sequence file produced is different from the one shown in the tutorial
Hi everyone,
I am working on the example given in the modeller tutorial http://salilab.org/modeller/wiki/Missing%20residues. I used the exact same script to generate the sequence file. Instead of the given pdb1qg8.ent , I used the 1qg8.pdb downloaded from www.rcsb.org. When I ran the script it resulted in the following sequence file (1qg8.seq)
>P1;1qg8 structureX:1qg8: 2 :A:+238 :A:MOL_ID 1; MOLECULE SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA; CHAIN A; ENGINEERED YES; OTHER_DETAILS GLYCEROL MAGNESIUM:MOL_ID 1; ORGANISM_SCIENTIFIC BACILLUS SUBTILIS; GENE SPSA; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_STRAIN BL 21: 1.50: 0.16 PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTR YAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNDIVKETVRPAAQVTWNAP CAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITEFVRNLPPQRNC RELRESLKKLGMG*
In the field 5, it says +238 whereas in the tutorial, in the resulting 1qg8.seq file it shows 256. Have I done any mistake? Would the above sequence file work just as fine as the one shown in the tutorial?
Thank you
Sajeewa Dewage
On 9/21/12 1:26 PM, Sajeewa Pemasinghe wrote: > In the field 5, it says +238 whereas in the tutorial, in the resulting > 1qg8.seq file it shows 256. Have I done any mistake? Would the above > sequence file work just as fine as the one shown in the tutorial?
The PIR alignment format is described at http://salilab.org/modeller/9.11/manual/node476.html
"+238" means "read 238 residues from the PDB file". "256" means "read until you reach the residue numbered "256" in the PDB file".
They should both result in the same thing. I suggest you run it and see.
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Sajeewa Pemasinghe