Re: [AMBER-Developers] Broken links in manual

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Wed, 3 Mar 2021 14:37:50 -0500

Hi Cristina,

Thank you so much for the reply. Yes, I've been following the tutorial, and
also the instructions in the manual, thanks!

My difficulty is the data I got from the experimentalists did not come in
the 7/8-column format. It came as a table with NOESY assignments, and later
with peak intensities. So, I've been trying to write the 7-column file
myself (by hand) based on this data. Then, I thought maybe I could use one
of the programs listed in the manual to build that table, but it turns
out none of the links work any longer... Also, today I found out also that
the NMRView program (mentioned in page 539), probably doesn't even exist
anymore, having been replaced by NMRViewJ, which in turn is in process of
being replaced by NMRFx Analyst... ( And none of them can read the NMR file
I got, which was prepared using MNova... \O/ )

Maybe this session of the manual is in need of updating...

Now, I do have some questions about the practical aspects of using the
NMR-refinement code, that maybe I'll send to the Amber-reflector list
instead (since they are not programming-related). I'd really appreciate
your input on them, if you don't mind.

Thank you so much! All the best,

--
Gustavo Seabra.
On Wed, Mar 3, 2021 at 10:16 AM Christina Bergonzo <cbergonzo.gmail.com>
wrote:
> Hi Gustavo,
>
> I still use Amber's internal programs to create NMR restraints, etc. and  I
> still find the NMR refinement tutorial helpful:
> http://ambermd.org/tutorials/advanced/tutorial4/index.php
> Things like, makeDIST_RST, makeANG_RST have still mostly worked for me
> (with some library tweaking and script modifying, but I mostly do RNAs).
> In some cases I gave up and wrote my own scripts to create Amber-readable
> restraint files (like RDCs).
> Mike Summers group released a toolkit for RNA refinement using Amber based
> on this paper (https://pubmed.ncbi.nlm.nih.gov/20549304/), but the
> download
> doesn't seem to exist anymore - I can send it to you (or maybe DAC knows
> since he's a coauthor), but again it's RNA-focused and I am not sure how
> well any of these currently work for proteins (though, if I had to guess,
> everything looks better for proteins).
>
> Hope this is helpful re: NMR refinement.
> -Christina
>
> On Tue, Mar 2, 2021 at 8:08 PM Gustavo Seabra <gustavo.seabra.gmail.com>
> wrote:
>
> > Hi All,
> >
> > I noticed that *all* links to external programs listed in page 539 of the
> > Amber manual, "that can assist in preparing input for [NMR-]structure
> > refinement in Amber" are broken:
> >
> > - http://ambermd.org/sane.zip
> > - http://garbanzo.scripps.edu/nmrgrp/wisdom/pipe/tips_scripts.html.
> > - http://picasso.ucsf.edu/mardihome.html
> >
> > Does anyone have up-to-date links to those programs (or something that is
> > used today)?
> >
> > Best,
> > --
> > Gustavo Seabra.
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
>
>
> --
> -----------------------------------------------------------------
> Christina Bergonzo
> Research Chemist
> Biomolecular Measurement Division, MML, NIST
> -----------------------------------------------------------------
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Received on Wed Mar 03 2021 - 12:00:02 PST