[modeller_usage] Re: Oligomer Missing Loop Residue Restrained Modeling, Broken Loop Issue

[Joel Subach <mjsubach AT ncsu.edu>]

Hello Ben thank you for your kind update:).

I tired the ModLoop, however, have 91 residues accordingly was rejected due
to length.
If there is way to work around this error let me know please, thanks:)

My Enter Loop Segment promoting this error.

88:A:100:A:
88:B:100:B:
88:C:100:C:
88:D:100:D:
88:E:100:E:
88:F:100:F:
88:G:100:G:

(I will continue with the other Advanced Tutorial.)

Best,
Joel 



On Thu, Sep 22, 2022 at 8:54 PM Modeller Caretaker <
modeller-care@ucsf.edu> wrote:

> On 9/22/22 9:57 AM, Joel Subach wrote:
> > In my case which tutorial should I follow for this loop refinement:
>
> The advanced tutorial at
> https://salilab.org/modeller/tutorial/advanced.html is the best place to
> start. The Cryo-EM tutorial scores the resulting loop models based on
> their fits into a cryo-EM map, so wouldn't make sense for you unless you
> also have such a map.
>
> Alternatively, you can use the ModLoop web server at
> https://modbase.compbio.ucsf.edu/modloop/
>
>         Ben Webb, Modeller Caretaker
> --
> modeller-care@ucsf.edu             https://salilab.org/modeller/
> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage
>

Hello Ben thank you for your kind update: ). I tired the ModLoop, however, have 91 residues accordingly was rejected due to length. If there is way to work around this error let me know please, thanks: ) My Enter Loop Segment promoting this error. 

ZjQcmQRYFpfptBannerStart

This Message Is From an External Sender

This message came from outside your organization.

 

ZjQcmQRYFpfptBannerEnd

Hello Ben thank you for your kind update:).

I tired the ModLoop, however, have 91 residues accordingly was rejected due to length.

If there is way to work around this error let me know please, thanks:)

My Enter Loop Segment promoting this error. 

88:A:100:A:
88:B:100:B:
88:C:100:C:
88:D:100:D:
88:E:100:E:
88:F:100:F:
88:G:100:G:

(I will continue with the other Advanced Tutorial.)

Best,

Joel ð???

On Thu, Sep 22, 2022 at 8:54 PM Modeller Caretaker <modeller-care@ucsf.edu> wrote:

On 9/22/22 9:57 AM, Joel Subach wrote:
> In my case which tutorial should I follow for this loop refinement:

The advanced tutorial at
https://salilab.org/modeller/tutorial/advanced.html is the best place to
start. The Cryo-EM tutorial scores the resulting loop models based on
their fits into a cryo-EM map, so wouldn't make sense for you unless you
also have such a map.

Alternatively, you can use the ModLoop web server at
https://modbase.compbio.ucsf.edu/modloop/

        Ben Webb, Modeller Caretaker
--
modeller-care@ucsf.edu             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage