Re: [AMBER] What would you like to see in visualization of chemical data?

From: Robert Molt <>
Date: Mon, 20 Jul 2020 07:31:50 -0400

For the record, this email is WAY too intimate for a professional
list-serv...I am sorry, but I think even reading this email would
qualify as infidelity to my wife :)

On 7/20/20 6:48 AM, Jan Mičan wrote:
> Dearest AMBER user,
> my name is Jan Mičan and I am (hopefully) a passionate computational
> chemist like you. I am also working on molecular visualization software
> development in VisITLab <>, where we are
> developing better tools for intuitive visual analysis of molecular
> dynamics, docking, and other chemical simulations data. It is bringing me
> lots of joy to see my wishes of what I would need in visualization tools to
> come true.
> But why am I writing this email?
> I am writing this email to know your wishes and dreams. In computational
> chemistry, each one of us is focused on just some molecular properties,
> protein families, etc...
> Our ideas and perspectives are converging in the periodic boundary
> conditions of our labs, topics of study, universities, towns, and
> conferences we attend. If we could only know what all the voices which we
> can't hear from there want! After some time of equilibration, we all start
> to treat our solvent of perspectives implicitly.
> We are in desperate need of a perturbation from YOU! We want you to know
> what you would appreciate in visualizing your data.
> Please tell me everything you would like to see in molecular visualization,
> what would you like to be able to do, explore, and how would you like to
> see your data, how these tools could help you.
> For your appreciated help, I will send you a poem about the fantastic world
> of molecular simulations dedicated to you.
> Just for inspiration, I have written a paragraph that looks like
> advertising our tools at first sight (which is against my principles of
> course). However, it is here for inspiring you by ideas about what we do so
> wishes about what would you like to see in molecular visualization appear
> more easily.
> Clever visualization and analysis tools can lead you to new ideas and
> perspectives, make analysis way easier or it can make you able to make
> analyses you could not before. Just to introduce you to what we do, we
> develop a tool called CAVER Analyst
> <> for viewing MD trajectories
> with a special emphasis on tunnels and channels analysis and other handy
> features such as caching which makes loading and analyzing very large
> trajectories fast. We also have developed tools for interactive exploration
> of protein unfolding <>, visualizing
> water trajectories
> <>, Comparative
> Visualization of Protein Secondary Structures
> <>,
> and much more <>.
> Thank you for reading this long email. I'll be thinking of you day and
> night, waiting for your reply.
> Yours faithfully,
> Jan Mičan
> Loschmidt Laboratories
> Department of Experimental Biology & RECETOX
> Faculty of Science, Masaryk University
> Kamenice 5/A13, 625 00 Brno, Czech Republic
> &
> VisITLab
> Faculty of Informatics, Masaryk University
> Botanická 554/68a, 620 00 Brno, Czech Republic
> _______________________________________________
> AMBER mailing list

Dr. Robert Molt Jr.
AMBER mailing list
Received on Mon Jul 20 2020 - 05:00:04 PDT
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