Re: [modeller_usage] Incorrect Number or residues/Starting position

[Modeller Caretaker <>]

Kevin Galens (RIT Student) wrote:
> I'm attempting to use modeller to use two templates to model on short 
> sequence.  I'm also creating the alignment file (PIR format) on my own 
> and I'm having some troubles with one of my sequences.  My alignment 
> file is as follows:
>
>  >P1;15c8
> structure:15c8:1:H:217:H::::
> EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQKPEQGLEWIAQI
> DPANGNTKYDPKFQGKATITADTSSNTAYLHLSSLTSEDSAVYY-----CA
> ADPPYYG--------------HGDYWGQGTTLTVSSAKTTPPSVYPLAPGS
> AAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSS
> SVTVPSSTWPSETVTCNVAHPASSTKVDKKIV-----*
>  >P1;1fns
> structure:1fns:1:H:225:H::::
> QVQLKESGPGLVAPSQSLSITCTVSGFSLTDYGVDWVRQPPGKGLEWLGMI
> WGD-GSTDYNSALKSRLSITKDNSKSQVFLKMNSLQTDDTARYYCVRDP--
> -------ADYGNYDYALDYWG------QGTSVTVSSAKTTPPSVYPLAPGS
> AAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSS
> SVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCG*
>  >P1;1f11
> sequence:1f11:1::15:::::
> ---------------------------------------------------
> --------------------------------------------CANDY--
> ---GSTY--------GFAYWG------------------------------
> ---------------------------------------------------
> -------------------------------------*

...

> openf5__224_> Open       11  OLD  SEQUENTIAL  pdb1fns.ent
> 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:  1: H
> rdabrk__288W> Protein not accepted:        2
> check_a_337E> Structure not read in:        2
>
> I'm running version 8v1 on Fedora core 3.  The best that I can decipher 
> is that modeller can't understand the starting position.  Or perhaps it 
> can't find the chain.  The pdb file has the same exact sequence (minus 
> the gaps of course) and chain id H. 

It can't find residue number '1' in chain 'H'. This isn't surprising, 
because PDB code 1fns has chain H numbered from 215 to 439. You should 
fix your alignment file.

> Interestingly (or confusingly) I also tried replacing the residue start 
> and end with the words 'FIRST' and 'LAST' leaving the chain
> H, thinking that Modeller could grab the chain without me telling it 
> where to start and end explicitly.  The end of the error file was as 
> follows:
...
> rdabrk__290E> Number of residues in the alignment and  pdb files are 
> different:
>      225      220
>               For alignment entry:        2
> rdabrk__288W> Protein not accepted:        2
> check_a_337E> Structure not read in:        2
>
>
> Okay, so modeller thinks there are 220 residues in the pdb file? Is it 
> looking at the right chain? The other chains in that file are length 217 
> and 195 (which isn't 220).  It's looking at the correct file, who knows 
> what chain it's going for.

There are 220 residues in chain H, since residues 352 through 356 were 
not located in the experiment (see the REMARK 465 lines). Since there is 
no structural information for these 5 residues, your alignment should 
probably have a gap of width 5 at that point.

Incidentally, there is a similar problem with your other structure 
(15c8); residues 131, 132, 155, and 158 through 161 are missing.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage