Hi, I tried to apply the script mutate_model.py to introduce a single point mutation on a protein, and I obtained an error: I'm attaching here the .log file. >From the error message, I see that mutate_model seems to be unable to manage a protein with chain breaks. I can obviously follow the suggestion and relabel the chains of my protein; however, chain breaks are a quite common situation in PDB files, therefore I wonder if there is a way to correct this problem without changing the chain ID as suggested in the log file (which is formally uncorrect since I don't have multiple chains in my protein). Any help will be appreciated. Many thanks in advance and best regards Anna Marabotti
__________________________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabotti@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
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On 11/30/2010 07:21 AM, Anna Marabotti wrote: > I tried to apply the script mutate_model.py to introduce a single point > mutation on a protein, and I obtained an error: I'm attaching here the > .log file.
Looks like you forgot to attach the file, or it got lost somewhere. Please send not just the log file, but also the inputs you use - otherwise we won't be able to figure out what's going wrong in your case.
> From the error message, I see that mutate_model seems to be unable to > manage a protein with chain breaks.
It shouldn't have any problem with proteins containing chain breaks, although it may be harder for you to select the residues you want to mutate if your chains are ambiguously labeled.
Ben Webb, Modeller Caretaker
Dear Ben, sorry for the missed attachments. However, in the mean time I found the solution by myself: in the PDB file there was a "TER" after the breaking of the chain, therefore probably the program interpretates (correctly!) this as the signal for a new chain (labelled with the same chain ID as the previous one) instead as of a chain breaking. After removing the TER line, the script worked properly. If you want to check the original PDB file for your information, the PDB code is 3BE8. It's the first time I see a chain breaking followed by a "TER" in a PDB file and I think it's an error. Many thanks anyway for your kind answer and best regards Anna Marabotti
-----Messaggio originale----- Da: modeller_usage-bounces@salilab.org [mailto:modeller_usage-bounces@salilab.org] Per conto di Modeller Caretaker Inviato: martedì 30 novembre 2010 20.05 A: Anna Marabotti Cc: modeller_usage@salilab.org Oggetto: Re: [modeller_usage] error using mutate_model.py
On 11/30/2010 07:21 AM, Anna Marabotti wrote: > I tried to apply the script mutate_model.py to introduce a single point > mutation on a protein, and I obtained an error: I'm attaching here the > .log file.
Looks like you forgot to attach the file, or it got lost somewhere. Please send not just the log file, but also the inputs you use - otherwise we won't be able to figure out what's going wrong in your case.
> From the error message, I see that mutate_model seems to be unable to > manage a protein with chain breaks.
It shouldn't have any problem with proteins containing chain breaks, although it may be harder for you to select the residues you want to mutate if your chains are ambiguously labeled.
Ben Webb, Modeller Caretaker
Dear Ben, just to add the proper information, I forgot to tell that I managed the original PDB file (which is correct, I've just checked it) in order to extract the chain A of the protein, and I used PyMol to do it. Probably this program added automatically the "TER" after each chain break. Thanks again and best regards Anna
-----Messaggio originale----- Da: Anna Marabotti [mailto:anna.marabotti@isa.cnr.it] Inviato: mercoledì 1 dicembre 2010 9.39 A: 'Modeller Caretaker' Cc: 'modeller_usage@salilab.org' Oggetto: R: [modeller_usage] error using mutate_model.py
Dear Ben, sorry for the missed attachments. However, in the mean time I found the solution by myself: in the PDB file there was a "TER" after the breaking of the chain, therefore probably the program interpretates (correctly!) this as the signal for a new chain (labelled with the same chain ID as the previous one) instead as of a chain breaking. After removing the TER line, the script worked properly. If you want to check the original PDB file for your information, the PDB code is 3BE8. It's the first time I see a chain breaking followed by a "TER" in a PDB file and I think it's an error. Many thanks anyway for your kind answer and best regards Anna Marabotti
-----Messaggio originale----- Da: modeller_usage-bounces@salilab.org [mailto:modeller_usage-bounces@salilab.org] Per conto di Modeller Caretaker Inviato: martedì 30 novembre 2010 20.05 A: Anna Marabotti Cc: modeller_usage@salilab.org Oggetto: Re: [modeller_usage] error using mutate_model.py
On 11/30/2010 07:21 AM, Anna Marabotti wrote: > I tried to apply the script mutate_model.py to introduce a single point > mutation on a protein, and I obtained an error: I'm attaching here the > .log file.
Looks like you forgot to attach the file, or it got lost somewhere. Please send not just the log file, but also the inputs you use - otherwise we won't be able to figure out what's going wrong in your case.
> From the error message, I see that mutate_model seems to be unable to > manage a protein with chain breaks.
It shouldn't have any problem with proteins containing chain breaks, although it may be harder for you to select the residues you want to mutate if your chains are ambiguously labeled.
Ben Webb, Modeller Caretaker
On 12/01/2010 12:39 AM, Anna Marabotti wrote: > sorry for the missed attachments. However, in the mean time I found the > solution by myself: in the PDB file there was a "TER" after the breaking of > the chain, therefore probably the program interpretates (correctly!) this as > the signal for a new chain (labelled with the same chain ID as the previous > one) instead as of a chain breaking. After removing the TER line, the script > worked properly.
Modeller has no problem with proteins containing multiple chains with the same ID - the warning is there simply because it will be hard to refer to the residues or atoms uniquely. For example, if you have two chains both with ID 'A', then mdl.residues['10:A'] will give you residue 10 in the *first* chain labeled 'A'. There is no way to get residue 10 in the *second* chain labeled A using this syntax; to distinguish them you'd have to refer to the chains numerically instead, i.e. mdl.chains[0].residues['10'] and mdl.chains[1].residues['10']
Since the mutate model script in the wiki uses the first syntax, it won't be able to find residues in the second chain with the same ID.
Ben Webb, Modeller Caretaker
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Anna Marabotti -
Modeller Caretaker