- Chimera-dev - RBVI Mailing Lists

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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Re: [chimera-dev] [Chimera-users] Parsing a new 3D file format
by ros 06 Jan '15

06 Jan '15

Dear Eric! Thank you for your detailed explanation and the time to write it! It will be my first time messing with the inner workings of chimera, but I will try it. I will use your advice as my starting point and ask following questions in the chimera-dev list. Thank you again and have a good day, Rodrigo. On Mon, Jan 5, 2015 at 8:43 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Hi Rodrigo, > There is code in Chimera to read XYZ files, which are somewhat similar, so > you could base you code off of that. The XYZ-reading code is in <your > Chimera>/share/ReadXYZ/__init__.py, the readXYZ() function. On a Mac, > "<your Chimera>" is actually Chimera.app/Contents/Resources. Anyway, there > is a lot of error-checking in that code so it may be hard to see the most > relevant parts for your purposes. Here's a digest version: > > import objects/functions we will be using > from chimera import Molecule, Element, Coord, connectMolecule > > create a new empty molecule > m = Molecule() > > create a residue named UNK in that molecule, with sequence position 1, no > chain ID, and no insertion code > r = m.newResidue("UNK", " ", 1, " ") > > assign a name to the molecule for display in the model panel and so forth > m.name = "molecule_name" > > create the appropriate chemical element > element = Element(text or integer) > > make a new atom with the appropriate name and element > a = m.newAtom("atom_name", element) > > add the atom to the residue > r.addAtom(a) > > assign the atom's xyz coordinate > a.setCoord(Coord(x, y, z)) > > assign a serial number to the atom > a.serialNumber = serial > > make appropriate bonds between the atoms > connectMolecule(m) > > return a list of models (Molecules) to open > return [m] > > Geez, that already was a lot. Anyway, let's ignore the file's "critical > points" for a second so that we can finish with getting this open in > Chimera. Basically, you will package this as an extension to Chimera that > doesn't put anything in the Tools menu (or model panel) but just adds to the > file types that Chimera knows how to open with the File->Open dialog and > with the "open" command (ala "open coords.xyz"). To do so, in the same > folder as your file-reading code you will need a file named > ChimeraExtension.py that has this in it: > > ---- > 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 above code assumes that the folder containing your code is named > "ReadAimall", that the file-reading function is named "readAimall", that it > is in a file named "__init__.py" in the folder, and that the files are > ".mgpviz" files. The second list in the register call (["mpgviz"]) allows > the file type to be specified with a "mpgviz:" prefix in an "open" command > should the file not actually have a .mgpviz suffix. > You can then get Chimera to find this extension by adding the folder above > the ReadAimall folder to the list in the Locations section of Chimera's > Tools preferences (remember to click Save afterward), i.e. you add the > folder containing new tools (in this case, the folder above ReadAimall) > rather than each tool folder itself. > > Okay, back to the critical points. Depending somewhat on what you want to > learn from them, I see four possible options: 1) fake atoms; 2) markers; > 3) sphere shapes; 4) bond colors. In the below, I tend to put the critical > points in their own model, since having fake atoms mixed into a real > molecule will mess up things like hydrogen bond finding, aromatic ring > determination, etc. > > 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. > > Markers > Markers are what the Volume Tracer tool uses to mark volume data. They're > really fake atoms, but have their own little support infrastructure. A > simple example of using them is in the markeruse.py script on our Scripts > page: http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts . They would have > the same limitation in that they could only connect to the "real" atoms via > pseudobonds. Also, they would only move in tandem with the real molecule as > long as both models are "active" (which is usually the case unless you > specifically do something to make their active states different). > > Sphere Shapes > These are shapes (surfaces, really) created by the "shape" command. > Probably the easiest way to create them is something like: > > from chimera import runCommand > runCommand("shape sphere radius rad center x,y,z modelName 'critical points' > modelId 100") > > which would put them all in model #100. If you wanted them in the same > model number as the molecule, that would require fancier code. You could > look at Aniso/__init__.py or at sphere_shape() in Shape/shapecmd.py for > examples of that. > > Bond Colors > If the critical points are really associated with bonds and are trying to > convey properties of the bonds, you could vary the thickness or color of the > bonds instead. To find the Bond object b between Atoms a1 and a2, you would > do this: > > b = a1.atomsMap(a2) > > To change the bond radius, you would show it as stick and change the radius: > > b.drawMode = chimera.Bond.Stick > b.radius = radius > > To change the color, you would make sure it wasn't in "halfbond" mode (each > half colored the same as its endpoint atom) and then set the color: > > b.halfbond = False > b.color = chimera.MaterialColor(red, green, blue, opacity) > > red / green / blue / opacity all in the range 0-1. > So finally, this is really a developer-oriented subject, so I have directed > follow ups to chimera-dev instead of chimera-users. Feel free to ask > additional questions there… > > --Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Jan 5, 2015, at 1:33 PM, ros <rodrigogalindo(a)gmail.com> wrote: > > Hello! > > I would like to ask for advice and starting directions to be able to > parse a new file format in Chimera so I can use Chimera's tools and > generate images. > > The file format that I want to be able to open is generated from the > Atoms in Molecules program AIMAll ( http://aim.tkgristmill.com/ ) > > The AIMAll program of course can also do visualization and is very > good at it. I am attaching an example of how a molecule looks. The > problem is that if you want to work with big biomolecules (like DNA), > the program is not very good to cloak/hide/select atoms so you have to > click atom by atom to hide it and make some sense of the > visualization. So, I will try to make a parser (or something that you > would recommend) to open the file in Chimera and use Chimera's masking > rules to select/deselect, hide/show atoms, which is very powerful. > > The text output generated by AIMAll has an XYZ list for each atom like this: > > Nuclear Charges and Cartesian Coordinates: > ------------------------------------------------------------------------------- > Atom Charge X Y Z > ------------------------------------------------------------------------------- > C1 6.0 0.0000000000E+00 2.3265459100E+00 > 0.0000000000E+00 > C2 6.0 0.0000000000E+00 0.0000000000E+00 > 1.7647056500E+00 > C3 6.0 0.0000000000E+00 0.0000000000E+00 > -1.7647056500E+00 > H4 1.0 1.6866221200E+00 3.4814514700E+00 > 0.0000000000E+00 > H5 1.0 -1.6866221200E+00 3.4814514700E+00 > 0.0000000000E+00 > C6 6.0 -2.0148478600E+00 -1.1632729600E+00 > 0.0000000000E+00 > H7 1.0 -2.1717143500E+00 -3.2013833400E+00 > 0.0000000000E+00 > H8 1.0 -3.8583364700E+00 -2.8006813000E-01 > 0.0000000000E+00 > C9 6.0 2.0148478600E+00 -1.1632729600E+00 > 0.0000000000E+00 > H10 1.0 2.1717143500E+00 -3.2013833400E+00 > 0.0000000000E+00 > H11 1.0 3.8583364700E+00 -2.8006813000E-01 > 0.0000000000E+00 > H12 1.0 0.0000000000E+00 0.0000000000E+00 > 3.8040484300E+00 > H13 1.0 0.0000000000E+00 0.0000000000E+00 > -3.8040484300E+00 > > > That is easy, I think. But as you can see from the attached image, I > want to be able to visualize the green spheres (which are called > critical points and represents special properties of the electron > density, extracted from quantum mechanical calculations). Those > points are represented in the output file as: > > CP# 16 Coords = 5.97894312844235E-20 1.21974356425640E+00 > -9.60854463947958E-01 > Type = (3,-1) BCP C1 C3 > Rho = 2.4067790431E-01 > GradRho = 3.5016504866E-18 -2.7948129921E-14 1.7716730860E-14 > HessRho_EigVals = -4.4278076226E-01 -4.3836581782E-01 > 3.5682199801E-01 > HessRho_EigVec1 = 1.0000000000E+00 0.0000000000E+00 > 0.0000000000E+00 > HessRho_EigVec2 = 0.0000000000E+00 -6.1321358320E-01 > 7.8991714842E-01 > HessRho_EigVec3 = 0.0000000000E+00 7.8991714842E-01 > 6.1321358320E-01 > DelSqRho = -5.2432458207E-01 > Bond Ellipticity = 1.0071370222E-02 > V = -2.5219393995E-01 > G = 6.0556397216E-02 > CP# 18 Coords = 1.05289204670721E+00 3.04112062239339E+00 > 1.96757752864282E-18 > Type = (3,-1) BCP H4 C1 > Rho = 2.9524693796E-01 > GradRho = 1.0061396161E-16 -1.6479873022E-16 1.6660693347E-18 > HessRho_EigVals = -7.9444808957E-01 -7.8708168641E-01 > 4.1039750300E-01 > HessRho_EigVec1 = -5.7017191910E-01 8.2152539989E-01 > 0.0000000000E+00 > HessRho_EigVec2 = 0.0000000000E+00 0.0000000000E+00 > 1.0000000000E+00 > HessRho_EigVec3 = 8.2152539989E-01 5.7017191910E-01 > 0.0000000000E+00 > DelSqRho = -1.1711322730E+00 > Bond Ellipticity = 9.3591342377E-03 > V = -3.7782718105E-01 > G = 4.2522056404E-02 > > etc etc etc > > First line indicates the critical point number followed by the XYZ > coordinate of the point, and the second line shows which atoms are > involved between that critical point. The rest is the electronic > properties of the critical point (nothing to visualize there) > > So, I am guessing that the critical points can be represented as dummy > atoms in Chimera following the XYZ coordinates? > > The idea is that first the molecule coordinates are parsed and the > molecule is displayed and then display the critical points of each > atom. If possible, show lines joining atoms that have a critical > point between them... > > I know it is a difficult task, but maybe you can provide some starting > directions? Anything will help because right now is double clicking > 1000+ atoms! > > Thank you so much and have a good day, > > Rodrigo.

