Tristan's home page

Making a marker in pymol

Posted on Mon 17 December 2018 in Notes

The pymol equivalent of Chimera's marker is named "Pseudoatom"

Exemple:

pseudoatom res40, resi=40, chain=A, vdw=2, color=red
show spheres, res40

Some bash

Posted on Tue 17 October 2017 in Notes

SSH escape sequences:

to terminate a connection

~.

to suspend ssh (fg to reactivate)

~^Z

for other

~?

Find commands:

today's files

$ find ~ -type f -mtime 0

files older than 10 days

$ find ~ -type f -mtime +10

todays's python files of the current directory in the next level of folder

$ find . -type …

GPU Boost

Posted on Tue 17 October 2017 in Notes

Display the current application clock:

$ nvidia-smi  -q -i 0 -d CLOCK

==============NVSMI LOG==============
[...]
Attached GPUs                       : 1
GPU 0000:03:00.0
    [...]
    Applications Clocks
        Graphics                    : 1404 MHz
        Memory                      : 5705 MHz
    Default Applications Clocks
        Graphics                    : 1404 MHz
        Memory                      : 5705 MHz
    Max Clocks
        Graphics                    : 1911 MHz
        SM                          : 1911 MHz
        Memory                      : 5705 MHz
        Video …

Git commands

Posted on Mon 09 October 2017 in Notes

Graph of git history with abbreviated commit hash.

git log --pretty=format:"%h %s" --graph --since=2.weeks

Checkout an old commit

git checkout 1588a65

HCA

Posted on Sat 07 October 2017 in Notes

Protein 1qmb.

The pymol script and the structure used to make this plot cand be downloaded.

The colors in the HCA plot below correspond to the colors used in the drawing of 1qmb.

Notes on pelican

Posted on Sat 07 October 2017 in Notes

To generate the website:

pelican /path/to/your/content/ [-s path/to/your/settings.py] [-t pelican-theme]
pelican content -t Flex

For local generation/visualization set the SITEURL variable to an empty string in the pelicanconf.py file.

...
SITEURL = ''
...

and change it back to the website domain name before publishing …

Content

Posted on Sat 12 August 2017 in Notes

My previous notes/thoughts written on various supports will be progressively migrated to this section.

You will also find here background informations and materials regarding my research projects.

On going..