April 2017 - Chimera-dev - RBVI Mailing Lists

Save PDB and Map before fitting
by Pablo Solar Rodríguez 14 May '17

14 May '17

Hi all, Hope everything is going fine! In my plugin, it is necessary to save the PDB and the map (ccp4) to disk before the exhaustive fitting process is executed. Is there any simple and efficient way of doing this? I've checked the scripts and haven't found anything about this and I wouldn't like to have to replicate the code from the Chimera source (OpenSave and the relative to maps). This question is quite related to the previous one I made about copying a molecule. Thank you all in advance and kind regards from Spain.

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Get values from other chimera dialogs
by Pablo Solar Rodríguez 08 May '17

08 May '17

Hello everyone! I feel you will get tired of me asking so many questions hehe Anyway, I continue developing my plugin and I'd like to know if there's any way to get values from other chimera dialogs although they are not open. For example, when my map is loaded I need the values, from the Volume Viewer, of the voxel size (in Coordinates panel) and the cutoff, but I didn't find how to get them and I really don't know if this is possible or not. Thank you in advance and, as usual, kind regards! Pablo.

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Chimera on Windows 10 store
by Marco Leonardi 29 Apr '17

29 Apr '17

Hi, I'm part of the UWP Open Source Community (https://github.com/UWP-Open-Source-Community) Our intent is to take Win32 Open Source applications and convert them into UWP apps through the Windows Bridge (Project Centennial). We like your app and that's why we decided to convert it. In case you would like to take charge of this app and publish it yourself on the store (make us very pleased) contact us the first possible please! Otherwise, we may be responsible for publishing your app. If you do not want to take over the publication on the Store, can you give us permission to do so? Sorry for my poor English. Thanks for your help. Regards, Marco Leonardi

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Re: [chimera-dev] ChimeraX
by Tom Goddard 11 Apr '17

11 Apr '17

Hi Matt, There is some information about how to install Python packages with Chimera in the programming FAQ https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b but I believe Eric here said the suggested approach to doing pip install no longer works. A more hacky approach is to simply copy site-packages/Mido (or whatever the module is called) from your system installed version into the Chimera Python site-packages (in chimera/lib/python2.7/site-packages or Chimera.app/Contents/Resources/lib/python2.7/site-packages on Mac). Tom > On Jan 13, 2017, at 2:26 PM, Dougherty, Matthew T <matthewd(a)bcm.edu> wrote: > > I have looked around at python midi packages. > I think I can get around modifying the tk/qt event loops by polling the midi port. > > I did a pip install of 'Mido' on my Mac laptop for testing using the OSx python environment. > > To install the Mido library into chimera, what do you recommend? > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > ================================================= > ================================================= > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Monday, November 21, 2016 12:53:04 PM > To: Dougherty, Matthew T > Cc: chimera-dev(a)cgl.ucsf.edu <mailto:chimera-dev@cgl.ucsf.edu> > Subject: Re: [chimera-dev] ChimeraX > > ***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe. > Hi Matt, > > The way to use MIDI in ChimeraX would be to include a MIDI / Qt5 library. Qt5 is the window toolkit used by ChimeraX and it controls the receiving of events from devices. I don’t know of an adequate Qt / MIDI library exists. Really we would want PyQt5 / MIDI since all Qt in ChimeraX is done in Python. The top Qt / MIDI hit is the QMidi library > > https://github.com/waddlesplash/QMidi <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_waddlesplas…> > > which apparently only handles output of MIDI events, and it sounds like you are primarily interested in input of MIDI events to ChimeraX. > > We welcome any recommendations on what PyQt library could handle incoming MIDI events. My quick web search turned up nothing. > > Tom > > > >> On Nov 18, 2016, at 9:47 AM, Dougherty, Matthew T wrote: >> >> 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… <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.amazon.com_Livid-2…> >> >> 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 >> ================================================= >> ================================================= >> _______________________________________________ >> 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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session files
by Dougherty, Matthew T 11 Apr '17

11 Apr '17

I was interested in writing/reading sessions as hdf datasets. Can you direct me into the code that does the IO? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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