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Direct standard output to Reply Log
by user 02 Dec '14

02 Dec '14

Hi, I am new to write Chimera code. Right now I am trying to run another program as a subprocess within Chimera. While I was trying to redirect the standard output from the subprocess to “Reply Log”, the results could be shown only after the subprocess finished but not simultaneously. I was wandering how should I redirect the output to “Reply Log” while the subprocess program is running. Right now I have something like this: def show(sub): for line in sub.stdout: replyobj.info(line) subproc = SM.Popen(cmd, stdin=None, stdout = SM.PIPE, stderr=SM.PIPE) subprog = SM.monitor(‘prog’, subproc, title=‘run’, task=task, afterCB=show(subproc)) If I run this block within the IDLE, then the result printed while it is running (seems still a bit delayed). Where should I change? Thank you in advance. Zhe

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Re: [chimera-dev] Getting distance values from runCommand
by Tom Goddard 18 Nov '14

18 Nov '14

Hi Alex, The Chimera 1 code should have a routine for finding the minimum distance between atoms, but it just isn’t written very well (I wrote that code). Chimera users who are not programming have always been our highest priority. But in Chimera 2 we are putting much more effort into the programming interfaces to encourage outside developers. We do not expect to have a release for some time (maybe a year). It will be open source. Tom On Nov 18, 2014, at 2:49 AM, Alex Voronov <alexey.voronov(a)gmail.com> wrote: > Hi Tom, > > After your explanation I understand that I'd have to implement some higher level measurement logic relying only on the distance between two atoms, and your example of handling selection and coordinates is very helpful! I looked earlier at measure/measure.py, but have not found a function that I can use out-of-the-box, now I understand why. > > It is great to hear that you are planning a new release. Will it be open source too? If you plan a beta release, I can volonteer to test some new features ;) > > Best Regards, > Alex > > On Tuesday, November 18, 2014, Tom Goddard <goddard(a)sonic.net> wrote: > Hi Alex, > > The “measure distance” code is the measure() function in > > chimera/share/Measure/measure.py > > It handles distances between atoms and also surfaces and can handle multiple distance calculations and prints the result but unfortunately does not return it as a Python value. I’ve attached some Python code to find the minimum distance between two sets of atoms. > > Unfortunately the Chimera Python programming interface is not documented. The programmer’s guide on the Chimera web side documentation page may be of some use, especially the examples, > > http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html > > and also the Chimera Python scripts on the Chimera developer web site can be of some use > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts > > Many of the simpler Chimera commands are in > > chimera/share/Midas/__init__.py > > To find others you can search all the Python under chimera/share for “addCommand(“ (for example on Linux or Mac shell command find . -type f -exec grep -nH -e "addCommand(" {} +) giving the attached file of command names and modules where the code is located. > > In our next generation Chimera we are making full reference documentation for Python programming. > > Tom >

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Re: [chimera-dev] [Chimera-users] Reading Chimera source ...?
by Tom Goddard 17 Nov '14

17 Nov '14

Hi Boris, Unfortunately Python programming in Chimera is not well documented. The “sel” variable means Selection, they are defined in chimera/share/selection/__init__.py. An example using Chimera selections is giving in the chimera-dev mailing list post http://plato.cgl.ucsf.edu/pipermail/chimera-dev/2014/001157.html with Python code http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/atomdist.py Tom On Nov 14, 2014, at 8:27 PM, Boris Steipe wrote: > Hi - > > I'm new to writing Chimera code; I've started poking around in the sample scripts and the modules but and I find it a bit slow to find my way around. For example I would like to perform some simple calculations on the coordinates of a set of selected atoms, and I see many functions that take a "sel" argument, but I can't seem to find documentation on exactly what that argument is expected to contain, or the function that would return such a selection list (is it even a list) of objects. I'm sure if I spend more time, through trial and error and dir() and grep, I'll eventually figure it out, but I wonder if there isn't a more principled approach - a document on the big picture of how the code is structured, and/or a searchable list of all functions? What's the best strategy to start reading and coding Chimera scripts? > > Thanks! > Boris > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Getting distance values from runCommand
by Alex Voronov 17 Nov '14

17 Nov '14

Hi, I'm measuring distance between two points. The measurement goes well and I get a correct value in the viewport. I would like to get the same value into a Python variable. Is it possible? I'm thinking about a code like this: d = chimera.runCommand('distance #1 #2') However, it seems to be impossible to get any value from runCommand, I always get None... Even parsing the log that appears in IDLE from commands 'distance #1 #2' or 'measure distance #1 #2' would sort-of work, but I don't know how to capture the log either... Is there a way to get values into variables from 'measure distance'? Thank you! Alex

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Chimera Python programming
by Tom Goddard 14 Nov '14

