- Chimera-dev - RBVI Mailing Lists

Get value of 'measure distance' command
by Hoai Thu NGUYEN 24 Mar '15

24 Mar '15

Hi, I need to calculate the minimum distance between 2 residues but It seems that I can't find the correct way to use the 'measure distance' command in python script. I tried: import Measure temp = Measure.measure_command('distance', 'distance :628.a :20.b') but it gave me the error: "No target atoms or surface" Can you please precise the correct syntax of this command? Thank you! Thu

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Re: [chimera-dev] volume display in my gui
by Tom Goddard 06 Mar '15

06 Mar '15

You can get a PIL (Python Image Library) image of the Chimera graphics window with import chimera image = chimera.viewer.pilImages()[0] You can supply optional width and height arguments in pixels otherwise the image size will match the graphics window size. An example using pilImages is the Chimera image saving code in the saveImage() routine share/chimera/printer.py Chimera moves the models and the Chimera always points along the -z axis. So to change the viewing angle you would rotate the models, for example: import chimera axis = chimera.Vector(1,0,0) angle = 30 r = chimera.Xform.rotation(axis, angle) chimera.openModels.setXform(r) The openModels code is in C++ and you can see the C++ header file for the OpenModels class which has equivalent Python methods here http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/_chimera/OpenMode… <http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/_chimera/OpenMode…> This stuff is all pretty hard to figure out. Unfortunately we do not have adequate programming documentation for Chimera. We are remedying this in our next generation Chimera 2 which is not yet released. Tom > On Mar 6, 2015, at 4:15 PM, hy liao wrote: > > Hi Tom: > > Thanks for the great details! A snapshot on the main Chimera window is good enough! I actually do not need interaction but just the correct display. In other words, given a volume data (density map) and a viewing angle (azimuthal and elevation angles), how do I get the corresponding 2D snapshot (a surface rendering) of the volume? Once I have this snapshot, I guess I can place it in my window by assigning it to my canvas object. > > Thanks again! > Stu > > > On Friday, March 6, 2015 6:27 PM, Tom Goddard wrote: > > > Hi Stu, > > The gui.py file I mentioned is shown with Chimera menu entry Tools / Volume Data / Values at Atom Positions. It does not embed volume images though. > > Chimera is not designed to handle multiple interactive 3-d renderings, so you cannot in any simple way embed the Chimera graphics in your own Tk window. The graphics is shown as a Togl widget (Tk OpenGL widget) that is drawn by Chimera C++ code. Why do you want do that? Why not just manipulate the view in the main Chimera graphics window? The only example of embedding 3d data display in another window is the Chimera side view (menu Favorites / Side View) which has Python code in > > chimera/share/chimera/viewing.py > > But it uses C++ code to handle the drawing. > > If your aim is to make a custom app with Chimera graphics and your own set of controls you could modify the Chimera main window with Python code in > > chimera/share/chimera/tkgui.py > > All of this is quite hard. Another route is to take a snapshot image from the main Chimera window to put it in your own window, but then you could not rotate it. > > Tom > > > >> On Mar 6, 2015, at 3:11 PM, hy liao wrote: >> >> Hi Tom: >> >> Thank you for your prompt reply. Sorry for my ignorance, but how can I run the script chimera/share/AtomDensity/gui.py and see the gui it actually produces? >> >> Alternatively, this might be another way of formulating my question: to display a picture in a gui using tkinter, one can create a frame object, then a canvas object, then set the position of the canvas, then create a photoimage object, and then indicate that the picture goes in the canvas. Now, instead of a picture, how do I do the same for a chimera type of volume display? Do I have to also go through creating a frame, a canvas, and then indicate that the volume must reside in the just created canvas. It would be great if you know of any example out there. I have been relying on examples so far. >> >> Thanks again! >> >> Stu >> >> >> On Friday, March 6, 2015 4:26 PM, Tom Goddard wrote: >> >> >> >> Hi Stu, >> >> To find out about Python functions that control volume display in Chimera that you could use from your Tkinter gui take a look at the Chimera Python scripts web page: >> >> http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> >> >> for example the readvol.py example shows how to access volume data values. In Python you can make use of commands that would be normally typed at the Chimera command-line in the following way >> >> from chimera import runCommand >> runCommand(‘volume #0 level 12.5 color pink’) >> >> or you could directly call functions in Python that change volume display, for example, >> >> import VolumeViewer as vv >> v0 = vv.volume_list()[0] >> v0.set_parameters(surface_levels = [12.5], surface_colors = [(1,.5,.5,1)]) >> >> To find those functions you can look at the Chimera Volume class Python code in your Chimera distribution >> >> chimera/share/VolumeViewer/volume.py >> >> (on Mac in Chimera.app/Contents/Resources/share/VolumeViewer/volume.py), and you can look at how the Chimera “volume” command does it >> >> chimera/share/VolumeViewer/volumecommand.py >> >> For making a Tk GUI look at a simple example in the Chimera distribution, for example, the values at atom positions dialog >> >> chimera/share/AtomDensity/gui.py >> >> >> Tom >> >> >> >>> On Mar 6, 2015, at 12:16 PM, hy liao wrote: >>> >>> Hi, I am developing a GUI with Tkinter, using anaconda's python 2.7.9. I like how chimera displays volumes (density maps), so I would like to a chimera-volume-display in my GUI. I am now disregarding anaconda and developing all within chimera's IDLE. However, I do not know which chimera commands I could use for my purpose; could you please point to some choices? >>> >>> I am new with developing chimera extension and tkinter, and I mostly look for code examples. I had a look at http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/ <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/>, "Working with the Chimera Extension Manager," but I do not know which commands I could use to have chimera display a volume in a grid of my GUI. >>> >>> Thanks! >>> Stu >>> _______________________________________________ >>> 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev> >> >> >> > > > >

