Sequence display error

[Maz S. Ardejani]

I load a fasta file (>molecule>read/write topology>sequence file) and then >Assign>Sequence and I get a blank .Seq window with this error:

can't use non-numeric string as operand of "%"
    ("if" test expression)
    invoked from within
"if {($iRes % 5) == 0} {
                $canvas create text $x $y -text $iRes -fill black -anchor s -font "Courier $pars(fontSize)"
                $c..."
    ("foreach" body line 89)
    invoked from within
"foreach "iRes rname"  $residues($entity) {
            incr resIndex
            incr j
            if {$iRes == "."} {
                break
        ..."
    ("foreach" body line 2)
    invoked from within
"foreach entity [mol entities $molName] {
        foreach "iRes rname"  $residues($entity) {
            incr resIndex
            incr j
            i..."
    (procedure "::nv::seq::makeCanvas" line 257)
    invoked from within
"::nv::seq::makeCanvas"
    (procedure "::nv::seq::makeGUI" line 105)
    invoked from within
"::nv::seq::makeGUI .seq"
    ("binding" script)

How can I fix this? Re-istalling NMRViewJ didn't help.

Cheers,

Maz. 

[brucej]

Reading a sequence from a file only works with the format where each residue is specified with three-letter code (for proteins) on single line of the file.  You can have an optional residue number on the line as well:

met 3

ala

gly

phe

If you want to use a single letter code description of the sequence you need to use the Sequence GUI (and check the single letter checkbox).

Hope this helps

Bruce

[Maz S. Ardejani]

Thanks a lot Bruce! I couldn't find this in the documentation. If this explanation is not in the documentation, it would be really helpful to have it there.

[brucej]

There's some discussion in the section on Molecular Topology, but it doesn't explicitly say that you can't read the FASTA format from a file.  Also, the formatting of that documentation is messed up so it's hard to read the file format section.  I'll try to fix that.

Bruce