14 Nov '14

Hi Nicolas, Yes, I am the right person to ask about Python programming with Chimera. Tom Ferrin, the head of our lab doesn’t do much programming these days. The good news is that all of the Chimera capabilities are accessible from Python, and all the those Python modules have the code included in the Chimera distribution. The bad news is we don’t have good programming documentation. You can look at our Programmer’s Guide under the Documentation link on the Chimera page http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html> but there is not much there. The Examples link which gives some programming examples might be the most useful part, but it doesn’t cover working with density maps. The Python scripts page on the Chimera developer site is a good source of example Python code that manipulates density maps http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> You ask how to use Chimera from your system Python. That is difficult. The Chimera distribution includes its own Python (version 2.7) and it include about 40 third party Python modules many compiled C code built for this specific Python. If your system Python is different in any way it will fail to work with those modules (e.g. I think our Python has a special option for unicode handling compiled in). Unfortunately the reality is Python is not very portable once you are using binary compiled C modules. But the normal solution is to just run the Chimera Python. This is troublesome though when you want to combine Chimera with other Python third-party packages that are not part of Chimera. The usual solution is to just install those extra packages into the Chimera Python. To run a Python script in Chimera just open it in Chimera (e.g. File / Open, or the Chimera open command, or start it from a shell “chimera myscript.py” or “chimera —nogui myscript.py” if you don’t need the graphical user interface). Let me know if there are more specific questions I can help with, or you can ask at chimera-dev(a)cgl.ucsf.edu <mailto:chimera-dev@cgl.ucsf.edu> and that way any of the Chimera programmers could answer your questions. Tom > On Nov 14, 2014, at 5:12 AM, Nicolas LEMERCIER wrote: > > Hello Thomas, > > I have been using Chimera for several years now. I writing a workflow to automatically treat my datas in cryoelectron tomography. The code is in Python 2.7.6 and I would like to launch chimera command directly from python without using the embedded version to intregrate in my workflow. I did not find the way to do this. Iguess it should be possible. > I send an e-mail to Thomas Ferrin a few days ago but I think you could help me more efficiently as you developped the volume viewer in chimera > Could you explain me how to control chimera from system python? > > Thanks a lot > > Best regards > > Nicolas > > Nicolas LEMERCIER, PhD > > Integrative Structural Biology Center > Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) > 1 rue Laurent Fries > 67404 Illkirch FRANCE

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Re: [chimera-dev] warped dome
by Tom Goddard 24 Oct '14

