http://blog.gmane.org/gmane.science.biology.xplor-nih.general hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1764 <pre>Hi charles and all A quick question about potentials, python potentials and swig to aid my understanding If i look for example at PyPot the signature of its constructor is PyPot.__init__(self,name). However, the signature of the underlying potential is PyPot(const String&amp; instanceName, PyObject* pyObject, Simulation* defaultSimulation); so my question is where does the Simulation* come from? My suspicion (from staring at the swig code; which is definitely painful) is that it is filled in by swig possibly using a default entry in the typemap, but I could be way off the mark here ;-) regards gary </pre> Gary Thompson 2013-06-11T09:33:38 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1761 <pre>Dear All (and charles!) I am trying to re-compile xplor on my computer from the source. However, the version of python distributed with my linux distribution doesn't match the python that xplor nih is compiled against. How do I control which version of python xplor nih compiles against when using make? regards gary </pre> Gary Thompson 2013-06-10T10:09:10 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1760 <pre> Dear All (most probably charles!) I am trying to generate a swig wrapper for a c++ class using the following command line (I am doing this outside xplor currently) swig -python -classptr -c++ -keyword -shadow -I/usr/include/python2.7 -I/home/garyt/programs/xplor-nih/2.31.0/CDSlib -I/home/garyt/programs/xplor-nih/2.31.0/common -I/home/garyt/programs/xplor-nih/2.31.0/intVar -I/home/garyt/programs/xplor-nih/2.31.0/nmrPot -I/home/garyt/programs/xplor-nih/2.31.0/vmd -I/home/garyt/programs/xplor-nih/2.31.0/surfD -I/home/garyt/programs/xplor-nih/2.31.0/cminpack -I/home/garyt/programs/xplor-nih/2.31.0/sparta -I/home/garyt/programs/xplor-nih/2.31.0/devel -I/home/garyt/programs/xplor-nih/2.31.0/fortlib -I. -I/home/garyt/programs/xplor-nih/2.31.0/python -o pyEnsemblePotProxy_wrap.cpp pyEnsemblePotProxy.i where pyEnsemblePotProxy.i contains an empty(ish) potential class // -*- c++ -*- #ifndef PY_ENSEMBLE_POT_PROXY_H #define PY_ENSEMBLE_POT_PROXY_H 1 #include "ensemblePot.hh" struct _object; typedef _object PyObject; class PyEnsemblePotProxy : public EnsemblePot { public: PyObject *m_obj; PyEnsemblePotProxy(const String&amp;, const String&amp;, Simulation*, PyObject *obj); virtual ~PyEnsemblePotProxy(); void doRun(); virtual void run(); float_type rms(); int violations(); int numRestraints(); }; #endif // !PY_ENSEMBLE_POT_PROXY_H however when I compile the resulting swig wrapper I get messages about missing declarations for ‘SWIGPY_POINTER_EXCEPTION’, ‘SWIGPY_ConvertPtr’ and ‘SWIGPY_fail' gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DCPLUSPLUS=1 -DUSE_CDS_NAMESPACE=1 -I/home/garyt/programs/xplor-nih/2.31.0/common -I/home/garyt/programs/xplor-nih/2.31.0/CDSlib -I/home/garyt/programs/xplor-nih/2.31.0/arch/Linux_i686/include -I/usr/include/python2.7 -I/home/garyt/programs/xplor-nih/2.31.0/CDSlib -I/home/garyt/programs/xplor-nih/2.31.0/common -I/home/garyt/programs/xplor-nih/2.31.0/intVar -I/home/garyt/programs/xplor-nih/2.31.0/nmrPot -I/home/garyt/programs/xplor-nih/2.31.0/vmd -I/home/garyt/programs/xplor-nih/2.31.0/surfD -I/home/garyt/programs/xplor-nih/2.31.0/cminpack -I/home/garyt/programs/xplor-nih/2.31.0/sparta -I/home/garyt/programs/xplor-nih/2.31.0/devel -I/home/garyt/programs/xplor-nih/2.31.0/fortlib -I. -I/home/garyt/programs/xplor-nih/2.31.0/python -I/home/garyt/programs/xplor-nih/2.31.0/python/bin.Linux_i686/include/python2.6 -c pyEnsemblePotProxy_wrap.cpp -o build/temp.linux-i686-2.6/pyEnsemblePotProxy_wrap.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for Ada/C/ObjC but not for C++ [enabled by default] pyEnsemblePotProxy_wrap.cpp: In function ‘PyObject* wrapPot(rc_Pot&amp;)’: pyEnsemblePotProxy_wrap.cpp:3269:45: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] pyEnsemblePotProxy_wrap.cpp: In function ‘PyObject* _wrap_new_PyEnsemblePotProxy__SWIG_0(PyObject*, PyObject*)’: pyEnsemblePotProxy_wrap.cpp:4164:11: error: ‘SWIGPY_POINTER_EXCEPTION’ was not declared in this scope pyEnsemblePotProxy_wrap.cpp:4165:31: error: ‘SWIGPY_ConvertPtr’ was not declared in this scope pyEnsemblePotProxy_wrap.cpp:4166:7: error: ‘SWIGPY_fail’ was not declared in this scope pyEnsemblePotProxy_wrap.cpp: In function ‘PyObject* _wrap_PyEnsemblePotProxy_setEnsWeights(PyObject*, PyObject*, PyObject*)’: pyEnsemblePotProxy_wrap.cpp:5911:43: error: ‘SWIGPY_ConvertPtr’ was not declared in this scope pyEnsemblePotProxy_wrap.cpp: In function ‘PyObject* _wrap_PyEnsemblePotProxy_setUseSimEnsWeights(PyObject*, PyObject*, PyObject*)’: pyEnsemblePotProxy_wrap.cpp:6065:27: error: ‘SWIGPY_ConvertPtr’ was not declared in this scope pyEnsemblePotProxy_wrap.cpp: In function ‘PyObject* _wrap_PyEnsemblePotProxy_setScale(PyObject*, PyObject*, PyObject*)’: pyEnsemblePotProxy_wrap.cpp:6383:29: error: ‘SWIGPY_ConvertPtr’ was not declared in this scope pyEnsemblePotProxy_wrap.cpp: In function ‘PyObject* _wrap_PyEnsemblePotProxy_setThreshold(PyObject*, PyObject*, PyObject*)’: pyEnsemblePotProxy_wrap.cpp:6537:29: error: ‘SWIGPY_ConvertPtr’ was not declared in this scope pyEnsemblePotProxy_wrap.cpp: In function ‘PyObject* _wrap_new_PyEnsemblePotProxy_LetterClass(PyObject*, PyObject*, PyObject*)’: pyEnsemblePotProxy_wrap.cpp:7383:29: error: ‘SWIGPY_ConvertPtr’ was not declared in this scope pyEnsemblePotProxy_wrap.cpp:7427:29: error: ‘SWIGPY_ConvertPtr’ was not declared in this scope /home/garyt/programs/xplor-nih/2.31.0/CDSlib/cdsString.hh: At global scope: /home/garyt/programs/xplor-nih/2.31.0/CDSlib/cdsString.hh:222:12: warning: ‘int cdsMapConvertToInt(const String&amp;)’ declared ‘static’ but never defined [-Wunused-function] /home/garyt/programs/xplor-nih/2.31.0/CDSlib/cdsMap.hh:134:12: warning: ‘int cdsMapConvertToInt(int)’ declared ‘static’ but never defined [-Wunused-function] /home/garyt/programs/xplor-nih/2.31.0/CDSlib/cdsMap.hh:135:12: warning: ‘int cdsMapConvertToInt(double)’ declared ‘static’ but never defined [-Wunused-function] pyEnsemblePotProxy_wrap.cpp:3283:15: warning: ‘String PyEnsemblePotProxy_help(PyEnsemblePotProxy*)’ declared ‘static’ but never defined [-Wunused-function] I presume the problem is that I need to do 1. sed 's/SWIG_/SWIGPY_/g' pyEnsemblePotProxy_wrap.cpp &gt; pyEnsemblePotProxy_wrap_new.cpp 2. ~/programs/xplor-nih/2.31.0/bin/includeCC pyEnsemblePotProxy_wrap_new.cpp --template-dir /home/garyt/programs/xplor-nih/2.31.0_test_swig/CDSlib --cc 'c++' -DX_MMAP_FLAGS=0 -DFORTRAN_INIT -O3 -DLINUX -D_REENTRANT -DNDEBUG -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/python/ -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/arch/Linux_i686/include -DSWIG_VERSION=20004 -I/usr/share/swig2.0/python -DCPLUSPLUS -DUSE_CDS_NAMESPACE -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/python/ -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/arch/Linux_i686/include -DSWIGPY_GLOBAL -I. -I/usr/include/python2.7 -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/CDSlib -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/common -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/intVar -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/nmrPot -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/vmd -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/surfD -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/cminpack -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/sparta -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/devel -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/fortlib -DNIHXPLOR_VERSION='"2.31-custom"' -DPYTHON_VERSION='"2.7"' -DSWIGPY_PYTHON_SILENT_MEMLEAK &gt; pyEnsemblePotProxy_wrap_new_2.cpp 3. c++ -c pyEnsemblePotProxy_wrap_new_2.cpp -DX_MMAP_FLAGS=0 -DFORTRAN_INIT -O3 -DLINUX -D_REENTRANT -DNDEBUG -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/python/ -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/arch/Linux_i686/include -DSWIG_VERSION=20004 -I/usr/share/swig2.0/python -DCPLUSPLUS -DUSE_CDS_NAMESPACE -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/python/ -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/arch/Linux_i686/include -DSWIGPY_GLOBAL -I. -I/usr/include/python2.7 -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/CDSlib -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/common -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/intVar -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/nmrPot -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/vmd -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/surfD -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/cminpack -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/sparta -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/devel -I/home/garyt/programs/xplor-nih/2.31.0_test_swig/fortlib -DNIHXPLOR_VERSION='"2.31-custom"' -DPYTHON_VERSION='"2.7"' -DSWIGPY_PYTHON_SILENT_MEMLEAK -DSWIGPY_NOINCLUDE are these all the step I need to do? nb swig -version gives me SWIG Version 2.0.4 Compiled with g++ [i686-pc-linux-gnu] Configured options: +pcre Please see http://www.swig.org for reporting bugs and further information regards gary </pre> Gary Thompson 2013-06-10T10:08:40 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1755 <pre>Hi, I have a model of a protein-protein complex, where several residues in a loop in the interface are undefined. I want to use xplor to add the loop residues, and put them in a location that does not clash with the rest of the protein or with the binding partner. I used addAtoms2.py to generate the loop residues without disturbing the rest of the structure. The loop that was generated clashed with the binding partner, so I wanted to run some dynamics to move the loop into a more suitable position, again without disturbing the rest of the model. I found the dock.py script has some features to treat the proteins as rigid bodies, and to prevent sidechain movement, while allowing some movement in a defined part of the protein(s). So I'm trying to use the dock.py script, with lines like: dyn_fix.group( 'resid 1022:1237') dyn_fix.group( 'resid 1238:1329' ) dyn_fix.group( 'resid 1338:1428' ) dyn_fix.fix( 'resid 1022:1237') dyn_fix.fix( 'resid 1238:1329') dyn_fix.fix( 'resid 1338:1428' ) I'm trying to set the protein without the modified loop as fixed, and the N-terminal and C-terminal parts of the other protein, before and after the loop as a fixed group, and let the loop itself be moved. However, no matter what I do, a bond at the C-terminal end of the loop is always broken. Is there a more appropriate approach to finding a possible conformation of a flexible loop, while keeping all other residues in a model fixed? Thank you, Katie Edmonds _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Katherine Edmonds 2013-06-05T16:36:10 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1753 <pre>Hi everyone, I am trying to backcalculate PREs from a pdb structure, in which I have a homodimer forming a complex with another protein. The paramagnetic centers are attached to the homodimer. I tried setting npc = 2 (pre.setNpc(2)) at runSBMF() function, using calc.py script as in (eginput/pre/fitting). I got the following error message: SystemError: xplor-nih error: Change npc to 1 I am not sure what additional parameter should be adjusted. For the input table (as zeros.tbl of eginput/pre/fitting), I wrote in the following manner: assign (resid 605 and name NS1) (resid 362 and name HN) 1.00 1.00 assign (resid 1605 and name NS1) (resid 362 and name HN) 1.00 1.00 I am not sure if that is the right way write the table for two paramagnetic centers. Or should I consider them as some sort of pseudo ambiguous restraint: assign ((resid 605 and name NS1) or (resid 1605 and name NS1)) (resid 362 and name HN) 1.0 1.0 Any help would be appreciated. Fernando ________________________________ UT Southwestern Medical Center The future of medicine, today. _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Fernando Correa 2013-06-04T21:30:03 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1751 <pre>Hi all, My apologies, There was a mistake in my last message, please exchange "thioester for thioether": I am having some trouble producing the structure of a lanthionine-containing peptide. I have taken the approach of supplying the peptide sequence including cysteines and adding a presidue to the topology file (essentially like using DISU but including the removal of an S): presidue THET ! Thioether linkage ...CYS - S - CYS... group delete atom 1HG end group delete atom 2HG end delete atom 2SG end modify atom 2CB type=CT end add bond 1SG 2CB add angle 1CB 1SG 2CB end I then get the following error: %HBUILD-ERR: error building hydrogen for donor: " 5 CYS CB " Some bond angles are missing in the topology and parameter file that involve this donor atom. %&lt;HBUILD&gt;-ERR: Unknown angles involving donor atom. I would greatly appreciate any help you can offer. Thanks, Chris </pre> Earl, Christopher 2013-05-29T17:27:57 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1750 <pre>Hi all, I am having some trouble producing the structure of a lanthionine-containing peptide. I have taken the approach of supplying the peptide sequence including cysteines and adding a presidue to the topology file (essentially like using DISU but including the removal of an S): presidue THES ! Thioester linkage ...CYS - S - CYS... group delete atom 1HG end group delete atom 2HG end delete atom 2SG end add bond 1SG 2CB add angle 1CB 1SG 2CB end I then get the following error: %HBUILD-ERR: error building hydrogen for donor: " 5 CYS CB " Some bond angles are missing in the topology and parameter file that involve this donor atom. %&lt;HBUILD&gt;-ERR: Unknown angles involving donor atom. I would greatly appreciate any help you can offer. Thanks, Chris </pre> Earl, Christopher 2013-05-29T16:39:24 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1746 <pre>Hello Charles, I have written a script for ensemble refinement based on dna_ensembe/ensemble.py and gb1_rdc/refine.py. The script is along with the mail below. When running the simulation, one of the child process stops working and in the log files I found this line : barrier: error reading from process 1 The simulation proceeds with computing only one structure. While the killed process has : StructureLoop: this process has no work. Exiting... Can you tell me where am I going wrong ? The below script is executed this way: xplor -smp 2 -py -o refine.out 5050.py xplor.requireVersion("2.17") numberOfStructures=1 ensembleSize=2 # number of ensemble members outFilename = "SCRIPT_%d_STRUCTURE_MEMBER.sa" % ensembleSize import protocol protocol.initRandomSeed() command = xplor.command protocol.initParams("protein") #load pdb and covalently minimize the protein protocol.loadPDB("model.pdb") xplor.simulation.deleteAtoms("not known") protocol.fixupCovalentGeom(maxIters=1000,useVDW=1) #initilize ensemble simulations from ensembleSimulation import EnsembleSimulation esim = EnsembleSimulation("ensemble",ensembleSize) # # a PotList contains a list of potential terms. This is used to specify which # terms are active during refinement. # from potList import PotList potList = PotList() # parameters to ramp up during the simulated annealing protocol # from simulationTools import MultRamp, StaticRamp, InitialParams rampedParams=[] highTempParams=[] # orientation Tensor - used with the dipolar coupling term # one for each medium # For each medium, specify a name, and initial values of Da, Rh. # from varTensorTools import create_VarTensor media={} expdatadir = 'xplor5050/' import os,re mediaList = open(expdatadir+'mediaList.txt').readlines() #media[medium] = create_VarTensor(medium) for mediaName in mediaList: mediaName = mediaName.strip() if not mediaName in media.keys(): media[mediaName] = create_VarTensor(mediaName) from rdcPotTools import create_RDCPot, scale_toNH,correctGyromagneticSigns correctGyromagneticSigns() bondTypes = ['NH','CAC','CAHA','CN','CHN'] #xplorBondTypes = {'NH':'NH','CN':'NCO','HNC':'CHN','CAHA':'CAHA', 'CAC':'CACO'} #bondTypeScales = {'NH':15, 'CAHA':3, 'CN':100, 'CAC':100, 'CHN':3} bondTypeScales = {'NH':1, 'CAHA':1, 'CN':1, 'CAC':1, 'CHN':1} rdcs = PotList('rdc') for medium in media.keys(): #rdc = create_RDCPot("%s_%s"%(medium,expt),file,media[medium]) for btype in bondTypes: if os.path.isfile(expdatadir+medium+'_'+btype+'.tbl'): rdc = create_RDCPot("%s_%s"%(medium,btype),expdatadir+medium+'_'+btype+'.tbl',media[medium]) rdc.setScale(bondTypeScales[btype]) rdc.setAveType("sum") # its set to be average by default rdc.setShowAllRestraints(1) rdcs.append(rdc) potList.append(rdcs) rampedParams.append( MultRamp(0.05,5.0, "rdcs.setScale( VALUE )") ) # calc. initial tensor orientation # and setup tensor calculation during simulated annealing # from varTensorTools import calcTensorOrientation, calcTensor for medium in media.keys(): calcTensor(media[medium]) rampedParams.append( StaticRamp("calcTensor(media['%s'])" % medium) ) pass #add other things about NOE later from avePot import AvePot from xplorPot import XplorPot potList.append( AvePot(XplorPot,'VDW') ) rampedParams.append( StaticRamp("protocol.initNBond()") ) rampedParams.append( MultRamp(0.9,0.8, "command('param nbonds repel VALUE end end')") ) rampedParams.append( MultRamp(.004,4, "command('param nbonds rcon VALUE end end')") ) potList.append( AvePot(XplorPot,"BOND") ) potList.append( AvePot(XplorPot,"ANGL") ) potList['ANGL'].setThreshold( 5 ) rampedParams.append( MultRamp(0.4,1,"potList['ANGL'].setScale(VALUE)") ) potList.append( AvePot(XplorPot,"IMPR") ) potList['IMPR'].setThreshold( 5 ) rampedParams.append( MultRamp(0.1,1,"potList['IMPR'].setScale(VALUE)") ) # Give atoms uniform weights, except for the anisotropy axis # protocol.massSetup() # IVM setup # the IVM is used for performing dynamics and minimization in torsion-angle # space, and in Cartesian space. # from ivm import IVM dyn = IVM() dyn.reset() for m in media.values(): m.setFreedom("varyDa, varyRh") #vary tensor Rh, Da, vary orientation protocol.torsionTopology(dyn) #for ending with cartesian minimzation minc = IVM() protocol.initMinimize(minc) for m in media.values(): m.setFreedom("varyDa, varyRh") #allow all tensor parameters float here pass protocol.cartesianTopology(minc) # object which performs simulated annealing # from simulationTools import AnnealIVM init_t = 3000. # Need high temp and slow annealing to converge cool = AnnealIVM(initTemp =init_t, finalTemp=25, tempStep =12.5, ivm=dyn, rampedParams = rampedParams) #criteria to accept a structure