Alignment sequence not found in PDB file
Hi!
when I get the following error message, I understand that the sequence in my PDB file does not correspond to that read from the alignment. Up to know, it was what had happened, and I always found the problem by trial and error, but this time .... :-(
rdpir___648E> Alignment sequence not found in PDB file: 2 ./1EL3.pdb
Is there some command or switch in modeller to get some more information on what the problem is? i.e. which amino acid does not match?
Thank you very much for any hint,
Karsten.
PS: here my commands:
SET OUTPUT_CONTROL = 1 1 1 1 0 READ_ALIGNMENT FILE = 'tcoffee.aln', ALIGN_CODES = 'all'
and the output:
Job starting time (YY/MM/DD HH:MM:SS): 2002/08/15 23:41:12.615
TOP_________> 2 2 READ_ALIGNMENT FILE = 'tcoffee.aln', ALIGN_CODES = 'all'
openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb rdpir___648E> Alignment sequence not found in PDB file: 1 ./1EL3.pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 8065909 7876.864 7.692
PPS: Attached are the input files (there is only one sequence in the alignment including gaps .. and the PDB file does only contain ATOM lines. That's because I eliminated all other stuff to see whether the error changes .. it doesn't, and I compared the sequences between the PDB file and the alignment - they are identical).
Replace the last zero in OUTPUT_CONTROL to 1. That will give you more info...
Bozidar
On Thu, 15 Aug 2002, Karsten Suhre wrote:
> > Hi! > > when I get the following error message, I understand that the sequence in my > PDB file does not correspond to that read from the alignment. Up to know, it > was what had happened, and I always found the problem by trial and error, but > this time .... :-( > > rdpir___648E> Alignment sequence not found in PDB file: 2 ./1EL3.pdb > > Is there some command or switch in modeller to get some more information on > what the problem is? i.e. which amino acid does not match? > > Thank you very much for any hint, > > Karsten. > > > > PS: here my commands: > > SET OUTPUT_CONTROL = 1 1 1 1 0 > READ_ALIGNMENT FILE = 'tcoffee.aln', ALIGN_CODES = 'all' > > and the output: > > > Job starting time (YY/MM/DD HH:MM:SS): 2002/08/15 23:41:12.615 > > TOP_________> 2 2 READ_ALIGNMENT FILE = 'tcoffee.aln', ALIGN_CODES = > 'all' > > openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln > openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb > openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln > openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb > rdpir___648E> Alignment sequence not found in PDB file: 1 ./1EL3.pdb > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Dynamically allocated memory at finish [B,kB,MB]: 8065909 > 7876.864 7.692 > > > PPS: Attached are the input files (there is only one sequence in the alignment > including gaps .. and the PDB file does only contain ATOM lines. That's > because I eliminated all other stuff to see whether the error changes .. it > doesn't, and I compared the sequences between the PDB file and the alignment > - they are identical). > >
Hi!
I already tried that - even set it to 2. But the fifth flag only controls dynamics memory allocation prints, which is not my problem here. I guess that something in my PDB file doesn't correspond to what modeller expects (my program runs with other PDB files).
Does anybody know which entries modeller reads and checks?
I had a similar problem reading the PIR alignments. You really need to put exactly 9 :'s into the header, and you must give the residues in upper case - while t_coffee writes them out in lower case. That problem I solved by experimentation. What I am seeking here is a way to obtain some more verbose output when modeller has problems reading my input (especially when you modify your alignments by hand errors slip in very easily).
Thanks a lot for giving my problems some consideration,
Kind regards, Karsten.