24 Oct '14

I’ll take a look next week. Tom On Oct 24, 2014, at 5:23 PM, Dougherty, Matthew T <matthewd(a)bcm.edu> wrote: > Hi Tom, > > Attached are two warp files and the spec: > * File example:: > * mode > * width height > * n0_x n0_y n0_u n0_v n0_i > * n1_x n1_y n1_u n1_v n1_i > * n2_x n1_y n2_u n2_v n2_i > * n3_x n3_y n3_u n3_v n3_i > * (...) > > > * First line is the image type the mesh is support to be applied to: 2 = fisheye, 1=radial > * The next line has the mesh dimensions > * Rest of the lines are the nodes of the mesh. Each line has x y u v i > * (x,y) are the normalized screen coordinates > * (u,v) texture coordinates > * i a multiplicative intensity factor > > * x varies from -screen aspect to screen aspect > * y varies from -1 to 1 > * u and v vary from 0 to 1 > * i ranges from 0 to 1, if negative don't draw that mesh node > */ > > Below is the extracted blender code to do the parsing and part of the code to do a similar warping on their mesh. > > Take a shot at it. If it looks like it will take a lot of your time let me know and I will give it a try. > > Thanks, > > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > =========================================================================== > ________________________________________ > From: Tom Goddard [goddard(a)sonic.net] > Sent: Friday, October 24, 2014 6:41 PM > To: Dougherty, Matthew T > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] warped dome > > Hi Matt, > > It would be a lot of fun to see Chimera used in some interactive dome visualization. Using a warping other than fisheye is pretty easy in the Chimera code because it is already using a mesh with texture coordinates that define the warping. The basic trick is what file can be read in, or what equation can be used to define the warping (x,y) -> (new x, new y) where x,y is fish eye, and new x, new y is warped position on the projector image. Alternatively you could define spherical coordinates phi,theta mapping to projector x,y coordinates. I thought you told me in the past there was a file format for defining a dome warping, but I never got a specification and example file from you. If you give me this I would give it a shot to allow interactive dome display with warping. What I’m talking about is for monoscopic dome display. Currently we don’t support stereoscopic dome display (except by recording each eye view separately for say a movie), so custom warped stereo dome display is a few steps away. > > Tom > > =========================================================================== > //mesh warp functions > typedef struct { > double x, y, u, v, i; > } WarpMeshNode; > > struct { > bool usemesh; > int mode; > int n_width, n_height; //nodes width and height > int imagesize; > int bufferwidth, bufferheight; > GLuint fboId; > vector <vector <WarpMeshNode> > nodes; > } warp; > > > > bool KX_Dome::ParseWarpMesh(STR_String text) > { > /* > * //Notes about the supported data format: > * File example:: > * mode > * width height > * n0_x n0_y n0_u n0_v n0_i > * n1_x n1_y n1_u n1_v n1_i > * n2_x n1_y n2_u n2_v n2_i > * n3_x n3_y n3_u n3_v n3_i > * (...) > * First line is the image type the mesh is support to be applied to: 2 = fisheye, 1=radial > * The next line has the mesh dimensions > * Rest of the lines are the nodes of the mesh. Each line has x y u v i > * (x,y) are the normalized screen coordinates > * (u,v) texture coordinates > * i a multiplicative intensity factor > * > * x varies from -screen aspect to screen aspect > * y varies from -1 to 1 > * u and v vary from 0 to 1 > * i ranges from 0 to 1, if negative don't draw that mesh node > */ > int i; > int nodeX=0, nodeY=0; > > vector<STR_String> columns, lines; > > lines = text.Explode('\n'); > if (lines.size() < 6) { > printf("Dome Error: Warp Mesh File with insufficient data!\n"); > return false; > } > columns = lines[1].Explode(' '); > if (columns.size() == 1) > columns = lines[1].Explode('\t'); > > if (columns.size() !=2) { > printf("Dome Error: Warp Mesh File incorrect. The second line should contain: width height.\n"); > return false; > } > > warp.mode = atoi(lines[0]);// 1 = radial, 2 = fisheye > > warp.n_width = atoi(columns[0]); > warp.n_height = atoi(columns[1]); > > if ((int)lines.size() < 2 + (warp.n_width * warp.n_height)) { > printf("Dome Error: Warp Mesh File with insufficient data!\n"); > return false; > } > else { > warp.nodes = vector<vector<WarpMeshNode> > (warp.n_height, vector<WarpMeshNode>(warp.n_width)); > > for (i=2; i-2 < (warp.n_width*warp.n_height); i++) { > columns = lines[i].Explode(' '); > if (columns.size() == 1) > columns = lines[i].Explode('\t'); > > if (columns.size() == 5) { > nodeX = (i-2)%warp.n_width; > nodeY = ((i-2) - nodeX) / warp.n_width; > > warp.nodes[nodeY][nodeX].x = atof(columns[0]); > warp.nodes[nodeY][nodeX].y = atof(columns[1]); > warp.nodes[nodeY][nodeX].u = atof(columns[2]); > warp.nodes[nodeY][nodeX].v = atof(columns[3]); > warp.nodes[nodeY][nodeX].i = atof(columns[4]); > } > else { > warp.nodes.clear(); > printf("Dome Error: Warp Mesh File with wrong number of fields. You should use 5: x y u v i.\n"); > return false; > } > } > } > return true; > } > > =========================================================================== > // constructor > KX_Dome::KX_Dome ( > RAS_ICanvas* canvas, > /// rasterizer > RAS_IRasterizer* rasterizer, > /// engine > KX_KetsjiEngine* engine, > > short res, //resolution of the mesh > short mode, //mode - fisheye, truncated, warped, panoramic, ... > short angle, > float resbuf, //size adjustment of the buffer > short tilt, > struct Text* warptext > > ): > dlistSupported(false), > canvaswidth(-1), canvasheight(-1), > m_drawingmode(engine->GetDrawType()), > m_resolution(res), > m_mode(mode), > m_angle(angle), > m_resbuffer(resbuf), > m_tilt(tilt), > m_canvas(canvas), > m_rasterizer(rasterizer), > m_engine(engine) > { > warp.usemesh = false; > fboSupported = false; > > if (mode >= DOME_NUM_MODES) > m_mode = DOME_FISHEYE; > > if (warptext) // it there is a text data try to warp it > { > char *buf; > buf = txt_to_buf(warptext); > if (buf) > { > warp.usemesh = ParseWarpMesh(STR_String(buf)); > MEM_freeN(buf); > } > } > > //setting the viewport size > const int *viewport = m_canvas->GetViewPort(); > > SetViewPort(viewport); > > switch (m_mode) { > case DOME_FISHEYE: > if (m_angle <= 180) { > cubetop.resize(1); > cubebottom.resize(1); > cubeleft.resize(2); > cuberight.resize(2); > > CreateMeshDome180(); > m_numfaces = 4; > } > else if (m_angle > 180) { > cubetop.resize(2); > cubebottom.resize(2); > cubeleft.resize(2); > cubefront.resize(2); > cuberight.resize(2); > > CreateMeshDome250(); > m_numfaces = 5; > } break; > } > > m_numimages =(warp.usemesh?m_numfaces+1:m_numfaces); > > CalculateCameraOrientation(); > > CreateGLImages(); > > if (warp.usemesh) > fboSupported = CreateFBO(); > > dlistSupported = CreateDL(); > } > =========================================================================== > void KX_Dome::CreateMeshDome180(void) > { > /* > * 1)- Define the faces of half of a cube > * - each face is made out of 2 triangles > * 2) Subdivide the faces > * - more resolution == more curved lines > * 3) Spherize the cube > * - normalize the verts > * 4) Flatten onto xz plane > * - transform it onto an equidistant spherical projection techniques to transform the sphere onto a dome image > */ > int i,j; > float uv_ratio = (float)(m_buffersize-1) / m_imagesize; > > m_radangle = DEG2RADF(m_angle); //calculates the radians angle, used for flattening > > //creating faces for the env mapcube 180deg Dome > // Top Face - just a triangle > cubetop[0].verts[0][0] = -M_SQRT2 / 2.0; > cubetop[0].verts[0][1] = 0.0; > cubetop[0].verts[0][2] = 0.5; > cubetop[0].u[0] = 0.0; > cubetop[0].v[0] = uv_ratio; > > cubetop[0].verts[1][0] = 0.0; > cubetop[0].verts[1][1] = M_SQRT2 / 2.0; > cubetop[0].verts[1][2] = 0.5; > cubetop[0].u[1] = 0.0; > cubetop[0].v[1] = 0.0; > > cubetop[0].verts[2][0] = M_SQRT2 / 2.0; > cubetop[0].verts[2][1] = 0.0; > cubetop[0].verts[2][2] = 0.5; > cubetop[0].u[2] = uv_ratio; > cubetop[0].v[2] = 0.0; > > nfacestop = 1; > > /* Bottom face - just a triangle */ > cubebottom[0].verts[0][0] = -M_SQRT2 / 2.0; > cubebottom[0].verts[0][1] = 0.0; > cubebottom[0].verts[0][2] = -0.5; > cubebottom[0].u[0] = uv_ratio; > cubebottom[0].v[0] = 0.0; > > cubebottom[0].verts[1][0] = M_SQRT2 / 2.0; > cubebottom[0].verts[1][1] = 0; > cubebottom[0].verts[1][2] = -0.5; > cubebottom[0].u[1] = 0.0; > cubebottom[0].v[1] = uv_ratio; > > cubebottom[0].verts[2][0] = 0.0; > cubebottom[0].verts[2][1] = M_SQRT2 / 2.0; > cubebottom[0].verts[2][2] = -0.5; > cubebottom[0].u[2] = 0.0; > cubebottom[0].v[2] = 0.0; > > nfacesbottom = 1; > > /* Left face - two triangles */ > > cubeleft[0].verts[0][0] = -M_SQRT2 / 2.0; > cubeleft[0].verts[0][1] = 0.0; > cubeleft[0].verts[0][2] = -0.5; > cubeleft[0].u[0] = 0.0; > cubeleft[0].v[0] = 0.0; > > cubeleft[0].verts[1][0] = 0.0; > cubeleft[0].verts[1][1] = M_SQRT2 / 2.0; > cubeleft[0].verts[1][2] = -0.5; > cubeleft[0].u[1] = uv_ratio; > cubeleft[0].v[1] = 0.0; > > cubeleft[0].verts[2][0] = -M_SQRT2 / 2.0; > cubeleft[0].verts[2][1] = 0.0; > cubeleft[0].verts[2][2] = 0.5; > cubeleft[0].u[2] = 0.0; > cubeleft[0].v[2] = uv_ratio; > > //second triangle > cubeleft[1].verts[0][0] = -M_SQRT2 / 2.0; > cubeleft[1].verts[0][1] = 0.0; > cubeleft[1].verts[0][2] = 0.5; > cubeleft[1].u[0] = 0.0; > cubeleft[1].v[0] = uv_ratio; > > cubeleft[1].verts[1][0] = 0.0; > cubeleft[1].verts[1][1] = M_SQRT2 / 2.0; > cubeleft[1].verts[1][2] = -0.5; > cubeleft[1].u[1] = uv_ratio; > cubeleft[1].v[1] = 0.0; > > cubeleft[1].verts[2][0] = 0.0; > cubeleft[1].verts[2][1] = M_SQRT2 / 2.0; > cubeleft[1].verts[2][2] = 0.5; > cubeleft[1].u[2] = uv_ratio; > cubeleft[1].v[2] = uv_ratio; > > nfacesleft = 2; > > /* Right face - two triangles */ > cuberight[0].verts[0][0] = 0.0; > cuberight[0].verts[0][1] = M_SQRT2 / 2.0; > cuberight[0].verts[0][2] = -0.5; > cuberight[0].u[0] = 0.0; > cuberight[0].v[0] = 0.0; > > cuberight[0].verts[1][0] = M_SQRT2 / 2.0; > cuberight[0].verts[1][1] = 0.0; > cuberight[0].verts[1][2] = -0.5; > cuberight[0].u[1] = uv_ratio; > cuberight[0].v[1] = 0.0; > > cuberight[0].verts[2][0] = M_SQRT2 / 2.0; > cuberight[0].verts[2][1] = 0.0; > cuberight[0].verts[2][2] = 0.5; > cuberight[0].u[2] = uv_ratio; > cuberight[0].v[2] = uv_ratio; > > //second triangle > cuberight[1].verts[0][0] = 0.0; > cuberight[1].verts[0][1] = M_SQRT2 / 2.0; > cuberight[1].verts[0][2] = -0.5; > cuberight[1].u[0] = 0.0; > cuberight[1].v[0] = 0.0; > > cuberight[1].verts[1][0] = M_SQRT2 / 2.0; > cuberight[1].verts[1][1] = 0.0; > cuberight[1].verts[1][2] = 0.5; > cuberight[1].u[1] = uv_ratio; > cuberight[1].v[1] = uv_ratio; > > cuberight[1].verts[2][0] = 0.0; > cuberight[1].verts[2][1] = M_SQRT2 / 2.0; > cuberight[1].verts[2][2] = 0.5; > cuberight[1].u[2] = 0.0; > cuberight[1].v[2] = uv_ratio; > > nfacesright = 2; > > //Refine a triangular mesh by bisecting each edge forms 3 new triangles for each existing triangle on each iteration > //Could be made more efficient for drawing if the triangles were ordered in a fan. Not that important since we are using DisplayLists > > for (i=0;i<m_resolution;i++) { > cubetop.resize(4*nfacestop); > SplitFace(cubetop,&nfacestop); > cubebottom.resize(4*nfacesbottom); > SplitFace(cubebottom,&nfacesbottom); > cubeleft.resize(4*nfacesleft); > SplitFace(cubeleft,&nfacesleft); > cuberight.resize(4*nfacesright); > SplitFace(cuberight,&nfacesright); > } > > // Turn into a hemisphere > for (j=0;j<3;j++) { > for (i=0;i<nfacestop;i++) > cubetop[i].verts[j].normalize(); > for (i=0;i<nfacesbottom;i++) > cubebottom[i].verts[j].normalize(); > for (i=0;i<nfacesleft;i++) > cubeleft[i].verts[j].normalize(); > for (i=0;i<nfacesright;i++) > cuberight[i].verts[j].normalize(); > } > > //flatten onto xz plane > for (i=0;i<nfacestop;i++) > FlattenDome(cubetop[i].verts); > for (i=0;i<nfacesbottom;i++) > FlattenDome(cubebottom[i].verts); > for (i=0;i<nfacesleft;i++) > FlattenDome(cubeleft[i].verts); > for (i=0;i<nfacesright;i++) > FlattenDome(cuberight[i].verts); > > } > > =========================================================================== > void KX_Dome::CreateMeshDome250(void) > { > /* > * 1)- Define the faces of a cube without the back face > * - each face is made out of 2 triangles > * 2) Subdivide the faces > * - more resolution == more curved lines > * 3) Spherize the cube > * - normalize the verts > * 4) Flatten onto xz plane > * - transform it onto an equidistant spherical projection techniques to transform the sphere onto a dome image > */ > > int i,j; > float uv_height, uv_base; > float verts_height; > > float rad_ang = m_angle * MT_PI / 180.0; > float uv_ratio = (float)(m_buffersize-1) / m_imagesize; > > m_radangle = m_angle * M_PI/180.0;//calculates the radians angle, used for flattening > /* > * verts_height is the exactly needed height of the cube faces (not always 1.0). > * When we want some horizontal information (e.g. for horizontal 220deg domes) we don't need to create and tessellate the whole cube. > * Therefore the lateral cube faces could be small, and the tessellate mesh would be completely used. > * (if we always worked with verts_height = 1.0, we would be discarding a lot of the calculated and tessellated geometry). > * > * So I came out with this formula: > * verts_height = tan((rad_ang/2) - (MT_PI/2))*sqrt(2.0); > * > * Here we take half the sphere(rad_ang/2) and subtract a quarter of it (MT_PI/2) > * Therefore we have the length in radians of the dome/sphere over the horizon. > * Once we take the tangent of that angle, you have the verts coordinate corresponding to the verts on the side faces. > * Then we need to multiply it by sqrt(2.0) to get the coordinate of the verts on the diagonal of the original cube. > */ > verts_height = tanf((rad_ang / 2.0f) - (float)(MT_PI / 2.0)) * (float)M_SQRT2; > > uv_height = uv_ratio * ( (verts_height / 2.0f) + 0.5f); > uv_base = uv_ratio * (1.0 - ((verts_height / 2.0f) + 0.5f)); > > //creating faces for the env mapcube 180deg Dome > // Front Face - 2 triangles > cubefront[0].verts[0][0] =-1.0; > cubefront[0].verts[0][1] = 1.0; > cubefront[0].verts[0][2] =-1.0; > cubefront[0].u[0] = 0.0; > cubefront[0].v[0] = 0.0; > > cubefront[0].verts[1][0] = 1.0; > cubefront[0].verts[1][1] = 1.0; > cubefront[0].verts[1][2] = 1.0; > cubefront[0].u[1] = uv_ratio; > cubefront[0].v[1] = uv_ratio; > > cubefront[0].verts[2][0] =-1.0; > cubefront[0].verts[2][1] = 1.0; > cubefront[0].verts[2][2] = 1.0; > cubefront[0].u[2] = 0.0; > cubefront[0].v[2] = uv_ratio; > > //second triangle > cubefront[1].verts[0][0] = 1.0; > cubefront[1].verts[0][1] = 1.0; > cubefront[1].verts[0][2] = 1.0; > cubefront[1].u[0] = uv_ratio; > cubefront[1].v[0] = uv_ratio; > > cubefront[1].verts[1][0] =-1.0; > cubefront[1].verts[1][1] = 1.0; > cubefront[1].verts[1][2] =-1.0; > cubefront[1].u[1] = 0.0; > cubefront[1].v[1] = 0.0; > > cubefront[1].verts[2][0] = 1.0; > cubefront[1].verts[2][1] = 1.0; > cubefront[1].verts[2][2] =-1.0; > cubefront[1].u[2] = uv_ratio; > cubefront[1].v[2] = 0.0; > > nfacesfront = 2; > > // Left Face - 2 triangles > cubeleft[0].verts[0][0] =-1.0; > cubeleft[0].verts[0][1] = 1.0; > cubeleft[0].verts[0][2] =-1.0; > cubeleft[0].u[0] = uv_ratio; > cubeleft[0].v[0] = 0.0; > > cubeleft[0].verts[1][0] =-1.0; > cubeleft[0].verts[1][1] =-verts_height; > cubeleft[0].verts[1][2] = 1.0; > cubeleft[0].u[1] = uv_base; > cubeleft[0].v[1] = uv_ratio; > > cubeleft[0].verts[2][0] =-1.0; > cubeleft[0].verts[2][1] =-verts_height; > cubeleft[0].verts[2][2] =-1.0; > cubeleft[0].u[2] = uv_base; > cubeleft[0].v[2] = 0.0; > > //second triangle > cubeleft[1].verts[0][0] =-1.0; > cubeleft[1].verts[0][1] =-verts_height; > cubeleft[1].verts[0][2] = 1.0; > cubeleft[1].u[0] = uv_base; > cubeleft[1].v[0] = uv_ratio; > > cubeleft[1].verts[1][0] =-1.0; > cubeleft[1].verts[1][1] = 1.0; > cubeleft[1].verts[1][2] =-1.0; > cubeleft[1].u[1] = uv_ratio; > cubeleft[1].v[1] = 0.0; > > cubeleft[1].verts[2][0] =-1.0; > cubeleft[1].verts[2][1] = 1.0; > cubeleft[1].verts[2][2] = 1.0; > cubeleft[1].u[2] = uv_ratio; > cubeleft[1].v[2] = uv_ratio; > > nfacesleft = 2; > > // right Face - 2 triangles > cuberight[0].verts[0][0] = 1.0; > cuberight[0].verts[0][1] = 1.0; > cuberight[0].verts[0][2] = 1.0; > cuberight[0].u[0] = 0.0; > cuberight[0].v[0] = uv_ratio; > > cuberight[0].verts[1][0] = 1.0; > cuberight[0].verts[1][1] =-verts_height; > cuberight[0].verts[1][2] =-1.0; > cuberight[0].u[1] = uv_height; > cuberight[0].v[1] = 0.0; > > cuberight[0].verts[2][0] = 1.0; > cuberight[0].verts[2][1] =-verts_height; > cuberight[0].verts[2][2] = 1.0; > cuberight[0].u[2] = uv_height; > cuberight[0].v[2] = uv_ratio; > > //second triangle > cuberight[1].verts[0][0] = 1.0; > cuberight[1].verts[0][1] =-verts_height; > cuberight[1].verts[0][2] =-1.0; > cuberight[1].u[0] = uv_height; > cuberight[1].v[0] = 0.0; > > cuberight[1].verts[1][0] = 1.0; > cuberight[1].verts[1][1] = 1.0; > cuberight[1].verts[1][2] = 1.0; > cuberight[1].u[1] = 0.0; > cuberight[1].v[1] = uv_ratio; > > cuberight[1].verts[2][0] = 1.0; > cuberight[1].verts[2][1] = 1.0; > cuberight[1].verts[2][2] =-1.0; > cuberight[1].u[2] = 0.0; > cuberight[1].v[2] = 0.0; > > nfacesright = 2; > > // top Face - 2 triangles > cubetop[0].verts[0][0] =-1.0; > cubetop[0].verts[0][1] = 1.0; > cubetop[0].verts[0][2] = 1.0; > cubetop[0].u[0] = 0.0; > cubetop[0].v[0] = 0.0; > > cubetop[0].verts[1][0] = 1.0; > cubetop[0].verts[1][1] =-verts_height; > cubetop[0].verts[1][2] = 1.0; > cubetop[0].u[1] = uv_ratio; > cubetop[0].v[1] = uv_height; > > cubetop[0].verts[2][0] =-1.0; > cubetop[0].verts[2][1] =-verts_height; > cubetop[0].verts[2][2] = 1.0; > cubetop[0].u[2] = 0.0; > cubetop[0].v[2] = uv_height; > > //second triangle > cubetop[1].verts[0][0] = 1.0; > cubetop[1].verts[0][1] =-verts_height; > cubetop[1].verts[0][2] = 1.0; > cubetop[1].u[0] = uv_ratio; > cubetop[1].v[0] = uv_height; > > cubetop[1].verts[1][0] =-1.0; > cubetop[1].verts[1][1] = 1.0; > cubetop[1].verts[1][2] = 1.0; > cubetop[1].u[1] = 0.0; > cubetop[1].v[1] = 0.0; > > cubetop[1].verts[2][0] = 1.0; > cubetop[1].verts[2][1] = 1.0; > cubetop[1].verts[2][2] = 1.0; > cubetop[1].u[2] = uv_ratio; > cubetop[1].v[2] = 0.0; > > nfacestop = 2; > > // bottom Face - 2 triangles > cubebottom[0].verts[0][0] =-1.0; > cubebottom[0].verts[0][1] =-verts_height; > cubebottom[0].verts[0][2] =-1.0; > cubebottom[0].u[0] = 0.0; > cubebottom[0].v[0] = uv_base; > > cubebottom[0].verts[1][0] = 1.0; > cubebottom[0].verts[1][1] = 1.0; > cubebottom[0].verts[1][2] =-1.0; > cubebottom[0].u[1] = uv_ratio; > cubebottom[0].v[1] = uv_ratio; > > cubebottom[0].verts[2][0] =-1.0; > cubebottom[0].verts[2][1] = 1.0; > cubebottom[0].verts[2][2] =-1.0; > cubebottom[0].u[2] = 0.0; > cubebottom[0].v[2] = uv_ratio; > > //second triangle > cubebottom[1].verts[0][0] = 1.0; > cubebottom[1].verts[0][1] = 1.0; > cubebottom[1].verts[0][2] =-1.0; > cubebottom[1].u[0] = uv_ratio; > cubebottom[1].v[0] = uv_ratio; > > cubebottom[1].verts[1][0] =-1.0; > cubebottom[1].verts[1][1] =-verts_height; > cubebottom[1].verts[1][2] =-1.0; > cubebottom[1].u[1] = 0.0; > cubebottom[1].v[1] = uv_base; > > cubebottom[1].verts[2][0] = 1.0; > cubebottom[1].verts[2][1] =-verts_height; > cubebottom[1].verts[2][2] =-1.0; > cubebottom[1].u[2] = uv_ratio; > cubebottom[1].v[2] = uv_base; > > nfacesbottom = 2; > > //Refine a triangular mesh by bisecting each edge forms 3 new triangles for each existing triangle on each iteration > //It could be made more efficient for drawing if the triangles were ordered in a strip! > > for (i=0;i<m_resolution;i++) { > cubefront.resize(4*nfacesfront); > SplitFace(cubefront,&nfacesfront); > cubetop.resize(4*nfacestop); > SplitFace(cubetop,&nfacestop); > cubebottom.resize(4*nfacesbottom); > SplitFace(cubebottom,&nfacesbottom); > cubeleft.resize(4*nfacesleft); > SplitFace(cubeleft,&nfacesleft); > cuberight.resize(4*nfacesright); > SplitFace(cuberight,&nfacesright); > } > > // Turn into a hemisphere/sphere > for (j=0;j<3;j++) { > for (i=0;i<nfacesfront;i++) > cubefront[i].verts[j].normalize(); > for (i=0;i<nfacestop;i++) > cubetop[i].verts[j].normalize(); > for (i=0;i<nfacesbottom;i++) > cubebottom[i].verts[j].normalize(); > for (i=0;i<nfacesleft;i++) > cubeleft[i].verts[j].normalize(); > for (i=0;i<nfacesright;i++) > cuberight[i].verts[j].normalize(); > } > > //flatten onto xz plane > for (i=0;i<nfacesfront;i++) > FlattenDome(cubefront[i].verts); > for (i=0;i<nfacestop;i++) > FlattenDome(cubetop[i].verts); > for (i=0;i<nfacesbottom;i++) > FlattenDome(cubebottom[i].verts); > for (i=0;i<nfacesleft;i++) > FlattenDome(cubeleft[i].verts); > for (i=0;i<nfacesright;i++) > FlattenDome(cuberight[i].verts); > } > <goDomeWarp-6m.data><CMU-DOME.data>

