Dear Sir, It gives me the following message:
Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153. 583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL align.ali rdpir___376W> Not enough fields in the second line of the sequence entry: struc tureX:1piea:9 : :396 : :galactokinase:Lactococcus lactis: 2.10 Actual fields, should be: 9 10 (Fields are separated by a colon, :) rdpir___376W> Not enough fields in the second line of the sequence entry: seque nce:galk:1 : :392 : :galk:Homo sapiens Actual fields, should be: 8 10 (Fields are separated by a colon, :)
Dynamically allocated memory at amaxbnd [B,kB,MB]: 8050641 7861. 954 7.678 openf5__224_> Open 11 OLD SEQUENTIAL align.ali rdpir___376W> Not enough fields in the second line of the sequence entry: struc tureX:1piea:9 : :396 : :galactokinase:Lactococcus lactis: 2.10 Actual fields, should be: 9 10 (Fields are separated by a colon, :) rdpir___376W> Not enough fields in the second line of the sequence entry: seque nce:galk:1 : :392 : :galk:Homo sapiens Actual fields, should be: 8 10 (Fields are separated by a colon, :)
Read the alignment from file : align.ali Total number of alignment positions: 402
# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1piea 388 1 1piea galactokinase 2 galk 392 1 galk galk TOP_________> 121 107 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND pdbnam__217W> Filename for PDB code not found: 1piea Directories: ./ Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 1 check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 8050641 7861. 954 7.678 Starting time : 2004/01/13 11:55:59. 546 Closing time : 2004/01/13 11:56:00. 718
Please guide me.
Thanking you,
> On Sun, Jan 11, 2004 at 10:20:34AM +0530, Jaimin Shah wrote: >> I am a novice for this program. I would really appreciate it if you can >> expedite matters for me by solving my hurdles. >> I am getting the message: >> check_a_343_> >> BEGINNING OF COMMAND >> check_a_337E> Structure not read in: 1 1 > > Perhaps you have a sequence mismatch between your structure and your > alignment? It's hard to tell from the output you've posted here. What > errors or warnings do you get prior to that? I suggest you also put > SET OUTPUT_CONTROL = 1 1 1 1 1 > at the start of your TOP file, if you haven't already, to increase the > amount of Modeller output. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage >
Jaimin Shah M.Sc. (Biotechnology) I.I.T. Powai