Jarrett Johnson

Senior Developer (PyMOL team) at @Schrodinger | UMich ChemBio PhD Grad | he/him/his

[Noeris @sirnoeris]

PYMOL 3 Tutorial - Carbon Nanotube Animation https://t.co/2h1FSMYA8a #pymol

[Jarrett Johnson @jarrettsjohnson]

@Ag_smith Thanks; I'll keep an eye out.

[Jarrett Johnson @jarrettsjohnson]

In Japan for the next 6 weeks. What a stunning country. 日本に六週間旅行してます、すごい国

[Sergey Ovchinnikov @sokrypton]

Looks like someone already implemented ESMfold API plugin in Pymol! 😎
https://t.co/TY4gbnr2jM

[Jarrett Johnson @jarrettsjohnson]

@bradyajohnston Great work! Glad to see Geometry Nodes and molecular biology coming together!

[Jarrett Johnson @jarrettsjohnson]

Can confirm this is not part of the PyMOL main. However, pull requests are always welcome! (I just can't guarantee that all PRs will be accepted😂)

[Edward Nirenberg 🇺🇦 @ENirenberg]

Oh my god is this real

[Jarrett Johnson @jarrettsjohnson]

@CathyAbbottLab @Cyberplasm @dineshsoares Right, `hide everything, chain A` to "hide" all representations of chain A, and if you wanted to show the cartoon again for chain A, `show cartoon, chain A`

[Jarrett Johnson @jarrettsjohnson]

@MartinStoermer @dr_benomycin The smooth command should be undoable as of PyMOL 2.5. If this isn't working then, it's probably a bug and I can investigate. As far as the second issue, I think something we can easily do as an improvement to our settings menu is filter them if different than defaults.

[Jarrett Johnson @jarrettsjohnson]

@chuckdoesbio I am. Thank you :)

[Jarrett Johnson @jarrettsjohnson]

@torusengoku @yam_cpp すみません、最新PyMOLをダウンロードしてお願いました。PyMOL 2.5.3はあの問題に関してバグ最新リリースだと思っています。

[Jarrett Johnson @jarrettsjohnson]

@nicholas_pearce @RolandDunbrack @DanielKeedy @fraser_lab But who actually knows about fnab ? ;) (relatively new)

[Jarrett Johnson @jarrettsjohnson]

One more week until the PyMOL Fellowship application deadline. :)

[Jarrett Johnson @jarrettsjohnson]

Applications for the Warren L. DeLano Memorial PyMOL Fellowship are now live for the 2022-2023 Academic Year. All Scientific/PyMOL open-source contributors and enthusiasts are welcome to apply! Deadline is Friday, August 26, 2022 https://t.co/M5Gk1Hor6S

[Jarrett Johnson @jarrettsjohnson]

Applications for the Warren L. DeLano Memorial PyMOL Fellowship are now live for the 2022-2023 Academic Year. All Scientific/PyMOL open-source contributors and enthusiasts are welcome to apply! Deadline is Friday, August 26, 2022 https://t.co/M5Gk1Hor6S

[Jarrett Johnson @jarrettsjohnson]

@RolandDunbrack @Schrodinger Hi, this is a known issue and we're currently working to resolve this. The two workarounds to this are to open the session file when PyMOL is already open (instead of opening by session file) or using the command `set use_shaders`

[Jarrett Johnson @jarrettsjohnson]

@bradyajohnston @biochem_bri There are features that are exclusively incentive https://t.co/gyFRlSqQXw . However, for features and bug fixes that affect both open-source and incentive PyMOL, open-source will be ahead since we continuously push commits to the open-source repo.

[Jarrett Johnson @jarrettsjohnson]

@stripp_lab One way to accomplish it is to export a movie program which does rocking. I've done an example here to show: https://t.co/UHOkxqHTai

Hope this helps.

[Jarrett Johnson @jarrettsjohnson]

@bradyajohnston Definitely agree that PyMOL could use some improvements visually. I've been working on some things currently to give it a more modern look and can't wait to share.

[Jarrett Johnson @jarrettsjohnson]

@Cascade21 No worries! I was a user too for years, so I can definitely relate. 😂