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Re: [chimera-dev] volume display in my gui
by Tom Goddard 06 Mar '15

06 Mar '15

Hi Stu, The gui.py file I mentioned is shown with Chimera menu entry Tools / Volume Data / Values at Atom Positions. It does not embed volume images though. Chimera is not designed to handle multiple interactive 3-d renderings, so you cannot in any simple way embed the Chimera graphics in your own Tk window. The graphics is shown as a Togl widget (Tk OpenGL widget) that is drawn by Chimera C++ code. Why do you want do that? Why not just manipulate the view in the main Chimera graphics window? The only example of embedding 3d data display in another window is the Chimera side view (menu Favorites / Side View) which has Python code in chimera/share/chimera/viewing.py But it uses C++ code to handle the drawing. If your aim is to make a custom app with Chimera graphics and your own set of controls you could modify the Chimera main window with Python code in chimera/share/chimera/tkgui.py All of this is quite hard. Another route is to take a snapshot image from the main Chimera window to put it in your own window, but then you could not rotate it. Tom > On Mar 6, 2015, at 3:11 PM, hy liao wrote: > > Hi Tom: > > Thank you for your prompt reply. Sorry for my ignorance, but how can I run the script chimera/share/AtomDensity/gui.py and see the gui it actually produces? > > Alternatively, this might be another way of formulating my question: to display a picture in a gui using tkinter, one can create a frame object, then a canvas object, then set the position of the canvas, then create a photoimage object, and then indicate that the picture goes in the canvas. Now, instead of a picture, how do I do the same for a chimera type of volume display? Do I have to also go through creating a frame, a canvas, and then indicate that the volume must reside in the just created canvas. It would be great if you know of any example out there. I have been relying on examples so far. > > Thanks again! > > Stu > > > On Friday, March 6, 2015 4:26 PM, Tom Goddard wrote: > > > Hi Stu, > > To find out about Python functions that control volume display in Chimera that you could use from your Tkinter gui take a look at the Chimera Python scripts web page: > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> > > for example the readvol.py example shows how to access volume data values. In Python you can make use of commands that would be normally typed at the Chimera command-line in the following way > > from chimera import runCommand > runCommand(‘volume #0 level 12.5 color pink’) > > or you could directly call functions in Python that change volume display, for example, > > import VolumeViewer as vv > v0 = vv.volume_list()[0] > v0.set_parameters(surface_levels = [12.5], surface_colors = [(1,.5,.5,1)]) > > To find those functions you can look at the Chimera Volume class Python code in your Chimera distribution > > chimera/share/VolumeViewer/volume.py > > (on Mac in Chimera.app/Contents/Resources/share/VolumeViewer/volume.py), and you can look at how the Chimera “volume” command does it > > chimera/share/VolumeViewer/volumecommand.py > > For making a Tk GUI look at a simple example in the Chimera distribution, for example, the values at atom positions dialog > > chimera/share/AtomDensity/gui.py > > > Tom > > > >> On Mar 6, 2015, at 12:16 PM, hy liao wrote: >> >> Hi, I am developing a GUI with Tkinter, using anaconda's python 2.7.9. I like how chimera displays volumes (density maps), so I would like to a chimera-volume-display in my GUI. I am now disregarding anaconda and developing all within chimera's IDLE. However, I do not know which chimera commands I could use for my purpose; could you please point to some choices? >> >> I am new with developing chimera extension and tkinter, and I mostly look for code examples. I had a look at http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/ <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/>, "Working with the Chimera Extension Manager," but I do not know which commands I could use to have chimera display a volume in a grid of my GUI. >> >> Thanks! >> Stu >> _______________________________________________ >> 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 > > >

