May 2010 - Chimera-dev - RBVI Mailing Lists

Re: [chimera-dev] Volume covered by a group of atoms
by Eric Pettersen 17 May '10

17 May '10

Hi Miguel, For finding clashes you would use the detectClash() method in the DetectClash module. It has a pretty long doc string so I think it will be clear how to call/use it. > Also, just a question: is there a way to access bonds as part of a > tree? I would like to select the atoms implicitly from the list of > bonds to be rotated. I'm reading this as: for a given torsion, what are the atoms that will be rotated? There is a function of Molecule (m.traverseAtoms()) that returns atoms in traversal order. Furthermore, that function can ignore (i.e. cross) "break points" (active torsions) or not cross them. That is the function you would use, but you would need to restructure your code so that you only have one torsion active at a time rather than all of them. Here's a loose outline: # activate torsion br = bondRotMgr.rotationForBond(b) # which atom is opposite the "anchor" side of the torsion (anchor == unmoving side) ma = b.otherAtom(br.anchorSide) # what is the "root" for graph-traversal purposes on that side root = ma.molecule.rootForAtom(ma, False) # the "False" means don't ignore active torsions # list of atoms on that side myatomlist = ma.molecule.traverseAtoms(root) ...do the stuff that drives the torsion... # deactivate torsion br.destroy() --Eric On May 13, 2010, at 4:13 AM, Miguel Ortiz Lombardia wrote: > Hi Eric and Tom, > > Thank you! Yes, I would like to improve the script so, it would be > great if you can give me pointers about clashes and filling the VDW > space! > > Also, just a question: is there a way to access bonds as part of a > tree? I would like to select the atoms implicitly from the list of > bonds to be rotated. > > Best regards, > > > Miguel > > Le 13 mai 2010 à 02:15, Eric Pettersen a écrit : > >> Hi Miguel, >> The script still is pretty useful! I've added it to the "Python >> Scripts" page on our wiki (Scripts – Chimera). You are right that >> improvements could be made, but it's a nice starting point. If you >> ever decide to refine the script, I could probably provide pointers >> on finding clashes, whereas Tom Goddard (whom I've cc'ed) would >> probably have to be the one to assist in filling a grid based on >> the atom's VDW radius (presumably scaling a three-dimensional >> gaussian or some such). >> >> --Eric >> >> On May 12, 2010, at 1:46 PM, Miguel Ortiz Lombardia wrote: >> >>> Le 12 mai 2010 à 19:00, Eric Pettersen a écrit : >>> >>>> Hi Miguel, >>>> I'm glad you got everything sorted out. Good luck. Feel free >>>> to shoot me any further questions you might have. >>>> >>>> --Eric >>>> >>> >>> Hi Eric, >>> >>> Thanks! I managed to make it work. I'm attaching the script in >>> case you or someone may find it useful. There is only a point I >>> haven't managed to solve: as it is, the script creates a grid >>> point at the atom center positions, while I would be more >>> interested in the van der Waals volume. Nevertheless, since this >>> is a very naive approach (it would be more interesting, for >>> example, to avoid any clashes) I'm using an external set of >>> programs (mapman and mama from the "Uppsala Software Factory") to >>> extend this volume by a couple of grid points. >>> >>> I'm attaching as well a figure so you see how it looks like (after >>> expansion with mapman/mama). >>> >>> Thanks for your advice, I have learnt a lot from this exercise. >>> >>> Best regards, >>> >>> >>> -- Miguel >>> >>> Architecture et Fonction des Macromolécules Biologiques (UMR6098) >>> CNRS, Universités d'Aix-Marseille I & II >>> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France >>> Tel: +33(0) 491 82 55 93 >>> Fax: +33(0) 491 26 67 20 >>> e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr >>> Web: http://www.pangea.org/mol/spip.php?rubrique2 >>> >>> >>> <C3vol.png><torspace.py> >>> >>> >> >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. > > -- Miguel > > Architecture et Fonction des Macromolécules Biologiques (UMR6098) > CNRS, Universités d'Aix-Marseille I & II > Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France > Tel: +33(0) 491 82 55 93 > Fax: +33(0) 491 26 67 20 > e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr > Web: http://www.pangea.org/mol/spip.php?rubrique2 > > > > >

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Re: [chimera-dev] Volume covered by a group of atoms
by Thomas Goddard 13 May '10

