Hi there
I got several contact matrices in XPM format generated by GROMACS trajectories for a series of protein mutants. How to compare them to extract the differences between atom contacts in each mutant?
Thanks in advance.
Hello Francisco,
We have very recently developed a small program that does all sorts of comparisons and statistical analysis on .xpm files created with the GROMACS gmx mdmat tool.
It can work directly with a single xpm or a time series-derived set of xpm files giving you differences (and other statistical analysis, as well as a contacts-based cluster analysis and a contacts-based principal component analysis) between xpm(s) as well as creating time-resolved videos of the contacts evolving in a MD trajectory. All you need is a single input file where you specify the path of your trajectory and/or coordinate file. You will need gromacs and some other very routinely used software to be installed.
The paper about it is soon to be published but a Github stable release can be found here, and it includes a detailed documentation:
https://github.com/HITS-MBM/conan
The tool is called CONAN - which is an acronym for Contact Analysis.
We tried to make the software as user friendly as possible.
Hope it will be useful to you (and others!). If something is not clear don't hesitate to ask!
Best
Davide
1. Convert the xpm files to postscript (text) files with xpm2ps.
2. Extract the arrays from the postscript files.
3. Calculate a differential array.
4. Plot the differential array with Matplotlib (imshow).
---
i am not a Gromacs user.
Hello Francisco,
We have very recently developed a small program that does all sorts of comparisons and statistical analysis on .xpm files created with the GROMACS gmx mdmat tool.
It can work directly with a single xpm or a time series-derived set of xpm files giving you differences (and other statistical analysis, as well as a contacts-based cluster analysis and a contacts-based principal component analysis) between xpm(s) as well as creating time-resolved videos of the contacts evolving in a MD trajectory. All you need is a single input file where you specify the path of your trajectory and/or coordinate file. You will need gromacs and some other very routinely used software to be installed.
The paper about it is soon to be published but a Github stable release can be found here, and it includes a detailed documentation:
https://github.com/HITS-MBM/conan
The tool is called CONAN - which is an acronym for Contact Analysis.
We tried to make the software as user friendly as possible.
Hope it will be useful to you (and others!). If something is not clear don't hesitate to ask!
Best
Davide
Dear Son
Ok.. If I run the script I convert the XPM to a text matrix. How to run the script?. After that how to do a comparison between two matrices?
Thanks in advance
Hi Davide... Superb!!... I will check it for sure and let you know. Thanks
Hi Davide
I ran conan, but I got this weird error at the end of the run, when the software was trying to do clustering. I am enclosing my input file for you to check. Do I need to install anything else in Numpy?. Thanks in advance.
***********************
mkdir: created directory ‘cluster_res’
Attempting k-medoids based on interaction lifetimes...
mkdir: created directory ‘cluster_res/lifetime’
Traceback (most recent call last):
File "../../conan-master/conan.py", line 1921, in
call_hierarchical("cluster_res/lifetime", vectors, trunc, trunc_inter, life_cond, xres, ks_res, "lifetime", None, 'res', xterm, xres, yterm, yres, asymm, matrices)
File "../../conan-master/conan.py", line 1332, in call_hierarchical
Z = linkage(condensed_dist, 'ward')
File "/usr/lib/python3/dist-packages/scipy/cluster/hierarchy.py", line 627, in linkage
raise ValueError("Valid methods when the raw observations are "
ValueError: Valid methods when the raw observations are omitted are 'single', 'complete', 'weighted', and 'average'.
***********************
Cheers
Paco
Hello Paco,
It sounds to me that you are running an old distribution of scipy where function is looking for a method to use. I'd advice you to install the latest version of Anaconda which should work out of the box.
On the other hand, if you could send me your .xpm map for testing I will have a look and test it on my machine.
Hope this helps.
Cheers,
Davide
Hi Davide
Sorry for my silence. You were right. I installed brand new Anaconda and everything runs smoothly. I am still quite bit puzzled about how to interpret the results, specially the clustering. Do you have any manual, or tutorial where I can find more info about?.. Thanks again for such a nice piece of work.
Best. Paco
Hello Francisco,
No problems. I am glad that everything is working now. We have a paper that is going to be published soon on BJ.
However, for now you can access ConAn documentation on the Github distr here:
https://github.com/HITS-MBM/conan/blob/master/docs/index.md
Sorry is a bit hidden. In the documentations, the clustering analysis and the other functionalities of ConAn are explained in detail.
Hope this will help.
Thanks!
Cheers,
Davide
Hello Joao,
Great to hearing from you! Glad that you like ConAn, very happy if it will be of any use, we tried to make it as user friendly as possible. May you have any question, please don't hesitate to message me. Thank you very much for dropping the message about the JCTC paper. :) Hope we will be able to meet sometime soon, let me know if you happen to be in or around ZH! :)
Davide
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