1 0

warped dome
by Dougherty, Matthew T 24 Oct '14

24 Oct '14

Hi, I am revisiting the problem of warping the fisheye camera so I can use chimera interactively in the dome which will be useful for research applications. Having gone through the warp code from Blender, I am contemplating how best to make the transfer into chimera. I am thinking the best insert would be the truncated dome camera option. I got word that Sriram Subramaniam & NLM are planning to replicate my dome at NIH, and CMU put in a facility last week. Want to make chimera the primary tool for their dome viz, so I would like to eventually get this into the distribution. Any suggestions on how to do this? Will involve C code. May need some help understanding the openGL calls in chimera. Realize you are moving to chimera2, want to make this as quick and easy for everybody. thanks, Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

2 1

extension widget
by Dougherty, Matthew T 15 Sep '14

15 Sep '14

Hi, I would like to create an extension that has tabs like the camera viewing gui. I am going to look through the chimera camera code. Is there a simpler code example I could look at? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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where to find public doc on Chimera test suite
by Jan Kosinski 19 Aug '14

19 Aug '14

Hi, I would like to create some unit tests for my extension. I found example tests in Chimera trunk that use "Chimera test suite" but I would like to have a look at the documentation. Apparently the doc is present at https://www.cgl.ucsf.edu/intranet/chimera-testsuite/README.html ( found the url at http://svn.cgl.ucsf.edu/svn/chimera/trunk/test/README) but I cannot access it due to password protection. Is there any public doc for Chimera test suite? Thanks, Jan

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BioPython on Mac OS X
by Mateusz Dobrychłop 14 Aug '14