def accept(potList): """ return True if current structure meets acceptance criteria """ #if potList['noe'].violations()&gt;0: # return False if potList['rdc'].rms()&gt;1.2: #this might be tightened some return False #if potList['CDIH'].violations()&gt;0: # return False if potList['BOND'].violations()&gt;0: return False if potList['ANGL'].violations()&gt;0: return False if potList['IMPR'].violations()&gt;1: return False return True def calcOneStructure(loopInfo): """ this function calculates a single structure, performs analysis on the structure, and then writes out a pdb file, with remarks. """ # initialize parameters for high temp dynamics. InitialParams( rampedParams ) # high-temp dynamics setup - only need to specify parameters which # differfrom initial values in rampedParams InitialParams( highTempParams ) # high temp dynamics # protocol.initDynamics(dyn, potList=potList, # potential terms to use bathTemp=init_t, initVelocities=1, finalTime=10, # stops at 10ps or 5000 steps numSteps=5000, # whichever comes first printInterval=100) dyn.setETolerance( init_t/100 ) #used to det. stepsize. default: t/1000 dyn.run() # initialize parameters for cooling loop InitialParams( rampedParams ) # initialize integrator for simulated annealing # protocol.initDynamics(dyn, potList=potList, numSteps=100, #at each temp: 100 steps or finalTime=.2 , # .2ps, whichever is less printInterval=100) # perform simulated annealing # cool.run() # final torsion angle minimization # protocol.initMinimize(dyn, printInterval=50) dyn.run() # final all- atom minimization # protocol.initMinimize(minc, potList=potList, dEPred=10) minc.run() #do analysis and write structure loopInfo.writeStructure(potList) pass from simulationTools import StructureLoop, FinalParams StructureLoop(numStructures=numberOfStructures, pdbTemplate=outFilename, structLoopAction=calcOneStructure, genViolationStats=1, averagePotList=potList, averageTopFraction=0.5, #report only on best 50% of structs averageAccept=accept, #only use structures which pass accept() averageContext=FinalParams(rampedParams), averageFilename="SCRIPT_ave.pdb", #generate regularized ave structure averageFitSel="name CA", averageCompSel="not resname ANI and not name H*" ).run() Thanks for your support, Santhosh _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> santhu kumar 2013-05-13T21:38:59 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1744 <pre>Hello, I've been doing some water refinements using the script from the gb1_rdc example in eginput and I get this term DIHE (it wasn't present while running the annealing script) that has rather large energies comparatively to noes or CDIH. How do I output those violations or how do I know what's creating this term. Shouldn't it be part of the IMPR term? Thanks, Marie </pre> Marie-Laurence Tremblay 2013-05-13T14:45:03 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1740 <pre>Hello Charles, I think I know the answer for these questions but just want to confirm with you. In refinement of structures using RDC's, we use 4 pseudo-atoms to define an axis and these are part of the PDB also. For more than one RDC dataset, we should have more than such 4 pseudo-atoms. Now the questions are : 1). Should the four atoms be created as a axis? I mean should O-XX be perpendicular to O-YY and so on? Or could it be any four atoms far away from the protein? In the examples, they are mostly perpendicular. 2). In case of multiple RDC constraints, would there be a problem if I overlap many such pseudo-atoms on top of each other? eg : ATOM 856 X ANI 500 322.383 -47.025 154.522 1.00 3.06 ATOM 857 Y ANI 500 322.080 -50.957 156.088 1.00 4.37 ATOM 858 Z ANI 500 323.128 -50.368 152.019 1.00 4.35 ATOM 859 OO ANI 500 324.205 -49.405 154.647 1.00 4.04 ATOM 860 X ANI 600 322.383 -47.025 154.522 1.00 3.06 ATOM 861 Y ANI 600 322.080 -50.957 156.088 1.00 4.37 ATOM 862 Z ANI 600 323.128 -50.368 152.019 1.00 4.35 ATOM 863 OO ANI 600 324.205 -49.405 154.647 1.00 4.04 Would this be fine as per VDW calculations or anything. I am hoping that they could overlap as I have many RDC datasets and it would be tricky to create many such random points. Thanks a lot, Santhosh _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> santhu kumar 2013-05-10T22:08:35 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1738 <pre>Hi all, I am trying to generate initial .pdb structures for a peptide RNA complex. My peptide contains nonstandard amino acids; I have already added their topology data to protein.top. When I try to run my script in xplor, I keep getting the following errors (see attached). I have checked to see that my NOE table assignments match what I have put