- Chimera-dev - RBVI Mailing Lists

Re: [chimera-dev] programming question: volume display
by Tom Goddard 10 Apr '17

10 Apr '17

Hi Matt, To get the current region and step for a volume ijk_min, ijk_max, ijk_step = v.region To avoid having the step adjust automatically in the new_region() call use new_region(..., adjust_step = False) Chimera adusts the step to show no more than some specified number of grid points (e.g. 2 million) and this parameter is v.rendering_options.voxel_limit = 1 # In millions of voxels v.rendering_options.limit_voxel_count = True # Whether to auto-adjust step These options are also present in the Volume Viewer dialog, menu Features / Data Display Options. Tom > On Apr 7, 2017, at 10:52 AM, Dougherty, Matthew T wrote: > > Got it, thx. Was wondering if there was an alternate API. > > > > having a problem with ijk_step using this: > > v.new_region(ijk_min=(i_min, j_min, k_min), ijk_max=(i_max, j_max, k_max), ijk_step=(1,1,1)) > > The min and max act correctly, but it jumps into other step sizes when I vary min & max. > would think the step size would be > > when the relative min/max is small (i.e., volume is small) the gui step size is one. > as the volume increases, the step size increases. > if I maximize the volume and manually set the gui step size to one, then the python call works as expected. > > Any ideas? > > also, if I wanted to get the min/max values for the region, how do I get that. > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > ================================================= > ================================================= > From: Tom Goddard <goddard(a)sonic.net> > Sent: Wednesday, April 5, 2017 2:13:06 PM > To: Dougherty, Matthew T > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] programming question: volume display > > Yes. In fact all that is done with the new_region() routine. (set step with the ijk_step argument, eg. ijk_step = (2,2,2). Set plane number by setting ijk_min, ijk_max to show one plane). > > Tom > > >> On Apr 5, 2017, at 12:00 PM, Dougherty, Matthew T <matthewd(a)bcm.edu <mailto:matthewd@bcm.edu>> wrote: >> >> thx >> >> is volume.py where I would find how to change step size, plane number & depth? >> >> Matthew Dougherty >> National Center for Macromolecular Imaging >> Baylor College of Medicine >> ================================================= >> ================================================= >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Wednesday, April 5, 2017 11:41:35 AM >> To: Dougherty, Matthew T >> Cc: chimera-dev(a)cgl.ucsf.edu <mailto:chimera-dev@cgl.ucsf.edu> >> Subject: Re: [chimera-dev] programming question: volume display >> >> ***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe. >> To change the region bounds of a volume v in Python: >> >> v.new_region((0,0,0), (50,60,70)) >> >> Here’s the Python declaration in chimera/share/VolumeViewer/volume.py where the Volume class is defined. >> >> def new_region(self, ijk_min = None, ijk_max = None, ijk_step = None, >> show = True, adjust_step = True, save_in_region_queue = True): >> >> Tom >> >> >>> On Apr 4, 2017, at 3:58 PM, Dougherty, Matthew T <matthewd(a)bcm.edu <mailto:matthewd@bcm.edu>> wrote: >>> >>> I am trying to modify the region bounds of the volume viewer using python. >>> What module should I be looking at to determine the api calls? >>> >>> thanks, >>> >>> Matthew Dougherty >>> National Center for Macromolecular Imaging >>> Baylor College of Medicine >>> ================================================= >>> ================================================= >>> _______________________________________________ >>> Chimera-dev mailing list >>> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mail…>

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(Smart) Copy Molecule to ModelPanel after fitting in plugin
by Pablo Solar Rodríguez 10 Apr '17

