R: modelling discarding part of a template
> 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 > > Is it algorithmically difficult to add a function that will select a range of residue in one template and Modeller will exclude them without touching the alignment? When having multiple templates and several unwanted regions this procedure becomes very tedious.
On 08/31/2010 08:25 AM, Thomas Evangelidis wrote: > Is it algorithmically difficult to add a function that will select a > range of residue in one template and Modeller will exclude them without > touching the alignment? When having multiple templates and several > unwanted regions this procedure becomes very tedious.
That is certainly a possibility for a future release. You can get something similar in the meantime by writing a simple Python script that reads in the model, makes a selection excluding the regions you don't like, then writes out the selection to a new PDB file which you then use for automodel.
Ben Webb, Modeller Caretaker
On 31 August 2010 19:42, Modeller Caretaker modeller-care@salilab.orgwrote:
> On 08/31/2010 08:25 AM, Thomas Evangelidis wrote: > >> Is it algorithmically difficult to add a function that will select a >> range of residue in one template and Modeller will exclude them without >> touching the alignment? When having multiple templates and several >> unwanted regions this procedure becomes very tedious. >> > > That is certainly a possibility for a future release. You can get something > similar in the meantime by writing a simple Python script that reads in the > model, makes a selection excluding the regions you don't like, then writes > out the selection to a new PDB file which you then use for automodel. > http://salilab.org/mailman/listinfo/modeller_usage
Along with the templates the script must also modify the alignment by introducing gaps. Realigning the truncated sequences doesn't necessary result to the same MSA as with the whole sequences.
If this is not algorithmically difficult then please add it to your TODO list for the upcoming release. I believe this would be a very useful feature for advanced comparative modeling.
participants (2)
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Modeller Caretaker -
Thomas Evangelidis