modelling discarding part of a template
Hi, sorry for a probable trivial question, but I couldn't find a solution browsing the mailing list by myself.
I want to model a protein using two different templates, in particular they differ in the position of a loop. My protein is very similar to template 1, but should have that loop in the same conformation found in template 2. So I'd like to "say" to modeller: please model my protein using template 1 as much as possible, but use only template 2 to model that loop. Please take in mind that both templates cover the entire sequence and show the loop (in different conformations). I tried to do this by replacing the residues that I would like to be discarded (in correspondence of the loop) in template 1 with gaps in the alignment. So for example:
target: AAAAAAAAAAAAAAAAA template 1: BBBB-------BBBBBB template 2: ZZZZZZZZZZZZZZZZZ (the part with gaps in template 1 is present in PDB file)
But Modeller returned me an error saying: Sequence difference between alignment and PDB: Alignment: BBBBBBBBBB Sequence: BBBBBBBBBBBBBBBBB
I understand that Modeller "interpret" my alignment as a gap would present in the structure, and since this is not the case, it returns me an error. The question is: how to correctly send information to Modeller in order to "force" it to follow only a template to model a portion of the sequence, even if the other template is present? It seems to me that there was a way to do it without modifying the PDB file of the first template in order to cancel this loop. Am I correct? Is there a solution? Thank you very much for kind assistance and best regards Anna
____________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabotti@isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
"If you think you are too small to make a difference, try sleeping with a mosquito"
On 5/5/10 3:57 AM, Anna Marabotti wrote: > I want to model a protein using two different templates, in particular > they differ in the position of a loop. My protein is very similar to > template 1, but should have that loop in the same conformation found in > template 2. So I'd like to "say" to modeller: please model my protein > using template 1 as much as possible, but use only template 2 to model > that loop. Please take in mind that both templates cover the entire > sequence and show the loop (in different conformations). > I tried to do this by replacing the residues that I would like to be > discarded (in correspondence of the loop) in template 1 with gaps in the > alignment. So for example: > target: AAAAAAAAAAAAAAAAA > template 1: BBBB-------BBBBBB > template 2: ZZZZZZZZZZZZZZZZZ > (the part with gaps in template 1 is present in PDB file) > But Modeller returned me an error saying: > Sequence difference between alignment and PDB:
You have to either keep the complete template sequence in the PDB file, or modify the template PDB to remove the residues you don't want. An alignment that achieves what you want without modifying the PDB is:
target: AAAAAAAAAAA-------AAAAAA template 1: BBBB-------BBBBBBBBBBBBB template 2: ZZZZZZZZZZZ-------ZZZZZZ
Ben Webb, Modeller Caretaker
Right! I knew that there was a simple trick to do it without modifying the PDB file, but I couldn't remember it... Thank you very much and best regards Anna
-----Messaggio originale----- Da: Modeller Caretaker [mailto:modeller-care@salilab.org] Inviato: mercoledì 5 maggio 2010 16.55 A: Anna Marabotti Cc: modeller_usage@salilab.org Oggetto: Re: [modeller_usage] modelling discarding part of a template
On 5/5/10 3:57 AM, Anna Marabotti wrote: > I want to model a protein using two different templates, in particular > they differ in the position of a loop. My protein is very similar to > template 1, but should have that loop in the same conformation found in > template 2. So I'd like to "say" to modeller: please model my protein > using template 1 as much as possible, but use only template 2 to model > that loop. Please take in mind that both templates cover the entire > sequence and show the loop (in different conformations). > I tried to do this by replacing the residues that I would like to be > discarded (in correspondence of the loop) in template 1 with gaps in the > alignment. So for example: > target: AAAAAAAAAAAAAAAAA > template 1: BBBB-------BBBBBB > template 2: ZZZZZZZZZZZZZZZZZ > (the part with gaps in template 1 is present in PDB file) > But Modeller returned me an error saying: > Sequence difference between alignment and PDB:
You have to either keep the complete template sequence in the PDB file, or modify the template PDB to remove the residues you don't want. An alignment that achieves what you want without modifying the PDB is:
target: AAAAAAAAAAA-------AAAAAA template 1: BBBB-------BBBBBBBBBBBBB template 2: ZZZZZZZZZZZ-------ZZZZZZ
Ben Webb, Modeller Caretaker
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Anna Marabotti -
Modeller Caretaker