into the topology file, but I am not sure what else to check from here. Any help? Jonesy _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Alisha Nicole Jones 2013-05-08T22:04:32 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1736 <pre>Hello I am new to Xplor-NIH and have done cartesian coordinate refinements using gromacs before. I have been through the relevant code and tutorials. The striking difference I have seen is that Xplor requires initial Da and Rh values to be provided. This makes sense when we are annealing from a completely unfolded chain but when refining from a good start point [structurally], and letting Da and Rh float [change], would it make a difference if we provide or not provide these initial estimates? And is there an easy way to compute Da and Rh values within xplor framework, given ensemble, RDC data without creating RDCpot ? [ for the initial estimate]. I could write a script in python which does the computation but if it could be done within xplor, it would be more convenient. Thanks Santhosh _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> santhu kumar 2013-04-30T14:11:15 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1732 <pre>Dear all, sorry if there is an obvious answer to this simple question, which I could not find. I wish to use angles constaints constraining three atoms, which are not related by bonds, to a certain angle. It seems it is only possible to constrain dihedral angles, and guess adding to the parameter file is not a good option. Is there a way to go? thanks in advance, best regards, Jakob Jakob Toudahl Nielsen, post doc Laboratory for Biomolecular NMR Spectroscopy inSPIN, Center for Insoluble Protein Structures Department of Chemistry, University of Aarhus and Interdisciplinary Nanoscience Center (iNANO) Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark Office: 1593-227 Phone: +45 871 56654 (office) &amp; 2993 8501 (cell) _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Jakob Toudahl Nielsen 2013-04-25T13:47:57 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1729 <pre>Hello I'm in the process of setting up a docking run using chemical shifts, and are running into problems with the generation of a input structure for one of the proteins in the docking. I'm docking 2 proteins, where one of the proteins is a Zinc-finger with 2 Zn2+ atoms, one coordinated by 4 Cys and the other one coordinated by 2 Cys &amp; 2 His. One histidine is coordinated by NE2 and the other by ND1. Based on answers from the mailing list and examples, I modified a topology file and parameter file for incorporating the two Zn. Upon running the file (see below) I can successfully generate the psf-file and a pdb-file. However, in the pdb-file, the Zn2+ and some N and C-terminal residues gets coordinates -9999.9. I have tried fixing that by running fixupCovalentGeom in the script, which causes the script to fail, saying missing atoms. What have I missed when setting up the protein and how can I fix this? I also want to mutate one residue to another in order to generate my version of the protein. The topology file is based on toph19.ion, where I generated bonds and angles, based upon how Zn2+ are handled in Aria/CNS. The file is as follows: PRESidue ZNK GROUP delete atom 1HG end MODIfy ATOM 1CB CHARge= 0.19 END MODIfy ATOM 1SG TYPE=S CHARge=-0.19 END ATOM 1ZN TYPE=ZN CHARGE=+2.0 END GROUP delete atom 2HG end MODIfy ATOM 2CB CHARge= 0.19 END MODIfy ATOM 2SG TYPE=S CHARge=-0.19 END GROUP delete atom 3HG end MODIfy ATOM 3CB CHARge= 0.19 END MODIfy ATOM 3SG TYPE=S CHARge=-0.19 END GROUP delete atom 4HG end MODIfy ATOM 4CB CHARge= 0.19 END MODIfy ATOM 4SG TYPE=S CHARge=-0.19 END ADD BOND 1ZN 1SG ADD BOND 1ZN 2SG ADD BOND 1ZN 3SG ADD BOND 1ZN 4SG ADD ANGLe 1CB 1SG 1ZN ADD ANGLe 2CB 2SG 1ZN ADD ANGLe 3CB 3SG 1ZN ADD ANGLe 4CB 4SG 1ZN ADD ANGLe 1SG 2SG 1ZN ADD ANGLe 1SG 3SG 1ZN ADD ANGLe 1SG 4SG 1ZN ADD ANGLe 2SG 3SG 1ZN ADD ANGLe 2SG 4SG 1ZN ADD ANGLe 3SG 4SG 1ZN END PRESidue C2HED GROUP delete atom 1HG end MODIfy ATOM 1CB CHARge= 0.19 END MODIfy ATOM 1SG TYPE=S CHARge=-0.19 END ATOM 1ZN TYPE=ZN CHARGE=+2.0 END GROUP delete atom 2HG end MODIfy ATOM 2CB CHARge= 0.19 END MODIfy ATOM 2SG TYPE=S CHARge=-0.19 END GROUP MODIFY ATOM 3ND1 TYPE=NR CHARge=-0.40 END GROUP MODIFY ATOM 4NE2 TYPE=NR CHARge=-0.40 END add bond 1ZN 1SG add bond 1ZN 2SG add bond 1ZN 3ND1 add bond 1ZN 4NE2 add angle 1SG 1ZN 2SG add angle 1SG 1ZN 3ND1 add angle 1SG 1ZN 4NE2 add angle 2SG 1ZN 3ND1 add angle 2SG 1ZN 4NE2 add angle 3ND1 1ZN 4NE2 add angle 1ZN 1SG 1CB add angle 1ZN 2SG 2CB add angle 1ZN 3ND1 3CG add angle 1ZN 3ND1 3CE1 add angle 1ZN 4NE2 4CG add angle 1ZN 4NE2 4CD2 END RESIdue ZN {* zinc *} GROUP ATOM ZN TYPE=ZN CHARGE=+2.0 END END and the parameter file is: bonds S ZN 500.0 2.30 BOND NR ZN 500.000 2.00 angles S ZN S 500.0 109.5 angles ZN S CH2E 70.0 120.0 angles ZN S CT 70.0 120.0 angles S ZN NR 500.0 109.5 angles NR ZN NR 500 109.5 ANGLes ZN NR CR1E 500.00 120.0000 ANGLes ZN NR CRH 500.00 120.0000 ANGLes ZN NR C5 500.00 120.0000 ! eps sigma eps(1:4) sigma(1:4) ! (kcal/mol) (A) ! --------------------------------------- NONBonded ZN 0.0430 3.3676 0.0430 3.3676 ! garbage I generate the psf-file using the following python-script, where I first patch histidine residues to the correct protonation and then I add the Zn-patches: xplor.parseArguments() import protocol protocol.loadPDB("1tota_cns.pdb") import psfGen protocol.initTopology("toph19.ion") protocol.initTopology("toph19.his") protocol.initParams("param19.ion") protocol.initParams("parhcsdx.pro") xplor.command(""" topology AUTO ANGLe=False DIHEdral=False END end patch HISE reference=nil=( resid 242 ) end patch HISD reference=nil=( resid 240 ) end patch ZNK reference=1=( resid 209 ) reference=2=( resid 212 ) reference=3=( resid 231 ) reference=4=( resid 234 ) end patch C2HED reference=1=( resid 222 ) reference=2=( resid 225 ) reference=3=( resid 242 ) reference=4=( resid 240 ) end """) xplor.command("write psf output=1tota_cns_zn.psf end") from pdbTool import PDBTool PDBTool("test.pdb").write() Best Regards Carl Diehl Post-Doc NNF CPR Copenhagen university, Denmark _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Carl Diehl 2013-04-23T14:42:38 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1726 <pre>Hi, How can I export H-bond violations from xplor-nih 2.32 so that they show up in the .stats file? I'm assuming that I have to add something to the anneal.py script but I'm not sure what exactly. Thanks, Marie </pre> Marie-Laurence Tremblay 2013-04-05T19:03:27 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1725 <pre>Hello, I am using TEMPO as a spin labeled to acquire PRE data to get distance restraints but I am not finding a TEMPO library in Xplor-nih, I could only find MTSL. Is there a TEMPO library? I really appreciate any help! Thanks so much. -Leah </pre> Leah Randles 2013-04-05T12:07:38 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1717 <pre>Hi All I'm trying to include a cisProline in water refinement calculations - I'm using a modified version of the script found in eginput/gb1_rdc/wrefine.py. In earlier posts on this matter its suggested that there are two ways of doing this: 1) load a pre-generated PSF using protocol.initStruct, and then load the structure with protocol.initCoords instead of protocol.loadPDB. I've used this method for the refine.py script loading in a single start structure and it works. If I try to do something similar for the wrefine.py script: from psfGen import seqToPSF protocol.initStruct("../generate/cov.psf") protocol.initCoords(inputStructures[0]) - have tried with a single structure as well - protocol.initCoords("../refine/refine_1.sa") xplor.simulation.deleteAtoms("not known") I get a lot of %CODANG-ERR: missing angle parameters errors and CODIMP-ERR: missing improper parameters in the log file and the run aborts. 2) load the structure with protocol.loadPDB, and then correct the PSF information using psfGen.cisPeptide. In the script I have: import psfGen protocol.loadPDB(inputStructures[0],deleteUnknownAtoms=True) psfGen.cisPeptide(110) In the log file I get the following error message: X-PLOR&gt; patch CIPP PATCH&gt; reference=-=( resid 110 and segid "") SELRPN: 19 atoms have been selected out of 2405 PATCH&gt; reference=+=( resid 111 and segid "") SELRPN: 14 atoms have been selected out of 2405 PATCH&gt; end %PATCH-ERR: atom C not found and the Proline is then trans. If I try the same thing in the refine.py script it works without error and I get a cis Proline. For the 2nd case if I move the import lines of the protein and apply the psfGen.cisPeptide before the Nilges topology/parameters for water then the CIPP patch is done correctly. However this then causes a major problem in the actual refinement. Comparing two structures calculated on a non-cis proline with just the position of when the structure is imported (either before or after the water parameters) with Molprobity I get the following: For water params then loadPDB - ClashScore = 12.73, Poor Rotamers = 2, Ramachandran Outliers = 1, Ramachandran favored = 91.75% For loadPDB then water params - ClashScore = 34.55, Poor Rotamers = 9, Ramachandran Outliers = 6, Ramachandran favored = 86.6% What's also interesting is that the reported DIHE violations in the pdb structure drops from 2355 (water, pdb) to 351 (pdb, water). any