13 May '10

Hi Miguel, For creating the volume occupancy map the molmap command creates a volume by placing a Gaussian centered at each atom. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html The Gaussian width is set by the molmap resolution parameter and is the same for all atoms. It does not use vdw radii. If you want to use vdw radii and if you want to sum over many torsion angles you might use a modified version of the molmap Python code. See the molecule_grid_data() routine in file chimera/share/MoleculeMap/molmap.py in your Chimera distribution. Tom > Hi Eric and Tom, > > Thank you! Yes, I would like to improve the script so, it would be great > if you can give me pointers about clashes and filling the VDW space! > > Also, just a question: is there a way to access bonds as part of a tree? > I would like to select the atoms implicitly from the list of bonds to be > rotated. > > Best regards, > > > Miguel > > Le 13 mai 2010 à 02:15, Eric Pettersen a écrit : > >> Hi Miguel, >> The script still is pretty useful! I've added it to the "Python >> Scripts" page on our wiki (Scripts – Chimera >> <http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts>). You are >> right that improvements could be made, but it's a nice starting point. >> If you ever decide to refine the script, I could probably provide >> pointers on finding clashes, whereas Tom Goddard (whom I've cc'ed) >> would probably have to be the one to assist in filling a grid based on >> the atom's VDW radius (presumably scaling a three-dimensional gaussian >> or some such). >> >> --Eric >> >> On May 12, 2010, at 1:46 PM, Miguel Ortiz Lombardia wrote: >> >>> Le 12 mai 2010 à 19:00, Eric Pettersen a écrit : >>> >>>> Hi Miguel, >>>> I'm glad you got everything sorted out. Good luck. Feel free to >>>> shoot me any further questions you might have. >>>> >>>> --Eric >>>> >>> >>> Hi Eric, >>> >>> Thanks! I managed to make it work. I'm attaching the script in case >>> you or someone may find it useful. There is only a point I haven't >>> managed to solve: as it is, the script creates a grid point at the >>> atom center positions, while I would be more interested in the van >>> der Waals volume. Nevertheless, since this is a very naive approach >>> (it would be more interesting, for example, to avoid any clashes) I'm >>> using an external set of programs (mapman and mama from the "Uppsala >>> Software Factory") to extend this volume by a couple of grid points. >>> >>> I'm attaching as well a figure so you see how it looks like (after >>> expansion with mapman/mama). >>> >>> Thanks for your advice, I have learnt a lot from this exercise. >>> >>> Best regards, >>> >>> >>> -- Miguel >>> >>> Architecture et Fonction des Macromolécules Biologiques (UMR6098) >>> CNRS, Universités d'Aix-Marseille I & II >>> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France >>> Web: http://www.pangea.org/mol/spip.php?rubrique2 >>> >>> >>> <C3vol.png><torspace.py> >>> >>> >> >> >> -- >> This message has been scanned for viruses and >> dangerous content by *MailScanner* <http://www.mailscanner.info/>, and is >> believed to be clean. > > -- Miguel > > Architecture et Fonction des Macromolécules Biologiques (UMR6098) > CNRS, Universités d'Aix-Marseille I & II > Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France > Web: http://www.pangea.org/mol/spip.php?rubrique2 > > > > >

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Re: [chimera-dev] [Chimera-users] Volume covered by a group of atoms
by Eric Pettersen 11 May '10

