- phenixbb - phenix-online.org

P3 pseudotranslation
by Ethayathulla A.S 15 Jan '13

15 Jan '13

Hello I am trying to solve a structure with P3 Pseudotranslation at 3.5A. The 3.5 dataset have cell of 150,150,200 and 5A dataset have smaller cell 150,150, 100. The data can be scaled in P321, p3221,p3121 with similar rsym (6 (54). Pointless gave me Spacegroups as P3221 or P3121 as soln. I tried Phenix.xtriage it showed me 40% Pseudotranslation peak ( 0,0,0.5) for 3.5A dataset as the c-axis is double that of 5A data. According to cell content analysis it can be dimer in 3.5A and monomer for 5A dataset. So I tried MR with both datasets with homology model build using similar fold protein. I got solns for dimer with LLGs with 1000's in P3221,P3121,P321 with 3.5A dataset. There were 28 solutions ++++++++++++++++++++++++++++++++++++++++++++++++++ SOLU SET RFZ=2.0 TFZ=8.2 PAK=0 LLG=259 TFZ==11.3 LLG=1181 TFZ==28.4 ( SOLU SPAC P 32 2 1) SOLU 6DIM ENSE partial EULER 94.4 2.7 25.5 FRAC -0.07 -1.07 -0.81 BFAC -1.00 Solution #2 annotation (history): SOLU SET RFZ=2.0 TFZ=8.2 PAK=0 LLG=225 LLG=1066 ( SOLU SPAC P 31 2 1) +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ So I refined the solns. of P3221, p321 it refined to 44/54 after that it doesn’t go down. The 0.5 Pseudotranslated molecule can been as symmetry molecule along c-axis. The packing looks very good. I have attached the image of it with native patt map. I deleted one monomer and refined to check the solution I could see clearly see the other molecule. I could see 2n+1 odd reflections to be weak. To check whether two fold can be due to twinning due to pseudotranslation I could not observe it. So I tried to see check whether the it can be P32 merohedral twinning with pseudotranslation with twinning of 0.36 (h,-h-k,-l) from yeates server. I try to use the dimer of P3212 and try for alternative spacegroup which yield me unique soln in P32. I refined the molecule four molecule which yielded me 46/49 and when I apply twinning fraction the r-factor decreases to 40/45. Similarly for 4.5A dataset I used dimer of 3.4 dataset dimer which yield me solution in P32 but cannot refine it gets struck for 45/50.I tried to use the dimer with 5A dataset I get unique solu and refine with merohedral twinning the r/freeR goes to 38/57. How I can check whether it is P32 merohedral twinning with Pseudotranslated or P3221. Also the patterson analysis another peak of height 4% ( 0.050, 0.102, 0.495 ) : 4.452 . Is it significant ? Any suggestion will be helpful Thank you Abdul ++++++++++++++++++++++++++++++++++++++++++++++++++ Patterson analyses from phenix.xtriage Frac. coord. : 0.000 0.000 0.500 Distance to origin : 103.157 Height (origin=100) : 40.427 p_value(height) : 2.740e-04 The full list of Patterson peaks is: x y z height p-value(height) ( 0.000, 0.000, 0.500 ) : 40.427 (2.740e-04) ( 0.050, 0.102, 0.495 ) : 4.452 (9.782e-01) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -- *********************************************** Dr. A.S. Ethayathulla Dept of biophysics AIIMS, new delhi ***********************************************

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fwd: Annual CCP4 summer school in USA, at APS, June 18-26
by Nathaniel Echols 15 Jan '13

15 Jan '13

---------- Forwarded message ---------- From: "Ruslan Sanishvili (Nukri)" <nukri(a)aps.anl.gov> To: phenixbb(a)phenix-online.org Cc: Date: Mon, 14 Jan 2013 17:46:48 -0600 (CST) Subject: Annual CCP4 summer school in USA, at APS, June 18-26 Dear Colleagues, We are pleased to announce the sixth annual CCP4 summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2013/index.php Title: "CCP4 school: From data collection to structure refinement and beyond" Dates: June 18 to 26. Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA The school content: Data collection workshop the first two days: beamline training and data collection on GM/CA-CAT beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three Sections – lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is April 5. The application form, the program, contact info and other details can be found at http: http://www.ccp4.ac.uk/schools/APS-2013/index.php Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers will arrange economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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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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