to model heterodimer protein of mossing residue
i tried a build a homology model of a heterodimer protein,since it contains missing residue i have to model that. But i am only familiar with single chain homology modelling and fro multi chain i am getting many errors like in greeting ali flie. and from tutorial also i am not getting everything clearly. can i get a detailed explantiojn on multi chain modelling
I think the only trick is not forgetting the chain break in the ali file: https://salilab.org/modeller/manual/node29.html
Best, Ajasja
PS: It's a very broad question, so I can only give a broad reply.
On Thu, 31 Aug 2023 at 09:12, Arun Dhanasekaran via modeller_usage < modeller_usage@salilab.org> wrote:
> i tried a build a homology model of a heterodimer protein,since it > contains missing residue i have to model that. But i am only familiar > with single chain homology modelling and fro multi chain i am getting many > errors like in greeting ali flie. and from tutorial also i am not getting > everything clearly. can i get a detailed explantiojn on multi chain > modelling > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/
Hi Arun how many residues in each chain total and how many residues are missing in each chain that need to be modeled? Best, Joel
On Thursday, August 31, 2023, Ajasja Ljubetič via modeller_usage < modeller_usage@salilab.org> wrote:
> I think the only trick is not forgetting the chain break in the ali file: > https://salilab.org/modeller/manual/node29.html > > Best, > Ajasja > > PS: It's a very broad question, so I can only give a broad reply. > > On Thu, 31 Aug 2023 at 09:12, Arun Dhanasekaran via modeller_usage < > modeller_usage@salilab.org> wrote: > >> i tried a build a homology model of a heterodimer protein,since it >> contains missing residue i have to model that. But i am only familiar >> with single chain homology modelling and fro multi chain i am getting many >> errors like in greeting ali flie. and from tutorial also i am not getting >> everything clearly. can i get a detailed explantiojn on multi chain >> modelling >> >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage@salilab.org >> https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/ > >
...and below is a link to the Modeller UsageHelp Forum indicating a methodology that I had used successfully to loop missing residue model via constraining the rest of the heptamer given residues successfully i.e. missing residue loop modeling within the Modeller website (although it maybe called something different). Good Luck:) On Thursday, August 31, 2023, Joel Subach mjsubach@alumni.ncsu.edu wrote:
> Hi Arun how many residues in each chain total > and how many residues are missing in each chain > that need to be modeled? Best, Joel > > On Thursday, August 31, 2023, Ajasja Ljubetič via modeller_usage < > modeller_usage@salilab.org> wrote: > >> I think the only trick is not forgetting the chain break in the ali file: >> https://salilab.org/modeller/manual/node29.html >> >> Best, >> Ajasja >> >> PS: It's a very broad question, so I can only give a broad reply. >> >> On Thu, 31 Aug 2023 at 09:12, Arun Dhanasekaran via modeller_usage < >> modeller_usage@salilab.org> wrote: >> >>> i tried a build a homology model of a heterodimer protein,since it >>> contains missing residue i have to model that. But i am only familiar >>> with single chain homology modelling and fro multi chain i am getting many >>> errors like in greeting ali flie. and from tutorial also i am not getting >>> everything clearly. can i get a detailed explantiojn on multi chain >>> modelling >>> >>> _______________________________________________ >>> modeller_usage mailing list >>> modeller_usage@salilab.org >>> https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/ >> >>
https://salilab.org/mm/hyperkitty/list/modeller_usage@salilab.org/thread/H56... On Thursday, August 31, 2023, Joel Subach mjsubach@alumni.ncsu.edu wrote:
> ...and below is a link to the Modeller UsageHelp Forum indicating a > methodology that I had used successfully to loop missing residue model via > constraining the rest of the heptamer given residues successfully i.e. > missing residue loop modeling within the Modeller website (although it > maybe called something different). Good Luck:) > On Thursday, August 31, 2023, Joel Subach mjsubach@alumni.ncsu.edu > wrote: > >> Hi Arun how many residues in each chain total >> and how many residues are missing in each chain >> that need to be modeled? Best, Joel >> >> On Thursday, August 31, 2023, Ajasja Ljubetič via modeller_usage < >> modeller_usage@salilab.org> wrote: >> >>> I think the only trick is not forgetting the chain break in the ali file: >>> https://salilab.org/modeller/manual/node29.html >>> >>> Best, >>> Ajasja >>> >>> PS: It's a very broad question, so I can only give a broad reply. >>> >>> On Thu, 31 Aug 2023 at 09:12, Arun Dhanasekaran via modeller_usage < >>> modeller_usage@salilab.org> wrote: >>> >>>> i tried a build a homology model of a heterodimer protein,since it >>>> contains missing residue i have to model that. But i am only familiar >>>> with single chain homology modelling and fro multi chain i am getting many >>>> errors like in greeting ali flie. and from tutorial also i am not getting >>>> everything clearly. can i get a detailed explantiojn on multi chain >>>> modelling >>>> >>>> _______________________________________________ >>>> modeller_usage mailing list >>>> modeller_usage@salilab.org >>>> https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/ >>> >>>
participants (3)
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Ajasja Ljubetič -
Arun Dhanasekaran -
Joel Subach