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, bcur001@ec.auckland.ac.nz 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. > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage