PyMol Trajectory Visualization

Posted 2022-08-03Updated 2025-02-23Notes / Toolsa minute read (About 133 words)

PyMol Trajectory Visualization

Visualize Amber nc trajectory in PyMol
I used to convert everything into .dcd file but it is a little complex. Now I found PyMol actually can directly read prmtop & nc file but just need little adjustment.

Posted 2021-12-25Updated 2022-07-12Notes / Tools13 minutes read (About 1999 words)

计算小分子机理研究的一般流程

This article is locked. This might include some personal or unpublished info.

Plot IGM analysis with PyMol

Posted 2021-08-03Updated 2022-08-03Notes / Toolsa minute read (About 167 words)

Plot IGM analysis with PyMol

Plot IGM analysis from Multiwfn using PyMol. IGM is an useful analysis of spatial distribution of steric hindrance. Plotting IGM result is much easier and looks better in PyMol.

Related Multiwfn Documents
http://sobereva.com/407

Related PyMol Documents
https://pymolwiki.org/index.php/Ramp_New

Posted 2020-12-05Updated 2022-08-03Notes / Toolsa few seconds read (About 30 words)

Misc Notes of PyMol

preventing redundant searching

PyMol Structure Amendment

Posted 2020-11-12Updated 2022-08-03Notes / Toolsa few seconds read (About 39 words)

PyMol Structure Amendment

Note for protein crystal structural amendment using PyMol.

PyMol & Multiwfn Electrostatic Potential (ESP) Visualization

Posted 2020-11-09Updated 2022-11-28Notes / Tools3 minutes read (About 422 words)

PyMol & Multiwfn Electrostatic Potential (ESP) Visualization

Generate ESP .cub file from the Multiwfn and plot it in PyMol

Related Multiwfn Documents
http://sobereva.com/443
http://sobereva.com/196

Related PyMol Documents
https://pymolwiki.org/index.php/Ramp_New

PyMol Orbital Visualization

Posted 2020-06-29Updated 2022-08-03Notes / Toolsa minute read (About 207 words)

PyMol Orbital Visualization

Notes for a Houk Group style molecular orbital visualization in PyMol