Sorry to take so long to get back to you.

I think the problem is that MMTKinter creates MMTKChimeraModel instances which derive from MMTK's ChemicalObjects.Molecule. Protein, on the other hand, derives from ChemicalObjects.Complex. So there is no compatible Protein object that you can pass to RigidMotionSubspace.

Looking at RigidMotionSubspace.__init__, it appears that it is expecting a list of atom-containing objects as the second argument. So instead of protein.residues(), I think you should be able to pass in a list of MMTKChimeraGroup instances. That's pretty easy to construct from an MMTKinter instance:

groups = [] for m in MMTKinter_instance.molecules: groups.extend(m.groups)

The only trick is that protein.residues() only returns residues from peptide chains. I'm not sure whether that's important for normal mode calculation or was just used for convenience in the example. If it's important to filter out non-amino acids, you will have to look at each group. I _think_ that a group has attribute "peptide" if and only if it is a standard amino acid.

Hope this helps.

Conrad

Victor Muñoz wrote:

Dear developpers,

I am trying to make an extension that allows normal mode calculations with MMTK into chimera. I have several problems beginning with the following.

I have first used the MMTKinter.py and added a new function called NM_ffm that calculates normal modes with a full atom force field. This works perfectly (although I am not yet able to make an animation in chimera that follows the vectors calculated...that will be a future question for you). Then I added another function (NM_mcm) that allows me to do NM calculations with the mechanical constraint (see http://dirac.cnrs-orleans.fr/MMTK/using-mmtk/mmtk-example-scripts/normal-mod...). For this I need to define a subspace that requires a universe.protein object (the functions are given at the end of the mail). Unfortunately, I can not pass the molecular object from the chimera space as a universe.protein object. We thought in putting self.universe.protein call into the _makeUniverse function in MMTKinter.py but that did not work. We tried other combinations but we now face the fact that we are blocked. May be we need another function in order to define subspaces but yet we still don't know how to pass chimera infos to MMTK.

Could you give me a hand so that I can define correctly subspaces on chimera molecules?

All the best and thank in advance for any help,

Victor

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Computational Biotechnological Chemistry @transmet

####Function for normal modes calculations in full atom ff def NM_ffm(self, nsteps, stepsize=0.02, interval=None, action=None, **kw): from chimera import replyobj timestamp("_minimize") from MMTK import Units from MMTK.ForceFields.Amber import AmberData from MMTK.Minimization import SteepestDescentMinimizer from MMTK.Trajectory import LogOutput # from JD to make NM calculations from MMTK.NormalModes import NormalModes from chimera import runCommand as run from chimera import selection as sele from chimera import Point, Vector import os, sys # JD'end import sys if not interval: actions = [] else: actions = [ LogOutput(sys.stdout, ["energy"], interval, None, interval) ] kw["step_size"] = stepsize * Units.Ang minimizer = SteepestDescentMinimizer(self.universe, actions=actions, **kw) if action is None or not interval: interval = None msg = "Initial energy: %f" % self.universe.energy() replyobj.status(msg) replyobj.info http://replyobj.info(msg) saveNormalizeName = AmberData._normalizeName AmberData._normalizeName = simpleNormalizeName remaining = nsteps while remaining > 0: timestamp(" minimize interval") if interval is None: realSteps = remaining else: realSteps = min(remaining, interval) minimizer(steps=realSteps) remaining -= realSteps if action is not None: action(self) timestamp(" finished %d steps" % realSteps) msg = "Finished %d of %d minimization steps" % ( nsteps - remaining, nsteps) replyobj.status(msg) replyobj.info http://replyobj.info(msg) replyobj.info http://replyobj.info("\n") #Calculate normal modes JD's trucho def despl(vec): run("sel #0") atoms=sele.currentAtoms() for a in atoms: a.setCoord(a.xformCoord()-10*(vec)) modes = NormalModes(self.universe) for mode in modes: print mode print mode.array L1=[] L2=[] L3=[] for mode in modes: y=6 u=len(mode.array) while y<u: L1.append(mode.array[y][0]) L2.append(mode.array[y][1]) L3.append(mode.array[y][2]) y+=1 y=0 run("sel:all") atoms=sele.currentAtoms() run("~sel") u=len(L1) a=0 o=len(atoms) while y<u: vec=Vector(float(L1[y]),float(L2[y]),float(L3[y])) atoms[a].setCoord(atoms[a].coord()-(vec)) a+=1 if a==o: a=0 raw_input() else: pass y+=1 #JD's end return modes AmberData._normalizeName = saveNormalizeName timestamp("end _minimize")

####Function for mechanical constraint def NM_mcm(self, nsteps, stepsize=0.02, interval=None, action=None, **kw): from MMTK import * from MMTK.Proteins import Protein from MMTK.ForceFields import Amber94ForceField from MMTK.NormalModes import NormalModes, SubspaceNormalModes from MMTK.Subspace import RigidMotionSubspace from MMTK.Minimization import ConjugateGradientMinimizer from MMTK.Trajectory import StandardLogOutput import numpy # Victor Modifications from chimera import replyobj timestamp("_minimize") from MMTK import Units from MMTK.ForceFields.Amber import AmberData from MMTK.Minimization import SteepestDescentMinimizer from MMTK.Trajectory import LogOutput from MMTK.NormalModes import NormalModes from chimera import runCommand as run from chimera import selection as sele from chimera import Point, Vector import os, sys #/end if not interval: actions = [] else: actions = [ LogOutput(sys.stdout, ["energy"], interval, None, interval) ] kw["step_size"] = stepsize * Units.Ang minimizer = SteepestDescentMinimizer(self.universe, actions=actions, **kw) if action is None or not interval: interval = None msg = "Initial energy: %f" % self.universe.energy() replyobj.status(msg) replyobj.info http://replyobj.info(msg) saveNormalizeName = AmberData._normalizeName AmberData._normalizeName = simpleNormalizeName remaining = nsteps while remaining > 0: timestamp(" minimize interval") if interval is None: realSteps = remaining else: realSteps = min(remaining, interval) minimizer(steps=realSteps) remaining -= realSteps if action is not None: action(self) timestamp(" finished %d steps" % realSteps) msg = "Finished %d of %d minimization steps" % ( nsteps - remaining, nsteps) replyobj.status(msg) replyobj.info http://replyobj.info(msg) replyobj.info http://replyobj.info("\n") # Construct system #self.universe = InfiniteUniverse(Amber94ForceField()) #self.universe.protein = self.universe # Set up the subspace: rigid-body translation and rotation for each residue self.subspace = RigidMotionSubspace(self.universe, self.universe.protein.residues())

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