VMD-L Mailing List

From: Robison, Keith (krobison_at_codondevices.com)
Date: Tue Jul 29 2008 - 08:22:24 CDT

Hello!

I installed VMD on my Windows box just a few days ago. I am running into
a problem with loading one particular structure file (2VBI) into
MultiSeq, which is causing the below error. I tried looking at the .tcl
file for this but I'm not a TCL programmer and I couldn't do much more
than verify that the source code (below) seems to have the correct
balancing of braces.

MultiSeq Error)
unmatched open brace in list
    while executing
"join [concat $genus " " $species"
    (procedure "::SeqData::Taxonomy::findNodeBySpecies" line 12)
    invoked from within
"::SeqData::Taxonomy::findNodeBySpecies [getName $sequenceID"
    (procedure "findTaxonomyNode" line 15)
    invoked from within
"findTaxonomyNode $seqNum"
    (procedure "::SeqData::addSeq" line 28)
    invoked from within
"::SeqData::addSeq $sequence $name "Y" $firstResidue $sources
[determineType $molID $chain $segname"
    (procedure "addVMDSequence" line 47)
    invoked from within
"addVMDSequence $molID $chain $segname $sequence "[getMoleculeName
$molID]$nameSuffix" [lindex $residues 0] $residues"
    (procedure "::SeqData::VMD::updateVMDSequences" line 115)
    invoked from within
"::SeqData::VMD::updateVMDSequences"

The procedure in question is

    proc findNodeBySpecies {name} {
        
        # Import global variables.
        variable speciesMap
        
        # Make sure the species map is loaded.
        loadSpeciesMap
        
        # See if we can identify the taxonomy node for this name.
        if {[info exists speciesMap($name)]} {
            return $speciesMap($name)
        } elseif {[regexp {^([^\s\_]+)[\s\_]([^\s\_]+)} $name unused
genus species] && [info exists speciesMap([join [concat $genus " "
$species]])]} {
            return $speciesMap([join [concat $genus " " $species]])
        } elseif {[regexp {^[^\s\_]+[\s\_]([^\s\_]+)[\s\_]([^\s\_]+)}
$name unused genus species] && [info exists speciesMap([join [concat
$genus " " $species]])]} {
            return $speciesMap([join [concat $genus " " $species]])
        } elseif {[regexp
{^[^\s\_]+[\s\_][^\s\_]+[\s\_]([^\s\_]+)[\s\_]([^\s\_]+)} $name unused
genus species] && [info exists speciesMap([join [concat $genus " "
$species]])]} {
            return $speciesMap([join [concat $genus " " $species]])
        }
        
        return ""
    }

Thanks in advance for any suggestions

Keith Robison, Ph.D.
Codon Devices Inc

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