Ilya Shlyakhter wrote: > I'm getting a "dynamic memory allocation failed" message on a very > small model. The test examples work fine, but when I modify > model-full.py for my own use it gives a problem. Below I give the > files I used, and the error message. I would appreciate any > suggestions.
I'm guessing that there was a typo in your message, and that really you had '*' as the sequence for 1yod, i.e.
>> P1;1yod > structureX:1yod:1:B:51:B:phospholamban:Homo sapiens: 1.80:0 > *
There is no residue 1 in chain B in PDB code 1yod, so Modeller fails to read in this sequence (notice that it's given as zero length):
> # Code #_Res #_Segm PDB_code Name > ------------------------------------------------------------------------------- > 1 1fjk 52 1 1fjk phospholamban > 2 1yod 0 0 1yod phospholamban
The final error message you got is, admittedly, rather cryptic, but I've just put in a more informative error (which will be in the next Modeller release).
The solution to your problem is to correct the start residue:chain for the 1yod sequence.
Ben Webb, Modeller Caretaker