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restraints for dna planarity
by John Lee 12 Sep '14

12 Sep '14

Hi, I'm refining a low resolution structure of a dna-protein complex (3.7A) & wondering if someone could help me with setting restraints in Phenix to maintain the base-pair planarity of the dna? With the restraints I have, even with a reference model, I'm getting 'puckering' of the base-pairs. Although the h-bonding distances seem to hold over time, I can't seem to find a way to keep the planarity intact. Thanks in advance for your help. -John

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Phenix-Rosetta integration tests fail with Rosetta MPI on RHEL 6.3
by Sina Masoud-Ansari 12 Sep '14

12 Sep '14

Hi there, I'm wondering anyone has managed to successfully run Phenix with Rosetta MPI on Red Hat Enterprise Linux 6.3 or similar? I currently have a non-MPI build of Rosetta that passes all of the tests in phenix_regression.wizards.test_command_line_rosetta_quick However when running these tests with the MPI build of Rosetta the following tests fail: Running test_relax ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ FAILED See log files test_relax/test_relax.log test_relax/test_relax_current.log ================================================================= Running test_relax_double ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ FAILED See log files test_relax_double/test_relax_double.log test_relax_double/test_relax_double_current.log ================================================================= Running test_relax_no_sol ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ FAILED See log files test_relax_no_sol/test_relax_no_sol.log test_relax_no_sol/test_relax_no_sol_current.log I have attempted to attach an archive of the logs. I'm working with Rosetta 3.5, more recent versions of Rosetta fail other tests in phenix_regression.wizards.test_command_line_rosetta_quick , please see https://www.rosettacommons.org/node/3721 for details. Rosetta 3.5 was compiled with GCC 4.4.6 using OpenMPI 1.6.4 Any help or advice is appreciated. -- Sina Masoud-Ansari Centre for eResearch 409.G21 24 Symonds Street University of Auckland e: s.ansari(a)auckland.ac.nz p: +64 9 3737599 ext 89369 w: http://www.eresearch.auckland.ac.nz

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phenix refine geometry restraints
by George Devaniranjan 12 Sep '14

12 Sep '14

Hi, I was trying to restrain the N-CA-C angle to 110.0 I updated the .def file as follows: angle { action = *add atom_selection_1 = name N atom_selection_2 = name CA atom_selection_3 = name C angle_ideal = 110.0 sigma = 2 I got the following: Sorry: More than one atom selected: "name N" Number of selected atoms: 86 I tried using N in quotes and it doesn't work either but the example in the website had this(below), what am I doing wrong? resname ALA and (name ca or name c or name n or name o) Thank you

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refinement for non-standard DNA base
by John Cheong 11 Sep '14

11 Sep '14

Hi, I have 5-fluoro-Uracil in my DNA:protein complex. I modeled 5-F-dU into the map, ran eLBOW for geometry file and did refinement. After the refinement, 5-F-dU is not connected to the neighboring nucleotides and the phosphate oxygens are rotated to wrong positions. Can anyone teach me how to refine with non-standard DNA base ? Any help or advice would be appreciated. John

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Occupancy refinement of anomalous scatters
by Chen Zhao 08 Sep '14

08 Sep '14

Hi all, I have a question about the occupancy refinement of the anomalous scatters. This is because when I went through all the HA sites, I found that some of them has too high B factor and too high occ. I manually adjusted the occ and fed the model into refinement, but the B factor and occ came back to around their original level again. It seems that those have a stronger peak in the anomalous difference Fourier map has a higher occupancy after refinement, but this does not necessarily equals to a strong density peak in 2Fo-Fc map (some of them even disappear after refinement), and this might be related to their high B factor. Am I doing something wrong in the refinement? I am basically using phenix.refine default setting, but with TLS+isotropic B factor refinement and occupancy refinement of a small region (5-8 residues). The resolution is 3 A, and the refinement is already at the final stage. I am still at the learning stage and your input will be greatly appreciated. Thank you! Sincerely, Chen

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Refinement and Density modification
by Ashu S 08 Sep '14

08 Sep '14

Dear all, I am working on a 3.6A Se SAD data. Autosol followed by autobuild gave a decent map (as expected at this resolution) with a moderate trace. After building poly ala trace and assigning few resides in and around Se positions when I refine the model, all the sharp features of the electron density map are lost. For example, a nice looking helical density becomes a tube. I presume that this happens because wilson B is high (~110 A2) and the map requires modification, sharpening etc. Is there a way to get the map with similar sharp features after model building and refinement as auto build gives? How could I follow exactly the same steps of density modification etc which auto build does? Thanks, Ashu

