------------------------
OK thanks.
I tried a different example, which did give me a (wrong) assignment -
is there any way of picking an alternative?
What partly confused me before and again was that this command assigns
the sequence but doesn't build the side chains - you have to use the
Fill Partial Residues command, I suppose
Also if I go back to the GUI for the same "molecule", it displays 2
sequences
Thanks again
Phil
---------------------------
then cootaneer
iv: 0 seq.size: 1
debug pythoning and
MHHHHHHLVPRGSHMIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ
in assign_sequence_from_string
storing sequence:
MHHHHHHLVPRGSHMIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ
for chain id: A
(assign-sequence-from-string 2 "A"
"MHHHHHHLVPRGSHMIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ
")
Sequence: ?KIEFT?
Confidence: 0.912518
On 4 Jun 2009, at 13:37, Bernhard Lohkamp wrote:
I guess you didnt give it a chain id. When sequencing the closest
fragment this information is required (maybe it shouldnt, or at
least it
should give the appropriate warning - I will look into it at some
point).
B
I'm trying to understand the Extensions-> Dock sequence dialogue.
How
does it work?
I've tried
Place helix here
Select Dock Sequence
choose Helix molecule
Load sequence from a file
click "Sequence closest fragment"
then I get
assign-sequence-from-file 2 "/Users/pre/Documents/Talks/
Crystallography/LMB-2009/MapFitting/Examples/amph2.seq")
iv: 0 seq.size: 1
debug pythoning and
MAEMGSKGVTAGKIASNVQKKLTRAQEKVLQKLGKADETKDEQFEQCVQNFNKQLTEGTRLQKDLRTYLASVKAMHEASKKLSECLQEVYEPEWPGRDEANKIAENNDLLWMDYHQKLVDQALLTMDTYLGQFPDIKSRIAKRGRKLVDYDSARHHYESLQTAKKKDEAKIAKPVSLLEKAAPQWCQGKLQAHLVAQTNLLRNQAEEELIKAQKVFEEMNVDLQEELPSLWNSRVGFYVNTFQSIAGLEENFHKEMSKLNQNLNDVLVSLEKQHGSNTFTVKAQPSDSAPEKGNKSPSPPPDGSPAATPEIRVNHEPEPASGASPGATIPKSPSQLRKGPPVPPPPKHTPSKEMKQEQILSLFDDAFVPEISVTTPSQFEAPGPFSEQASLLDLDFEPLPPVASPVKAPTPSGQSIPWDLWEPTESQAGVLPSGEPSSAEGSFAVAWPSQTAEPGPAQPAEASEVVGGTQEPGETAASEATSSSLPAVVVETFSATVNGAVEGSTTTGRLDLPPGFMFKVQAQHDYTATDTDELQLKAGDVVLVIPFQNPEEQDEGWLMGVKESDWNQHKELEKCRGVFPENFTERVQ
apply the sequence info here
then cootaneer
ERROR:: the input contains an invalid chain and/or sequence
BL ERROR:: something went wrong assigning the sequence
What should I have done? (Coot 0.6-pre 1 1941, OSX)
Best wishes
Phil