11 May '10

On May 9, 2010, at 10:14 PM, Miguel Ortiz Lombardia wrote: > Dear all, > > I would like to represent as a volume the space that would be > covered by a set of atoms that are bound by "torsionable" bonds when > one systematically modifies those torsion angles. An example would > be the side-chain of an amino acid; imagine I would like to have a > glimpse of what part of the space could be occupied by that side- > chain. As a first approximation I wouldn't care about clashes. > > I would appreciate if someone can point me to an existing way of > obtaining such representation or to an algorithm that could be > implemented within chimera (which I would be happy to share with > other interested people; if I manage to code it, that's it!) Hi Miguel, This problem has two parts: adjusting the torsions and visualizing the result. Adjusting the Torsions If you're adjusting the chi angles of an amino acid, then this is easy in Chimera. Each such residue has chi1/chi2/chi3 attributes that you can set, e.g.: for chi1 in range(0, 360, 10): r.chi1 = chi1 for chi2 in range(0, 360, 10): r.chi2 = chi2 for chi3 in range(0, 360, 10): r.chi3 = chi3 do something You'd probably actually want to write the code as a recursive routine, since otherwise it is awkward to handle the fact that some residues have different numbers of chi angles than others. You might also want to change your angle increment based on the recursion depth. If you're changing torsions that aren't the well-known amino acid chi angles, then you'll have to resort to Chimera's more generic torsion- adjustment facilities, the core of which are in the BondRotMgr module. Specifically, if 'b' is the bond you want to adjust, then: from BondRotMgr import bondRotMgr torsion = bondRotMgr.rotationForBond(b) and then torsion.increment(amount) will increment the torsion angle by 'amount' degrees (from its current position). If you want to set the dihedral to a certain value (rather than just increment from the current position) then you will have to measure the dihedral you care about with: chimera.dihedral(a1.xformCoord(), a2.xformCoord(), a3.xformCoord(), a4.xformCoord()) and then use the appropriate increment value, or use chimera.phipsi._setAngle(bond, newAngle, curAngle) [in the latter case you don't have to call rotationForBond yourself]. Visualizing the Result There are a bunch of possibilities of course. I'll touch on two: a bunch of spheres, and an actual volume. 1) As you change the torsion, you can use each atom's .coord() method to get Point instances which can be used to place helium atoms at those positions with BuildStructure.placeHelium(). You could put the heliums in the same model or in a new model (by providing a model name to your first call of placeHelium()). 2) Computing a volume is not too hard conceptually. Basically you decide on a grid spacing and then make a dictionary that maps xyz grid addresses to occupancy counts (omitting counts of zero). Then you find the lower and upper bounds for each axis, create a 3D array with corresponding dimensions, and populate that array with your counts. Then you can open that in Volume Viewer and use all the Volume Viewer facilities to look at the occupancy. There is code that does just this in Movie.gui, it's MovieDialog's computeVolume method. The line: gridData = {} initializes the occupancy-count dictionary and the loop that immediately follows that populates the dictionary. Most of the loop isn't relevant for you (getting the right coordinate set and adjusting for "hold selection steady") but the very end of the loop is, the part that maps coordinates into xyz grid addresses and adjusts the corresponding count. Then after that the loop the "generate volume" and "show volume" sections are largely relevant. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Tiled Wall Display Extension
by christopher lau 05 May '10

05 May '10

Hi, I have developed a Tiled Wall Display Extension for ViewDock in Chimera. I was in contact with Greg and Tom during the summer regarding development of the extension. According to the Chimera license agreement it states that we need to contact the developers directly and seek permission to distribute files that modify the original Chimera source code. Can we receive permission to allow our code to be publicly available via our website? P.S. I did not release the URL of our website on this list-serv because we haven't received official approval from Chimera. Best Regards, Christopher Lau UCSD, Department of Bioengineering

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Re: [chimera-dev] [Chimera-users] place fragment (again)
by Eric Pettersen 04 May '10

04 May '10

On May 4, 2010, at 7:44 AM, Elisabeth Ortega wrote: > Dear all, > > We are trying to place a fragment in an exact position. We created a > fragment with tetrahedral symmetry and we are trying to link an atom > of > other molecule at 2.00 A of the central atom of the new fragment and > making a certain angle (120 degrees for example) with one of the > substituents to get the correct orientation of the new fragment. > > Has anybody an idea that how can we do that? Hi Elisabeth, I think you'll find that you've under-defined the positioning -- I think you'll need another angle and a dihedral at least to uniquely position the fragment, but nonetheless I can provide some code to get you pointed in the right direction. First, of course, you would use placeFragment() to get your fragment to some (arbitrary) initial position. The function will return a Residue that contains your fragment's atoms. From this you can find the central atom, etc. So let's say you've found the relevant atoms for positioning and you have these variables: fca = central fragment atom fsa = fragment substituent atom (for angle positioning) oa = atom from other atom (for distance) r = fragment residue --- start code --- # make fca-oa distance 2.0 [assumes fragment in same model as other molecule] dv = fca.coord() - oa.coord() dv.length = 2.0 - dv.length for a in r.atoms: a.setCoord(a.coord() + dv) # make fsa-fca-oa angle 120 from chimera import cross, angle, Point, Xform fscrd, fccrd, ocrd = [a.coord() for a in (fsa, fca, oa)] axis = cross(fscrd-fccrd, fccrd-ocrd) # axis the rotation will be around delta = 120.0 - angle(fscrd, fccrd, ocrd) v = fccrd - Point(0.0, 0.0, 0.0) # rotation is about origin, so move center atom there trans1 = Xform.translation(v) # translation to origin v.negate() trans2 = Xform.translation(v) # translation back from origin trans1.multiply(Xform.rotation(axis, delta)) trans1.multiply(trans2) for a in r.atoms: a.setCoord(trans1.apply(a.coord())) --- end code --- If your initial positioning of the fragment places the center atom in the proper direction from the other molecule atom you may be able to get away with only one angle (may still need a dihedral though). I am working on a function for bonding molecules together that would have been helpful here but it isn't done yet (the partially-completed function is bind() which you can look at in BuildStructure/ __init__.py). Also, I cc'ed chimera-dev on this and redirected replies there since this is pretty programming intensive. Good luck and don't hesitate to ask more questions. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Chimera-dev May 2010