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Refinement and Density Modification
by Ashu S 08 Sep '14

08 Sep '14

Dear all, I am working on a 3.6A Se SAD data. Autosol followed by autobuild gave a decent map (as expected at this resolution) with a moderate trace. After building poly ala trace and assigning few resides in and around Se positions when I refine the model, all the sharp features of the electron density map are lost. For example, a nice looking helical density becomes a tube. I presume that this happens because wilson B is high (~110 A2) and the map requires modification, sharpening etc. Is there a way to get the map with similar sharp features after model building and refinement as auto build gives? How could I follow exactly the same steps of density modification etc which auto build does? Thanks, Ashu

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refine anomalous
by Andreas Förster 08 Sep '14

08 Sep '14

Dear all, I've solved a structure from a SAD dataset collected at 1.54 Å. The structure contains a good number of sulfurs and also what I think is a potassium ion. To verify, I chose a refinement strategy including "Anomalous groups". This worked well in an important way - R values down by 2 percentage points - but the refined f' and f" values are way off. I start out with these parameters in *.eff: anomalous_scatterers { group { selection = (name SD or name SG) f_prime = 0.319342 f_double_prime = 0.557592 refine = *f_prime *f_double_prime } group { selection = name K f_prime = 0.365562 f_double_prime = 1.06736 refine = *f_prime *f_double_prime } } What I get back is: Anomalous scatterer group: Selection: "(name SD or name SG)" Number of selected scatterers: 15 f_prime: -1.15797 f_double_prime: 0.00577091 refine: f_prime f_double_prime Anomalous scatterer group: Selection: "name K" Number of selected scatterers: 1 f_prime: -4.41689 f_double_prime: 0.00271946 refine: f_prime f_double_prime I thought I'd get close to the book values for S and would be able to identify the other anomalous scatterer by the refined f'/f" values. Naiveté or stupidity? Thank you. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

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Fwd: Re: Sculptor
by Gabor Bunkoczi 08 Sep '14

08 Sep '14

Apologies, this was meant for the BB. -------- Original Message -------- Subject: Re: [phenixbb] Sculptor Date: 2014-09-08 10:41 From: Gabor Bunkoczi <gb360(a)cam.ac.uk> To: Marie Elizabeth Fraser <frasm(a)ucalgary.ca> Hi Marie, please check the extension of your alignment. If it is .pir, the second line is supposed to be a comment line, and it is therefore ignored. You can either change the extension to .ali, or insert an empty line after the ones starting with ">". If this is not the problem, then this is not supposed to happen. Please send me the logfile in the first instance, although I may need the actual alignment and the PDB file as well (you can delete the target sequence if you wish, an alignment with a single sequence is perfectly valid). BW, Gabor On 2014-09-08 01:22, Marie Elizabeth Fraser wrote: > Hello, > I'm running Sculptor from the Phenix GUI, trying to improve a > molecular replacement model. I've given the pdb file and a sequence > alignment. Sculptor does not appear to accept the first residues > aligned in the sequence alignment. In the alignment, these residues > are residue numbers 42 to 60, so they are on the second line of the > fasta file (the first line after the title) and Sculptor starts at > residue 61 (the subsequent line). Residues 42 to 60 of the target are > to match the first residues of the pdb model, so in the alignment, > there are 41 dashes before the beginning of the sequence for the pdb > file. Am I giving an incorrectly formatted sequence alignment, > misinterpreting what Sculptor does or is Sculptor supposed to do this? > Thank you, Marie > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

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Sculptor
by Marie Elizabeth Fraser 07 Sep '14

07 Sep '14

Hello, I'm running Sculptor from the Phenix GUI, trying to improve a molecular replacement model. I've given the pdb file and a sequence alignment. Sculptor does not appear to accept the first residues aligned in the sequence alignment. In the alignment, these residues are residue numbers 42 to 60, so they are on the second line of the fasta file (the first line after the title) and Sculptor starts at residue 61 (the subsequent line). Residues 42 to 60 of the target are to match the first residues of the pdb model, so in the alignment, there are 41 dashes before the beginning of the sequence for the pdb file. Am I giving an incorrectly formatted sequence alignment, misinterpreting what Sculptor does or is Sculptor supposed to do this? Thank you, Marie

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