14 Aug '14

Dear Chimera Team, I'm currently trying to install BioPython using Chimera's Python copy on Mac OS X. Thanks to the Chimera Programming FAQ, I've already managed to install BioPython succesfully on Ubuntu, but on Mac OS X I get the following error: Error while importing Combine from /Applications/Chimera.app/ Contents/Resources/share: Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/extension/base.py", line 349, in _importExtension __import__(module) File "/Applications/Chimera.app/Contents/Resources/share/Combine/ChimeraExtension.py", line 32, in <module> balloon="Combine molecular models into new model", moleculesOnly=True) File "/Applications/Chimera.app/Contents/Resources/share/ModelPanel/base.py", line 40, in addButton "Button named '%s' already exists" % name KeyError: "Button named 'copy/combine...' already exists" Error while importing Ramachandran from /Applications/Chimera.app/ Contents/Resources/share: Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/extension/base.py", line 349, in _importExtension __import__(module) File "/Applications/Chimera.app/Contents/Resources/share/ Ramachandran/ChimeraExtension.py", line 29, in <module> ModelPanel.addButton("Ramachandran plot...", emo.modelPanelCB) File "/Applications/Chimera.app/Contents/Resources/share/ModelPanel/base.py", line 40, in addButton "Button named '%s' already exists" % name KeyError: "Button named 'Ramachandran plot...' already exists" running install running build running build_py running build_ext Error while processing 'setup.py install': TypeError: argument of type 'NoneType' is not iterable File "/Applications/Chimera.app/Contents/Resources/frameworks/ Python.framework/Versions/2.7/lib/python2.7/_osx_support.py", line 185, in _find_appropriate_compiler if 'llvm-gcc' in data: See reply log for Python traceback. Is there anything I can do to solve this problem? Best, Mateusz

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Re: [chimera-dev] [Chimera-users] Feature request
by Elaine Meng 11 Aug '14

11 Aug '14

Dear Xavier, I personally don’t recommend the Chimera/Povray approach… my neon/conic suggestion is better-looking, but not as easy as the feature you request. There is limited programmer time, so I can’t say it will happen, but we can put it on the list of requests. You can enable showing backbone atoms at the same time as ribbon with command “ribbackbone” — then try displaying the carbonyls. You may also need to unchain (avoid drawing long bonds between different carbonyls, e.g. command: setattr m autochain 0). However, the default ribbon path is smoothed, so in some places the backbone atoms will appear to be floating away from the ribbon. You can try reducing that problem by using a different method to calculate the ribbon path, for example, with command: ribspline cardinal smooth strand …but see the manual for other command options and parameters. The cardinal spline tries to follow CA positions, so it is still possible you won’t be able to totally eliminate spaces between ribbon and C atoms. It may be necessary to show the C atoms as balls (slightly larger than stick-ends) to obscure the gapping. The ribbackbone and ribbon path issues are discussed in more detail here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo…> I hope this helps, Elaine On Aug 11, 2014, at 1:48 AM, F.Xavier Gomis-Rüth <xgrcri(a)ibmb.csic.es> wrote: > Dear Elaine & Eric, > thanks again for your and Eric's suggestions. The issue is that the POV-Ray rendering is not as attractive as the CHIMERA rendering. > Would it be possible to kindly and humbly request that this minor feature be implemented at a certain time point in a new version > of the program :-) ? > Another issue I have currently problems with: > it would be very helpful to be able to display the main-chain carbonyls sticking out from the ribbon at the right place. I tried with the > licorize option of the ribbon trace but it was not solving the problem. This is particularly helpful when representing e.g. metal-binding sites. > Thanks again for your help and dedication to constantly improve this fantastic program. > Best wishes, > Xavier > > On 1/8/14 9:11 PM, Elaine Meng wrote: >> A few caveats of the Povray approach: >> In my tests (current daily build), it always makes cylinders with the same aspect ratio regardless of whether I am showing the lines as dotted or dashed in Chimera. Also, it is hard to tell they are cylinders unless you make the linewidth fairly large. >> >> Elaine >> >> On Aug 1, 2014, at 11:28 AM, Eric Pettersen >> <pett(a)cgl.ucsf.edu> >> wrote: >> >> >>> Hi Xavier, >>> In addition to Elaine's neon suggestion, if when you save an image you change the rendering from "Chimera" to "POV-Ray" then any dashed or dotted lines will be converted into equivalent cylinders and spheres in the POV-Ray image. I've attached an image that shows how a distance looks. >>> >>> --Eric >>> >>> > > -- > <fxgr_signanew.jpg> _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Feature request
by "F.Xavier Gomis-Rüth" 01 Aug '14

01 Aug '14

Dear CHIMERA team, I moved from SETOR to CHIMERA for preparing nice protein structure images for publication already some time ago and am totally happy. Thre is, however, one single feature that was possible in SETOR but I still miss in CHIMERA: to draw pseudobonds as dashed sticks or small spheres. Is it be really not possible to implement this nuisance? I known Elaine negatively answered a similar question some time ago within the BB but I would herewith strike a blow for it again. Best wishes and thanks for maintaining and devloping such a fantastic program, Xavier --

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how to write documentation for an extension
by Jan Kosinski 25 Jul '14

25 Jul '14

Hi, I wrote a custom extension and now I want to create a documentation page that upon clicking a Help button opens a web page similarly to some other Chimera tools. Is there any html template, style guide or any important instructions I should follow for implementing it? Thanks in advance, Jan

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warped dome
by Dougherty, Matthew T 24 Jun '14

24 Jun '14

I was able to fish out the Paul Bourke warp dome python code from blender. I should be able to get it into a form that could be put into chimera. Would like to discuss how this might be passed off into official releases. Also, the material science lab at Carnegie Mellon is replicating my 9ft lab dome, which uses spherical mirror to create the warped dome. The full fisheye is critical for getting chimera output into regular permanent planetariums doing animation. The warp dome would be critical for interactive lab research. As an aside, Marc DeGraef has also been developing and HDF5 format for their EM & Xray datasets. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Does chimera support molecules from MMTK
by Jean-Didier Maréchal 18 Jun '14

18 Jun '14

Dear all, I would like to avoid gaff assignation with the dock prep interface (basically, I need to work with some organometallic compounds) and I was wondering if chimera accepts MMTK molecules ( as can be found in lib/site-packages/MMTK/Database/Molecules). I believe this would be of the best way to expand the force field inside chimera. Cheers, JD

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Impossible to download Chimera Source Code
by Alfonso Avino 03 Jun '14

03 Jun '14

Hi, I get this error downloading the source code of the last Chimera: svn: REPORT of '/svn/chimera/!svn/vcc/default': Could not read response body: connection was closed by server (http://svn.cgl.ucsf.edu) Thanks for your help. -- Alfonso Avino Informatica IBMB-CSIC C/ Baldiri Reixac 15, 3 A17 08028, Barcelona, España Tel. (+34)934020244

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Plugin installation from a web link
by Alex 03 Jun '14

03 Jun '14

Hello Chimera developers, If I remember well, during a visit in your lab in January, Conrad Huang showed me a way to package a Python plugin that can be installed just by opening the package with Chimera. Do you have an example? I found something vaguely related here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.h… But I don't see how to include commands to copy libraries or python modules into the lib or share directories, or to make sure Chimera can remember where to find the files in the future. Many thanks for your help, Alex

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(no subject)
by maryam.khoshnejat 03 Jun '14