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volume display in my gui
by hy liao 06 Mar '15

06 Mar '15

Hi, I am developing a GUI with Tkinter, using anaconda's python 2.7.9. I like how chimera displays volumes (density maps), so I would like to a chimera-volume-display in my GUI. I am now disregarding anaconda and developing all within chimera's IDLE. However, I do not know which chimera commands I could use for my purpose; could you please point to some choices? I am new with developing chimera extension and tkinter, and I mostly look for code examples. I had a look at http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/, "Working with the Chimera Extension Manager," but I do not know which commands I could use to have chimera display a volume in a grid of my GUI. Thanks!Stu

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UnitCell.molecule_center(): Attribute does not exist
by Alejandro Virrueta 11 Feb '15

11 Feb '15

Hello all, I'm trying to execute the script to fill out the crystal unit cell found here: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q13 However, I get the error that UnitCell does not have the 'molecule_center' attribute (code line ~12). I checked with dir(), and yeah, it's not there: ['ModelessDialog', 'Unit_Cell_Dialog', '__builtins__', '__doc__', '__file__', '__name__', '__package__', '__path__', 'chimera', 'dialogs', 'find_model_by_name', 'outline_box', 'place_molecule_copies', 'remove_extra_copies', 'show_unit_cell_dialog'] Where did the attribute go? Is there some other module I could use? Could someone explain (or direct me to some webpage that explains) the process of expanding the ASU and I can write my own script. Any help is greatly appreciated! Thanks! Alex

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Re: [chimera-dev] [Chimera-users] Find subsequence programatically
by Thomas Hrabe 22 Jan '15

22 Jan '15

Hi Eric , I have an algorithm that returns some subsequences of a structure and i want to color the corresponding structure segment automatically. Thanks Thomas from the road Am 22.01.2015 um 16:37 schrieb Eric Pettersen <pett(a)cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>>: On Jan 22, 2015, at 4:21 PM, Thomas Hrabe <thrabe(a)sanfordburnham.org<mailto:thrabe@sanfordburnham.org>> wrote: Hi Chimera Team, How can I automate the Sequence View -> Edit -> Find Subsequence Tool programmatically with the Chimera shell or better within python? I don't know what your context is here exactly, but if you have a Sequence object you can use its regexMatch or prositeMatch methods to find subsequences. They return lists of (start, end) tuples. If you need more info, provide some more detail about your usage context and I can help better. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [chimera-dev] [Chimera-users] Ringer/Chimera/IDLE
by Greg Couch 21 Jan '15

