[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
>_______________________________________________
>phenixbb mailing list
>phenixbb at phenix-online.org
>http://phenix-online.org/mailman/listinfo/phenixbb
>

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     Dr Gabor Bunkoczi

     Cambridge Institute for Medical Research
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     Cambridge CB2 0XY
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