VMD-L Mailing List

From: Robison, Keith (krobison_at_codondevices.com)
Date: Tue Jul 29 2008 - 13:32:19 CDT

Thanks for the quick response.

Strange, it wouldn't load anything (same problem each time) but now I've
quit & restarted it's behaving -- but I had tried that once before. Now
on 2 restarts it is working.

Thanks again -- apologies apparently reporting a local gremlin

-----Original Message-----
From: Elijah Roberts [mailto:erobert3_at_scs.uiuc.edu]
Sent: Tuesday, July 29, 2008 2:17 PM
To: Robison, Keith
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Multiseq refusing to load a structure due to
taxonomy problem

Hi Keith, I was able to load the structure 2VBI on a Mac successfully.
Have you been able to load any other structures into MultiSeq?

Elijah

Robison, Keith wrote:
> 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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