... not sure where to look next. thanks for any suggestsions. -bryan

2 1

Nino Campobasso is out of the office.
by Nino.2.Campobasso＠gsk.com 11 Nov '09

11 Nov '09

I will be out of the office starting 11-Nov-2009 and will not return until 12-Nov-2009.

1 0

Failed to make map after phenix.refine
by Zhou, Tongqing (NIH/VRC) [E] 11 Nov '09

11 Nov '09

Hi, All I am having problem with the new 1.5.2. After few rounds of refinement, the program failed to write out maps. It ended with: "Sorry: Duplicate mtz_label_amplitudes:FOFCWT" Here is the portion in my param file which worked fine before: electron_density_maps { map_format = *xplor map_coefficients_format = mtz *phs suppress = None map { mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" likelihood_weighted = True obs_factor = 2 calc_factor = 1 } map { mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" likelihood_weighted = True obs_factor = 1 calc_factor = 1 } } Thanks in advance for your help. Tongqing

2 1

C-ter amidation of peptide
by Nate Nicely 10 Nov '09

10 Nov '09

Dear all, How best to handle a C-terminally amidated peptide in phenix? I defined the atom as 'N' and the resname as 'NH2' following a structure I found that also bears a C-terminally amidated peptide. However phenix.refine seems not to be making the linkage between the amide and the preceding residue. Putting the structure into phenix.elbow returns, "No unknown residues." Thanks, Nate N.

3 2

Glycan refinement
by Zhou, Tongqing (NIH/VRC) [E] 10 Nov '09

10 Nov '09

Dear All, I am refining a structure with a N-linked glycosylation site. There is density that goes beyond the first NAG, at least to MAN3. I know in Phenix there is data_link = NAG-ASN for the ASN-NAG connection, but I don't know how to do the "apply_cif_link' for the extensions such NAG-NAG, NAG-MAN, MAN-MAN...., any suggestions are appreciated. 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. ******************************************************************

5 9

Problem reading ".edits" parameter file
by John Pascal 06 Nov '09

06 Nov '09

Hello, On a previous version of PHENIX, 1.4-153, I was able to read in a parameter file with geometry constraints. Upon loading the file, the program asked when to execute the commands, I said at run time, and everything worked fine. Using the same parameter file in PHENIX 1.5-2, I am no longer asked about when to execute the file, and when I proceed to run the refinement, the program quits stating an unexpected character. I can't find anything obviously wrong with the parameter file. Any suggestions? The previous version of PHENIX (the one that worked) is no longer located on my server, so I can't easily return to that version. 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.

2 1

Phaser question : RMS deviation and FOM
by Peter Grey 06 Nov '09

06 Nov '09

Dear Phenix developers, The expected RMS deviation input to Phaser affects the FOM estimation of phases quality. This in-turn affects the sigmaa weighted maps and most importantly the density modification steps that follow phaser. I would like to ask if, based on the phaser solution and the LLG parameter, one could optimize the RMS estimation or know the real RMS deviation that would result in more true FOM. Thanks, Peter With condolences to the family of Warren DeLano who will be sorely missed

2 1

Analyzing MIR datasets
by Rajagopalan, Senapathy 06 Nov '09

06 Nov '09

Hi All, I am a new user to Phenix and am trying to process MIR datasets from a parameter file typing 'phenix.autosol mir.eff' and keep running into the error message saying: _______________ Possible choices: /Users/sena/data/crystallography/raw1025/Processing/iafinal_d212121.mtz:I,SIGI,merged /Users/sena/data/crystallography/raw1025/Processing/iafinal_d212121.mtz:IPR,SIGIPR,merged Please use scaling.input.xray_data.obs_labels to specify an unambiguous substring of the target label. 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_mir: Sorry, there is something wrong with the file /Users/sena/data/crystallography/raw1025/Processing/iafinal_d212121.mtz ... xtriage cannot analyze it? ******************************************************************************** ___________________ The 'mir.eff' file contains: ------------------ # autosol { seq_file = sequence.dat #scaling.input.xray_data.obs_labels='I SIGI' # xray_data_labels = FP, SIGFP # autosol.input.xray_data.labels=FP labels='I SIGI' crystal_info { space_group = p212121 unit_cell = 49.020 73.140 187.350 90.000 90.000 90.00 } native { data = iafinal_d212121.mtz } deriv { data = s10final_d212121.mtz atom_type = I sites = 2 inano = noinano *inano anoonly } deriv { data = s13final_d212121.mtz atom_type = I sites = 1 inano = noinano *inano anoonly } deriv { data = s23final_d212121.mtz atom_type = I sites = 1 inano = noinano *inano anoonly } } ----------------- I guess the error comes because the program is not able to make a choice as to which columns to take from the mtz file. But no matter what 'label' syntax I use or where I use it, it doesn't seem to help. Obviously, I am missing something here. So could someone please help me with this. Also, I tried the same thing using the phenix wizard and it still gives me the same error. Thanks Sena Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Ranked No. 8 on FORTUNE magazine's list of the "100 Best Companies to Work For" in 2009 Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

2 1

molecular replacement - restricting rotation around a specified orientation
by Christine Gee 06 Nov '09

06 Nov '09

Dear Phenix developers, We have a protein with two sub domains (N-lobe and C-lobe) we are trying to solve by MR. The C-terminal sub domain solves fine (TFZ 11.1), but the N-terminal lobe is not being placed correctly. I read in the online documentation that you can specify a limited rotation range around the orientation you would expect for the N-lobe based on the C-lobe orientation. My question is, how do specify what orientation to start with? I know I need some Euler numbers, but are they just the same ones that the C-lobe writes out with and I use an N- lobe that is basically the other half of the C-lobe pdb (ie the X,Y,Z co-ordinates are consistent with each other at the beginning of the search)? Or do I need to position the N-lobe with the solution C-lobe and write it out for use in the search model, and then how do I specify the Euler? Also we were going to try and use normal mode perturbation to generate an ensemble and I was wondering if there is more documentation somewhere on how to do that? Regards Christine

2 1

about Turbo Frodo
by Zhongli Cui 06 Nov '09

06 Nov '09

Dear all, I have ever used Turbo Frodo as the modelling software in protein crystallography. It is a very convinient software to learn. But it seems that the lience email of turbo is out of work. Does anyone know if Turbo is still maintained by AFMB and the new email for lience? Thanks Zhongli ---------------- Cui Zhongli Professor, Ph.D Dept. of Microbiology College of Life Sciences Nanjing Agricultural University 1 Weigang, Nanjing, 210095 Jiangsu Province P.R. China. Mail: czl(a)njau.edu.cn Tel: 86-25-84396753 Mob: (0)13951080529

1 0

Running Phenix 1.5.2 with Martin Horvath
by Raghav Kalia 04 Nov '09

04 Nov '09

I recently downloaded and installed phenix 1.5-2. I can launch the GUI by double clicking on the phenix icon. However, I cannot get to run phenix.refine on the command line. How does one set paths so that phenix.refine will be recognized in a terminal window? Raghav Kalia

