- phenixbb - phenix-online.org

sculptor modifications
by Emilia C. Arturo (Emily) 21 Jun '17

21 Jun '17

Hello All, Is there a way to identify quickly the changes to a model that Sculptor has made? I am running the Phenix GUI to use Sculptor. I have read through the out-put log file, and understand (mostly) the sculpt protocol as it relates to the circumstances under which modifications to main chain or side chains are made, but it would be nice to see (in a list format, perhaps) what changes (if any...) were made. Regards, Emily. -- "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell "I'm not afraid of storms for I'm learning to sail my ship." - Louisa May Alcott

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phenix.map_to_model input mtz file failure
by dancingdream＠163.com 18 Jun '17

18 Jun '17

Dear Phenix bb, I intend to build a initial model by phenix.map_to_model. And the command line is as follows: phenix.map_to_model_1.12rc0-2787 map_coeffs_file=../rep_dm.mtz map_coeffs_labels="'FP,SIGFP' 'PHIDM' 'FOMDM'" seq_file=../resolve.seq is_crystal=True use_sg_symmetry=True density_select=False truncate_at_d_min=True and the feedback like this: Sorry: No initial assignment made for map_coeffs. Labels used: FP,SIGFP PHIDM FOMDM. Available labels: ['PHIB', 'FOM', 'HLA,HLB,HLC,HLD', 'FP,SIGFP', 'PHIDM', 'FOMDM', 'FDM', 'HLADM,HLBDM,HLCDM,HLDDM'] NOTE: grouped labels like 'FP,SIGFP' must stay together, have commas, and have no spaces. If they come from an MTZ file, they must be in adjacent columns as well. Suggested labels to use: PHIDM FOMDM I try many other input format of map_coeffs_labels, such as map_coeffs_labels="FP,SIGFP PHIDM FOMDM" map_coeffs_labels=["FP,SIGFP PHIDM FOMDM"] ... ... but the result is the same. Dose anyone can tell me how to fix this problem? Thank a lot. -- Wei Ding P.O.Box 603 The Institute of Physics,Chinese Academy of Sciences Beijing,China 100190 Tel: +86-10-82649083 E-mail: dingwei(a)iphy.ac.cn

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Overall anisotropic ADP in phenix.real_space_refine?
by Oliver Clarke 17 Jun '17

17 Jun '17

Hi, I wonder in phenix.real_space_refine whether it may be worth adding refinement of a single overall anisotropic ADP to the model - or a single TLS group with modeled anisotropic ADPs - in order to model the effects of overall orientation errors (which affect resolution more substantially towards the periphery) and preferred orientation (which tends to give rise to anisotropic resolution across the volume). Maybe this would be helpful at least in generating a calculated map that is better for difference map calculation, for example? Cheers Oli

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real_space_refine questions
by Daniel Larsson 14 Jun '17

14 Jun '17

I'm have some questions about doing real space refinements using phenix.real_space_refine. I am refining a model for an intermediate-resolution (3.79 Å) cryo-EM map. As the starting point I use a model from a higher-resolution map (3.25 Å) of the same system in another conformation. My idea is to first do rigid body fitting of domains and then gradually relax constrains and restraints. - Is it possible to restrain the position of certain parts of the model (i.e. "freeze" them so that they move at all) to do focused refinement of subdomains or loops? - In the instructions it says that you can do both NCS constraints and restraints. How you do the latter? I can only do the former by default or by defining ncs_constraints=True and give a NCS definition file. - When I do a run with run=rigid_body, some rigid body groups move in to each other and overlap. Is there no collision detection using this algorithm? If I do a run=minimization_global, things work a bit better in this regard, but is not really what I want (at this stage). Am I doing something wrong? Here is the run command and the rigid body definition file: phenix.real_space_refine \ model.pdb \ map.ccp4 \ rigid.eff \ resolution=8.0 \ ncs_constraints=False \ rotamer_restraints=True \ ramachandran_restraints=True \ c_beta_restraints=True \ run=rigid_body \ macro_cycles=10 # rigid.eff: refinement { rigid_body { group = chain A and resseq 101:266 group = chain A and resseq 273:388 group = chain B and resseq 101:266 group = chain B and resseq 273:388 group = chain C and resseq 104:266 group = chain C and resseq 273:388 } } Regards, Daniel Larsson

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 13 Jun '17

13 Jun '17

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission for the July 2017 issue is 30 June 2017. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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preparing DL-Malic acid stock solution
by Sebastiano Pasqualato 08 Jun '17

08 Jun '17

Dear all, we’ve recently having trouble preparing a 3 M stock solution of DL-Malic Acid, pH 7 (which we had, so it’s doable!). When we reach pH 3 - 4 the solution turns milky white and does not goes back to a clear solution even when the pH is raised. Does anybody have any advice on how to get a clear solution? Has anyone gone through the same? Thanks in advance, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEOXtalUnit

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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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