help is greatly appreciated Richard _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Richard Harris 2013-04-01T14:50:07 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1715 <pre>Hi, I get this message at the start of my structure calculations: round10_new.py(278): randomizeTorsions(dyn) AT_Build::buildNode: cycle link found between atoms 28 PRO 3 CD and 19 PRO 3 N removing bond. AT_Build::buildNode: cycle link found between atoms 74 PHE 7 CD2 and 71 PHE 7 CG removing bond. AT_Build::buildNode: cycle link found between atoms 948 PHE 69 CD2 and 945 PHE 69 CG removing bond. AT_Build::buildNode: cycle link found between atoms 1090 PRO 78 CD and 1081 PRO 78 N removing bond. AT_Build::buildNode: cycle link found between atoms 1180 TYR 86 CD2 and 1177 TYR 86 CG removing bond. AT_Build::buildNode: cycle link found between atoms 1238 PHE 90 CD2 and 1235 PHE 90 CG removing bond. AT_Build::buildNode: cycle link found between atoms 1309 PHE 95 CD2 and 1306 PHE 95 CG removing bond. AT_Build::buildNode: cycle link found between atoms 1993 PHE 146 CD2 and 1990 PHE 146 CG removing bond. AT_Build::buildNode: cycle link found between atoms 2122 TYR 156 CD2 and 2119 TYR 156 CG removing bond. AT_Build::buildNode: cycle link found between atoms 2273 TYR 169 CD2 and 2270 TYR 169 CG removing bond. AT_Build::buildNode: cycle link found between atoms 2314 PRO 172 CD and 2305 PRO 172 N removing bond. AT_Build::buildNode: cycle link found between atoms 2346 PRO 175 CD and 2337 PRO 175 N removing bond. AT_Build::buildNode: cycle link found between atoms 2392 PRO 179 CD and 2383 PRO 179 N removing bond. AT_Build::buildNode: cycle link found between atoms 2425 TYR 182 CD2 and 2422 TYR 182 CG removing bond. AT_Build::buildNode: cycle link found between atoms 2445 PRO 183 CD and 2436 PRO 183 N removing bond. AT_Build::buildNode: cycle link found between atoms 2466 PRO 185 CD and 2457 PRO 185 N removing bond. AT_Build::buildNode: cycle link found between atoms 2530 PRO 191 CD and 2521 PRO 191 N removing bond. AT_Build::buildNode: cycle link found between atoms 2545 PHE 192 CD2 and 2542 PHE 192 CG removing bond. AT_Build::buildNode: cycle link found between atoms 2607 PHE 197 CD2 and 2604 PHE 197 CG removing bond. round10_new.py(282): from varTensorTools import calcTensorOrientation round10_new.py(288): InitialParams( rampedParams ) I've read in the mailing list that this pops up with disulfide bonds or metal ion binding. How do I prevent XPLOR from removing those bonds, which should be there. Is there a setting somewhere? Thanks </pre> Marie-Laurence Tremblay 2013-03-19T12:20:13 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1713 <pre>Hi, Our lab recently switched from XPLOR-NIH version 2.19 to version 2.33. It would seem that the former proton stereospecificity (HD** or HG**) in the NOE restraint files have changed to only accept HD(1 or 2)* or HG(1 or 2)*. My methyl protons aren't stereospecifically assigned and I was wondering how XPLOR is treating those proton and how we keep the ambiguity? Do we have to use the potential described in: Kuszewski, J., Gronenborn, A.M. &amp; Clore, G.M. (1996) A potential involving multiple proton chemical shift restraints for non-stereospecifically assigned methyl and methylene protons. J. Magn. Reson. Series B 112, 79-81 Thanks </pre> Marie-Laurence Tremblay 2013-03-18T13:46:07 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1710 <pre>Dear, My email is j.fazavana&lt; at &gt;ymail.com_______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Judicael Fazavana 2013-03-13T20:16:44 http://comments.gmane.org/gmane.science.biology.xplor-nih.general/1708 <pre>Dear Charles, Recently I have tested the water refinement script (Xplor-NIH 2.31). The run completed fine, but upon inspection I noticed the aromatic side chains had their planarity distorted. For example, CG-CD-CE-CZ dihedral in Phe side chain was 4.8 degrees, the ring adopting a chair conformation. For topology/parameters initialization I have used the values in the GB1 example: protocol.parameters['protein']="waterRef/parallhdg5.3.pro.new" protocol.parameters['water'] ="waterRef/parallhdg5.3.sol" protocol.topology['protein'] ="waterRef/topallhdg5.3.pro.new" protocol.topology['water'] ="waterRef/topallhdg5.3.sol" protocol.initParams(("protein","ion.par")) I was also surprised to see very little change in the side chains after the run. Even in the scenarios where a positive and negative residues were one turn from each other on an alpha-helix, there was little side chain rearrangement. Thank you, Vitaly </pre> V.V 2013-02-23T06:38:57 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.science.biology.xplor-nih.general