May 2011 - phenixbb - phenix-online.org

error from loop fitting
by Kendall Nettles 09 May '11

09 May '11

I'm trying the loop fitting for the first time and keep getting this error: Reading in sequence probability info and matching to input PDB List of segments read from input PDB file: Segment 0 Start: 225 End: 380 ChainID: 'A' NO MATCH What should be in the sequence file? it is fasta format?it is the entire sequence, or just the loop? I've played with different combinations and keep getting the same error. Best regards, Kendall Nettles

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Diffraction anisotropy
by Ina Lindemann 06 May '11

06 May '11

Hi, I am refining a structure of 2.3A resolution. The R values with and without bulk solvent and anisotropic scale are quite different as you can see here: Start R-work = 0.3751, R-free = 0.5562 (no bulk solvent and anisotropic scale) Final R-work = 0.3741, R-free = 0.5557 (no bulk solvent and anisotropic scale) Start R-work = 0.2298, R-free = 0.2974 Final R-work = 0.2261, R-free = 0.2970 I checked the anisotropy of the data with different tools: Results from Xtriage: Maximum likelihood isotropic Wilson scaling ML estimate of overall B value of None: 39.25 A**2 Estimated -log of scale factor of None: -2.59 Maximum likelihood anisotropic Wilson scaling ML estimate of overall B_cart value of None: 50.10, 0.00, 0.00 50.10, -0.00 25.47 Equivalent representation as U_cif: 0.63, -0.00, -0.00 0.63, 0.00 0.32 Eigen analyses of B-cart: Value Vector Eigenvector 1 : 50.103 ( 0.71, 0.71, -0.00) Eigenvector 2 : 50.103 (-0.71, 0.71, -0.00) Eigenvector 3 : 25.473 (-0.00, 0.00, 1.00) ML estimate of -log of scale factor of None: -2.57 Correcting for anisotropy in the data Results from PHASER: Principal components of anisotropic part of B affecting observed amplitudes: eigenB (A^2) direction cosines (orthogonal coordinates) 8.178 0.9961 0.0879 0.0000 8.178 -0.0879 0.9961 0.0000 -16.357 -0.0000 -0.0000 1.0000 Anisotropic deltaB (i.e. range of principal components): 24.535 Results from Ctruncate: ANISOTROPY CORRECTION (using intensities): Anisotropic scaling (orthogonal coords): | -0.2272 -0.0000 -0.0000 | | -0.0000 -0.2272 0.0000 | | -0.0000 0.0000 0.4543 | Anisotropic U scaling (fractional coords): | -4.451e-05 -5.622e-23 -1.266e-21 | | -5.622e-23 -4.451e-05 -8.929e-22 | | -1.266e-21 -8.929e-22 4.717e-06 | Anisotropic B scaling (fractional coords): | -3.514e-03 -4.439e-21 -9.995e-20 | | -4.439e-21 -3.514e-03 -7.050e-20 | | -9.995e-20 -7.050e-20 3.725e-04 | Eigenvalues: 0.7728 0.7728 1.4543 Eigenvalue ratios: 0.5314 0.5314 1.0000 Resolution limit in weakest direction = 3.156 A Now I am not sure about the severeness of anisotropy and the necessary procedure and would be very pleased if anyone could help. The electron density maps look okay related to the resolution. Has anyone experience with the diffraction anisotropy server or ellipsoidal truncation with data with comparable anisotropy? Thank you for your help in advance Ina Ina Lindemann Philipps-Universität Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908

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phenix.mr_rosetta error
by Jermaine Jenkins 05 May '11

05 May '11

Hi, I am trying to use phenix.mr_rosetta supplying a local.hhr file and using only the top alignment which is an NMR structure and the pre_refine option. It finishes the mr.model_preparation and writes out two pdbs ( _sculpt and _chain that each have 10 ensembles) but then writes out a empty alignment.ali file (should be 100% identity between the template and the search model). Below is the error I get in the RUN_1.log file. Wrote dummy alignment to /pre_refine/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/alignment.ali ******************* ERROR ENDING *************** Sorry, the alignment file ['/pre_refine/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/alignment.ali'] does not have enough lines (6 required, 0 found): Note: last line needs to be '--' ******************* ERROR ENDING *************** Sorry, the alignment file ['../pre_refine/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/alignment.ali'] does not have enough lines (6 required, 0 found): Note: last line needs to be '--' Thanks, JJ

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Off topic: Apologize for linkedin invitation accident
by Nian Huang 03 May '11

03 May '11

Dear fellows, I am really sorry for the massive invitations from my linkedin account. I was certain that I skipped the sending invitation step from my contact lists and I am not sure how it could still happen in the end. Please delete those emails as you wish and I thank the people who have already added me to the connection. Nian Huang, Ph.D. Dept. of Biochemistry UT Southwestern Medical Center

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Invitation to connect on LinkedIn
by Nian Huang via LinkedIn 03 May '11

03 May '11

LinkedIn ------------Nian Huang requested to add you as a connection on LinkedIn: ------------------------------------------ Felix, I'd like to add you to my professional network on LinkedIn. - Nian Accept invitation from Nian Huang http://www.linkedin.com/e/rc00ja-gn8i47ba-4i/_D6v-a9jXU1vVlzLNqYGbefdvPFwhu… View invitation from Nian Huang http://www.linkedin.com/e/rc00ja-gn8i47ba-4i/_D6v-a9jXU1vVlzLNqYGbefdvPFwhu… ------------------------------------------ Why might connecting with Nian Huang be a good idea? Have a question? Nian Huang's network will probably have an answer: You can use LinkedIn Answers to distribute your professional questions to Nian Huang and your extended network. You can get high-quality answers from experienced professionals. http://www.linkedin.com/e/rc00ja-gn8i47ba-4i/ash/inv19_ayn/ -- (c) 2011, LinkedIn Corporation

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Sulfate ion on 2-fold axis
by J. Fleming 01 May '11

01 May '11

Hi all, I have a sulfate ion sitting on a 2-fold axis of symmetry. If I set all the atom occupancies to 0.5 and refine using phenix.refine (Phenix v. 1.5-2) the occupancies are changed to 0.00 for the sulfur, 1.00 for three of the oxygen's, and 0.72 for the fourth oxygen. Can anyone explain this? Thanks in advance, Jon

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