Dear Sir, This is your post regarding modelling of the dimer protein on dimeric template. I have done the required changes in the ali file (alignment file), do I need to change the PAP file also, because I am getting following error while running Script 4 : Number of residues in the alignment and the pdb files are different. With Regards, Bhavik
Hi,
If you have a dimer as template and want to model a dimer with the same organisation, you just need to include a "/" character as chain breaker in the alignment file (between your 2 monomers).
I join an exemple of alignment for a dimer.
On Thu, 12 Jun 2003, Difei Wang wrote:
> Hi, All > > I am wondering if it is possible to model a dimer structure from a dimer > template. > I can not find anything in the manual. I tried to model each of them first and > then > put them together. However, I am not sure it is good or not for the packing in > the > contact region. Thanks for your help. > > Difei >
Dear Bhavik,
If you still have not resolved your issue vis-a-vis the modeling of dimeric protein, please have a look @ http://structuropedia.org (which is an interface to MODELLER).
Structuropedia automizes such model building with user opting to either upload his(er) own dimer template or defaulting to an automatic template selection with Blast search. Have a look at it. It could help you trouble-shoot your issue as it will also provide you with an alignment file so that you can see how MODELLER handles dimeric structures.
With warmest regards,
*AMJAD FAROOQ PhD DIC | Associate Professor*Dept of Biochemistry, University of Miami School of Medicine *Location*: Gautier Building, Suite 217 *Address*: 1011 NW 15th Street #217, Miami , FL 33136, USA *Contact*: amjad@farooqlab.net | 305-243-2429 *Labpage*: farooqlab.net | structuropedia.org
On Mon, May 25, 2015 at 12:10 PM, Bhavik Sawhney bhavik@cdfd.org.in wrote:
> > Dear Sir, > This is your post regarding modelling of the dimer protein on dimeric > template. I have done the required changes in the ali file (alignment > file), do I need to change the PAP file also, because I am getting > following error while running Script 4 : Number of residues in the > alignment and the pdb files are different. > With Regards, > Bhavik > > Hi, > > If you have a dimer as template and want to model a dimer with the same > organisation, you just need to include a "/" character as chain breaker in > the alignment file (between your 2 monomers). > > I join an exemple of alignment for a dimer. > > > > > On Thu, 12 Jun 2003, Difei Wang wrote: > > > Hi, All > > > > I am wondering if it is possible to model a dimer structure from a dimer > > template. > > I can not find anything in the manual. I tried to model each of them > first and > > then > > put them together. However, I am not sure it is good or not for the > packing in > > the > > contact region. Thanks for your help. > > > > Difei > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >
On 05/25/2015 09:10 AM, Bhavik Sawhney wrote: > This is your post regarding modelling of the dimer protein on dimeric > template. I have done the required changes in the ali file > (alignment file), do I need to change the PAP file also
No, the PAP file is not used in modeling.
> getting following error while running Script 4 : Number of residues > in the alignment and the pdb files are different.
Your alignment file is incorrectly formatted. If you can't figure it out, post it here so we can see what the problem is.
Ben Webb, Modeller Caretaker
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Amjad Farooq -
Bhavik Sawhney -
Modeller Caretaker