Re: [modeller_usage] Alignment file not recognizing a chain break?
To: "Kolmus, Elizabeth K." <>, "" <>
Subject: Re: [modeller_usage] Alignment file not recognizing a chain break?
From: Modeller Caretaker <>
Date: Tue, 09 Jun 2015 09:54:59 -0700
On 06/09/2015 08:32 AM, Kolmus, Elizabeth K. wrote:
I am attempting to model a target sequence from multiple templates. When
I check the alignment, I'm getting an error I can't resolve either on my
own or by consulting previous entries on the mailing list. It appears
that the program is concatenating the end of one chain directly onto the
beginning of the other and ignoring a gap.
Modeller doesn't do anything special. It reads the PDB file strictly
sequentially. Every residue in the PDB file needs to also be in the
alignment file, in the same order. Gaps (and chain breaks) are used to
align the template sequence with the target - they have no effect on the
matching between alignment file and PDB.
"This command can raise ... a
SequenceMismatchErrorif a 'PIR' sequence does not match that read from
PDB (when an empty range is given)" - does this mean that automodel will
not run on the alignment? What is the appropriate fix?
The fix is simple - your alignment sequence must match the primary
sequence from the PDB. Looking at 3TNP from PDB, it does not match your
alignment.
I suspect I may also have trouble down the line with matching the chains
together, given that 3TNP is formatted as 1-2-1-2 and 3J4Q is formatted
as 3-1-1-2-2. Will this be an issue, and if so, what is the workaround?
Modeller doesn't care what order the chains are in in your PDB files, as
long as you put them in the same order in the alignment file. All the
information it uses to build the model is structural. If you want to
change the order, edit the input PDB files accordingly.