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Improving picture quality of ED map in PYMOL
by Raja Dey 02 Sep '09

02 Sep '09

Dear Friends, Sorry, for the of topic question. Does anyone can tell how to improve the quality of a picture showing the electron density map of dna in a complex using PYMOL. I created the figure, but not happy with the quality as it is now. Might be there is a way to improve which I don't know. I want the lines in the mesh to be more sharp and fine. Any suggested program to prepare a publication quality figure to show the ED map would be of great help. Thanking you in advance... Raja

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Source for Nightlys Location?
by Andrew Ring 02 Sep '09

02 Sep '09

Is it possible to get a source distribution for the nightlys? If so, where is it located? I can only finding the builds on the nightlys downloads page. For my systems and uses, the --openmp switch on version 1.4-3 has given encouraging results and I would like to investigate with something newer. -- =================================== Andrew Ring System Administrator Kuriyan Laboratory http://jkweb.qb3.berkeley.edu/ Doudna Laboratory http://rna.berkeley.edu/ University of California, Berkeley Office: 542 Stanley Hall Shipping: 176 Stanley Hall, QB3 Berkeley, CA 94720-3220 tel: (510) 643 0166 fax: (510) 643 2352 ====================================

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R-work is too low
by Sam Stampfer 01 Sep '09

01 Sep '09

Hi, I'm refining a 2.88 Angstrom structure and am getting a difference of greater than 6% between the R-work and R-free. The best result (I think) is what I have from minimization alone: Start R-work = 0.3219, R-free = 0.3505 (no bulk solvent and anisotropic scale) Final R-work = 0.2424, R-free = 0.3174 (no bulk solvent and anisotropic scale) Start R-work = 0.3220, R-free = 0.3500 Final R-work = 0.2411, R-free = 0.3176 The results from simulated annealing are the following: Start R-work = 0.3219, R-free = 0.3505 (no bulk solvent and anisotropic scale) Final R-work = 0.2454, R-free = 0.3322 (no bulk solvent and anisotropic scale) Start R-work = 0.3220, R-free = 0.3500 Final R-work = 0.2403, R-free = 0.3333 I have also done the refinement with ncs but ncs is probably not appropriate for my structure. The final R-free ends up being higher (though the difference between R-free and R-work ends up being 6-7%) My PI (who is on vacation until next week) said that it was a problem if R-work was more than 0.06 lower than R-free. Any recommendations for me? Is it possible to reduce this difference? Is it worth it to rebuild the refined pdb if the R-work is this different from the R-free? My refinement script is: phenix.refine ss46_p3_cv.mtz ss46_rebuilt.pdb \ output.prefix=results/ss46_rebuilt_sa \ strategy=individual_sites+group_adp cif_link.params nag-nag.cif \ twin_law="h,-h-k,-l" \ simulated_annealing=true (the cif_link.params and nag-nag.cif files are made to handle the N-glycosylation sites, I think). Thanks for your help! -Sam

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error TLS refinement
by Marjolein Thunnissen 01 Sep '09

01 Sep '09

I'm trying to finish refining a structure that has been almost refined completely about a year ago with an older version of Phenix.refine. When I start TLS refinement I get the following error message: RuntimeError : mean_weighted() argument is an empty array Traceback: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 259, in OnExcept raise event.data RuntimeError: mean_weighted() argument is an empty array I do not get this error when refining without TLS, only when I switch it on. The program advises me to post the error here so... Thanks Marjolein ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)46-22 24584 Associate Professor Fax +46-(0)46-22 24692 Dept of Molecular Biophysics, Lund University http://www.mbfys.lu.se PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator I911 (Max-lab): MAD and fixed-wavelength stations for macromolecular crystallography ________________________________________________________________________

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Specifying the number of processors to run phenix with
by Sam Stampfer 31 Aug '09