21 Jan '15

(This question is a developer question and not a user question, but since it was asked on chimera-users, the response is there as well. Followups should go to chimera-dev(a)cgl.ucsf.edu.) The "ValueError: missing default material" means that the script was not run by chimera, which we don't support. We also don't support using an IDLE other than the one you get by running chimera and using Tools / General Tools / IDLE. We only support using chimera's Python code in scripts that are invoked by chimera. That is why the ringer shell script is: "$CHIMERA_HOME"/bin/chimera --nogui --silent --script "$RINGER"/ringer/main.py -- "$@" In the same vein, if you replaced "$RINGER"/ringer/main.py with the following 2 line script: import chimera print chimera.MaterialColor(1, 1, 1) Everything works. Long ago, we considered what it would take to get chimera's Python code working in a different application. In that scenario, you would need to: 1. Set the CHIMERA environment variable to the root of the Chimera installation 2. Set other environment variables that are set in CHIMERA/bin/chimera for your platform 3. Add $CHIMERA/share to your Python's sys.path 4. import chimeraInit; chimeraInit.init([], nogui=True, eventloop=False, exitonquit=False) But since chimera uses a modified Python, that is insufficient. For example, chimera changes Python's default string to unicode conversion to use utf-8 instead of ASCII. We've also backported some of Python 3's unicode support that chimera depends on. If you are lucky, your use of chimera's Python code will not be affected by those changes. HTH, Greg P.S. Your immediate problem might be fixed by calling chimera.initializeColors(), but that is a hack that is not guaranteed to keep working. On 01/16/2015 12:20 PM, Alejandro Virrueta wrote: > Hello, > > I am modifying some Ringer files for my own needs, but I am running > into a weird issue. If I run Ringer via typical means: > > $RINGER/ringer/ringer -i ringer_in_${pdb_ID}.txt -o > ringer_out_${pdb_ID}.txt > > it works fine. However, when I step through it in what I think is my > version of IDLE ("$CHIMERA_HOME/bin/chimera --nogui --nostatus > --script `which idle2.7` > /usr/bin/idle2.7", with `which idle2.7` returning "/usr/bin/idle2.7"), > I run into this error: > > Traceback (most recent call last): > File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 233, in > <module> > main() > File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 161, in main > move_set, pdb = structureFile(parameters, path) > File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 65, in > structureFile > pdb = chimera.openModels.open(parameters.pdbfileName) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", > line 1817, in open > checkForChanges=False, noprefs=noprefs) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", > line 1644, in add > makePseudoBondsToMetals(realMolecules) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", > line 1961, in makePseudoBondsToMetals > cmPBG = mol.metalComplexGroup(issueHint=True) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", > line 119, in _getMetalPbg > am.color = preferences.get(MOLECULE_DEFAULT, MOL_COMPLEX_COLOR) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", > line 608, in get > forPrefSave=forPrefSave) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", > line 179, in get > return self._options[name].get(forPrefSave=forPrefSave) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", > line 80, in get > return self.prefToVal(self.value) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/tkoptions.py", > line 1229, in _prefToColor > return getColorByName(pref) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/colorTable.py", > line 87, in getColorByName > color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0) > ValueError: missing default material > > Any suggestions? > > Cheers, > Alex > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Alternate conformations in residues
by Alejandro Virrueta 21 Jan '15

21 Jan '15

Hello all, Is there a way to get the all the information for an alternate conformation from a residue object? I have res.altLocs resulting in set([a,b]), but how can I get chi1-4 for conformation b for example? Thanks! Alex

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Re: [chimera-dev] AIMAll extension update 1
by Eric Pettersen 09 Jan '15