2 1

Re: [phenixbb] phenixbb Digest, Vol 48, Issue 4
by Leo Sazanov 04 Nov '09

04 Nov '09

Thanks, restore results works fine for what I need now. phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: re-run jobs in GUI (Nathaniel Echols) > 2. Elbow ligand building (Joe Krahn) > 3. Re: Elbow ligand building (Nigel W Moriarty) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 4 Nov 2009 08:34:24 -0800 > From: Nathaniel Echols <NEchols(a)lbl.gov> > Subject: Re: [phenixbb] re-run jobs in GUI > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <529970F2-E319-4152-B4F1-E46184755554(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes > > On Nov 4, 2009, at 8:08 AM, Leo Sazanov wrote: > >> Hi, in a new GUI how can one re-run previous jobs (to make some >> modifications to them)? >> > > Open the main GUI (the command 'phenix', or click the home button on > the toolbar of any other program), click the "job history" toolbar > button, select a job from the list, and click "restore results". This > should restore both the results tab or window, and the configuration. > There is also a "restore last job [for the current project]" button on > the toolbar. Any inconsistencies here are definitely a bug, but it > was working for most programs in 1.5-2. (The main exception is the > reflection file editor, but that will also save/restore results in the > next available nightly build.) > > >> If I just try to open parameter (.eff) file from the main file menu in >> Autobuild, the file does not show up, even though it exists. >> Just adding it to the list of input files works, but the information >> is >> not passed on into GUI? >> > > > It's a little complicated right now. If you want to apply the > contents of a parameter file, this is best done at startup - e.g. drag > and drop the file onto the launch icon, or use it as a command line > argument ('phenix.autobuild params.eff'). For phenix.refine, you can > also save default parameters (Preferences->Refinement, or project > settings, or from the utilities menu) and it will start with them pre- > loaded. Once the program window is drawn, however, it's clumsier - > files *should* be passed down to the command-line module (if not, also > a bug), but they won't immediately be applied to the GUI, because of > the way it tracks parameters internally. > > I can't promise that every pre-existing configuration file will be > processed cleanly by the GUI - it's difficult to anticipate what users > will try to do. If you encounter cases where the parameters are > misinterpreted, let me know. > > -------------------- > Nathaniel Echols > Lawrence Berkeley Lab > 510-486-5136 > NEchols(a)lbl.gov > > > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 04 Nov 2009 12:35:01 -0500 > From: Joe Krahn <krahn(a)niehs.nih.gov> > Subject: [phenixbb] Elbow ligand building > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <4AF1BB45.20707(a)niehs.nih.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > I am having some problems building ligand parameters with elbow. > > I have an accurate reference structure, but elbow seems to "regularize" > the coordinates in a way the distorts the structure. Is there a way to > disable this? > > With --opt, QM optimization should hopefully remove distortions, but it > is not doing a very good job for this molecule. So, I decided to > optimize using Gaussian, and a better basis set. > > It seems that the Gaussian interface is still fairly simple, and it > seems that you have to edit the Gaussian.csh template. So, I did that, > but got the "Gaussian does not seem to be installed" message. > Unfortunately, elbow runs the Gaussian script with output to /dev/null, > so there is no way to see any error messages. Maybe that should be done > only when the --quiet flag is given. > > I edited the Python source to let errors go to the tty, and found that > the problem is in the way the script is invoked using "csh -c %s.csh". > That only works if "." is in your $PATH, which is often the case. It > also invokes an extra instance of csh, because it is invoked as a system > command. The correct way to run a shell script is to leave out the '-c'. > Elbow makes the script executable, so an even better approach is to just > leave out "csh", and do "os.system('./%s.csh' % project)". Then, the > script can be in sh/bash/etc. Maybe the was the intent of using '-c'? > > Thanks, > Joe Krahn > > > ------------------------------ > > Message: 3 > Date: Wed, 04 Nov 2009 10:09:47 -0800 > From: Nigel W Moriarty <NWMoriarty(a)lbl.gov> > Subject: Re: [phenixbb] Elbow ligand building > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <4AF1C36B.3010500(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Joe > > On 11/4/09 9:35 AM, Joe Krahn wrote: > >> I have an accurate reference structure, but elbow seems to "regularize" >> the coordinates in a way the distorts the structure. Is there a way to >> disable this? >> >> > eLBOW will always run a simple optimisation unless you specify the final > geometry you like using > > phenix.elbow --final-geometry accurate.pdb > > Naturally, you are smart to use a better input format thus > > phenix.elbow filename.sdf --final-geometry accurate.pdb > >> With --opt, QM optimization should hopefully remove distortions, but it >> is not doing a very good job for this molecule. So, I decided to >> optimize using Gaussian, and a better basis set. >> >> > Good thinking. > >> It seems that the Gaussian interface is still fairly simple, and it >> seems that you have to edit the Gaussian.csh template. So, I did that, >> but got the "Gaussian does not seem to be installed" message. >> Unfortunately, elbow runs the Gaussian script with output to /dev/null, >> so there is no way to see any error messages. Maybe that should be done >> only when the --quiet flag is given. >> >> > Maybe I'll implement this with a --verbose flag. > >> I edited the Python source to let errors go to the tty, and found that >> the problem is in the way the script is invoked using "csh -c %s.csh". >> That only works if "." is in your $PATH, which is often the case. It >> also invokes an extra instance of csh, because it is invoked as a system >> command. The correct way to run a shell script is to leave out the '-c'. >> Elbow makes the script executable, so an even better approach is to just >> leave out "csh", and do "os.system('./%s.csh' % project)". Then, the >> script can be in sh/bash/etc. Maybe the was the intent of using '-c'? >> > This is old code from before PHENIX had a smart module for running > commands. I'll update to code. > > Nigel > > -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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Elbow ligand building
by Joe Krahn 04 Nov '09

