[modeller_usage] R: error using mutate_model.py

[Anna Marabotti <>]

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:] 
Inviato: mercoledì 1 dicembre 2010 9.39
A: 'Modeller Caretaker'
Cc: ''
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: 
[">mailto:] Per conto di Modeller Caretaker
Inviato: martedì 30 novembre 2010 20.05
A: Anna Marabotti
Cc: 
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
-- 
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
_______________________________________________
modeller_usage mailing list

https://salilab.org/mailman/listinfo/modeller_usage