Hi,
Thanks for the suggestions. I tried by changing the the line with the
suggested line and rerun the program from command prompt both in 32 and 64
bit version, but it gave the following error.
----------------------------------------------------------------------------------------------------------------------------------
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
###############################################################################
### ARP/wARP Program Suite: LOOP BUILDING 0.1 Krista Joosten (17-11-2005)
###
### F77 lib: V. Lamzin
###
############ Copyright 2005 , NKI, A. Perrakis Laboratory
#####################
###############################################################################
<!--SUMMARY_END--></FONT></B>
Starting time : Mon Jul 30 09:31:00 2007
MIGHT ABORT NOW, error message is : ERROR** : Couldn't find any loop to build
Quitting now... encountered an error (exception) : N4warp4CMsgE
Message is :
Couldn't find any loop to build
Ending time : Mon Jul 30 09:31:01 2007
CPU usage loop building: 0.49s.
---------------------------------------------------------------------------
May be this error could be a trival one, I am not able to get what exactly
mission, as I run this loop module first time. I am also enclosing the
input file I used.
------------------------------------------------------------------------------
INPUT FILE
------------------------------------------------------------------------------
<arp-warp>
<loop>
<MessageFilename>
/home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/loopy.msg
</MessageFilename>
<XMLOutputFilename>
/home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/loopy.xml
</XMLOutputFilename>
<AbortLevel> 8 </AbortLevel>
<MessageLevel> 4 </MessageLevel>
<ProgramName> loopy </ProgramName>
<DictionaryFilename>
/home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/AAbis_extension.XYZ
</DictionaryFilename>
<UniformAtomBFactor> 20 </UniformAtomBFactor>
<UniformAtomRadius> 0.74 </UniformAtomRadius>
<AntiBumpFactor> 1. </AntiBumpFactor>
<SymmetryFilename>
/home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/syminfo.lib
</SymmetryFilename>
<SpaceGroup> 19 </SpaceGroup>
<XtalCell> 60.489 112.116 133.838 90.00 90.00 90.00 </XtalCell>
<KeepSideChain> 1 </KeepSideChain>
<KeepFragmentLongerThan> 0 </KeepFragmentLongerThan>
<UseCDummyResidue> 1 </UseCDummyResidue>
<StructureFilenameToC>
/home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/set_1200_2C_my_0.3b_cos_log.llh
</StructureFilenameToC>
<StructureFilenameToN>
/home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/set_1200_2N_my_0.3b_cos_log.llh
</StructureFilenameToN>
<CADistance> 3.8 </CADistance>
<RandomGrid> 0 </RandomGrid>
<GridNumber> 378 </GridNumber>
<DisregardNegativeDensity> 1 </DisregardNegativeDensity>
<KeepNegDensityHalfway> 0 </KeepNegDensityHalfway>
<NormalizeDensity> 1 </NormalizeDensity>
<BFactorForBuildSideChain> 26 </BFactorForBuildSideChain>
<LikelihoodThreshold> -4.5 </LikelihoodThreshold>
<WeightDensityLLH> 1. </WeightDensityLLH>
<WeightDistanceLLH> 1. </WeightDistanceLLH>
<WeightStructuralLLH> 1. </WeightStructuralLLH>
<OldComputation> 0 </OldComputation>
<CheckFirstAngle> 1 </CheckFirstAngle>
<UseCubicFitTarget> 1 </UseCubicFitTarget>
<OverlapRejectionThreshold> 0.1 </OverlapRejectionThreshold>
<DummyRejectionThreshold> 0.1 </DummyRejectionThreshold>
<LoopBuildAll> 0 </LoopBuildAll>
<ExtendGapSmallerThan> 0 </ExtendGapSmallerThan>
<LoopBothWays> 1 </LoopBothWays>
<LoopToC> 1 </LoopToC>
<LoopLength> </LoopLength>
<LoopOverlap> 0 </LoopOverlap>
<LoopDensityCutoffNo> 100 </LoopDensityCutoffNo>
<MinimalDistance> 0.3 </MinimalDistance>
<MaxNoCAsKept> 6 </MaxNoCAsKept>
<ForceMinCAsKept> 2 </ForceMinCAsKept>
<LoopRMS> 0.7 </LoopRMS>
<LoopStructureThreshold> -1.5 </LoopStructureThreshold>
<LoopStructureCutoffNo> 50 </LoopStructureCutoffNo>
<LoopStructureMinNo> 15 </LoopStructureMinNo>
<LoopMainChainDensNo> 5 </LoopMainChainDensNo>
<LoopsToBuild> C104<8>C112 </LoopsToBuild>
<LoopSequence> PNHVTYSGD </LoopSequence>
<UseLoopSequence> 1 </UseLoopSequence>
<InputPDB> /home/vijay/divya/ps39_3/refinement/cns/denzo1/04_model.pdb
</InputPDB>
<IncludeChains> </IncludeChains>
<InputMTZ>
/home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/ps39_3_refmac4.mtz
</InputMTZ>
<OutputMapFromMTZ> /tmp/vijay/ps39_3_loopy1.map </OutputMapFromMTZ>
<FWTLabel> FWT </FWTLabel>
<PHIWTLabel> PHWT </PHIWTLabel>
<SaveResult> 0 </SaveResult>
<SaveBestLoopSets> 1 </SaveBestLoopSets>
<SaveBestNumber> 5 </SaveBestNumber>
<SaveLoopsDir> /home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac
</SaveLoopsDir>
<SaveLoopsBasename> 04_model_loop </SaveLoopsBasename>
<SaveProposedPDBDir> /home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac
</SaveProposedPDBDir>
<SaveProposedPDBBasename> 04_model_proposed </SaveProposedPDBBasename>
<SaveUseLoopDef> 0 </SaveUseLoopDef>
<WeightMainChain> 1. </WeightMainChain>
<WeightSideChain> 0. </WeightSideChain>
</loop>
</arp-warp>
----------------------------------------------------------------------------------------------------
> Hi -
>
>
> On 28 Jul 2007, at 13:59, Karthikeyan S. wrote:
>
>> Dear CCP4BB members,
>>
>> I am using the loop building module of new arp/warp 7.0 version in
>> RHEL. I
>> am sure during installation everthing went well. But when I try to
>> run the
>> program the following error occured. I think the problem is
>> somewhere in
>> the xml file format.
>
> I am afraid you run in a weird bug ...
>
> Look at the following line from the file you sent:
>
>> <LoopsToBuild> C104<8>C112 </LoopsToBuild>, Was not considered.
>
> In the script file we do try and substitute '<' and '>' with 'lt' and
> 'gt', since <,> are invalid XML characters.
> Somehow, that does not happen in your system and at least one more
> system we know of.
>
> This line should look like
>
> <LoopsToBuild> C104<4>C112 </LoopsToBuild>
>
> if you edit it in the file you sent and then rerun from the command line
> (copying from your log file)
>
> /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/loop -
> paramfile=/tmp/vijay/v3_8_1_com.tmp
>
> it should work.
>
> If anyone has a clue why the substitution works in some systems but
> in some does not, please help us !
> A user has seen it once before, but I cant reproduce in OSX, FC5 ...
> Any clues would be appreciated.
>
> Tassos
>
