VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Jan 23 2008 - 09:19:12 CST

Hi Axel:
I am too busy in these days to fully understand the answers to my call for a
tcl script. For the moment, I'll carry out that mapping around the ligand with
Chimera. I know how to do that. Thanks (incidentally, I can assure those in
doubt that I know what I do)
francesco

--- Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:

> michel,
>
> [...]
>
> > If you can get TCL scripting working for grant proposal writing,
> > please let us know! :))
>
> i suspect we first have to invent a new language for that.
> GPL (Grant Proposal Language) would be a proper name. ;-)
>
> e.g.:
>
> if (num(postdoc) == 2) incr(paper(nature))
> ...
>
> > > ...and then, of course, there is the problem, that (too?) many people
> don't
> > > submit their scripts or script fragments to the VMD script library, so a
> lot
> > > of useful stuff is lost when they move on to other projects.
> >
> > That is true. This could happen, in part, because we think that our
> > lousy scripts are too simple or too specific and wouldn't be useful
> > for other people. We also assume that there are other people who can
> > do a better job at writing useful scripts, yet clean and elegant...
>
> ...but what about: if it is good enough for you, somebody else
> could use and may even improve it. why should people have to
> re-invent _everything_ when there is an option to just improve on
> what is already mostly there. most people just need the ideas,
> i.e. we can have a 'dump' for script fragments, for ideas, rather
> than completed scripts. as you may have seen from the original
> question, there is most likely no script that can do _exactly_ what
> is needed, but there is a higher probability that somebody has
> a framework, that could be adapted. most of the time this is sufficient
> to get people started. but when there is nothing to look at.
>
> ... and don't forget. everybody has to start somewhere. nobody
> is born to be an expert and how else can one learn to become
> better than by getting feedback by others on the stuff that one
> has written.
>
> > > other than that, there is also the alternative of sponsoring somebody
> > > with the proper expertise to write a custom script. since people spend
> > > a lot of money on computers and (commercial) software, i am always
> > > wondering why there is nobody offering 'incentives' to get their specific
> > > problem solved (by and expert and quickly).
> >
> > this is because... Science is selfless and altruistic! :)
>
> oh, i must have missed that one. ;-)
>
> but seriously, i personally have found that helping other people
> can be _very_ selfish. my 'drug' is solving (challenging) problems,
> so if other people provide me with interesting challenges, i am
> always inclined to give it a try (time permitting) and since in most
> cases, people just need a few ideas or pointers, i can have the fun
> of coming up with ideas, while the others have to do the legwork
> of programming and in the end we're all happy (i have learned whether
> my idea works without having to do it myself and the person asking
> got his/her problem solved fast(er)).
>
> also, since only few people want to do it, this is a "seller's market"
> and over the time people have been very generous in many ways,
> not to mention excellent job opportunities that start popping up.
>
> > Seriously, I thought the same myself. For example, I consider myself a
> > bad (really bad sometimes) programmer, so I usually find myself
> > spending a couple of hours trying to write a simple script. This is a
> > huge waste of time. Unfortunately, I'm not really sure if there are
> > people out there who want to deal with these issues in a regular basis
> > (even when getting incentives!). This might be in part because most of
> > the people here want to focus on the science and get their work done
> > (very valid thing to do). And the talented TCL-script writers (like
> > you or John) are just too busy with many other things!
>
> well, on one side, a lot might depend on the type of incentive,
> but also, if people would realize, that there _was_ a market, this
> might change a lot. i've recently some discussions with people
> on this issue and more or less i came to the conclusion that science
> needs to offer jobs (and train people for it) with a new job description:
> something like scientific software support, much like the technical
> support you need for running a spectrometer or alike.
>
> with the ongoing invasion of computers and software into every
> part of research, but the limited willingness to treat this in a professional
> manner (how many clusters are managed these days by graduate
> students or post docs who barely manage to keep them working
> without making too much of a mess? how many clusters are run
> in an very inefficient way, since the computer scientists running it
> have no idea of what the workflow and requirements of scientific
> computing are?) i am very concerned about what will happen in
> the future. once the few idealists and 'dinosaurs', who were forced
> to learn how computers and operating systems work inside out to
> be able to use them at all, die out, we could run into a situation
> where we have lots of facilities wasted, because there is nobody
> around who knows how to use them (well).
>
> cheers,
> axel.
>
> >
> > Cheers,
> > Michel
> >
> > >
> > > i'd be very interested to learn how people here on this mailing list
> > > see the perspective of having their technical problems sort of
> > > 'contracted out' so they can focus on the science...
> > >
> > > cheers,
> > > axel.
> > >
> > >
> > > >
> > > > In doing that from prmtop/mdcrd (I am working with Amber in this
> moment) I
> > > > guess that atoms names should be read from a pbd generated from
> prmtop/mdcrd,
> > > > and given to the script in their precise format (I mean, for example,
> that atom
> > > > names in ff99SB for the protein are uppercase, while those for the
> ligand in
> > > > GAFF ff are lowercase).
> > > >
> > > > That applies also to Luis Gracia's RMSD Traj Tool that I am finding
> extremely
> > > > useful and time saving.
> > > >
> > > > Thanks
> > > > francesco pietra
> > > >
> > > >
> > > >
>
____________________________________________________________________________________
> > > > Looking for last minute shopping deals?
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> > > >
> > > >
> > >
> > >
> > > --
> > > =======================================================================
> > > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > > Center for Molecular Modeling -- University of Pennsylvania
> > > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> > > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> > > =======================================================================
> > > If you make something idiot-proof, the universe creates a better idiot.
> > >
> >
> >
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>

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