March 2016 - Chimera-users - RBVI Mailing Lists

Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Mirrored density artefact
by Morris, Kyle 13 Apr '16

13 Apr '16

Dear Chimera dev and community, I am using "vop cover” to extract a box of density around a PDB and making the box quite large with the following: $ vop cover #0 atomBox #1 pad 55 I have noticed in the extracted density that as I increase the pad size the true density gets duplicated and mirrored on the opposite edge of the cell containing the volume. This seems like strange behaviour to me, is there something wrong or that I am doing wrong? Many thanks for your help. Best, Kyle

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ACA 2016 SAS Workshop
by Kushol Gupta 02 Apr '16

02 Apr '16

On behalf of the organizing committee, I am pleased to announce a workshop on "Computational Approaches to the Structural Modelling of Biological Macromolecules using Small Angle Scattering." This workshop will take place on Friday, July 22nd, 2016 at this year's American Crystallographic Association (ACA) Meeting in Denver, Colorado, U.S.A. The meeting itself will run from July 22-26. WK.02 Computational Approaches to the Structural Modelling of Biological Macromolecules using Small-Angle Scattering. This one-day workshop will focus on computational approaches to structural modelling and analysis. In the first session, a brief reprise of fundamental concepts will be provided, with a focus on pitfalls in data acquisition and reduction that can affect subsequent data analysis and modelling. The remainder of the day will be allocated to the hand-on application of the leading software packages to the analysis of solution scatter. This workshop will feature direct participation from the creators of the most prevalent software packages currently used (including BIOSAXS(EMBL), SIBYLS, CCP-SAS, FoXs and IMP). The participating groups will present their software, including the basis for the algorithms employed, and further deliver guided hands-on tutorials for workshop participants. This approach will introduce and train participants on the appropriate application of these tools, including experimental design, model preparation, comparison of structural models using both SAS and complementary information, validation, and most importantly the limitations of interpretation with regards to the biological conclusions that can be made. The workshop format will include lectures, and a selection of hands-on practical exercises. Students will be expected to bring laptops with appropriate pre-installed software as necessary. Prior to the workshop, a website will be made available containing installation instructions and software for each tutorial. Tentative Program Schedule Basic Theory and Methods Joint Session 8:00 am - 9:30am - Introduction: what is SAS data good for? (short) - Theory Essentials: How to get your scattering profiles - SAXS and SANS: common pitfalls, how to ensure the data is suitable for modelling - Cross Checks and Validation 9:30 AM - 10:00 AM Coffee Break Software Application and Tutorial Session 10 am - 7pm 10:00 AM - 11:30 AM BIOSAXS(EMBL) lectures and guided tutorial 11:30 AM - 12:30 PM Lunch and Discussions (vendor presentations in the form of 'lunch and learn') 12:30 PM - 2:00 PM IMP Lectures and Guided Tutorial 2:30 PM - 3:00 PM Coffee Break 3:00 PM - 4:30 PM SIBYLS lectures and guided tutorial 4:30 PM - 6:00 PM CCP-SAS lectures and guided tutorial 6:00 PM - 7:00 PM Discussion Pre-registration is mandatory. The fee to attend is: . Student (undergrad, grad or postdoctoral) - $140 . Corporate - $275 . Non corporate or non student - $140 Lunch will be included. Organizers: . Angela Criswell Rigaku Americas Corporatio Angela.Criswell(a)rigaku.com . Richard Gillilan Cornell CHESS reg8(a)cornell.edu . Kushol Gupta Perelman School of Medicine, University of Pennsylvania kgupta(a)upenn.edu . Michal Hammel SIBYLS group at The Advanced Light Source (ALS) mhammel(a)lbl.gov . Susan Krueger NIST Center for Neutron Research/CCP-SAS susan.krueger(a)nist.gov . Maxim Petoukhov BIOSAXS group at the European Molecular Biology Laboratory (EMBL) maxim.petoukhov(a)embl-hamburg.de . Adam Round EMBL Grenoble around(a)embl.fr . Dina Schneidman Institute of Life Science, Hebrew University of Jerusalem dina.schneidman(a)mail.huji.ac.il . Jill Trewhella University of Sydney jill.trewhella(a)sydney.edu.au More information is available at: http://www.amercrystalassn.org/wk.02-saxs http://www.amercrystalassn.org/2016-meeting-homepage Kushol Gupta, Ph.D. Research Assistant Professor Department of Biochemistry and Biophysics Perelman School of Medicine at The University of Pennsylvania <mailto:kgupta@upenn.edu> kgupta(a)upenn.edu / 215.573.7260 / 267.259.0082 / <http://www.stwing.upenn.edu/~kgupta> www.stwing.upenn.edu/~kgupta

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Issues loading RESTServer extension on Headless Linux installation
by tom＠pine-biotech.com 30 Mar '16

