# How to pull ligand in negative/opposite direction of axis? **URL:** \ **Category:** User discussions\ **Created:** [May 5, 2024, 6:13am UTC](https://gromacs.bioexcel.eu/t/how-to-pull-ligand-in-negative-opposite-direction-of-axis/9060 "2024-05-05T06:13:34Z")\ **Posts on this page:** 11\ **Page:** 2
**Author:** ![Manish](https://avatars.discourse-cdn.com/v4/letter/m/a6a055/32.png) [@Manish](https://gromacs.bioexcel.eu/u/Manish)\ **Post date:** [May 14, 2024, 9:15am UTC](https://gromacs.bioexcel.eu/t/how-to-pull-ligand-in-negative-opposite-direction-of-axis/9060/21 "2024-05-14T09:15:06Z")
sir I have attached the files below and I want to pull the ligand from -y axis becz it shows important interactions towards that side. (Attachment newbox.txt.gro is missing) ---
**Author:** ![Manish](https://avatars.discourse-cdn.com/v4/letter/m/a6a055/32.png) [@Manish](https://gromacs.bioexcel.eu/u/Manish)\ **Post date:** [May 14, 2024, 9:22am UTC](https://gromacs.bioexcel.eu/t/how-to-pull-ligand-in-negative-opposite-direction-of-axis/9060/22 "2024-05-14T09:22:14Z")
sir how to send it unable attach newbox file,therefore attached image ![newboximage](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/1a4589bd1cf80e1d6302a909e1a5fbd5a5649731.png) ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [May 14, 2024, 10:49am UTC](https://gromacs.bioexcel.eu/t/how-to-pull-ligand-in-negative-opposite-direction-of-axis/9060/23 "2024-05-14T10:49:37Z")
image is not clear, zoom out and show the system , looks like you need to rotate the whole system that it aligns to the positive y axis, that makes everything easy. ---
**Author:** ![Manish](https://avatars.discourse-cdn.com/v4/letter/m/a6a055/32.png) [@Manish](https://gromacs.bioexcel.eu/u/Manish)\ **Post date:** [October 5, 2024, 6:42am UTC](https://gromacs.bioexcel.eu/t/how-to-pull-ligand-in-negative-opposite-direction-of-axis/9060/24 "2024-10-05T06:42:29Z")
sir how can i align this system , can u please tell. ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [October 5, 2024, 7:28pm UTC](https://gromacs.bioexcel.eu/t/how-to-pull-ligand-in-negative-opposite-direction-of-axis/9060/25 "2024-10-05T19:28:24Z")
I have sent you 3 file in your email, please update the status here so that community can get benefit @Manish ---
**Author:** ![Manish](https://avatars.discourse-cdn.com/v4/letter/m/a6a055/32.png) [@Manish](https://gromacs.bioexcel.eu/u/Manish)\ **Post date:** [October 8, 2024, 5:23am UTC](https://gromacs.bioexcel.eu/t/how-to-pull-ligand-in-negative-opposite-direction-of-axis/9060/26 "2024-10-08T05:23:32Z")
Thank you so much sir for your quick guidance. I wanted to ask if you changed anything in the structure, if yes what is it and how did you do it. Also do we need to change anything in the pull.mdp file. ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [October 9, 2024, 9:14pm UTC](https://gromacs.bioexcel.eu/t/how-to-pull-ligand-in-negative-opposite-direction-of-axis/9060/27 "2024-10-09T21:14:49Z")
i have rotated the whole structure towards particular axis- so that it is easy to pull. check the orientation and select the direction you wanted to pull. ---
**Author:** ![Manish](https://avatars.discourse-cdn.com/v4/letter/m/a6a055/32.png) [@Manish](https://gromacs.bioexcel.eu/u/Manish)\ **Post date:** [October 10, 2024, 2:55am UTC](https://gromacs.bioexcel.eu/t/how-to-pull-ligand-in-negative-opposite-direction-of-axis/9060/28 "2024-10-10T02:55:57Z")
Thank you sir, canyou please tell by what source or technique you rotated the whole structure towards a particular axis, so that i could use it in future. ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [October 10, 2024, 4:07am UTC](https://gromacs.bioexcel.eu/t/how-to-pull-ligand-in-negative-opposite-direction-of-axis/9060/29 "2024-10-10T04:07:22Z")
pymol ---
**Author:** ![Manish](https://avatars.discourse-cdn.com/v4/letter/m/a6a055/32.png) [@Manish](https://gromacs.bioexcel.eu/u/Manish)\ **Post date:** [October 10, 2024, 4:31am UTC](https://gromacs.bioexcel.eu/t/how-to-pull-ligand-in-negative-opposite-direction-of-axis/9060/30 "2024-10-10T04:31:19Z")
ok sir i will also try to do the same with other proteins. Thank you so much sir. ---
**Author:** ![Manish](https://avatars.discourse-cdn.com/v4/letter/m/a6a055/32.png) [@Manish](https://gromacs.bioexcel.eu/u/Manish)\ **Post date:** [October 15, 2024, 5:14am UTC](https://gromacs.bioexcel.eu/t/how-to-pull-ligand-in-negative-opposite-direction-of-axis/9060/31 "2024-10-15T05:14:12Z")
sir, please can you tell the commands you followed in pymol to set the axis of protein for proper alignment, as I am unable to do it. [Previous page](https://gromacs.bioexcel.eu/t/how-to-pull-ligand-in-negative-opposite-direction-of-axis/9060.md?page=1)