04 Nov '09

I am having some problems building ligand parameters with elbow. I have an accurate reference structure, but elbow seems to "regularize" the coordinates in a way the distorts the structure. Is there a way to disable this? With --opt, QM optimization should hopefully remove distortions, but it is not doing a very good job for this molecule. So, I decided to optimize using Gaussian, and a better basis set. It seems that the Gaussian interface is still fairly simple, and it seems that you have to edit the Gaussian.csh template. So, I did that, but got the "Gaussian does not seem to be installed" message. Unfortunately, elbow runs the Gaussian script with output to /dev/null, so there is no way to see any error messages. Maybe that should be done only when the --quiet flag is given. I edited the Python source to let errors go to the tty, and found that the problem is in the way the script is invoked using "csh -c %s.csh". That only works if "." is in your $PATH, which is often the case. It also invokes an extra instance of csh, because it is invoked as a system command. The correct way to run a shell script is to leave out the '-c'. Elbow makes the script executable, so an even better approach is to just leave out "csh", and do "os.system('./%s.csh' % project)". Then, the script can be in sh/bash/etc. Maybe the was the intent of using '-c'? Thanks, Joe Krahn

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re-run jobs in GUI
by Leo Sazanov 04 Nov '09

04 Nov '09

Hi, in a new GUI how can one re-run previous jobs (to make some modifications to them)? If I just try to open parameter (.eff) file from the main file menu in Autobuild, the file does not show up, even though it exists. Just adding it to the list of input files works, but the information is not passed on into GUI? -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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low resolution, high B, low R
by gerwald jogl 03 Nov '09

03 Nov '09

Hi All, I am working on a 4.2 A structure and feel somewhat uneasy about my refinement results. First, my R/Rfree at the moment is 0.18/0.25. The refinement is not complete and weights are not optimized, so the gap may get smaller. It's just that at 4.2 A, I don't quite expect such low R factors... There is nothing funny with the data, no messing around, no conversions - straightforward data set and a basic rigid body, individual_sites+group_adps, simulated annealing, no tls yet, no ncs. I am aware that one possible answer is that phenix is just really good... The other issue is about B factors. Phenix will happily refine B factors to values of 300 if there is no density in the region and that brings up the question about how to deal with disordered regions in general. Are there any current opinions out there about what would constitute 'reasonable' B factors? Conversely, when would a B factor indicate that it is better to remove the residue from the model instead of leaving it and calling it disordered. Also, this is after group_adp at 4.2 A - should I maybe take this as an indication that this is asking too much from the data and go back to a single adp per chain and tls? All comments are appreciated. Thanks! Gerwald

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Re: [phenixbb] phenixbb Digest, Vol 48, Issue 2
by Xuewu Zhang 03 Nov '09

03 Nov '09

You are right. It started in the 2nd macro cycle. I should have been a little more patient. Sorry about it. Thanks, Xuewu On Tue, Nov 3, 2009 at 2:00 PM, <phenixbb-request(a)phenix-online.org> wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: optimization of wxc and wxu (Xuewu Zhang) > 2. Re: optimization of wxc and wxu (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 3 Nov 2009 08:28:58 -0600 > From: Xuewu Zhang <xuewu.zhang(a)gmail.com> > Subject: Re: [phenixbb] optimization of wxc and wxu > To: phenixbb(a)phenix-online.org > Message-ID: > <926abad50911030628h31d09c53m59c2c84f1d024596(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi phenix developers/gurus, > > I am using the latest night build of phenix on OS X snow leopard. I found > that phenix ignores these lines in my custom refinement file: > > refinement.target_weights.optimize_wxc="True" > refinement.target_weights.optimize_wxu="True" > > Manually setting up the scale factors however works. I am not sure whether > this is a bug or a platform related issue. > > Thanks, > Xuewu Zhang >

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