- Chimera-dev - RBVI Mailing Lists

Register-Unregister Chimera Extension (Plugin) to check source code changes
by Pablo Solar Rodríguez 21 Feb '17

21 Feb '17

Hi all again, While I try how to debug my plugin with Chimera (I posted that question here), I downloaded the 'Fit in map' tool source code to create my own plugin from it. So I changed the name in ChimeraExtension.py and loaded it in Tools -> Volume Data to check that my new plugin was loaded succesfully. The point now is that when I make some changes in my code, they are not immediately visible when I open the plugin again. Even more, I am not capable to "reload" the plugin with the new changes. Any solution to this? As I told you before, I'm fully newbie with Chimera and I feel pretty lost Thank you in advance!

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Debugging own extension in Mac OS X
by Pablo Solar Rodríguez 21 Feb '17

21 Feb '17

Hello all, My name is Pablo Solar and I am newbie in a real BioInformatics work, specifically in Chimera. Due to my new project requirements, I want/need to write a Chimera Extensión which executes an existing tool for fitting maps in an exhaustive way. I started to read the documentation available and the programmers guide, but the fist question that came to my mind is about debugging. I would like to know how could I debug my extension python code while I work with Chimera at the same time. Is this possible? I mean, opening my extension in Chimera (Tools -> preferences and so on) and starting to debug the _init_py and the rest of my files. How should I configure my environment? What framework to use? That kind of things Thank you in advance. I think I will post questions frequently because, as I said, this is totally new to me. By the way, I suscribed to the mailing list with my personal mail (pablosolar.r(a)gmail.com) I would like to give you all kind regards and hope to learn from you as much as possible. Just need a bit of patience... :) Keep in touch and thank you in advance, Pablo Solar.

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Linking Chimera with Tetr
by Gordon Gibb 08 Feb '17

08 Feb '17

Dear developers, I have been working on integrating Tetr (a command line tool to construct/modify molecular systems for use in computational chemistry codes such as CASTEP and CP2K - http://nms.kcl.ac.uk/lev.kantorovitch/codes/lev00/index.html <http://nms.kcl.ac.uk/lev.kantorovitch/codes/lev00/index.html>) with Chimera. To do this we have written a plugin to Chimera that runs an instance of Tetr in a console, with the user being able to type commands into Tetr. The aim is to have Chimera visualise the system being constructed in Tetr, and to update the visualisation based to changes made in Tetr. At present whenever a command is send to Tetr (which in response to this command may re-write a file containing the molecular system), the plugin looks to see if this file has changed, and if so gets Chimera to reload this file and visualise it. As far as I can tell, there isn’t a ‘reload’ option in Chimera, so instead I close the model (saving its xform matrix first), then open the modified file, and set its xform matrix to restore the old viewing angle etc. For example: #save xform matrix and close model xf=model.openState.xform chimera.openModels.close(model) #open updated file into model number baseId chimera.openModels.open(filename,baseId=baseId) #retrieve model from the list of open models modlist=chimera.openModels.list() for mod in modlist: if mod.id == baseId: model=mod break #set the xform matrix model.openState.xform=xf What I was wondering was 1) if this is a sensible way to go about things, and 2) if there is a way to retrieve and store visualisation information such as displaying the molecule as ball and stick, wireframe etc such that this can be re-applied to the newly opened model, since at present any visualisation information is not retained when re-opening a file. Thanks in advance, Gordon ----------------------------------------------- Dr Gordon P S Gibb EPCC, The University of Edinburgh The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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(no subject)
by Kavya Shankar 02 Feb '17

02 Feb '17

Hi, Is it possible to find the distance between a point and a line in chimera? I am trying to find the distance from the center of mass of the protein to the 2 fold axis of the homodimer. Thanks. Regards, Kavya

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midi
by Dougherty, Matthew T 31 Jan '17

31 Jan '17

Hi, I got the midi interface working with chimera, thanks. I ended up using the rtmidi package instead of mido. https://pypi.python.org/pypi/python-rtmidi Midi will significantly reduce my reliance on accelerators. It will give me the ability to pass multivariate parameters from hardware and modify LED displays on those devices. Previous efforts directly working with USB has be difficult because of lack of compliance and limited open source methods. The software I developed allows the DS1 control surface to easily control volume rendering and stereographics. http://lividinstruments.com/products/ds1/ I am anticipating this will improve operational viz for tomograms. If users demonstrate value in device, will release as an chimera extension. Internal NCMI testing begins next week. Also looking at other inexpensive midi devices. Recommending chimera ship with rtmidi library. thanks, Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Automate Energy Minimization of pdb files
by Ajay Pal 20 Jan '17

