Re: [modeller_usage] Alignment file.

[Eswar Narayanan <>]

You should convert your sequence (1005) to upper case. MODELLER  
interprets some of the smaller case single-letter residue codes as  
other residues (see $LIBS/restyp.lib).

Eswar.

On Oct 13, 2004, at 5:19 AM,  wrote:

> I'm doing something wrong, I'm a novice though, so I know what what.
> I'm using a fairly simple TOP script to generate a model a  
> nitroreductase.
> I've used blast on NCBI to find a simialr protein to the one I have  
> the pdb
> model for. The blast results look like this :
>
> Query: 1    
> MDIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARV 60
>            MDIISVALKRHSTKAFDASKKLT E+AE+IKTLLQYSPSSTNSQPWHFIVASTEEGKARV
> Sbjct: 1    
> MDIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARV 60
>
> Query: 61   
> AKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKG 120
>            AKSAAG YVFNERKMLDASHVVVFCAKTAMDD WL+ VVDQE+ADGRF TPEAKAAN KG
> Sbjct: 61   
> AKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKG 120
>
> Query: 121  
> RKFFADMHRKDLHDDAEWMAKQVYLNVGNFXXXXXXXXXXXXPIEGFDAAILDAEFGLKE 180
>            R +FADMHR DL DD +WMAKQVYLNVGNF            PIEGFDAAILD EFGLKE
> Sbjct: 121  
> RTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKE 180
>
> Query: 181 KGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTE 216
>            KG+TSLVVVPVGHHSVEDFNATLPKSRLP +  +TE
> Sbjct: 181 KGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTE 216
>
>
> How do I then transform this into a successful alignment file?
> My attempt looks something like this:
> > P1;1OO5
> structureX:1OO5:   2 :A: 217 :D:undefined:undefined:-1.00:-1.00
> mdiisvalkrhstkafdaskkltpeqaeqiktllqyspsstnsqpwhfivasteegkarvaksaagnyvfn 
> erkml
> dashvvvfcaktamddvwlklvvdqedadgrfatpeakaandkgrkffadmhrkdlhddaewmakqvylnv 
> gnfll
> gvaalgldavpiegfdaaildaefglkekgytslvvvpvghhsvedfnatlpksrlpq nitltev*
>
> > P1;1NEC
> sequence:1NEC:   2 :A: 216 :D:undefined:undefined:-1.00:-1.00
> DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNE 
> RKML
> DASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNV 
> GNFL
> LGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTE*
>
> I've basically taken the Query sequence (1OO5) which I have the pdb  
> file for and
> placed it in the sequence section, then taken the result sequence  
> which has
> been matched to it (1NEC) and placed it in the second position of the  
> alignment
> file with the sequence label.
> However, when I run it, in my mod.log file, I'm getting the error:
>
> Dynamically allocated memory at         amaxseq [B,kB,MB]:      2205269
> 2153.583     2.103
> openf5__224_> Open       11  OLD  SEQUENTIAL  1OO5.ali
>
> Dynamically allocated memory at         amaxbnd [B,kB,MB]:      5377489
> 5251.454     5.128
> openf5__224_> Open       11  OLD  SEQUENTIAL  1OO5.ali
> read_al_375E> Unknown residue type,position,sequence:  m        1       
>   1
> recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
>
>
>
> As far as I can gatherThis means that it doesn't like the residue at  
> position
> one. I don't however know what it doesn't like about the residue at  
> that
> position. Am I creating the alignment file in the wrong manner? Is  
> there
> something else wrong?
>
> In case it of any use, the top file looks like:
> INCLUDE                             # Include the predefined TOP  
> routines
> SET OUTPUT_CONTROL = 1 1 1 1 1      # uncomment to produce a large log  
> file
> SET ALNFILE  = '1ICV.ali'           # alignment filename
> SET KNOWNS   = '1ICV'               # codes of the templates
> SET SEQUENCE = '1NEC'               # code of the target
> # SET HYDROGEN_IO = on
> SET HETATM_IO = on
> SET ATOM_FILES_DIRECTORY = '../pdb' # directories for input atom files
> SET STARTING_MODEL= 1               # index of the first model
> SET ENDING_MODEL  = 10              # index of the last model
>                                     # (determines how many models to  
> calculate)
> SET PDB_EXT = '.modlr.pdb'
> SET MD_LEVEL = 'refine_5'
> SET LIBRARY_SCHEDULE = 1
> CALL ROUTINE = 'model
>
>
> Thanks.
> Ben.
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