- Chimera-dev - RBVI Mailing Lists

Freeing chimera memory after combining two molecules
by Daniel VH 05 Oct '18

05 Oct '18

Hi, In my python script I'm using the combine() function to merge a protein and a molecule into one model and since I'm doing this multiple times and only use the combined result to save it with pdbWrite I want to free the memory of the object combination right after that, but after the instructions chimera.openModels.close(combination), del combination, chimera.update.checkForChanges(), gc.collect(), chimera.closeSession() the memory is not freed. This is the code that reproduces the problem, it uses the molecules in the zipfile I have attatched. import chimera from Combine import combine import zipfile import time import gc import os #from memory_profiler import profile for itemnum in range(3): #@profile def pathmaker(itemnum): dirpath = os.path.dirname(os.path.realpath(__file__)) zippath=dirpath+'/'+'test1_000.zip' torsionpath=zipfile.ZipFile(zippath).extract('Pathway_000_Pathway.txt') proteinpath=zipfile.ZipFile(zippath).extract('Protein_000_Protein.mol2') ligandpath=zipfile.ZipFile(zippath).extract('Ligand_000_Ligand.mol2') opened = chimera.openModels.open(proteinpath) protein = opened[0] opened1 = chimera.openModels.open(ligandpath) mol=opened1[0] combination=combine([mol,protein],protein) totalnum=str(itemnum).zfill(3)+'_'+str(i).zfill(3) chimera.pdbWrite([combination], chimera.Xform(), 'testpdb%s.pdb' %totalnum) print('writing testpdb%s.pdb' %totalnum) chimera.openModels.close(combination) del combination chimera.update.checkForChanges() gc.collect() chimera.closeSession() for i in range(20): pathmaker(itemnum) #this stops the code and shows memory increase for each iteration print('pause 6 seconds...') time.sleep(6)

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Auto set threshold boundaries and colors
by Benjamin Looker 24 Sep '18

24 Sep '18

Hello! My name is Benjamin Looker, and I have recently become acquainted with your software for visualization of molecular orbital calculations that my group does with some regularity. I was wondering whether the statement on this page refers to a specific preferences file in the Chimera program files. : ( http://www.rbvi.ucsf.edu/chimera/1.8/docs/ContributedSoftware/volumeviewer/… ) "For unsigned data types, an initial threshold is set so that 1% of voxels" The reason I ask is because it would be much simpler, given a known color code and level, to standardize the import of files into Chimera for any sort of publication, especially in the event that many molecular orbitals needed to be visualized at once for a project. Best, -- Benjamin G. Looker Graduate Student Lancaster Group

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Asking about installation
by Utid Suriya 04 Sep '18

04 Sep '18

Dear, Chimera developer First of all, I would like to introduce myself; I am a graduate student in Thailand and my work is focusing on Drug Discovery. I am interested in using Chimera in visualization so, I downloaded and already installed it by accepting license and condition. However, I cannot open the Chimera program at all. I am not sure what are the related possible problems. One possibility is that I use Window 8. But I am not sure whether it is a bottleneck problem. Thank you very much Utid Suriya Department of chemistry, faculty of science, Chiang Mai university, Thailand 50200

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Re: [chimera-dev] [Chimera-users] Is there any tool to write some calculated attribute into a header format?
by Sergio Garay 31 Jul '18

