Re: [ccp4bb] ARP/wARP 7.0 error

[Serge Cohen]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello Karthik;
Indeed the problem seems to lie in the XML produced by the CCP4 GUI  
which is very likely to contain a first (or few initial) line(s)  
which makes "loop" to believe it has to deal with NON-XML input while  
indeed the input is XML...

Hence (as stated by the first warning) it turns to the fall-back  
'plain-text' format for parsing the parameter file but then it is  
confused as soon as it encounters the body of the file which is NOT  
"plain-text" but XML.

One thing you should try is to :

1. look at the parameter file in an editor (file /tmp/vijay/ 
v3_8_1_com.tmp)
2. If as mentioned above it contains a few plain text lines at the  
beginning, delete them.
3. Also you have to check that the loop which is defined by  
"<LoopsToBuild> C104<8>C112 </LoopsToBuild>" should indeed be  
"<LoopsToBuild> C104&lt;8&gt;C112 </LoopsToBuild>" (because plain <  
and > are not valid in XML, unless marking a tag). (indeed this alone  
would produce the error you see).
4. Then re-run loop :
/home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/loop - 
paramfile=/tmp/vijay/v3_8_1_com.tmp

Last remark : We had some trouble while testing on 64b x86 (AMD or  
intel x86 processor running in 64b mode). If you encounter more  
troubles we are very interested in your feed-back. In the meantime  
(if encountering 'Illegal Instruction' or other kind of core-dump),  
you can run using the x86 32bit version which is likely to run also  
on your computer :

/home/programs/linux/arp_warp_7.0/bin/bin-i686_64-Linux/loop - 
paramfile=/tmp/vijay/v3_8_1_com.tmp

Please do not hesitate to send any more question, bug report...

Cheers;

Serge.


Le 28 juil. 07 à 13:59, Karthikeyan S. a écrit :

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.

Any help is highly appreciated!

Thanks
Karthik

(Sorry for the long log file)


---------------------------------------------------------------------- 
--------

#CCP4I VERSION CCP4Interface 1.4.4.2
#CCP4I SCRIPT LOG loopy
#CCP4I DATE 24 Jul 2007  09:20:39
#CCP4I USER vijay
#CCP4I PROJECT v3
#CCP4I JOB_ID 8
#CCP4I SCRATCH /tmp/vijay
#CCP4I HOSTNAME localhost.localdomain
#CCP4I PID 28599

## This script run with the command   ##########
# /home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/loop
-paramfile=/tmp/vijay/v3_8_1_com.tmp
################################################
loop - WRNG* : CConfig::processStream File isn't in proper XML format