30 Mar '16

Hi all, Using the unsupported headless linux x64 installer, chimera-1.10.2-linux_x86_64_osmesa.bin, I can run Chimera at the command line but am having a very difficult time running the RESTServer extension. Using my ~/.chimera/preferences file from my OS X install where a location for Extensions was selected in the preferences and saved, and copied to linux and edited to contain the /opt/UCSF/Chimera64-1.10.2/share location instead, it does open a bunch of packages on start, unlike before when it refused to load any extension. However, it still cannot start RESTServer. [root@dfw share]# chimera Package "DBPuppet" already exists and tool(s) in it will not be loaded [snip, for full output see http://pastebin.com/s3GH7mbz ] > start RESTServer Starting extension 'RESTServer' failed As such, the one reason I wanted to run Chimera headless on linux does not seem to work. I know it's unsupported so I'm not expecting anything, but perhaps this is something that can be resolved simply. I've done a few fruitless google searches and this mailing list kept coming up. Thanks for your time, Tom

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RR Distance to make a Difference Plot
by Edward J Brignole 30 Mar '16

30 Mar '16

Dear Chimera folks, I've been looking into making Difference Distance Matrix Plots (a la Richards & Kundrot, Proteins 1988) to evaluate domain movements between two models. Chimera's RR Distance plots get most of the way there and since they start from sequence alignments do a nice job handling different patches of missing residues between the two models. In addition to plotting Avg and Std Distances would it be possible to compute the differences between RR distances of two structures. Or if you don't want to implement this function in the RR Distance GUI, at least some sort of python script that could access the distance matrices from the RR Distance function and direct that to some sort of output either with matplotlib or the data as text to plot with another program. Thanks for considering it, Ed

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How to calculate the angle between two helix in a protein structure
by Elaine Meng 30 Mar '16

30 Mar '16

> Date: Wednesday, March 30, 2016 9:20 AM > Subject: How to calculate the angle between two helix in a protein structure > > Dear community, > > I want to calculate the angle between two helix in a protein structure. Does anybody know how to calculate it precisely? > Please help me. Thanks a lot. > > Best regards, > Bing Wang > National Institute of Biological Sciences, Beijing Dear Bing Wang, It can be done either with graphical interfaces (tool dialogs) or with commands. You can calculate and display helix axes with the Axes/Planes/Centroids tool (in menu under Tools… Structure Analysis) or the “define” command. The axes objects will be listed in in a dialog, and you can measure the angle between any two by choosing them in the dialog with the mouse, or by specifying their identifiers (as listed in the dialog) in the “angle” command. See manual pages: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/str…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html> Example commands (start Command Line from the Favorites menu): open 2gbp define axis perHelix true angle a3 a10 This reports in the Reply Log (open from Favorites menu) that the angle between a3 and a10 is 22.893 degrees. The dialog shows that I have axes a1-a10 calculated from the 10 helices in the structure 2gbp. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. Chimera questions should be sent to the chimera-users email address CC’d here… looks like you accidentally sent the question to just “chimera” instead

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Automatic Bond Rotating Script
by Lisa Rohrwasser 29 Mar '16

29 Mar '16

Hello, I am currently trying to write a python script to rotate different bonds automatically many many times. The idea is to randomly chose a bond of a .pdb-File and rotate it by a certain angle. In principle the command line tool "rotation" is exactly what I would like to use, but i have difficulties implementing it. To start with rotating only one bond I already got: import chimera from chimera import runCommand as rc opened = chimera.openModels.open('~/Documents/rho.pdb') #open protein rho = opened[0] #get random bond (it is set to bond 10 for now) b = rho.bonds[10] #gives back both atoms corresponding to the bond (atom IDs are needed for command line tool "rotation") b.atoms #select bond-atoms a1 = b.atoms[0] a2 = b.atoms[1] #now i would like to use command line tool "rotation", which gives many errors rc("rotation a1 a2 <angle>") So i think the problems are 1) objects a1, a2 have the wrong datatype 2) rc does not have access to a1, a2 Now i wonder if there is a solution at all to these problems or if i have to think of a completely different way? Thanks in advance, Lisa

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ribbackbone
by Edward J Brignole 29 Mar '16

29 Mar '16

Dear Chimera developers and users, I'm trying to make a figure that shows hbond contacts with a ligand but am having a problem displaying contacts while simultaneously displaying residues and ribbons. I know that ribbackbone will allow simultaneous display of ribbon and backbone, but the problem is that this attribute is set for the entire model, not per residue. To keep the display as uncomplicated as possible I want to just show side chains except when there's a backbone contact then I want to show backbone for that residue as well. The problem arises when contacting residues are adjacent, if ribbackbone is on, then the CA's are connected, but if I turn ribbackbone off then I lose the backbone atoms I'd like to show except an occasional floating carbonyl oxygen. My workflow is basically: sel #0:LIG findhbond spec #0 sel cross intermodel F intraMol F intraRes F makePseudobonds T reveal T distSlop 0.7 angleSlop 40 ac cs ribbackbone #0 transparency 75,r #0 I'm sure there's a way to accomplish this but I haven't been able to figure it out. I saw there has been some discussion previously on the chimera-users list about ribbackbone display but I didn't find any posts that would solve this particular problem. My apologies if this situation has already been discussed. Thank you for your help, Ed

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Finding and depicting intermolecular interactions
by Henrique C. S. Junior 27 Mar '16

27 Mar '16

Dear Chimera list, I'm Interested in finding and showing halogen bonds and pi stackings. Is that possible? Attached is an example made using Schrodinger's Maestro. Thanks in advance -- *Henrique C. S. Junior* Químico Industrial - UFRRJ Mestrando em Química Inorgânica - UFRRJ Centro de Processamento de Dados - PMP

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