31 Jul '18

Thank you very much, Eric. Unhappily I am not familiar with Python scripting, so I will have to wait that someone with that skill adds this useful tool into Chimera code! But for now I will take Elaine's hints! Thank you again Sergio On Tue, Jul 31, 2018 at 3:38 PM Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Hi Sergio, > If you are comfortable writing Python code, there is a provision for > adding custom header types to Multalign Viewer. Look at the MAVHeader > module in your Chimera distribution (<your Chimera>/share/MAVHeader), > particularly the file ChimeraExtension.py which defines headers for charge > variation and CA/backbone/full RMSDs and registers those headers with > Multalign Viewer. I imagine you will have questions (LOL!) so I have > directed responses to the chimera-dev mailing list, which would seem more > appropriate in this case. > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > On Jul 31, 2018, at 11:22 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Sergio, > Sorry, there isn’t a way to automatically make residue attributes into a > header. We had imagined that people would be calculating properties > outside of Chimera, and then using a script or even manually creating a > file in the header format to load them as a header. > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/d… > > > > However, you can change the sequence lettering colors to match the ribbon, > so if you first colored ribbon by some residue attribute (with Render by > Attribute or command “rangecolor”), it could be reflected back into the > sequence window in that way. To do that, use sequence window menu > Preferences… Appearance, and then for residue letter coloring (near the > bottom), choose “coloring scheme: ribbon”. I realize this might not be > optimal if some of the coloring makes the letters hard to read. > > I attached an example image with my protein colored by residue average > bfactor (blue -> red -> yellow) and using “ribbon” coloring of the > associated sequence in the alignment. > > With a header you could only have one value per column, but with ribbon > coloring you could have different values (colors) in the same column if > there are multiple structures associated. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > <Screen Shot 2018-07-31 at 11.18.18 AM.png> > > > On Jul 31, 2018, at 6:05 AM, Sergio Garay <sergio.alberto.garay(a)gmail.com> > wrote: > > Hi All! > > I would like to know: > Is there any way or tool to write some calculated attribute into a header > format? > > I want to see the same color values obtained for some a calculated > attribute projected onto a sequence. > > I have read in the chimera list the inverse process: exporting a header > from a sequence window to be read as an attribute. > > Thank you in advance. > > -- > Sergio Garay > Dr. en Ciencias Biológicas > Facultad de Bioquimica y Cs. Biológicas > Universidad Nacional del Litoral > Santa Fe - Argentina > C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA > Argentina > Ph. +54 (342) 4575-213 > Fax. +54 (342) 4575-221 > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > -- *Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *

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Save density map as a mesh
by עמיחי הולצר 30 Jul '18

30 Jul '18

Hi Chimera support, I have 2 questions: 1. How does Chimera calculate the mesh from the density map? 2. How can I save the mesh as a file? Thanks a lot, Amichai Holzer Huji

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Re: [chimera-dev] Dust Clean in cryo-EM maps
by עמיחי הולצר 16 Jul '18

16 Jul '18

Hi, I like the density map after hide density map, is there any way to save the density map after dust hide? Every time I save the density map, it saved the original map instead of density map after hidden dust. Thanks, Amichai 2018-07-13 17:16 GMT+03:00 עמיחי הולצר <amiholz(a)gmail.com>: > Chimera System Hi, > > I am a student in computational structural biology lab in the Hebrew > University of Jerusalem. We are developing software for modelling with electron > microscopy density maps. > > I'm using chimera to display the density maps, and the specific using thr > feature in chimera called clean dust, which shows the map seamlessly. > My question is whether there is a possibility to save the map without the > "dust"? > Because now there is only an option to eliminate dust, but not to save the > clean map. > > Thank in advance, > Amichai Hozler > Hebrew University >

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Visualize 3D structure of Peptide
by Mohammadreza Behi 22 May '18

22 May '18

Dear Sir/Madam, I am trying to visualize a peptide and a protein using Chimera, yet I am not sure if the peptides may have an ID to fetch the structure by ID. Even I could not find the ID for my protein. Can you please let me know how I may find the ID for these items? Or if there is not any ID how to visualize them for further studies? Kind regards, Reza

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Pointer to model when opened
by Pablo Solar Rodríguez 24 Apr '18

24 Apr '18

Hello Eric and the rest of mates! I would like to know if when you open a PDB through Midas 'open' method, the opened model is returned. I need to have access to that specific model all the time, even when IDs in the Model Panel are changed due to some other models are closed or opened. The idea is something like: if os.path.exists(model_path): from Midas import open self.model_path_pointer = open(model_path, filetype="pdb") And whenever I need, make: self.model_path_pointer.name self.model_path_pointer.id .... *Thank you in advance and kind regards!*

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Renaming a PDB loaded the Model Panel
by Pablo Solar Rodríguez 12 Apr '18

12 Apr '18

Hello all! I am introducing some features in my plugin and I would like to know if there is any smart of way to rename a PDB that is loaded in the Model Panel. I've seen the renameDialog.py module in ModelPanel package but didn't see any way to call it from my plugin. Thank you in advance and kind regards!

