# Distance restraints **URL:** \ **Category:** Uncategorized\ **Created:** [July 19, 2020, 8:34am UTC](https://ask.bioexcel.eu/t/distance-restraints/2342 "2020-07-19T08:34:24Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![yululu](https://avatars.discourse-cdn.com/v4/letter/y/cab0a1/32.png) [@yululu](https://ask.bioexcel.eu/u/yululu)\ **Post date:** [July 19, 2020, 8:34am UTC](https://ask.bioexcel.eu/t/distance-restraints/2342/1 "2020-07-19T08:34:24Z")
Helloļ¼ŒI want to ask a question about the Distance restraints, I know restraints are in CNS format, I want to know how to generate the restraints(TBL file) ,Thanks! ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [July 19, 2020, 12:10pm UTC](https://ask.bioexcel.eu/t/distance-restraints/2342/2 "2020-07-19T12:10:18Z")
By hand šŸ™‚ The restraint format is described in our Nature Protocol paper. See: ``` http://www.nature.com/nprot/journal/v5/n5/abs/nprot.2010.32.html ``` Also relevant: ``` https://www.nature.com/articles/s41596-018-0017-6.epdf?author_access_token=PCOdao9At6UPBnGnXKot19RgN0jAjWel9jnR3ZoTv0OMpdiCTExLiiIVHnJ_GM9iTFHQzhmzv8TQRpN4UoHo_SftIscahWHWSW2Cs2suSVugc9yUnz0hK1botwaQ0W5FoANSwLHc7l2f0LB1mRH94g%3D%3D ``` Examples are also given is various of our online tutorials. And I am also describing it in a recent BioExcel webinar about the new features of the 2.4 web server: ``` https://www.youtube.com/watch?v=9dWdaJ5jBqo ``` ---
**Author:** ![yululu](https://avatars.discourse-cdn.com/v4/letter/y/cab0a1/32.png) [@yululu](https://ask.bioexcel.eu/u/yululu)\ **Post date:** [July 20, 2020, 3:30am UTC](https://ask.bioexcel.eu/t/distance-restraints/2342/3 "2020-07-20T03:30:27Z")
Thanks for your help,I also want to ask another question. For the Protein-peptide docking ,how many amino acids should the peptide contain? ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [July 20, 2020, 6:54am UTC](https://ask.bioexcel.eu/t/distance-restraints/2342/4 "2020-07-20T06:54:38Z")
Conformational flexibility / changes are the challenges when dealing with peptides. So the shorter you can make you sequence the more change you will have to get some reasonable results. I would really try to remain below 20 a.a. or even less if possible. ---
**Author:** ![yululu](https://avatars.discourse-cdn.com/v4/letter/y/cab0a1/32.png) [@yululu](https://ask.bioexcel.eu/u/yululu)\ **Post date:** [July 20, 2020, 7:35am UTC](https://ask.bioexcel.eu/t/distance-restraints/2342/5 "2020-07-20T07:35:18Z")
OKļ¼Thanks for your answer,it helped me a lot. Then I want to ask you another question,for my protein-peptide docking, the peptide contains 30 aa, so will it be bad to do protein-peptide docking using HADDOCK ? ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [July 20, 2020, 7:46am UTC](https://ask.bioexcel.eu/t/distance-restraints/2342/6 "2020-07-20T07:46:45Z")
You can always try - but it will be challenging. It also all depends if you have some knowledge on the conformation of your peptide when bound or not (e.g. is it helical?). Any software will have a hard time with such a peptide. ---
**Author:** ![yululu](https://avatars.discourse-cdn.com/v4/letter/y/cab0a1/32.png) [@yululu](https://ask.bioexcel.eu/u/yululu)\ **Post date:** [July 27, 2020, 2:54am UTC](https://ask.bioexcel.eu/t/distance-restraints/2342/7 "2020-07-27T02:54:19Z")
Helloļ¼Œ I am doing Protein-peptide docking, and as described in protein-peptide docking protocol using the HADDOCK webserver, we can use the build\_seq.py script to generate the starting structures,I want to know how can i get the build\_seq.py script and use it.Please help me, thanks very much[pymol\_peptide|690x252](https://ask.bioexcel.eu/uploads/short-url/q42mJNpXB00SHtLPv20nJyvHiK7.png) ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [July 27, 2020, 7:27am UTC](https://ask.bioexcel.eu/t/distance-restraints/2342/8 "2020-07-27T07:27:37Z")
Should be available as supplementary material. But here is the script. Do change the extension from `.pdf` too `.py` since the forum does not allow to upload python files[3c\_build\_seq.pdf](https://ask.bioexcel.eu/uploads/short-url/voqBoD9Rom7pJf9VD9aSZqXUYYl.pdf) (6.8 KB)