09 Jan '15

Hi Rodrigo, I covered this in my initial, novella-length response: Fake Atoms In this scenario, you would create a second Molecule as you read the file and add the critical points as atoms to that. You include the additional Molecule in the list of models you return ("return [m, m2]"). You would not call connectMolecule() on the second Molecule, but might add pseudobonds from the critical points to the appropriate atoms (you can't add regular bonds between models). The second molecule will have the same ID and sub-ID # as the first one, and will move in tandem with it. It will show up in the model panel. There really is no such thing as a fake Molecule per se. You just use the Molecule class in exactly the same way as for a normal molecule. It's just that what you're trying to depict isn't an actual chemical entity. One thing I probably should have added, is that for the "fake" Molecule that will hold the critical points you should set the attribute "isRealMolecule" to False, like so: m2.isRealMolecule = False This will prevent the critical-points Molecule from being listed in various interfaces that really only want to list actual chemical entities (e.g. the Minimize interface). --Eric On Jan 7, 2015, at 11:59 AM, ros <rodrigogalindo(a)gmail.com> wrote: > That did the trick, the bonds are now correctly being displayed! Thank you! > > Could you please provide an example for drawing or placing a fake > atom? I do not seem to find the correct command in the Programmers > manual. > > Thank you again, > > Rodrigo. > > On Wed, Jan 7, 2015 at 12:50 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: >> On Jan 7, 2015, at 11:45 AM, Eric Pettersen <pett(a)cgl.ucsf.EDU> wrote: >> >> So I guess the question is: what is up with the AIMAll coordinates? >> >> >> I see. AIMAll units are bohrs. So you need to multiply by 0.52918. >> >> --Eric >>

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AIMAll extension update 1
by ros 07 Jan '15

07 Jan '15

Hello! Thanks to the recommendations from Dr. Eric, I was able to code an extension for Chimera that reads mgpviz files generated from the AIMAll program. Right now, only the XYZ and atom type information is parsed and the molecule is displayed. Although, I do not know why it shows no connectivity. I am including a screenshot that shows how Chimera displays the molecule (left) and how does it look in AIMAll (right). I do use the command connectMolecule() but I do not know if I have to include some other argument for that function. I based the code from the ReadXYZ extension. My code (I am no coder, so it might be super ugly (: ) ChimeraExtension.py ------------------------------------------------------------------------------ def aimallOpen(fileName): from ReadAimall import readAimall return readAimall(fileName) import chimera chimera.fileInfo.register("AIMAll mgpviz", aimallOpen, [".mgpviz"], ["mpgviz"], category=chimera.FileInfo.STRUCTURE) the readAimall function: ----------------------------------------------------------------------------------- ## Extension to read a file output from AIMALL ## based on the code ReadXYZ def readAimall(fileName): from OpenSave import osOpen from chimera import UserError, Molecule, Element, openModels, replyobj from chimera import Coord, connectMolecule anums = {} ## Open the file getatoms = osOpen(fileName) ## Search for the string: ## 'Number of NACPs' ## which gives us the number of atoms ## and store it in numAtoms for data in getatoms: data = data.strip() if data.startswith("Number of NACPs"): a,b,c,d,e = data.split() numAtoms = int(e) getatoms.close() f = osOpen(fileName) readAtoms = 1 state = "init" ## Skip the 26 header lines from the mpgviz file f = f.readlines()[26:] ## cycle through the file until it reaches ## the number of Atoms for line in f: if readAtoms == numAtoms: break line = line.strip() if state == "init": state = "post" m = Molecule() r = m.newResidue("UNK", " ", 1, " ") state = "atoms" serial = 1 if not line: continue elem, charge, x, y, z = line.split() x, y, z = [float(c) for c in [x,y,z]] ## Remove the number from the atomic symbol elem = filter(lambda x: x.isalpha(), elem) element = Element(elem) anum = anums.get(element.name, 0) + 1 anums[element.name] = anum a = m.newAtom("%s%d" % (element.name, anum), element) r.addAtom(a) a.setCoord(Coord(x, y, z)) a.serialNumber = serial serial += 1 readAtoms += 1 #f.close() connectMolecule(m) return [m] --------------------------------------------------------------------------------------------------- I couple of questions: 1- Do I have to include something in the connectMolecule function to enable the display of bonds? 2- At the end, what would be your recommendation, based on your experience, to display the critical points and bonds between atoms? We were considering: Fake atoms, Markers, Sphere shapes and bond colors. What we are trying to achieve is to be able to turn off certain critical points and leave some on to show how molecules interact. Thank you for your help and let me know what you think!! Rodrigo.

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