[phenixbb] Fwd: Re: Sculptor

Gabor Bunkoczi gb360 at cam.ac.uk
Mon Sep 8 03:28:06 PDT 2014

Apologies, this was meant for the BB.

-------- Original Message --------
Subject: Re: [phenixbb] Sculptor
Date: 2014-09-08 10:41
 From: Gabor Bunkoczi <gb360 at cam.ac.uk>
To: Marie Elizabeth Fraser <frasm at ucalgary.ca>

Hi Marie,

please check the extension of your alignment. If it is .pir, the second 
line is supposed to be a comment line, and it is therefore ignored. You 
can either change the extension to .ali, or insert an empty line after 
the ones starting with ">".

If this is not the problem, then this is not supposed to happen. Please 
send me the logfile in the first instance, although I may need the 
actual alignment and the PDB file as well (you can delete the target 
sequence if you wish, an alignment with a single sequence is perfectly 

BW, Gabor

On 2014-09-08 01:22, Marie Elizabeth Fraser wrote:
> Hello,
>  I'm running Sculptor from the Phenix GUI, trying to improve a
> molecular replacement model. I've given the pdb file and a sequence
> alignment. Sculptor does not appear to accept the first residues
> aligned in the sequence alignment. In the alignment, these residues
> are residue numbers 42 to 60, so they are on the second line of the
> fasta file (the first line after the title) and Sculptor starts at
> residue 61 (the subsequent line). Residues 42 to 60 of the target are
> to match the first residues of the pdb model, so in the alignment,
> there are 41 dashes before the beginning of the sequence for the pdb
> file. Am I giving an incorrectly formatted sequence alignment,
> misinterpreting what Sculptor does or is Sculptor supposed to do this?
>  Thank you, Marie
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