- Chimera-dev - RBVI Mailing Lists

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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(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 28 Feb '17

28 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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