[modeller_usage] Multi-chain/multi-template Modeling

Hey there Modellers,

I appreciate the input I received from my previous questions, but have run into something I need more clarification on. I'm attempting to product models using multiple templates and multiple chains. I'll detail my steps below:

Step 1:

Build individual chain profiles using build_profile.py, as seen in the basic tutorial (select PDBs based on e-val and identity thresholds).

Step 2:

Use the multiple template salign.py program as seen in the advanced tutorial (the first script in the tutorial), on PDBs selected in step 1.

Step 3:

Here I attempted to combine alignment profiles. I wrote a quick python script to do so. I'll show a snippet of the output below, please note that some structures only offer one chain that could be used as a template, if this was the case I use a hyphen a placeholder... which I think is the source of at least one of my problems.

>P1;2bnu
structure:2bnu:   1 :A:252 :B:::-1.00:-1.00
--QEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGRST
LYIAASQPGDSATYLCAVRPTSGGSYIPTFGRGTSLIVHPYIQNPDPAVYQLRRSKSSDKSVCLFTDFDSQTNVS
QSKD--SDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS-----/
--GVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFP
LRLLSAAPSQTSVYFCASSYVG-N-TGELFFGEGSRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATG
FYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWT
QDRAKPVTQIVSAEAWGRAD-------*

>P1;5bs0
structure:5bs0:   1 :D:252 :E:::-1.00:-1.00
-AQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLYVRPYQREQTSGRLNASLDKSSGRST
LYIAASQPGDSATYLCAVRPGGAGPFFVVFGKGTKLSVIPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVS
QSKD--SDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIP------------/
---------------------------------------------------------------------------
---------------------------------------------------------------------------
---------------------------------------------------------------------------
---------------------------*

>P1;4grm
structure:4grm:   1 :A:252 :B:::-1.00:-1.00
--------------------------------------------------------------------------
--------------------------------------------------------------------------
--------------------------------------------------------------/
--GVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFP
LRLLSAAPSQTSVYFCASRPGL---QPEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATG
FYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWT
QDRAKPVTQIVSAEAWGRAD-------*
>P1;2pye
sequence:2pye:   1 :A:252 :B:::-1.00:-1.00
MKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGSST
LYIAASQPGDSATYLCAVRPLLDGTYIPTFGRGTSLIVHPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVS
QSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNS/
MGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGTTDQGEVPNGYNVSRSTIEDFPL
RLLSAAPSQTSVYFCASSYLGNTGELFFGEGSRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYP
DHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDR
AKPVTQIVSAEAWGRAD*

Step 4:
Next, I attempted to use the second salign.py script in the advanced tutorial, hoping for PDB-multi.ali and PDB-multi.prf files which I did not receive. The error code was as seen below:

_modeller.ModellerError: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT 
(or the alignment file header) was not found; requested starting position: residue number " 1", chain " A"; atom file name:  2bnu.pdb

I'm assuming this has to do with the pdbID_fit.pdb files outputted by the program in step 2. So am I merging my alignment file too late? I'm also assuming the pdbID_fit.pdb file must contain both chains. Regardless any guidance for producing models from this would be very useful.
Best,
Ryan