On Thursday 15 August 2002 23:58, Bozidar Yerkovich wrote: > Replace the last zero in OUTPUT_CONTROL to 1. That will give you more > info... > > Bozidar > > On Thu, 15 Aug 2002, Karsten Suhre wrote: > > Hi! > > > > when I get the following error message, I understand that the sequence in > > my PDB file does not correspond to that read from the alignment. Up to > > know, it was what had happened, and I always found the problem by trial > > and error, but this time .... :-( > > > > rdpir___648E> Alignment sequence not found in PDB file: 2 > > ./1EL3.pdb > > > > Is there some command or switch in modeller to get some more information > > on what the problem is? i.e. which amino acid does not match? > > > > Thank you very much for any hint, > > > > Karsten. > > > > > > > > PS: here my commands: > > > > SET OUTPUT_CONTROL = 1 1 1 1 0 > > READ_ALIGNMENT FILE = 'tcoffee.aln', ALIGN_CODES = 'all' > > > > and the output: > > > > > > Job starting time (YY/MM/DD HH:MM:SS): 2002/08/15 23:41:12.615 > > > > TOP_________> 2 2 READ_ALIGNMENT FILE = 'tcoffee.aln', ALIGN_CODES > > = 'all' > > > > openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln > > openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb > > openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln > > openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb > > rdpir___648E> Alignment sequence not found in PDB file: 1 > > ./1EL3.pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > > Dynamically allocated memory at finish [B,kB,MB]: 8065909 > > 7876.864 7.692 > > > > > > PPS: Attached are the input files (there is only one sequence in the > > alignment including gaps .. and the PDB file does only contain ATOM > > lines. That's because I eliminated all other stuff to see whether the > > error changes .. it doesn't, and I compared the sequences between the PDB > > file and the alignment - they are identical).
I know this might sound like a wichcraft, but I was just helping a fellow MODELLER off the list, who had a similar problem, and I found out that non-visible 'return' sign at the end of his SET OUTPUT_CONTROL line was causing MODELLER not to read in PDB structure. After I entered 'return' and deleted the created new empty line (where this coruptet 'return' simbol was) everything was fine.
I think this might have to do how some text editors interpret carry-over ASCII simbol.
As for more log info, OUTPUT_CONTROL is the only way. Excceptions are some commands that have switches for their outputs (i.e. LONG, SHORT, etc).
Good luck, Bozidar Yerkovich
On Fri, 16 Aug 2002, Karsten Suhre wrote:
> Hi! > > I already tried that - even set it to 2. But the fifth flag only controls > dynamics memory allocation prints, which is not my problem here. I guess that > something in my PDB file doesn't correspond to what modeller expects (my > program runs with other PDB files). > > Does anybody know which entries modeller reads and checks? > > I had a similar problem reading the PIR alignments. You really need to put > exactly 9 :'s into the header, and you must give the residues in upper case - > while t_coffee writes them out in lower case. That problem I solved by > experimentation. What I am seeking here is a way to obtain some more verbose > output when modeller has problems reading my input (especially when you > modify your alignments by hand errors slip in very easily). > > Thanks a lot for giving my problems some consideration, > > Kind regards, Karsten. > > > On Thursday 15 August 2002 23:58, Bozidar Yerkovich wrote: > > Replace the last zero in OUTPUT_CONTROL to 1. That will give you more > > info... > > > > Bozidar > > > > On Thu, 15 Aug 2002, Karsten Suhre wrote: > > > Hi! > > > > > > when I get the following error message, I understand that the sequence in > > > my PDB file does not correspond to that read from the alignment. Up to > > > know, it was what had happened, and I always found the problem by trial > > > and error, but this time .... :-( > > > > > > rdpir___648E> Alignment sequence not found in PDB file: 2 > > > ./1EL3.pdb > > > > > > Is there some command or switch in modeller to get some more information > > > on what the problem is? i.e. which amino acid does not match? > > > > > > Thank you very much for any hint, > > > > > > Karsten. > > > > > > > > > > > > PS: here my commands: > > > > > > SET OUTPUT_CONTROL = 1 1 1 1 0 > > > READ_ALIGNMENT FILE = 'tcoffee.aln', ALIGN_CODES = 'all' > > > > > > and the output: > > > > > > > > > Job starting time (YY/MM/DD HH:MM:SS): 2002/08/15 23:41:12.615 > > > > > > TOP_________> 2 2 READ_ALIGNMENT FILE = 'tcoffee.aln', ALIGN_CODES > > > = 'all' > > > > > > openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln > > > openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb > > > openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln > > > openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb > > > rdpir___648E> Alignment sequence not found in PDB file: 1 > > > ./1EL3.pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > > > > Dynamically allocated memory at finish [B,kB,MB]: 8065909 > > > 7876.864 7.692 > > > > > > > > > PPS: Attached are the input files (there is only one sequence in the > > > alignment including gaps .. and the PDB file does only contain ATOM > > > lines. That's because I eliminated all other stuff to see whether the > > > error changes .. it doesn't, and I compared the sequences between the PDB > > > file and the alignment - they are identical). >
Thank for that hint - but that wasn't it neither.
