I am not scanning against PDB95 but rather working on multi-chain PDBs locally.
For instance, if a PDB has 4 chains (say A, D, F, P) and I am interested in extracting the chain ID of the second segment (D) that best aligns with my query sequence, I do not believe you can extract that from PIR alignment file, which only provides chain IDs of the first (A) and the last chain (P).
Also, how would I know if my query sequence aligned up against chain D unless I look at the alignment file manually. I want to automate this procedure. In other words, have a python script extract the chain ID of the aligned segment in a multi-chain PDB and automatically proceed to next step for homology modeling--that is I only want to use segment D as a template during homology modeling rather than the whole multi-chain PDB, which compromises the quality of the alignment and hence the model.
Thanks!
On Mon, Oct 28, 2013 at 2:36 PM, Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 10/27/2013 11:08 AM, Amjad Farooq wrote: > >> Is it possible to perform an automatic search of a multi-chain PDB >> template with a known protein sequence that is to be modeled (say >> 100-200 residues in length) and then extract the chain ID of the segment >> of the PDB template that best matches with the query sequence. >> > > If I understand you correctly, this is straightforward. If you're scanning > against our PDB95 database, for example, all the templates are single > chain, and the chain ID is simply the last character in the align code. > > If you're trying to align against a multi-chain template (presumably a > local alignment) you could extract the chain ID trivially from the > alignment object. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/**modeller/http://www.salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/**listinfo/modeller_usagehttps://salilab.org/mailman/listinfo/modeller_usage >
On 10/28/2013 12:01 PM, Amjad Farooq wrote: > For instance, if a PDB has 4 chains (say A, D, F, P) and I am interested > in extracting the chain ID of the second segment (D) that best aligns > with my query sequence, I do not believe you can extract that from PIR > alignment file, which only provides chain IDs of the first (A) and the > last chain (P).
No, but you can read in the corresponding PDB and extract the chains from that.
Ben Webb, Modeller Caretaker
Ben,
Can you please clarify this for me:
1) I have a multi-chain PDB 2) I have a protein sequence that only matches against one of the chains in the PDB
So, how do I automatically, say using a python script and my protein sequence as a query, extract the chain ID of the PDB segment to which it matches? Is a script like that available in MODELLER? If so, can you please guide me to it. I have tried most of them but I cannot figure this one out.
The closest I came across is the "make_chains.py". But that only spits out all the possible chains in a PDB file into individual alignment files.
Thanks very much, Amjad
On Mon, Oct 28, 2013 at 3:37 PM, Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 10/28/2013 12:01 PM, Amjad Farooq wrote: > >> For instance, if a PDB has 4 chains (say A, D, F, P) and I am interested >> in extracting the chain ID of the second segment (D) that best aligns >> with my query sequence, I do not believe you can extract that from PIR >> alignment file, which only provides chain IDs of the first (A) and the >> last chain (P). >> > > No, but you can read in the corresponding PDB and extract the chains from > that. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/**modeller/http://www.salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/**listinfo/modeller_usagehttps://salilab.org/mailman/listinfo/modeller_usage >
On 10/28/13 12:56 PM, Amjad Farooq wrote: > Can you please clarify this for me: > > 1) I have a multi-chain PDB > 2) I have a protein sequence that only matches against one of the chains > in the PDB > > So, how do I automatically, say using a python script and my protein > sequence as a query, extract the chain ID of the PDB segment to which it > matches? Is a script like that available in MODELLER?
No - you would need to write your own. But it is really elementary Python - I recommend the tutorial on the Python website.
Ben Webb, Modeller Caretaker
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