Re: [ccp4bb] Rcrane error, update
I figured it out. Rcrane works fine if I remove the hydrogens before going into Coot. Ursula On Wed, Jun 21, 2017 at 12:04 PM, Ursula Schulze-Gahmen < uschulze-gah...@lbl.gov> wrote: > I am trying to use Rcrane in stand-alone coot version 0.8.8. The Rcrane > window opens and I am able to calculate new conformations for my nucleic > acid. But when I am trying to accept a conformation, I am getting an error > message: > > Traceback (most recent call last): > File "/home/programs/x86_64-linux/ccp4/7.0/ccp4-7.0/lib/python2. > 7/site-packages/coot/rcrane/reviewSuitesGui.py", line 1041, in __accept > self.__pseudoMolecule.finalMoleculeCleanup(fixSegids = > bool(self.__pseudoMolecule.hasSavedCoordinates())) > File "/home/programs/x86_64-linux/ccp4/7.0/ccp4-7.0/lib/python2. > 7/site-packages/coot/rcrane/pseudoMolecule.py", line 1735, in > finalMoleculeCleanup > curRes[3].sort(key = lambda x: self.__reorderAtomsOrder[str( > curRes[2])][x[0][0].strip()]) > File "/home/programs/x86_64-linux/ccp4/7.0/ccp4-7.0/lib/python2. > 7/site-packages/coot/rcrane/pseudoMolecule.py", line 1735, in > curRes[3].sort(key = lambda x: self.__reorderAtomsOrder[str( > curRes[2])][x[0][0].strip()]) > KeyError: "H5'" > > Any suggestions what might be wrong, and how I can fix this? > > Thanks > > -- > Ursula Schulze-Gahmen, Ph.D. > Project Scientist > UC Berkeley, QB3 > 360 Stanley Hall #3220 > Berkeley, CA 94720-3220 > (510) 643 9491 <(510)%20643-9491> > -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491
Re: [ccp4bb] Rcrane error, update
I'm thinking a nomenclature issue. H5 ? Should be H5' no? Have you run your structure through a pdb remediator? http://kinemage.biochem.duke.edu/software/remediator.php is my favorite. You will want to play around with the flags to get the right output. I think rCrane likes old style nomenclature (asterisks instead of apostrophes). F On Jun 21, 2017, at 3:04 PM, Ursula Schulze-Gahmen wrote: > I am trying to use Rcrane in stand-alone coot version 0.8.8. The Rcrane > window opens and I am able to calculate new conformations for my nucleic > acid. But when I am trying to accept a conformation, I am getting an error > message: > > Traceback (most recent call last): > File > "/home/programs/x86_64-linux/ccp4/7.0/ccp4-7.0/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py", > line 1041, in __accept > self.__pseudoMolecule.finalMoleculeCleanup(fixSegids = > bool(self.__pseudoMolecule.hasSavedCoordinates())) > File > "/home/programs/x86_64-linux/ccp4/7.0/ccp4-7.0/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py", > line 1735, in finalMoleculeCleanup > curRes[3].sort(key = lambda x: > self.__reorderAtomsOrder[str(curRes[2])][x[0][0].strip()]) > File > "/home/programs/x86_64-linux/ccp4/7.0/ccp4-7.0/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py", > line 1735, in > curRes[3].sort(key = lambda x: > self.__reorderAtomsOrder[str(curRes[2])][x[0][0].strip()]) > KeyError: "H5'" > > Any suggestions what might be wrong, and how I can fix this? > > Thanks > > -- > Ursula Schulze-Gahmen, Ph.D. > Project Scientist > UC Berkeley, QB3 > 360 Stanley Hall #3220 > Berkeley, CA 94720-3220 > (510) 643 9491
[ccp4bb] Rcrane error, update
I am trying to use Rcrane in stand-alone coot version 0.8.8. The Rcrane window opens and I am able to calculate new conformations for my nucleic acid. But when I am trying to accept a conformation, I am getting an error message: Traceback (most recent call last): File "/home/programs/x86_64-linux/ccp4/7.0/ccp4-7.0/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py", line 1041, in __accept self.__pseudoMolecule.finalMoleculeCleanup(fixSegids = bool(self.__pseudoMolecule.hasSavedCoordinates())) File "/home/programs/x86_64-linux/ccp4/7.0/ccp4-7.0/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py", line 1735, in finalMoleculeCleanup curRes[3].sort(key = lambda x: self.__reorderAtomsOrder[str(curRes[2])][x[0][0].strip()]) File "/home/programs/x86_64-linux/ccp4/7.0/ccp4-7.0/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py", line 1735, in curRes[3].sort(key = lambda x: self.__reorderAtomsOrder[str(curRes[2])][x[0][0].strip()]) KeyError: "H5'" Any suggestions what might be wrong, and how I can fix this? Thanks -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491