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Write-Open
by Pablo Solar Rodríguez 12 Mar '18

12 Mar '18

Hello all! I'm looking to the scripts ( http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/) and can not see a simple example of how to open a PDB. What I need to my extension is to save a PDB relative to a map and then open it to the model panel. Copying it to the model panel does not make sense to me because I need to fix the positions of the moved PDB relative to the map. Could it be something like this? * # Get opened molecule (the one selected in the menu)* * m = self.object_menu.getvalue()* * # Make copy using the copy_molecule native functionality from Chimera* * from Molecule import copy_molecule* * mc = copy_molecule(m)* * # Set copy name* * mc.name <http://mc.name> = m.name.split('.')[0] + '_' + self.chosen_solution + '.pdb'* * copy_path = self.cwd + mc.name <http://mc.name>* * from Midas import open, write* * write(mc, self.map_menu.volume(), self.cwd)* * open(self.cwd)* Thank you in advance!

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cdf output
by White, Tommi A. 05 Feb '18

05 Feb '18

Hello. We are intrigued by a new document format called "CDF". https://www.wolfram.com/cdf/ Are the developers of Chimera... 1) Aware this format exists? 2) Actively seeking ways to output cdf formatted renderings? From a structural biology community standpoint, the ability to break free of the traditional static image figure and have the ability to render in 3D for a more interactive way would be AMAZING for the structural biology community Just wanted to give you a heads up that this exists. If we could output our "images" into cdf files, and further rendered in a document...:) Tommi A. White, Ph.D. Assistant Professor of Biochemistry Director, Electron Microscopy Core Facility University of Missouri W117 Veterinary Medicine Building 1600 East Rollins Street Columbia, MO 65211 573-882-8304 WhiteTo(a)missouri.edu<mailto:WhiteTo@missouri.edu> http://emc.missouri.edu<http://emc.missouri.edu/>

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Running Chimera through Python script
by Evan Seitz 29 Jan '18

29 Jan '18

Hi - I’m trying to follow Example 1 on http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html>, but after entering the code precisely as it is written, am getting back the ModuleNotFoundError: No module named ‘chimera’. I’ve tried running the script using both Python2.7 and Python3, and both have resulted in the same error. As a sub-question, is Chimera supported in Python3, or is it best practice to still use Python2? Thank you, Evan Seitz Chimera version: 1.12.0 OS: macOS High Sierra 10.13.2

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Chimera's default directory
by Shuto Araki 01 Nov '17

01 Nov '17

Hi everyone, My name is Shuto Araki, a Computer Science student at DePauw University in Indiana. I’m currently helping a research in biochemistry department using Chimera and Python. My program reads a csv file and manipulate and visualize its data on Chimera. I’m trying to read a csv file, but it only works on my computer because I have to use the absolute path for the csv file. Is there a way to set the path relative? How can I set the default directory to the one that I set in the Tool Preferences —> Locations? I tried os.getcwd() to see the default directory but the IDLE only returns “/“ and I’m confused because it is supposed to return a string representing the current working directory. Could you please help me figure out what’s happening? Sincerely, Shuto

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GUI question
by Daniel Gurnon 29 Oct '17