10 Apr '17

Hi all! Hope everything is ok! :) I would like to know if there is any smart way to copy/duplicate a Molecule directly to the Model Panel. The plugin I am developing for an exahustive fitting generates N solutions on the same opened Molecule. In this situation, when the process has finished, the user can choose a solution and the Molecule rotates and translates to the associated position. That is, N different positions for each solutions. What I want is to let the user be able to "save" the solution it wants and show it in the Model Panel. An example: _I've got a chainH.pdb and a ccp4 map. After my exhaustive fitting process, 10 solutions are generated, so chainH can be moved into 10 different positions. Next step is that if user choses the solution number 7, chainH will move and rotate to that 7 solution and the user can save this into the Model Panel with solution7_chainH.pdb name_. Is there a simple way to do this? I've checked the Copy/Combine source code (http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/Combine [1]) but I want to know if there is a better way and not to "replicate" this code. Thank you all in advance! Pablo Solar Rodríguez pablo.solar(a)delogica.com Delógica - www.delogica.com [2] España: C/Nuñez de Balboa 31, 2ª Planta - 2, 28001 Madrid, Tel.: (34) 91 431 31 09 Colombia: Edificio Torre Zimma - Carrera 15 88-70 Bogotá, PBX (571) 3000302 ------------------------- _ POR FAVOR, ANTES DE IMPRIMIR ESTE MENSAJE, ASEGÚRATE DE QUE ES NECESARIO. AYUDEMOS A CUIDAR EL MEDIO AMBIENTE. _ _Este mensaje puede contener información confidencial o privilegiada. Si le ha llegado por error, rogamos no haga uso del mismo, avise al remitente y bórrelo. Consulte aviso legal. _ _This message may contain confidential or privileged information. If it has been sent to you in error, please do not use it, notify the sender of the error and delete it. See legal notice._ Links: ------ [1] http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/Combine [2] http://www.delogica.com

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Re: [chimera-dev] programming question: volume display
by Tom Goddard 05 Apr '17

05 Apr '17

Yes. In fact all that is done with the new_region() routine. (set step with the ijk_step argument, eg. ijk_step = (2,2,2). Set plane number by setting ijk_min, ijk_max to show one plane). Tom > On Apr 5, 2017, at 12:00 PM, Dougherty, Matthew T <matthewd(a)bcm.edu> wrote: > > thx > > is volume.py where I would find how to change step size, plane number & depth? > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > ================================================= > ================================================= > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Wednesday, April 5, 2017 11:41:35 AM > To: Dougherty, Matthew T > Cc: chimera-dev(a)cgl.ucsf.edu <mailto:chimera-dev@cgl.ucsf.edu> > Subject: Re: [chimera-dev] programming question: volume display > > ***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe. > To change the region bounds of a volume v in Python: > > v.new_region((0,0,0), (50,60,70)) > > Here’s the Python declaration in chimera/share/VolumeViewer/volume.py where the Volume class is defined. > > def new_region(self, ijk_min = None, ijk_max = None, ijk_step = None, > show = True, adjust_step = True, save_in_region_queue = True): > > Tom > > >> On Apr 4, 2017, at 3:58 PM, Dougherty, Matthew T <matthewd(a)bcm.edu <mailto:matthewd@bcm.edu>> wrote: >> >> I am trying to modify the region bounds of the volume viewer using python. >> What module should I be looking at to determine the api calls? >> >> thanks, >> >> Matthew Dougherty >> National Center for Macromolecular Imaging >> Baylor College of Medicine >> ================================================= >> ================================================= >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mail…>

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(no subject)
by Kavya Shankar 05 Apr '17

05 Apr '17

Hi, I am trying to open the same pdb file twice and apply mm command on the chains. The following script loops through the files in the folder so i open the same pdb twice: #!/bin/bash for file in `ls tmp_d2` do chimera --nogui --silent tmp_d2/$file tmp_d2/$file tmp_d2/$file tmp_d2/$file chim.cmd > test_A.pdb mv test_A.pdb temper/$file echo "$file" done File "chim.cmd" has the following: mm #0:.A:.B #1:.B:.A pair ss measure rotation #0 #1 I get the following error: 1c9o_1.pdb Error while sourcing chim.cmd, line 1: "measure rotation #0 #1" Rotation angle is near zero (0 degrees) I should be getting an angle of 180 degrees because they are all dimers. I have two versions of chimera on my system 1.7 and 1.11.2, does that make a difference? Thank you. Regards, Kavya Shankar

