June 2017 - phenixbb - phenix-online.org

Re: [phenixbb] AutoSol invalid MTZ column_types error
by Terwilliger, Thomas Charles 08 Jun '17

08 Jun '17

Hi Mintu, I'm sorry about this problem! I should have fixed it already but missed this message from Phil Evans that he posted in January: "Columns N(+) and N(-), both of type I, are recent additions to the output file from Aimless. They are the number of observations merged into I(+) and I(-) respectively" AutoSol doesn't know about these columns and can accidentally guess that they are data. To get around this column, use a command like this to create a data file that does not contain the N(+) and N(-) columns: phenix.reflection_file_converter aimless.mtz --mtz=aimless_noN.mtz --label="I(+" ?where the --label=xxxx command specifies the first few characters of the columns you want to use as I+/I- data. Then use aimless_nonN.mtz instead of aimless.mtz as input to autosol. I will fix this in autosol. Let me know if that does not do it! All the best, Tom T Dear all, I am getting an error message "Invalid MTZ column_types for the given miller_array." while I try to run AutoSol. The last line in the log is "Adding array ['N(+)', 'N(-)'] to output file with type II". Do you have any suggestion how to fix this error? Thanks a lot in advance. Best, Mintu

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comfortable OS X level
by Patrick Loll 07 Jun '17

07 Jun '17

I’m still running Yosemite on my Macs, both because I’m change-averse and because folks reported problems with some crystallographic software upon upgrading the OS. These reports have now faded into the haze of the past, and so I ask, have the issues been resolved? Is it safe to move to Sierra? Thanks as always, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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ligand - protein close contact
by Nikos Pinotsis 06 Jun '17

06 Jun '17

Dear all, I have a protein-ligand structure with several chains in the AU. After refinement one of the ligands forms a close contact 1.8A with the protein. For the rest of the protein-ligand chains the same interaction is as expected to 2.7-2.8 A forming an H-bond. I tried to adjust this ligand with coot but everytime I am getting back the same 1.8 A close contact. There is enough density for the ligand and I can even see that it can fit better to distance 2.4-2.5A H-bond with the protein Is there a way to constrain this distance to more than 2A? Should I fix the ligand atom that interacts? Unless I am missing something more fundamental. The ligand cif file is the default in phenix, the data set is a quite decent 2.3A. thanks in advance for any suggestions Nikos -- Dr. Nikos Pinotsis Institute of Structural and Molecular Biology Department of Biological Sciences, 3rd Floor, R313 Birkbeck College Malet Street London WC1E 7HX T: +44 (0)207 631 6827 F: +44 (0)207 631 6803 M: +44 (0)792 384 3593

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Composite omit map
by Sam Tang 05 Jun '17

05 Jun '17

Dear all Sorry for a very basic question about generating an omit map. I am trying to generate a SA-omit map for only my ligand but not the protein core of my complex. I presume I can use phenix.composite_omit_map GUI and specify my ligand chain in Atom Selection? All other parameters being the same, I notice that when I did not select any atom the whole structure was divided to 30-40 regions but when I selected my ligand chain it now divides into 89 regions. Is there a reason why and is there any advantage to manually adjust the number of omit regions? Many thanks and regards Sam Biochemistry Programme, School of Life Sciences, CUHK

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Fitting ligand with DM map?
by Sam Tang 03 Jun '17

03 Jun '17

Dear community I guess it may not be a standard practice but I wonder if anyone has tried to use a density modified map for ligand building. My situation is that I am trying to fit a single strand DNA ligand into an enzyme model. The dataset is at 3 Ang, P1 space, with overall completeness of only about 88%. MR was done by the apo-enzyme and the density for the first two-third of the ligand is very good and could easily be modelled. Towards the last one-third the density becomes much weaker so nucleotides cannot be easily put. This is the only dataset so far, so multi-crystal averaging / map averaging is not possible at this stage. NCS averaging is also not possible. We did try to sharpen map during refinement. I understand that DM is usually used to improve phase at the initial stage esp. with experimental phasing. With MR would you think density modification could produce a better map to aid the modelling of the last one-third ligand? Can I use the denmod.mtz directly for manual model building? Any input would be very much appreciated. Best Sam Biochemistry Programme, CUHK

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