I had some issues today using some PDBs generated by Modeller, and I tracked the error to the fact the TER fields inside the PDB have more columns (which should not be there)
For example
ATOM 1393 C2' DT D 35 81.341 17.516 55.945 1.00 48.63 C ATOM 1394 C3' DT D 35 82.152 18.800 55.754 1.00 48.81 C ATOM 1395 O3' DT D 35 83.036 19.108 56.819 1.00 49.40 O *TER 1396 DT D 35* ATOM 1397 N SER A 20 33.719 48.929 107.140 1.00 49.89 N ATOM 1398 CA SER A 20 34.080 48.490 108.522 1.00 50.05 C ATOM 1399 CB SER A 20 33.010 48.924 109.527 1.00 50.13 C
I understand that the TER separator is not supposed to have anything afterwards. Is there a particular reason why Modeller is writing my TER records like that? It should read only "TER"
Best Pedro
On 6/17/20 10:13 AM, Pedro Guillem wrote: > I had some issues today using some PDBs generated by Modeller, and I > tracked the error to the fact the TER fields inside the PDB have more > columns (which should not be there) [...] > *TER 1396 DT D 35* [...] > I understand that the TER separator is not supposed to have anything > afterwards. Is there a particular reason why Modeller is writing my TER > records like that? It should read only "TER"
You are incorrect - Modeller writes correct TER records; see http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#T...
Ben Webb, Modeller Caretaker
Thanks for the quick reply.
The weird part is that in my original PDB, the TER lines (6 in total) are not followed by anything. They just read TER. After performing mutations with modeller and saving the file, the output of the 6 TER lines has additional columns.
Is there a particular reason for modeller to be doing this? (I can provide the input file and output files)
Pedro
El mié., 17 jun. 2020 a las 19:21, Modeller Caretaker (< modeller-care@salilab.org>) escribió:
> On 6/17/20 10:13 AM, Pedro Guillem wrote: > > I had some issues today using some PDBs generated by Modeller, and I > > tracked the error to the fact the TER fields inside the PDB have more > > columns (which should not be there) > [...] > > *TER 1396 DT D 35* > [...] > > I understand that the TER separator is not supposed to have anything > > afterwards. Is there a particular reason why Modeller is writing my TER > > records like that? It should read only "TER" > > You are incorrect - Modeller writes correct TER records; see > > http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#T... > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >
On 6/18/20 5:06 AM, Pedro Guillem wrote: > The weird part is that in my original PDB, the TER lines (6 in total) > are not followed by anything. They just read TER. > After performing mutations with modeller and saving the file, the output > of the 6 TER lines has additional columns. > > Is there a particular reason for modeller to be doing this? (I can > provide the input file and output files)
I don't see how that's weird. You gave Modeller an invalid PDB file and it made a best effort to read it anyway. It output a valid PDB. If for some reason your pipeline needs invalid PDB files, mangle them with a Perl or Python script to remove the extra fields from the TER records. Alternatively, if you don't need the TER records at all, you can set no_ter=True when you call model.write(): https://salilab.org/modeller/9.24/manual/node181.html
Ben Webb, Modeller Caretaker
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Pedro Guillem