Hello,
I try to build a modele with 2 protein templates. I want to modelise just one loop of 1pkg, part of it on the template 3A2M, the rest of the loop de novo. The rest of 1pkg must not be changed, so I put it as BLK:
P1;1pkg structureX:1pkg:1:A:280:A:::: .............................................................................. ........................................-------------------------------------- -------------------------------------------................................... .............................................................................. .................................................* P1;3A2M structureX:3A2M:283:A:305:A:::: ------------------------------------------------------------------------------ ----------------------------------------QEDHADAIGRSVAGWIAGIEAVR--------------- ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ -------------------------------------------------* P1;KID sequence:KID:1:A:361:A:::: .............................................................................. ........................................KRDSFICSKQEDHAEAALYKNLLHSKESSCSDSTNEYM DMKPGVSYVVPTKADKRRSVRIGSYIERDVTPAIMEDDELALD................................... .............................................................................. .................................................*
I get a model with 3 chains instead of one. How can I get a one-chain model? All atoms in the pdb files are like "ATOM". Should I change it in "HETATM"?
Thanks a lot in advance, Isaure
On 1/24/11 6:56 AM, Isaure Chauvot de Beauchene wrote: > I try to build a modele with 2 protein templates. I want to modelise > just one loop of 1pkg, part of it on the template 3A2M, the rest of the > loop de novo. The rest of 1pkg must not be changed, so I put it as BLK:
BLK residues are really designed for modeling ligands and other things that are not proteins. If you only want Modeller to optimize part of your protein, see http://salilab.org/modeller/9v8/manual/node23.html
Ben Webb, Modeller Caretaker