03 Jun '14

hello could you help me? i should model specific mutant residue of protein . i have PDB file and rotamer of mutant residue how can i find coordination of mutant residue based on backbone and CB coordination of native residue , rotamer and atom bonding distance i need a code for finding coordination of mutant residue regards

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how to remove chimera file load history?
by Dennis N Bromley 12 May '14

12 May '14

Hi all, Whenever I try and load a file into chimera, it tries to open the windows file load dialog in the last directory I loaded a file from (I guess that is what is happening, at any rate). But that directory now has around 10K pdb files in it and chimera hangs trying to enumerate them all (maybe due to windows/samba/etc). As a result, I can no longer even use chimera because it hangs every time I try and load a file. Is there a way to clear this so that I can load files again? thanks! -denny-

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read file by python script and color pdb file with script
by Sanjeev Sariya 24 Apr '14

24 Apr '14

I am having 2 coordinates in check file. I want to take/read them and paint my pdb file loaded in chimera. I have chimera in my ~/bin/ System specs: ubuntu 64 bit, 13.10, 4gb ram Below is the command I have used for script-chimera communication $ chimera64-1.8.1 --script "y.py check" -- Q6UXT6.pdb I am storing values in listu and want to use them for coloring my file loaded. rc("color blue :"+listu[0]+"-"+listu[1]) This works well, if hard coded rc ("color red :55-86") I do not get any error. The particular protein length is not colored. attached 3 files. Kindly suggest, how do I proceed. -- Regards Sariya

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Re: [chimera-dev] Help with "looping through PDB IDs" script
by Eric Pettersen 21 Apr '14

21 Apr '14

Hi Navya, This later mail of yours provides some additional details that help. So for one thing you might also want to look at the Programmer's Examples (Examples), particularly the first one ("Chimera's Object Model"). At any rate, the obvious problem with the script you have so far is that you haven't defined the 'residues' variable. Let's say you are trying to work with residues 50.A, 55.A, and 70.A. Here's a little code snippet that will get those residues into the 'residues' variable once you've opened your structure: rc("sel :50.a:55.a:70.a") from chimera.selection import currentResidues residues = currentResidues() Now, I don't know where you're storing your lists of residues. Are they in the same file as the IDs? A separate file? I don't know if you need more help with that or not. So once you have the residues, then printing the atomic surface areas and bfactors is: for r in residues: for a in r.atoms: print>>outf, a, a.areaSAS, a.bfactor Getting the CASTp information is another whole can of worms however, since Chimera stores that info in the CASTp dialog rather than with the atoms and residues. Nonetheless, once you've got the rest of your script working you could try to do that part. In would involve copying the processCastpID function from CASTp/__init__.py (in your Chimera installation's 'share' folder) and deleting the last two lines and instead return the cavity list. Each CastpCavity instance has 'mouthInfo' and 'pocketInfo' attributes which are dictionaries that have an 'atoms' key. The value for the 'atoms' key is a chimera.selection.ItemizedSelection instance. You can use the contains() method of those ItemizedSelections to see if a particular atom is in the ItemizedSelection. The pocketInfo dictionary also has 'SA volume' and 'MS volume' keys you can use to get the desired volume info. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 16, 2014, at 12:44 PM, Navya Shilpa Josyula <njosyu2(a)uic.edu> wrote: > Hi, > > I need a help in chimera scripting. I have text file with list of PDB IDs and corresponding residue list. I am trying to write a chimera command which will scan this file, open each PDB ID and select the corresponding residues listed in the file. After selecting, it should write out the values of atomic areaSAS, atomic Bfactor and which atom belong to CASTp identified pockets (with pocket volume). I know I am asking a lot here but I am new to chimera scripting and I searched the users mailing list and found the "looping" script, > > http://www.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007281.html > > but it is not working for me. Attached is the script I have till now. > > Please help me on this. > > Thank you in advance, > Navya > <test.py> import os from chimera import runCommand as rc # use 'rc' as shorthand for runCommand from chimera import replyobj # for emitting status messages # change to folder with data files os.chdir("C:/Users/Navya Shilpa/Desktop/thesis/All_Proteins/nonred") # open file of PDB IDs f = open("C:/Users/Navya Shilpa/Desktop/thesis/All_Proteins/nonred/nr-list.txt", 'r') # loop through the IDs, opening, processing, and closing each in turn for line in f: pdbID = line.strip() replyobj.status("Processing " + pdbID) # show what PDB we're working on rc("open " + pdbID) rc("surf") # surface receptor outf = open(pdbID, "w") for r in residues: print>>outf, r, r.areaSAS outf.close() rc("close all") # uncommenting the line below will cause Chimera to exit when the script is done #rc("stop now") # note that indentation is significant in Python; the fact that # the above command is exdented means that it is executed after # the loop completes, whereas the indented commands that # preceded it are executed as part of the loop.

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Fwd: [Chimera-users] Working with several proteins
by Elaine Meng 16 Apr '14

16 Apr '14

Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Working with several proteins > Date: April 16, 2014 3:16:07 PM PDT > To: Navya Shilpa Josyula <njosyu2(a)uic.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Reply-To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu>, "chimera-dev(a)cgl.ucsf.edu" <chimera-dev(a)cgl.ucsf.edu> > > Dear Navya, > This would require Python programming because not all of these tasks can be done with Chimera commands. See the Chimera programmer's guide: > <http://www.rbvi.ucsf.edu/chimera/current/docs/ProgrammersGuide/index.html> > > You did not say if your structures are from the PDB database or whether you generated them somehow (for example, from a simulation). If they are in the PDB database, it is possible they are also in the CASTp database, in which case you could open each with a Chimera command something like: > > open castp:2gbp > > CASTp finds a lot of pockets for one structure, and each pocket would have a separate volume value and list of residues. > <http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/castp.html#pocketl…> > > If the structures are not in the CASTp database, you would have to upload them individually for a calculation at the CASTp web server, and this cannot be done from inside Chimera. After you got the CASTp results by email, you could open them in Chimera. Even if the structure is already in CASTp, it might just be better to get the CASTp results files directly from their website and not use Chimera. If showing CASTp results in Chimera, you would then have to use python to write out the desired information to a file anyway. > > CASTp search at their website: > <http://sts-fw.bioengr.uic.edu/castp/index.php> > CASTp upload for new structure calculation: > <http://sts-fw.bioengr.uic.edu/castp/calculation.php> > > For bfactor, again you can just get the values directly from the text of the PDB files, no need to go through Chimera. Just like for CASTp, it may be simpler to write your own scripts to get the values from these files. > > Back to Chimera: To calculate areaSAS you have to show the surface (for example, command: surface). Attribute values can be written out to a file using the File menu of the Render by Attribute tool (in menu under Tools… Depiction), > <http://www.rbvi.ucsf.edu/chimera/current/docs/ContributedSoftware/render/re…> > ...but again to process many structures instead of using the GUI, you would have to use python scripting because there isn't a command. There is a similar script attached to this previous post (get the writeAttr.py attachment using the URL near the bottom, unfortunately it will be named attachment.bin but it is really a text file containing the script): > <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003531.html> > > Best, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Apr 15, 2014, at 7:29 PM, Navya Shilpa Josyula <njosyu2(a)uic.edu> wrote: > >> Hi, >> >> I am working on a set of 400 proteins and for all these proteins I have specific list of amino acid residues. I wanted to know if there is any available script or a command to get the following >> • atomic areaSAS >> • atomic B-factor values >> • CASTp identified pocket residues and >> • CASTp identified pocket volumes >> for all the residues of these 400 proteins to be written in a single file. Kindly help me at your earliest. >> >> Thank you in advance for your help. >> Regards, >> Navya > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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