Dear Sir, 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 Thanking you, Sincerely, Jaimin Shah M.Sc. (Biotechnology) I.I.T. Powai
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
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
Concerning your specific query about the BEGINNING OF COMMAND error :
On Tue, 13 Jan 2004 11:54:44 +0530 (IST) "Jaimin Shah" jaimin@iitb.ac.in wrote:
> 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
The line beginning 'pddbnam__217W' actually says what the error is. MODELLER cannot find 1piea.atm, 1piea.pdb, 1piea.ent, or 1piea.crd in any of the directories given in ATOM_FILES_DIRECTORY.
When you have problems with MODELLER, you should examine the output very carefully. It has given you some warnings (these lines begin with a code like : afuncnam__123W> The W> indicates a warning message. E> indicates an error message (which may have arisen because of the previous warnings).
There are several warnings given in the output, telling you that the PIR headers in your alignment file are incorrect (these are lines like : structure:1pdb:Start:C:End:C:.:.:.:.
In your case, you need to add some extra ':' separated fields in each of the PIR headers in the alignment file. Look at the example above : I have used'.' as a wildcard, to specify that there is no required value for these fields.
Hope this helps, j.
______________________________________________________________________ Dr JB Procter:Biomolecular Modelling at ZBH - Center for Bioinformatics Hamburg http://www.zbh.uni-hamburg.de/staff.php
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J B Procter -
Jaimin Shah -
Modeller Caretaker