loop - WRNG* : Couldn't read XML parameter file for warp::CConfig.
loop - WRNG* : CConfig::processStream Handling parameter file as  
non-xml.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <arp-warp>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <loop>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <MessageFilename>
/home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/loopy.msg
</MessageFilename>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <XMLOutputFilename>
/home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/loopy.xml
</XMLOutputFilename>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <AbortLevel> 8 </AbortLevel>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <MessageLevel> 4 </MessageLevel>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <ProgramName> loopy </ProgramName>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <DictionaryFilename>
/home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/ 
AAbis_extension.XYZ
</DictionaryFilename>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <UniformAtomBFactor> 20 </UniformAtomBFactor>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <UniformAtomRadius> 0.74 </UniformAtomRadius>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <AntiBumpFactor> 1. </AntiBumpFactor>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <SymmetryFilename>
/home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/syminfo.lib
</SymmetryFilename>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <SpaceGroup> 19 </SpaceGroup>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <XtalCell> 60.489 112.116 133.838 90.00 90.00 90.00 </XtalCell>,  
Was not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <KeepSideChain> 1 </KeepSideChain>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <KeepFragmentLongerThan> 0 </KeepFragmentLongerThan>, Was not  
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <UseCDummyResidue> 1 </UseCDummyResidue>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <StructureFilenameToC>
/home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/ 
set_1200_2C_my_0.3b_cos_log.llh
</StructureFilenameToC>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <StructureFilenameToN>
/home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/ 
set_1200_2N_my_0.3b_cos_log.llh
</StructureFilenameToN>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <CADistance> 3.8 </CADistance>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <RandomGrid> 0 </RandomGrid>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <GridNumber> 378 </GridNumber>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <DisregardNegativeDensity> 1 </DisregardNegativeDensity>, Was 
not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
		<KeepNegDensityHalfway> 0 </KeepNegDensityHalfway>, Was not  
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <NormalizeDensity> 1 </NormalizeDensity>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <BFactorForBuildSideChain> 26 </BFactorForBuildSideChain>, Was 
not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
		<LikelihoodThreshold> -4.5 </LikelihoodThreshold>, Was not  
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <WeightDensityLLH> 1. </WeightDensityLLH>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <WeightDistanceLLH> 1. </WeightDistanceLLH>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <WeightStructuralLLH> 1. </WeightStructuralLLH>, Was not 
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <OldComputation> 0 </OldComputation>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <CheckFirstAngle> 1 </CheckFirstAngle>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <UseCubicFitTarget> 1 </UseCubicFitTarget>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
		<OverlapRejectionThreshold> 0.1 </OverlapRejectionThreshold>, Was  
not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <DummyRejectionThreshold> 0.1 </DummyRejectionThreshold>, Was 
not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <LoopBuildAll> 0 </LoopBuildAll>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
		<ExtendGapSmallerThan> 0 </ExtendGapSmallerThan>, Was not  
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <LoopBothWays> 1 </LoopBothWays>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <LoopToC> 1 </LoopToC>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <LoopLength> </LoopLength>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <LoopOverlap> 0 </LoopOverlap>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
		<LoopDensityCutoffNo> 100 </LoopDensityCutoffNo>, Was not  
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <MinimalDistance> 0.3 </MinimalDistance>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <MaxNoCAsKept> 6 </MaxNoCAsKept>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <ForceMinCAsKept> 2 </ForceMinCAsKept>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <LoopRMS> 0.7 </LoopRMS>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <LoopStructureThreshold> -1.5 </LoopStructureThreshold>, Was not
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
		<LoopStructureCutoffNo> 50 </LoopStructureCutoffNo>, Was not  
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <LoopStructureMinNo> 15 </LoopStructureMinNo>, Was not 
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <LoopMainChainDensNo> 5 </LoopMainChainDensNo>, Was not 
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <LoopsToBuild> C104<8>C112 </LoopsToBuild>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <LoopSequence> PNHVTYSGD </LoopSequence>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <UseLoopSequence> 1 </UseLoopSequence>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
		<InputPDB> /home/vijay/divya/ps39_3/refinement/cns/ 
denzo1/04_model.pdb
</InputPDB>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <IncludeChains>  </IncludeChains>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <InputMTZ>
/home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac/ 
ps39_3_refmac4.mtz
</InputMTZ>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
		<OutputMapFromMTZ> /tmp/vijay/ps39_3_loopy1.map </ 
OutputMapFromMTZ>, Was
not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <FWTLabel> FWT </FWTLabel>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <PHIWTLabel> PHWT </PHIWTLabel>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <SaveResult> 0 </SaveResult>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <SaveBestLoopSets> 1 </SaveBestLoopSets>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <SaveBestNumber> 5 </SaveBestNumber>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
                <SaveLoopsDir> 
/home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac
</SaveLoopsDir>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <SaveLoopsBasename> 04_model_loop </SaveLoopsBasename>, Was not  
considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <SaveProposedPDBDir>
/home/vijay/divya/ps39_3/refinement/cns/denzo1/refmac
</SaveProposedPDBDir>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <SaveProposedPDBBasename> 04_model_proposed </ 
SaveProposedPDBBasename>,
Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <SaveUseLoopDef> 0 </SaveUseLoopDef>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <WeightMainChain> 1. </WeightMainChain>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  <WeightSideChain> 0. </WeightSideChain>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  </loop>, Was not considered.
loop - WRNG* : CConfig::readLine Invalid line read from parameter  
file :
  </arp-warp>, Was not considered.
loop - WRNG* : CConfig::CConfig : Some argument of the command line  
(was)
were not parsed by CConfig, ie not understood by libwarp.

<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 : Tue Jul 24 09:20:39 2007

loop - ERROR** : Unable to open file with name : ''. Hence unable to
create a dictionary of Amino Acids!
********************************************************************** 
*****
* Information from CCP4Interface script
********************************************************************** 
*****
The program run with command:
/home/programs/linux/arp_warp_7.0/bin/bin-x86_64-Linux/loop
-paramfile=/tmp/vijay/v3_8_1_com.tmp
has failed with error message
:51: parser error : StartTag: invalid element name
<LoopsToBuild> C104<8>C112 </LoopsToBuild>
                    ^
Parameter Stream does NOT contain XML!!!
MIGHT ABORT NOW, error message is : ERROR** : Unable to open file with
name : ''. Hence unable to create a dictionary of Amino Acids!
********************************************************************** 
*****


#CCP4I TERMINATION STATUS 0 ":51: parser error : StartTag: invalid  
element
name <LoopsToBuild> C104<8>C112 </LoopsToBuild>                     ^
Parameter Stream does NOT contain XML!!! MIGHT ABORT NOW, error  
message is
: ERROR** : Unable to open file with name : ''. Hence unable to  
create a
dictionary of Amino Acids!"
#CCP4I TERMINATION TIME 24 Jul 2007  09:20:40
#CCP4I MESSAGE Task failed

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.3 (Darwin)

iD8DBQFGqz7C5EPeG5y7WPsRAojHAJ9r8zjDNR6N+9aaZr76LSnS8glDIACfYlGm
ejakSCG6I76aZOpCan7oLZw=
=k1Y2
-----END PGP SIGNATURE-----