Missing Residues Script File Inquiry
Hello must I create the script files to fill in missing residues? If not where would they be?
Thanks:) Joel
On 8/26/22 12:30 PM, Joel Subach via modeller_usage wrote: > Hello must I create the script files to fill in missing residues? > If not where would they be?
There is a demonstration of filling in missing residues in the Modeller wiki: https://salilab.org/modeller/wiki/Missing_residues
Ben Webb, Modeller Caretaker
Hello Ben thank you for your kind update:).
Yes the link that you had emailed is what I am using as my template to fill in my missing residues but where are the script files for this? Must I create all of my own? I completed your first tutorial where all the script files were given i.e. the below but my understanding is that I would need similar files to complete my missing residues. Thanks if you can answer this inquiry since its particular. Tutorial ------------------------------ Basic example: Modeling lactate dehydrogenase from *Trichomonas vaginalis* based on a single template. *.tar.gz format (for Unix/Linux) https://salilab.org/modeller/tutorial/basic-example.tar.gz.*
On Sat, Aug 27, 2022 at 12:33 AM Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 8/26/22 12:30 PM, Joel Subach via modeller_usage wrote: > > Hello must I create the script files to fill in missing residues? > > If not where would they be? > > There is a demonstration of filling in missing residues in the Modeller > wiki: > https://salilab.org/modeller/wiki/Missing_residues > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >
...and Ben I believe I may not need any script files i.e. all I would need is my proteins sequence and 3-D coordinate files if there is any other script file that I would need to create a use please feel free to let me know, thanks Ben:). (I had seen in a youtube Windows tutorial the user using three Python Script files that he did not exhibit hence my inquiry.)
On Sat, Aug 27, 2022 at 8:35 AM Joel Subach mjsubach@ncsu.edu wrote:
> Hello Ben thank you for your kind update:). > > Yes the link that you had emailed is what I am using as my template to > fill in my missing residues > but where are the script files for this? Must I create all of my own? I > completed your first tutorial > where all the script files were given i.e. the below but my understanding > is that I would need similar > files to complete my missing residues. Thanks if you can answer this > inquiry since its particular. > Tutorial > ------------------------------ > Basic example: > Modeling lactate dehydrogenase from *Trichomonas vaginalis* based on a > single template. > *.tar.gz format (for Unix/Linux) > https://salilab.org/modeller/tutorial/basic-example.tar.gz.* > > On Sat, Aug 27, 2022 at 12:33 AM Modeller Caretaker < > modeller-care@salilab.org> wrote: > >> On 8/26/22 12:30 PM, Joel Subach via modeller_usage wrote: >> > Hello must I create the script files to fill in missing residues? >> > If not where would they be? >> >> There is a demonstration of filling in missing residues in the Modeller >> wiki: >> https://salilab.org/modeller/wiki/Missing_residues >> >> Ben Webb, Modeller Caretaker >> -- >> modeller-care@salilab.org https://salilab.org/modeller/ >> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >> >
Hi Ben I made it through the missing residue tutorial error free without any python scripts, accordingly you may disregard my last email(s) thanks and sorry, next time ill be sure to exhaust things on my end before emailing you to manage time.
Best, Joel
On Sat, Aug 27, 2022 at 9:10 AM Joel Subach mjsubach@ncsu.edu wrote:
> ...and Ben I believe I may not need any script files i.e. all I would need > is my proteins sequence and 3-D coordinate files > if there is any other script file that I would need to create a use please > feel free to let me know, thanks Ben:). (I had seen > in a youtube Windows tutorial the user using three Python Script files > that he did not exhibit hence my inquiry.) > > On Sat, Aug 27, 2022 at 8:35 AM Joel Subach mjsubach@ncsu.edu wrote: > >> Hello Ben thank you for your kind update:). >> >> Yes the link that you had emailed is what I am using as my template to >> fill in my missing residues >> but where are the script files for this? Must I create all of my own? I >> completed your first tutorial >> where all the script files were given i.e. the below but my understanding >> is that I would need similar >> files to complete my missing residues. Thanks if you can answer this >> inquiry since its particular. >> Tutorial >> ------------------------------ >> Basic example: >> Modeling lactate dehydrogenase from *Trichomonas vaginalis* based on a >> single template. >> *.tar.gz format (for Unix/Linux) >> https://salilab.org/modeller/tutorial/basic-example.tar.gz.* >> >> On Sat, Aug 27, 2022 at 12:33 AM Modeller Caretaker < >> modeller-care@salilab.org> wrote: >> >>> On 8/26/22 12:30 PM, Joel Subach via modeller_usage wrote: >>> > Hello must I create the script files to fill in missing residues? >>> > If not where would they be? >>> >>> There is a demonstration of filling in missing residues in the Modeller >>> wiki: >>> https://salilab.org/modeller/wiki/Missing_residues >>> >>> Ben Webb, Modeller Caretaker >>> -- >>> modeller-care@salilab.org https://salilab.org/modeller/ >>> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >>> >>
participants (2)
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Joel Subach -
Modeller Caretaker