Software

Useful

FATCAT: Sequence alignment taking structural alignment into account.

How to use python3 on Amber machines

scl enable rh-python36 bash

Or you can find python3 installed under /opt/rh. I enabled the Software Collections on Centos 7 read this.

pyMBAR

conda create -n pymbar python=2.7
conda install -n pymbar -c omnia pymbar

I will suggest put the source code under /opt and use super link to access

cd /opt
git clone https://github.com/MobleyLab/alchemical-analysis.git

Everytime you use it

conda activate pymbar
cd /your/wokr/directory
ln -s /opt/alchemical-analysis/alchemical_analysis.py .
python alchemical-analysis/alchemical_analysis.py -h

Modeler

conda create -n modeller
conda config --add channels salilab
conda install -n modeller modeller
conda activate modeller

vi /Users/ukevi/opt/anaconda3/lib/modeller-9.24/modlib/modeller/config.py

The license is

MODELIRANJE

Rosetta

Academic_User
Xry3x4

PyMOL

Download here. I just share my token (chan.773@osu.edu). -Kevin

jun2020
alphahelix

License:

INCREMENT PYMOL_MAIN SCHROD 999 01-jun-2020 uncounted HOSTID=ANY \
	ISSUED=01-Oct-2019 NOTICE="PyMOL for educational use only" \
	START=01-Nov-2019 TS_OK SIGN="07EB 97C4 AE1C 8ACF 39AE 9CAA \
	BBF6 D760 4330 9573 6C5C 0841 FB52 ED60 8A37 1F55 0CE4 2ADA \
	3BDD 0881 327E DA85 FD83 DD75 EE39 CFF1 4C48 2886 4298 B2DF" \
	SIGN2="1448 4CC9 7083 19E8 A4E3 8A83 B5D1 B5A5 113E C465 15E7 \
	76AC 368E B80D DB08 1406 2D0C E68C 060D FBFE C8B4 AD55 2734 \
	9131 D67D CB04 6F54 C5E4 D535 D10B"

Check PDB clashes

MolProbity