[phenixbb] sculpt program
Dr G. Bunkoczi
gb360 at cam.ac.uk
Mon Apr 12 02:02:04 PDT 2010
Hi Shya,
this (admittedly cryptic) message usually indicates that the chain sequence
does not match any sequences in the alignments you provide. In the current
version, the program actually stops with an error message saying that no
alignment has been found (for a certain chain), and is hopefully more
self-explanatory.
If you find no mismatches, could you send me (not the list!) the files in
question, and I will investigate.
Sculptor tolerates common modifications (e.g. oxidation, glycosylation) to
residues, but is not tolerant towards mismatches. One particularly vicious
case is seleno-methionine, which is (as a special case) recognized by
sculptor as M, but often put down as X in the sequence/alignment file. I am
currently in two minds whether this special case should be kept as it
creates more confusion than the additional sequence check it provides.
Best wishes, Gabor
On Apr 10 2010, sbiswas2 at ncsu.edu wrote:
>Dear all,
>
>I was trying to generate a model using the sculpt program in phenix. when
>I run it with both alignment file and pdb file I get the following
>message:
>Processing PDB...
>Next model: ''...
>Next chain 'A'...
>No matching alignment for chain 'A'; delete
>PDB output requested
>Executing design...
>Everything is deleted; output file empty
>
>Any help with this...
>
>thanks,
>Shya
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>phenixbb at phenix-online.org
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>
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Dr Gabor Bunkoczi
Cambridge Institute for Medical Research
Wellcome Trust/MRC Building
Addenbrooke's Hospital
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Cambridge CB2 0XY
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