20 Jan '17

Dear Developers I am trying to build a chimera integrated python script to energy minimize protein pdb files. I have a list of ~400 pdb files (clean homology models) which I need to Energy minimize Can you please help me with this matter: like how to select files from directory adding H-atoms selecting the forcefield, etc how can I automate this whole process ? Thank you, I would appreciate all your help. Ajay -- Ajay Pal PhD Research Student Dublin Institute of Technology, Dublin -- This email originated from DIT. If you received this email in error, please delete it from your system. Please note that if you are not the named addressee, disclosing, copying, distributing or taking any action based on the contents of this email or attachments is prohibited. www.dit.ie Is ó ITBÁC a tháinig an ríomhphost seo. Má fuair tú an ríomhphost seo trí earráid, scrios de do chóras é le do thoil. Tabhair ar aird, mura tú an seolaí ainmnithe, go bhfuil dianchosc ar aon nochtadh, aon chóipeáil, aon dáileadh nó ar aon ghníomh a dhéanfar bunaithe ar an ábhar atá sa ríomhphost nó sna hiatáin seo. www.dit.ie Tá ITBÁC ag aistriú go Gráinseach Ghormáin – DIT is on the move to Grangegorman <http://www.dit.ie/grangegorman>

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chimerax and write pdb files question
by Wolfgang Lugmayr 18 Jan '17

18 Jan '17

dear chimerax developers, i found out, that you skipped writing pdb files and use only mmcif/pdbx. i need to write the selected structures as pdb for the usage with the rosetta modeling software. in chimera1 i used your save as dialog for this. are you (or somebody else) planning to also implement a pdb file writer for chimerax? cheers, wolfgang -- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Institute of Molecular Biotechnology (IMBA) Dr. Bohr-Gasse 3-7 (Room 6.14) 1030 Vienna, Austria Tel.: +43 (1) 790 44-4649 Email: w.lugmayr(a)uke.de http://www.cssb-hamburg.de/ -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

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opening file in extension.
by Devin Haslam 14 Jan '17

14 Jan '17

I am developing an extension for the newest version of chimera. At the moment, my extension takes several .pdb files as input and opens them in the viewer. Currently, I am using the chimera.openmodels.open() to display these pdb files. This was not a problem until I started using .pdb files that consisted of hundreds of points. Because I am opening multiple .pdb files, the call to "setCategory()" does not execute fast enough and the root will have changed. In summary, what will I have to do in code to open multiple .pdb files made up of hundreds of points? -- Devin Haslam Old Dominion University, Norfolk, Virginia

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chimerax - registering an external tool problem
by Wolfgang Lugmayr 12 Jan '17

12 Jan '17

dear chimera developers, i'm currently porting one of our chimera 1.x plugins called starmap to chimerax. basic questions: 1. should the package be e.g. chimerax-starmap or just starmap? 2. is there a recommended way when i should upload to the toolshed repository? my current problem: i use chimerax's python3.5 pip to install and remove my tests. my test package is called chimerax.starmapx (+.__init.py__) i had a look at your toolshed and added test categories like follows to the metadata (installed version): Classifier: ChimeraX :: Bundle :: Volume data :: 1,1 :: chimerax.starmap :: chimerax.starmap :: Classifier: ChimeraX :: Tool :: StarMapX :: Volume data :: Run Rosetta refinements Classifier: ChimeraX :: Command :: apix :: Volume data :: Run Rosetta apix Requires-Dist: ChimeraX-Core (>=0.1) Requires-Dist: pyparsing i also used "General" instead of "Volume data" for debugging. i have overriden the BundleAPI get_class, start_tools, register_command similar to blastprotein. unfortunatly my test plugin never shows up in chimerax (e.g. ts list) and the command "stm apix" is not registered. i debugged the toolshed (standalone - not in chimerax) and if i print the contents of line 720 - end of_load_bundle_infos() i get ...using SteamVR]], ChimeraX-StarMap (installed) [version: 0.1.2] [api package: chimerax.starmap] [category: Volume data] [tool: StarMap [categories: Volume data] [synopsis: Run Rosetta refinements]] [command: apix [categories: Volume data] [synopsis: Run Rosetta refinements]], ChimeraX-Stringdb (installed) [version: 0.1]... and a little bit before ('checking', <InstalledDistribution 'ChimeraX-StarMap' 0.1.2 at '/projects/marlovits/lugmayr/workspace/ChimeraX/lib/python3.5/site-packages/ChimeraX_StarMap-0.1.2.dist-info'>) do i miss something during the registration process? cheers, wolfgang --- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Institute of Molecular Biotechnology (IMBA) Dr. Bohr-Gasse 3-7 (Room 6.14) 1030 Vienna, Austria Tel.: +43 (1) 790 44-4649 Email: w.lugmayr(a)uke.de http://www.cssb-hamburg.de/ -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

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ChimeraX on Centos7
by Wolfgang Lugmayr 02 Jan '17

02 Jan '17

dear chimera users, if you want to test/use the daily releases of chimerax on centos7 and have an error like ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /opt/chimerax/0.1-daily/lib/python3.5/site-packages/chimerax/core/geometry/_geometry.so) you might find the following link useful: http://www.marlovitslab.org/chimerax/ the provided libraries could also work on other linux distributions, so just try. cheers, wolfgang -- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Institute of Molecular Biotechnology (IMBA) Dr. Bohr-Gasse 3-7 (Room 6.14) 1030 Vienna, Austria Tel.: +43 (1) 790 44-4649 Email: w.lugmayr(a)uke.de http://www.cssb-hamburg.de/ -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

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