January 2015 - Chimera-dev - RBVI Mailing Lists

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

2 1

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

1 0

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

1 0

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 >>

2 4

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.

2 2

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.

2 2

Chimera-dev January 2015