However, by shuffling around the lines in my input files, I got things eventually working.
Is it true that the order of the structures in the alignment file has to be the same as that in the SET KNOWNS command (maybe I missed this in the manual)?
Kind regards, Karsten.
On Friday 16 August 2002 19:28, you wrote: > I know this might sound like a wichcraft, but I was just helping a fellow > MODELLER off the list, who had a similar problem, and I found out that > non-visible 'return' sign at the end of his SET OUTPUT_CONTROL line was > causing MODELLER not to read in PDB structure. After I entered 'return' > and deleted the created new empty line (where this coruptet 'return' > simbol was) everything was fine. > > I think this might have to do how some text editors interpret carry-over > ASCII simbol. > > As for more log info, OUTPUT_CONTROL is the only way. Excceptions > are some commands that have switches for their outputs (i.e. LONG, SHORT, > etc). > > Good luck, > Bozidar Yerkovich > > On Fri, 16 Aug 2002, Karsten Suhre wrote: > > Hi! > > > > I already tried that - even set it to 2. But the fifth flag only controls > > dynamics memory allocation prints, which is not my problem here. I guess > > that something in my PDB file doesn't correspond to what modeller expects > > (my program runs with other PDB files). > > > > Does anybody know which entries modeller reads and checks? > > > > I had a similar problem reading the PIR alignments. You really need to > > put exactly 9 :'s into the header, and you must give the residues in > > upper case - while t_coffee writes them out in lower case. That problem I > > solved by experimentation. What I am seeking here is a way to obtain some > > more verbose output when modeller has problems reading my input > > (especially when you modify your alignments by hand errors slip in very > > easily). > > > > Thanks a lot for giving my problems some consideration, > > > > Kind regards, Karsten. > > > > On Thursday 15 August 2002 23:58, Bozidar Yerkovich wrote: > > > Replace the last zero in OUTPUT_CONTROL to 1. That will give you more > > > info... > > > > > > Bozidar > > > > > > On Thu, 15 Aug 2002, Karsten Suhre wrote: > > > > Hi! > > > > > > > > when I get the following error message, I understand that the > > > > sequence in my PDB file does not correspond to that read from the > > > > alignment. Up to know, it was what had happened, and I always found > > > > the problem by trial and error, but this time .... :-( > > > > > > > > rdpir___648E> Alignment sequence not found in PDB file: 2 > > > > ./1EL3.pdb > > > > > > > > Is there some command or switch in modeller to get some more > > > > information on what the problem is? i.e. which amino acid does not > > > > match? > > > > > > > > Thank you very much for any hint, > > > > > > > > Karsten. > > > > > > > > > > > > > > > > PS: here my commands: > > > > > > > > SET OUTPUT_CONTROL = 1 1 1 1 0 > > > > READ_ALIGNMENT FILE = 'tcoffee.aln', ALIGN_CODES = 'all' > > > > > > > > and the output: > > > > > > > > > > > > Job starting time (YY/MM/DD HH:MM:SS): 2002/08/15 23:41:12.615 > > > > > > > > TOP_________> 2 2 READ_ALIGNMENT FILE = 'tcoffee.aln', > > > > ALIGN_CODES = 'all' > > > > > > > > openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln > > > > openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb > > > > openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln > > > > openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb > > > > rdpir___648E> Alignment sequence not found in PDB file: 1 > > > > ./1EL3.pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 > > > > 1 > > > > > > > > Dynamically allocated memory at finish [B,kB,MB]: > > > > 8065909 7876.864 7.692 > > > > > > > > > > > > PPS: Attached are the input files (there is only one sequence in the > > > > alignment including gaps .. and the PDB file does only contain ATOM > > > > lines. That's because I eliminated all other stuff to see whether the > > > > error changes .. it doesn't, and I compared the sequences between the > > > > PDB file and the alignment - they are identical).
Yes it has to be the same, otherwise MODELLER will reassign them, which can cause a mess...
Bozidar
> Is it true that the order of the structures in the alignment file has to be > the same as that in the SET KNOWNS command (maybe I missed this in the > manual)? > > Kind regards, Karsten. > > > > On Friday 16 August 2002 19:28, you wrote: > > I know this might sound like a wichcraft, but I was just helping a fellow > > MODELLER off the list, who had a similar problem, and I found out that > > non-visible 'return' sign at the end of his SET OUTPUT_CONTROL line was > > causing MODELLER not to read in PDB structure. After I entered 'return' > > and deleted the created new empty line (where this coruptet 'return' > > simbol was) everything was fine. > > > > I think this might have to do how some text editors interpret carry-over > > ASCII simbol. > > > > As for more log info, OUTPUT_CONTROL is the only way. Excceptions > > are some commands that have switches for their outputs (i.e. LONG, SHORT, > > etc). > > > > Good luck, > > Bozidar Yerkovich > > > > On Fri, 16 Aug 2002, Karsten Suhre wrote: > > > Hi! > > > > > > I already tried that - even set it to 2. But the fifth flag only controls > > > dynamics memory allocation prints, which is not my problem here. I guess > > > that something in my PDB file doesn't correspond to what modeller expects > > > (my program runs with other PDB files). > > > > > > Does anybody know which entries modeller reads and checks? > > > > > > I had a similar problem reading the PIR alignments. You really need to > > > put exactly 9 :'s into the header, and you must give the residues in > > > upper case - while t_coffee writes them out in lower case. That problem I > > > solved by experimentation. What I am seeking here is a way to obtain some > > > more verbose output when modeller has problems reading my input > > > (especially when you modify your alignments by hand errors slip in very > > > easily). > > > > > > Thanks a lot for giving my problems some consideration, > > > > > > Kind regards, Karsten. > > > > > > On Thursday 15 August 2002 23:58, Bozidar Yerkovich wrote: > > > > Replace the last zero in OUTPUT_CONTROL to 1. That will give you more > > > > info... > > > > > > > > Bozidar > > > > > > > > On Thu, 15 Aug 2002, Karsten Suhre wrote: > > > > > Hi! > > > > > > > > > > when I get the following error message, I understand that the > > > > > sequence in my PDB file does not correspond to that read from the > > > > > alignment. Up to know, it was what had happened, and I always found > > > > > the problem by trial and error, but this time .... :-( > > > > > > > > > > rdpir___648E> Alignment sequence not found in PDB file: 2 > > > > > ./1EL3.pdb > > > > > > > > > > Is there some command or switch in modeller to get some more > > > > > information on what the problem is? i.e. which amino acid does not > > > > > match? > > > > > > > > > > Thank you very much for any hint, > > > > > > > > > > Karsten. > > > > > > > > > > > > > > > > > > > > PS: here my commands: > > > > > > > > > > SET OUTPUT_CONTROL = 1 1 1 1 0 > > > > > READ_ALIGNMENT FILE = 'tcoffee.aln', ALIGN_CODES = 'all' > > > > > > > > > > and the output: > > > > > > > > > > > > > > > Job starting time (YY/MM/DD HH:MM:SS): 2002/08/15 23:41:12.615 > > > > > > > > > > TOP_________> 2 2 READ_ALIGNMENT FILE = 'tcoffee.aln', > > > > > ALIGN_CODES = 'all' > > > > > > > > > > openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln > > > > > openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb > > > > > openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln > > > > > openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb > > > > > rdpir___648E> Alignment sequence not found in PDB file: 1 > > > > > ./1EL3.pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 > > > > > 1 > > > > > > > > > > Dynamically allocated memory at finish [B,kB,MB]: > > > > > 8065909 7876.864 7.692 > > > > > > > > > > > > > > > PPS: Attached are the input files (there is only one sequence in the > > > > > alignment including gaps .. and the PDB file does only contain ATOM > > > > > lines. That's because I eliminated all other stuff to see whether the > > > > > error changes .. it doesn't, and I compared the sequences between the > > > > > PDB file and the alignment - they are identical). >
participants (2)
-
Bozidar Yerkovich -
Karsten Suhre