10 Apr '17

We don’t have volume erase in ChimeraX yet. Probably not coming for at least 6 months other new tools and more commonly used capabilities will come first. But when it does arrive allowing a box eraser instead of a sphere should be easy. Tom > On Apr 10, 2017, at 2:20 PM, Dougherty, Matthew T <matthewd(a)bcm.edu> wrote: > > thx > understood. > is this a feature in chimeraX? > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > ================================================= > ================================================= > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Monday, April 10, 2017 3:44:54 PM > 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 > > Volume eraser shows a sphere. There is no code to show a box. Would not be too hard to add such code, but we are not making such feature improvements to Chimera since our development of new features is in the next generation ChimeraX. > > Tom > >> On Apr 10, 2017, at 11:22 AM, Dougherty, Matthew T <matthewd(a)bcm.edu <mailto:matthewd@bcm.edu>> wrote: >> >> thx >> >> I noticed in the source and the accelerators that I can erase a box (inside or out). How can I display the box instead of the sphere? >> I assume I would disable the sphere graphic and write a box graphic, i.e. there is no api I am missing. >> >> Matthew Dougherty >> National Center for Macromolecular Imaging >> Baylor College of Medicine >> ================================================= >> ================================================= >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Monday, April 10, 2017 12:15:12 PM >> 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 >> >> Hi Matt, >> >> If you want to erase inside the sphere displayed by the volume erase dialog, first get that dialog then call its erase method: >> >> from VolumeEraser.gui import volume_erase_dialog >> d = volume_eraser_dialog(create = True) >> d.erase_inside_sphere() >> >> Tom >> >> >> >>> On Apr 7, 2017, at 5:37 PM, Dougherty, Matthew T wrote: >>> >>> here is a related question, let me know if I should open a new thread. >>> >>> The VolumeEraser code does this for erasing: self.erase_inside_sphere() >>> >>> writing python code, how can I activate that code in my modules? >>> assuming I have issued a 'start Volume Eraser' command to get the gui up. >>> >>> >>> Matthew Dougherty >>> National Center for Macromolecular Imaging >>> Baylor College of Medicine >>> ================================================= >>> ================================================= >>> From: Dougherty, Matthew T >>> Sent: Friday, April 7, 2017 2:03:55 PM >>> To: Tom Goddard >>> Cc: chimera-dev(a)cgl.ucsf.edu <mailto:chimera-dev@cgl.ucsf.edu> >>> Subject: Re: [chimera-dev] programming question: volume display >>> >>> thx >>> >>> Matthew Dougherty >>> National Center for Macromolecular Imaging >>> Baylor College of Medicine >>> ================================================= >>> ================================================= >>> From: Tom Goddard >>> Sent: Friday, April 7, 2017 12:58:14 PM >>> 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 >>> >>> 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 >>>> Sent: Wednesday, April 5, 2017 2:13:06 PM >>>> 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 >>>> >>>> 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 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 >>>>> 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 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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Re: [chimera-dev] programming question: volume display
by Tom Goddard 10 Apr '17

10 Apr '17

Volume eraser shows a sphere. There is no code to show a box. Would not be too hard to add such code, but we are not making such feature improvements to Chimera since our development of new features is in the next generation ChimeraX. Tom > On Apr 10, 2017, at 11:22 AM, Dougherty, Matthew T <matthewd(a)bcm.edu> wrote: > > thx > > I noticed in the source and the accelerators that I can erase a box (inside or out). How can I display the box instead of the sphere? > I assume I would disable the sphere graphic and write a box graphic, i.e. there is no api I am missing. > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > ================================================= > ================================================= > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Monday, April 10, 2017 12:15:12 PM > 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 > > Hi Matt, > > If you want to erase inside the sphere displayed by the volume erase dialog, first get that dialog then call its erase method: > > from VolumeEraser.gui import volume_erase_dialog > d = volume_eraser_dialog(create = True) > d.erase_inside_sphere() > > Tom > > > >> On Apr 7, 2017, at 5:37 PM, Dougherty, Matthew T wrote: >> >> here is a related question, let me know if I should open a new thread. >> >> The VolumeEraser code does this for erasing: self.erase_inside_sphere() >> >> writing python code, how can I activate that code in my modules? >> assuming I have issued a 'start Volume Eraser' command to get the gui up. >> >> >> Matthew Dougherty >> National Center for Macromolecular Imaging >> Baylor College of Medicine >> ================================================= >> ================================================= >> From: Dougherty, Matthew T >> Sent: Friday, April 7, 2017 2:03:55 PM >> To: Tom Goddard >> Cc: chimera-dev(a)cgl.ucsf.edu <mailto:chimera-dev@cgl.ucsf.edu> >> Subject: Re: [chimera-dev] programming question: volume display >> >> thx >> >> Matthew Dougherty >> National Center for Macromolecular Imaging >> Baylor College of Medicine >> ================================================= >> ================================================= >> From: Tom Goddard >> Sent: Friday, April 7, 2017 12:58:14 PM >> 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 >> >> 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 >>> Sent: Wednesday, April 5, 2017 2:13:06 PM >>> 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 >>> >>> 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 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 >>>> 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 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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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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