31 Aug '09

Hi- anyone know how to specify the number of processors to run phenix under in linux? Or how to tell what the default is? I'm running linux (fedora) with 4 processors and can't tell whether phenix is using all of them or not. I do the refinement with .csh files and tried doing "myfile.csh --nproc=4". The file ran but no faster- I can't tell if it is using 4 by default or if that's the incorrect command to specify the use of 4 processors. Thanks for your help! -Sam

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Best first map for RESOLVE after MR
by Peter Grey 31 Aug '09

31 Aug '09

Hello all, I try to solve the structure of a big complex at rather low resolution. I have a molecular replacement solution with a partial model from Phaser. I would like to use RESOLVE for density modification. I ask for your advice regarding the first map that should be the input into RESOLVE. Should it be the 2mFo-DFc map directly from Phaser or would it be better to do rigid body refinement in phenix.refine and use the bulk solvent corrected 2mFo-DFc map ? Many thanks in advance for your suggestions, Peter.

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high resolution bin statistics
by Sebastiano Pasqualato 31 Aug '09

31 Aug '09

Hi there, i just wanted to know how is determined the number of bins for which the statistics of refinement are given in the header of the pdb refined with phenix.refine, and if there's a way to have more than the number of bins that is default output. For example, what if I'd like to have statistics for the 2.6-2.5 bin, here: REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.4159 - 3.9625 0.99 2545 131 0.1921 0.2232 REMARK 3 2 3.9625 - 3.1460 1.00 2447 116 0.1650 0.2289 REMARK 3 3 3.1460 - 2.7486 1.00 2433 121 0.1917 0.2682 REMARK 3 4 2.7486 - 2.4974 1.00 2405 130 0.2244 0.2890 thanks a lot in advance, ciao s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094

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question about kick map
by crystallogrphy 29 Aug '09

29 Aug '09

Hi, I am trying to use kick map to remove model bias with the following script phenix.refine MR.1_refine_data.mtz MR.1_refine_001_refine_001.pdb output.prefix=refine-090828a simulated_annealing=True simulated_annealing.start_temperature=8000 strategy=individual_sites refine.params However, the program says: Sorry: Unknown file format: refine.params I do not understand why the format of refine.params cannot be read, which has the following contents. Does anyone know why? refinement { electron_density_maps { map { mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked= True fill_missing_f_obs_with_weighted_f_model=True } map { mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked= True fill_missing_f_obs_with_weighted_f_model=True } }

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reflection file utility and use of modified phases in refinement
by Engin Ozkan 28 Aug '09

28 Aug '09

Hi everybody, I had some trouble with the reflection file utility today. I've been trying to import Rfree-flag column from one of the mtz's to my combined mtz, and it never does. The R-free flag is always left out of the output even when I have it selected. Have you guys seen this (I'm using 147)? Another question I have is about the output of phenix.autobuild. Phenix.autobuild tells me to use modified phase probabilities (HLAM, etc.) in refinement. I am assuming this is density-modified phases. But I've always thought that this would be bad practice (possibly because of unrealistically high FOMs and possible flattening of loops, etc, but maybe resolve does a better job than, say DM). Any ideas on that one? Thanks, Engin -- Engin Özkan Post-doctoral Scholar Dept of Molecular and Cellular Physiology Howard Hughes Medical Institute Stanford University School of Medicine ph: (650)-498-7111

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Tracing and refining b-strands at 3.3A resolution
by Gino Cingolani 28 Aug '09

28 Aug '09

Hi Phenix community, I'm tracing a 3.3A averaged electron density map of a large macromolecular complex (~18,500 residues in the asymmetric unit). The map has great continuity and appears quite 'tubular'. While it is easy to interpret in a-helical regions, b-strands are more challenging, as I can't see the 'bump' corresponding to the carbonyl. If I built b-strands into the tubular density, refinement usually 'undoes' them and turns them into pseudo-loops/turns. On the positive side, a related molecule (~70% identical to mine) was solved to 1.9A resolution. So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement? Thanks in advance for the feedback, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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