29 Oct '17

Hi everyone, I'm working with a undergraduate computer science student, Shuto Araki, on a Chimera development project that involves creating a GUI. I'm not a programmer, and he's learning Python as he goes- so we've run into the inevitable snag, and we're looking for some help. Here's how Shuto describes the issue: ---- I am trying to create a Chimera GUI extension that asks Chimera to fetch a PDB ID and then to highlight residue positions within the structure, with the PDB and positions taken from a CSV file. I started with a Python script, and it works as intended if I import it from IDLE. However, when I tried to create a GUI using this guide https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/ Examples/Main_ExtensionUI.html I ran into an error. When I click on the button that I added on toolbar, the callback function does not seem to work properly. It just pops up an empty window with OK, Apply and Cancel buttons. The code snippet is as follows: ############################################################## class MutationDialog(ModelessDialog): name = "mutation highlighter" title = "Rare Genetic Mutation Highlighter” master = Tk() master.title("Rare Genetic Disease Mutation Highlighter") master.geometry('{}x{}'.format(500, 100)) global var var = StringVar(master) var.set(proteinNames[0]) # proteinNames is a list of protein options that a user chooses options = OptionMenu(master, var, *proteinNames) options.pack() def Apply(): # this functionality works protein_num = proteinMap[var.get()] mh.highlightMutation(filename, protein_num) button = Button(master, text = "Apply", command = Apply) button.pack() chimera.dialogs.register(MutationDialog.name, MutationDialog) dir, file = os.path.split(__file__) icon = os.path.join(dir, 'ExtensionUI.tiff') chimera.tkgui.app.toolbar.add(icon, lambda d=chimera.dialogs.display, n=MutationDialog.name: d(n), 'Highlight Mutations', None) ############################################################## I suspect that MutationDialog class is not working as a proper callback class. *Do you have any suggestions for the proper structure of the class?* We're also Sincerely, Shuto --- Thanks for any advice! Dan ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry Director, Science Research Fellows Program DePauw University Greencastle, IN 46135

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per-frame python script
by James Prestegard 21 Jul '17

21 Jul '17

I'm trying to write a script to be used in the per-frame operation of chimera MD Movie (I'm not an accomplished python programmer). The script I wrote calculates order parameters and internal relaxation elements. It appears that I have to import some chimera commands as well as the python math library to do this. Everything works on a single frame, but I need to pass some variables from frame to frame, and the import commands appear to reset all variables at each new frame. Is there a way to set some global variables or to do the imports only once outside the pre-frame script? Jim James H. Prestegard Professor and GRA Eminent Scholar, Emeritus Complex Carbohydrate Research Center University of Georgia Athens, Georgia, 30602, USA 706-542-6281

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Finding central Axis of Strand
by Devin Haslam 20 Jul '17

20 Jul '17

Hello, I am developing my own extension to find the central axis of a strand. I am using the nitrogen atoms of a strand to estimate this line, but I have not been able to estimate the end of the strand so that it follows the ribbon. I have attached an image below that displays this error. Currently I am using the next nitrogen atom on the loop to extend my line, but I was wondering how Chimera does this with the ribbon. As you can see in the image, one end of the strand is very accurate, but the side with the arrow head has some problems. Thanks for your help. -- Devin Haslam Old Dominion University, Norfolk, Virginia

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Chimera Plugin Question
by Broyde, Joshua E. 03 Jul '17

03 Jul '17

Hi, I was wondering if it is possible to develop a custom plugin for Chimera that users would be able to download an use? Does Chimera allow this, or must all functionalities in Chimera be designed by the UCSF team? Ideally, this custom plugin would include new buttons to the chimera GUI as well. Sincerely, Joshua Broyde

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Open MD Movie Trajectorie from plugin
by Pablo Solar Rodríguez 16 May '17

16 May '17

Hello all! It is possible to open the MD Movie trajectory with a custom format and a file from a plugin? I am trying to do this: *from Movie.gui import MovieDialogfrom Trajectory import EnsembleLoaderEnsembleLoader.loadEnsemble(MovieDialog, movieFile="/Users/ME/Desktop/movie.pdb")* **But I get this error *ValueError: Unknown trajectory format: 'MODEL 0'* * File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/EnsembleLoader.py", line 131, in loadEnsemble* * raise ValueError("Unknown trajectory format: '%s'" % format)* *See reply log for Python traceback.* I think it is because I need to set the format (self.curFormat in the EnsembleLoader class) but it is not possible. How can I solve this? Thank you so much -- *Pablo Solar Rodríguez* *pablosolar.r(a)gmail.com <pablosolar.r(a)gmail.com>*

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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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