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programming question: volume display
by Dougherty, Matthew T 05 Apr '17

05 Apr '17

I am trying to modify the region bounds of the volume viewer using python. What module should I be looking at to determine the api calls? thanks, Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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(no subject)
by Kavya Shankar 29 Mar '17

29 Mar '17

Hi, Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures. Thank you. Regards, Kavya Shankar

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Send PDB and CCP4 selected to an external program
by Pablo Solar Rodríguez 27 Feb '17

27 Feb '17

Hello again dear mates! I've been working those days in my extension and the GUI es almost finished. Now I want to fill this skeleton with the process logic. To understand between us, I have an external compiled program that is executed in shell this way: ./bin/myProgram ./dir1/pdbselected.pdb ./dir/mapselected.ccp4 arg3 arg3 arg4 And for sure, in my .py test, it has to be executed as: import subprocess subprocess.call(["./Users/Solar/Desktop/parent/child1/child2/bin/myProgram", "/Users/Solar/Desktop/parent/child1/child2/dir1/pdbselected.pdb", "/Users/Solar/Desktop/parent/child1/child2/dir1/mapselected.ccp4", "arg3", "arg4", "arg5"]) The problem is to execute this in Chimera as an extension. The coding I made for the PDB and the Map it's similar to the FitMap tool (in Volume Data), where I use: ... # PDB from chimera import Molecule mlist = [m for m in fit_object_models() if isinstance(m, Molecule)] fstart = mlist[0] if mlist else None from chimera.widgets import ModelOptionMenu om = ModelOptionMenu(ff, labelpos = 'w', label_text = 'Fit ', initialitem = fstart, listFunc = fit_object_models, sortFunc = compare_fit_objects, command = self.object_chosen_cb) om.grid(row = 0, column = 0, sticky = 'w') self.object_menu = om # Map fm = Volume_Menu(ff, ' in map ') fm.frame.grid(row = 0, column = 1, sticky = 'w') self.map_menu = fm -- The question is, how can I pass the PDB to the compiled program as it is expected? Or, another possible solution, the paths of the PDB and the Map loaded in Chimera? I didn't found any friendly doc (methods, info and so on) about this and and I'm a mess :/ Thank you in advance dear coworkers! Pablo

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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 30 Jan '17

30 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 13 Jan '17

13 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 11 Jan '17

11 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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ChimeraX
by Dougherty, Matthew T 21 Nov '16

21 Nov '16

Many of the USB devices I have been looking at for control surfaces are midi-centric, primarily coming out of the music industry. For simple devices, not going the midi-route is usually straight forward, although can get complex supporting cross-platform. For complex devices such as DS1, midi appears to be the best method for dial boxes. There is also economical advantages and an ongoing evolution of such devices. https://www.amazon.com/Livid-Instruments-Portable-Digital-Mixer/dp/B00M4OEW… It also allows one to take advantage of manufacturer software in configuring baseline operational conditions (setting dial colors, ranges, toggling action of buttons). We have talked about midi in the event loop before. At the time it was not clear how/if this could work under chimeraX. Any further ideas? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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CHIMERA download
by Samir Al-Hilfi 16 Nov '16

16 Nov '16

Dear all, I read about the software and it seems useful to my research please any idea how to get it ? Regards Samir Al-Hilfi PhD student National Graphene Institute Room 2.008

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(no subject)
by Kavya Shankar 07 Nov '16

07 Nov '16

Hi, I have to find the normal of the protein and I am writing a python script that can do this. But when I run it, the normal is different. On chimera, I select *chain A* and *chain B* to get the plane. import chimera import os from cStringIO import StringIO from StructMeasure import centroid from StructMeasure import plane from chimera import numpyArrayFromAtoms for filename in os.listdir("test_python1"): print filename model1 = chimera.openModels.open('test_python1/'+filename) mol1 = model1[0] p = plane(numpyArrayFromAtoms(mol1.atoms)) print p.normal axis = chimera.Vector(p.normal) angle = 120 xf = chimera.Xform.rotation(axis,angle) #matrix = chimera.Xform.getOpenGLMatrix(xf) mol1.openState.localXform(xf) mem =StringIO() chimera.pdbWrite(model1,chimera.Xform.identity(),mem) words=filename.split('_') with open('test_python1/'+words[0]+'_2.pdb','w') as f: f.write(mem.getvalue()) Can you tell me where I am going wrong? For some proteins, it gives me the right plane and for others its different. Ex: 1l9q_1.pdb Opening 1l9q_1.pdb... #3, chain A: Cu-NIR #3, chain B: Cu-NIR #3, chain C: Cu-NIR 0.98101 0.0805021 0.176463 and Model #0 is 1l9q.pdb Distance information Angles/Torsions Axes axis name, length, center, direction Planes plane name, center, normal, radius plane: ( 19.690, 39.732, 48.459) (-0.981, -0.081, -0.176) 46.305 Centroids centroid name, center centroid: ( 19.690, 39.732, 48.459) Thanks. Regards, Kavya Shankar

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Fwd:
by Kavya Shankar 07 Nov '16

07 Nov '16

Hi, My thesis is on protein symmetry and I have been using the chimera's "Axes/Plane/Centroid" feature a lot. May I know what algorithm is being used in order to get the plane? Thanks. Regards, Kavya Shankar

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(no subject)
by Kavya Shankar 26 Oct '16

26 Oct '16

Hi, I am attempting to find the centroid of a protein and then translating it based on the output. Is there any function that does this? model = chimera.openModels.open('test_python/'+filename) mol = model[0] axis = chimera.Vector(1,1,1) angle = 180 xf = chimera.Xform.rotation(axis,angle) I am using chimera.Xform functions for my implementation. Also, Is there a documentation that lists down all functions that are currently available to manipulate proteins? Thank you. Regards, Kavya Shankar

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Rotating models using python scripting in chimera
by Kavya Shankar 25 Oct '16

25 Oct '16

Hi, I am new to chimera and I am attempting to write a python script that would rotate the models by some angle and then writing it to another pdb file with changed coordinates. import chimera import os from cStringIO import StringIO for filename in os.listdir("test_python"): print filename model = chimera.openModels.open('test_python/'+filename) mol = model[0] axis = chimera.Vector(1,1,1) angle = 180 xf = chimera.Xform.rotation(axis,angle) matrix = chimera.Xform.getOpenGLMatrix(xf) print mol.openState.xform mol.openState.localXform(xf) print mol.openState.xform mem =StringIO() chimera.pdbWrite(model,mol.openState.xform,mem) print mol.openState.xform with open('converted.pdb','w') as f: f.write(mem.getvalue()) This is my code so far. When I run it, the converted.pdb file does not contain any changed coordinates. The coordinates of the atoms are same as before. Am I making some mistake? Is there any other way of doing this easily? Thanks. Regards, Kavya Shankar

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Crystallographic symmetry
by Airlie McCoy 06 Sep '16

06 Sep '16

Hi, This is just a quick questions about your plans for chimera x. Do the plans include the ability to extend electron density maps with crystallographic symmetry, the way that e.g. Coot does? It is rather important, of course, for crystallographers! Ta, Airlie

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B factor
by Bashayer Althufairi 27 Jul '16

27 Jul '16

Hello As you know many crystallographers need to determine the ave. B factor of selected amino acids or sometimes they wanna know B factor of N-termius Vs. C-terminus of a protein. I'm working on a protein where I need to predict B factor of certain amino acids sequence as well as difference between the values for analysis. Is this possible by Chimera? If yes, I'd like to know Please the way step be step, If no, I wish you could recommend a simple way to do it by educational simple software like PyMol. Thank You in Advance -- Bashayer Althufairi Medicinal Chemistry department Virginia Commonwealth University

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