- phenixbb - phenix-online.org

Ligand building/refinement woes
by Machius, Mischa Christian 14 Jan '13

14 Jan '13

I seem to be having the hardest time building/refining NADPH (PDB code NAP). When fetching this common ligand from within coot, Phenix (1.81-1168) subsequently does not seem to accept it and bombs noting all kinds of violations. When I have Phenix automatically build NAP into the density, it does place NAP (albeit completely out of otherwise quite nice density). When I then take the coordinates, read them into coot together with the CIF that Phenix writes into the ligand_build directory, placing and refinement in coot works well, but subsequent refinement in Phenix, using the very same CIF, again bombs. Since hydrogens are often an issue when going from coot to Phenix I remove them before running Refine. I have also tried just refining the coordinates as they came out of ligand_build. But Phenix still bombs and doesn't seem to accept its own CIF. I would have thought that a ligand as common as NAP wouldn't require a lot of gymnastics, perhaps not even reading CIF information, and that it would go all automatically.That's probably too optimistic on my part. It's probably something silly, but I can't figure out what it is. Any ideas? Many thanks in advance, MM

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Fwd: WCPCW21
by Nathaniel Echols 14 Jan '13

14 Jan '13

---------- Forwarded message ---------- From: "Williams, John Charles" <jwilliams(a)coh.org> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Cc: Date: Mon, 14 Jan 2013 10:29:12 -0800 Subject: WCPCW21 Dear All, The West Coast Protein Crystallography Workshop is rapidly approaching. The standard rates close Jan 21st. Also, we are now able to accept credit cards. Due to IT security issues, the CC number needs to be called in to Ariadna Bello, senior secretary in Dept of Molecular Medicine, City of Hope. Finally, please submit your abstracts as soon as possible as we will start to select oral presentations. Best, John

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Electron Density
by CPMAS Chen 14 Jan '13

14 Jan '13

Thanks, Nat, If the density level(map or coefficient) of phenix is not an absolute level, then I really do not need to worry what shows up by coot. I used the Fourier map generated by phenix, .mtz file. Thanks! 6. density level (CPMAS Chen) > 7. Re: density level (Nathaniel Echols) > 9. Re: density level (Pavel Afonine) > > > > ------------------------------ > > > Message: 7 > Date: Sun, 13 Jan 2013 12:21:00 -0800 > From: Nathaniel Echols <nechols(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] density level > Message-ID: > <CALeAa1Mty9= > U-CFcmhJ1ZRWAiuXMeOS0RHVT4YtXpOVBO0EDyQ(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Sun, Jan 13, 2013 at 11:38 AM, CPMAS Chen <cpmasmit(a)gmail.com> wrote: > > I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To my > > surprise, the absolute electron density on the 2Fo-Fc map is quite > > different. > > The electron density maps (or coefficients) generated by Phenix are > not on an absolute scale, and the values displayed by Coot are more or > less irrelevant. The scaling method changed significantly between > 1.6.4 and 1.8, so I'm not surprised that the map levels did too. > > > By the way, is there a simple way to keep only F and SIGF column of the > > autoxds generated truncate.mtz via phenix? the GUI does not allow to > reduce > > columns. I normally use IMEAN and SIGIMEAN to do refinement, but this may > > not be necessary as it is pointed in the maillist, since the intensity is > > already transformed to amplitude after truncation in autoxds. > > > > I can specify labels by xray_data.labels = "F, SIGF", but apparently > phenix > > treats it as containing anomalous data. the following is extracted from > the > > refine pdb file > > > > MIN(FOBS/SIGMA_FOBS) : 1.16 > > REMARK 3 COMPLETENESS FOR RANGE (%) : 97.11 > > REMARK 3 NUMBER OF REFLECTIONS : 143207 > > REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247 > > > > Also, in the auto generated def file, > > xray_data.labels = "F, SIGF, DANO, SIGDANO" > > This is intentional - why would you want to throw out information? > However, you can always use either the reflection file editor (in the > latest builds) or the French & Wilson GUI to convert IMEAN to F. > > > -Nat > > > > > ------------------------------ > > Message: 9 > Date: Sun, 13 Jan 2013 21:19:17 -0800 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] density level > Message-ID: <50F39555.8000000(a)lbl.gov> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi, > > what kind of file you use to see the map in Coot: Fourier map > coefficients (MTZ file) or actual map (CCP4 binary formatted file with > the map)? I need to know this before offering a first guess on what may > be the reason for this. > > Pavel > > On 1/13/13 11:38 AM, CPMAS Chen wrote: > > Dear PhenixBBer, > > > > I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To > > my surprise, the absolute electron density on the 2Fo-Fc map is quite > > different. > > > > https://www.dropbox.com/s/prs0z8ayb73kg9k/Screenshot_sigma.png > > > > At the same sigma level(1.5), the absolute density of the violet map > > is 0.32e/A^3 (phenix-dev-1266), while that of the blue map is > > 0.01e/A^3(phenix-1.6.4-486). Besides the different phenix used, there > > is no other difference on the data and model used. > > > > Sam encountered a similar problem on the density. > > > > http://phenix-online.org/pipermail/phenixbb/2012-December/019226.html > > > > By the way, is there a simple way to keep only F and SIGF column of > > the autoxds generated truncate.mtz via phenix? the GUI does not allow > > to reduce columns. I normally use IMEAN and SIGIMEAN to do refinement, > > but this may not be necessary as it is pointed in the maillist, since > > the intensity is already transformed to amplitude after truncation in > > autoxds. > > > > I can specify labels by xray_data.labels = "F, SIGF", but apparently > > phenix treats it as containing anomalous data. the following is > > extracted from the refine pdb file > > > > MIN(FOBS/SIGMA_FOBS) : 1.16 > > REMARK 3 COMPLETENESS FOR RANGE (%) : 97.11 > > REMARK 3 NUMBER OF REFLECTIONS : 143207 > > REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247 > > > > Also, in the auto generated def file, > > xray_data.labels = "F, SIGF, DANO, SIGDANO" > > > > Or there is a work round for this issue? > > > > Thanks! > > > > -- > > > > *************************************************** > > > > Charles Chen > > > > Research Associate > > > > University of Pittsburgh School of Medicine > > > > Department of Anesthesiology > > > > ****************************************************** > > > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > >

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density level
by CPMAS Chen 14 Jan '13

14 Jan '13

Dear PhenixBBer, I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To my surprise, the absolute electron density on the 2Fo-Fc map is quite different. https://www.dropbox.com/s/prs0z8ayb73kg9k/Screenshot_sigma.png At the same sigma level(1.5), the absolute density of the violet map is 0.32e/A^3 (phenix-dev-1266), while that of the blue map is 0.01e/A^3(phenix-1.6.4-486). Besides the different phenix used, there is no other difference on the data and model used. Sam encountered a similar problem on the density. http://phenix-online.org/pipermail/phenixbb/2012-December/019226.html By the way, is there a simple way to keep only F and SIGF column of the autoxds generated truncate.mtz via phenix? the GUI does not allow to reduce columns. I normally use IMEAN and SIGIMEAN to do refinement, but this may not be necessary as it is pointed in the maillist, since the intensity is already transformed to amplitude after truncation in autoxds. I can specify labels by xray_data.labels = "F, SIGF", but apparently phenix treats it as containing anomalous data. the following is extracted from the refine pdb file MIN(FOBS/SIGMA_FOBS) : 1.16 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.11 REMARK 3 NUMBER OF REFLECTIONS : 143207 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247 Also, in the auto generated def file, xray_data.labels = "F, SIGF, DANO, SIGDANO" Or there is a work round for this issue? Thanks! -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Refining anomalous groups
by Brennan Bonnet 13 Jan '13

13 Jan '13

Hi All, I hope everyone had relaxing holidays to begin the new year. I am back to work trying to refine anomalous groups using phenix.refine. I have managed to merge my files so that my exptl_fobs_phases_flags_1_with_hl_anom.mtz now contains F(+), SIGF(+), F(-), SIGF(-). Now I have a new problem which was not occurring before the break. Usually I check the box for "Anomalous groups", then select "Modify selections for: Anomalous groups" which brings up a screen for atom selection and definition of f' and f''. In the past, clicking on the View/pick button launches Coot for selection of the atoms. Sadly, now clicking on the View/pick doesn't launch Coot and instead crashes Phenix. Does anyone else have this problem or know how to fix it? Please help! Thanks, ~Brennan~

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Problem rebuilding ligand structure
by bsubedi＠btk.fi 12 Jan '13

12 Jan '13

Hi, I am using Phenix 1.0-1069 for refinement and coot 0.7-pre-1 for visualization and rebuilding. I used SMILES in coot to build the ligand and then merged them with PDB.I had to do this as a separate step for both chains and the .cif file so produced was not accepted for refinement. I used readyset to obtain the restrains for refinement using .pdb file, even though my refinement works, when i try to run real build refine in coot I get this error message: Failed to match (to the dictionary) the following model atom names: HB3 O6 C10 C11 C12 O7 C13 O5 C8 C9 ...... That would cause exploding atoms, so the refinement didn't start. Could someone help me with fixing this problem. Best regards, Bishwa

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symmetry related bond restraint in R3 space group
by Xiang Li 11 Jan '13

11 Jan '13

I am trying to add some restraints between symmetric molecule with symmetry operation. However, I found it is not correct to use the operation information directly provided in Coot. The crystal I worked on has R3 symmetry. The symmetry operation in Coot shows to be -x+y,-x,z+ (1,1,0) and it did not work in Phenix refine. I read one previous email on this topic about the difference of symmetry operation in Coot and Phenix. However, I do not know how to do the conversion between the two when the numbers changed. Could you help me to work out on correct the symmetry operation in Phenix and talk some more on how to do the conversion please? I really appreciate your help! Sincerely, Xiang

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AutoSol error
by Luca Pellegrini 11 Jan '13

11 Jan '13

AutoSol (phenix 1.8.1-1168) stops at the build stage with the following message: *** ERROR MESSAGE: The cell appears to have changed during the run Original cell: [49.22, 91.325, 103.285, 113.16, 97.64000000000001, 76.74] New cell : [49.173301696777344, 92.32479858398438, 103.37100219726562, 66.54070281982422, 82.29070281982422, 76.58550262451172] If running from a script, please specify the space group in the input file. The incorrect space group may be coming from another wizard... *** Can you please advice as to what might be wrong? I am running AutoSol from the GUI and it did pick up the space group from the mtz file. What AutoSol refers to as the 'new cell' is actually my original cell. I was running two AutoSol jobs simultaneously from two mtz files with the same cell dimensions, and they both failed with the same message. Thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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DEN refinement and reference model
by Luca Pellegrini 08 Jan '13

08 Jan '13

Phenix.den_refine (1.8.1-1168) stops and complains that: "Sorry: Reference model contains SEGIDs that do not match the working model." I have four chains in both working and reference model, ordered in the same way (A to D). Chains A and C are the same molecule, and chains B and D are also the same. Can you please advice? Some of the chains in the reference model contain more residues, is this a problem? Thanks for your help. Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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dev-1261 wizard.test fail
by Morten Groftehauge 08 Jan '13

08 Jan '13

Hi guys, I just updated Rosetta to 3.4 and it seems to have compiled correctly (at least no error interruptions). I've done this enough to not be satisfied by that and ran > phenix_regression.wizards.test_command_line_rosetta_quick which goes past the Rosetta tests correctly but fails at ================================================================= Running test_prerefine ------------------------------------------------------------ Numbers do not match: 0.47825 0.53601 r {{ 0.87799 0.06946 -0.47362} {-0.02049 0.99396 0.10779} { 0.47825 -0.08494 0.87411}} --- r {{ 0.84375 0.06393 -0.53291} {-0.02789 0.99676 0.07541} { 0.53601 -0.04877 0.84280}} ------------------------------------------------------------ FAILED See log files test_prerefine/test_prerefine.log test_prerefine/test_prerefine_current.log ================================================================= Running test_prerefine_double OK ================================================================= Running test_prerefine_no_data ------------------------------------------------------------ Numbers do not match: 0.47825 0.53601 r {{ 0.87799 0.06946 -0.47362} {-0.02049 0.99396 0.10779} { 0.47825 -0.08494 0.87411}} --- r {{ 0.84375 0.06393 -0.53291} {-0.02789 0.99676 0.07541} { 0.53601 -0.04877 0.84280}} ------------------------------------------------------------ FAILED See log files test_prerefine_no_data/test_prerefine_no_data.log test_prerefine_no_data/test_prerefine_no_data_current.log ================================================================= When I look in the log there are no error messages. I don't need to prerefine so I'm good but I still find it weird. I tried again with Rosetta 3.3 and got no error flags. Is it because the quick tests are checking the result against the results that you got earlier and the algorithm has been changed between 3.3 and 3.4? Cheers, Morten PS Really enjoyed the talks at the CCP4 study weekend. -- Morten K Grøftehauge, PhD Pohl Group Durham University

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