VMD-L Mailing List

From: Chris Neale (candrewn_at_gmail.com)
Date: Wed Apr 01 2020 - 01:48:32 CDT

For what it's worth, I am pasting an email I got from John Keller that
showed me how to load a .cif into Jmol and write out a pdf that VMD could
open. It worked like a charm and with only a minute of doing the jmol
installation I now have the (multi-step) functionality I needed to load
.cif files into vmd. I think John Keller may have also posted this reply to
the VMD mailing list, but I thought I would risk the cross posting to
ensure that those on this thread are aware of this relatively easy fix for
those in need right now since I am not sure if John Keller's post made it
to the VMD list (and my browser is having trouble loading a single page
with the last many thousand VMD mailing list posts so I can't be sure).
John Keller: I hope it's OK that I am pasting your helpful reply here.

Hi Chris,

Jmol 14.29.6 will open and display .cif files. Then, in the console, do $
write pdb c:/path/cholesterol-cif.pdb

And then open it in VMD.

Jmol will write a bunch of different formats. See the help page at
https://chemapps.stolaf.edu/jmol/docs/#writemodel

Best Regards from Alaska,

John Keller

University of Alaska Fairbanks

On Wed, Apr 1, 2020 at 12:18 AM John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi guys,
> I'm still short on time, we had some significant computing disruptions
> here and being under lockdown slowed down our responses significantly,
> and I haven't had a chance to get caught up yet.
>
> The big difference between the C++11 issue for a plugin vs. VMD itself is
> that a plugin that has unresolved dependencies will not crash the entire
> VMD session, whereas code included in VMD itself will. There are still
> some gotchas for me to compile the C++11 code that I'll have to work
> through,
> but there have always been a few plugins that required special non-standard
> compilation, so my VMD build system can handle this case without much
> difficulty I think.
>
> In the short term I do expect to continue to make builds that support older
> distros like CentOS 6.x. This isn't motivated by official end of support
> dates for RHEL6/CentOS 6.x, but rather because those distros are some of
> the last ones that provide completely trouble-free support for
> stereoscopic displays (LCD shutter glasses, clone-mode passive stereo
> projection systems, 3-D TVs, etc). We managed to get a CentOS 7.x
> system to "limp" with stereoscopic display support, but it's been a
> comparative nightmare. I haven't tried CentOS 8.x yet, and I've heard
> it's near hopeless on Ubuntu from what others have said. The stereoscopic
> display users are a minority among the full VMD user community, but
> that's one of the "hold out" groups from upgrades to newer distros.
>
> In any case, I plan to have a look at Francois-Xavier's plugin this
> week and I'll let you know more as I put effort into building it and Gemmi
> on a few different platforms. I'll report back when I've had a chance
> to do this, and what my results on various platforms look like.
>
> Best,
> John Stone
>
>
> On Sun, Mar 29, 2020 at 11:04:55AM -0400, Giacomo Fiorin wrote:
> > Hi John, thanks for clarifying that the issues are different. It was
> > unclear to me (and probably will be clearer when you write back on
> Monday)
> > how this would work. For most of us, there isn't a clear distinction
> > between how VMD and the plugins are built, since their builds are
> bundled
> > together anyway.
> > It is possible that what you have in mind could be the solution to
> > problems with other C++11 code, which would otherwise need to wait
> until a
> > version later than 1.9.4 to become available in an official VMD build.
> > Giacomo
> > On Sat, Mar 28, 2020 at 11:11 PM John Stone <[1]johns_at_ks.uiuc.edu>
> wrote:
> >
> > Hi,
> > Â I'm pressed for time, but I never said that the plugin can't
> > make it into the official builds. I said that on systems that
> > lack the necessary C++11 runtime, it would fail to load.Â
> > That's a different issue altogether. I will explain all of
> > this in more detail when I have the time on Monday since it seems
> > there are some misunderstandings here.Â
> >
> > Best,
> > Â John
> >
> > On Sun, Mar 29, 2020 at 01:35:14AM +0100, FX wrote:
> > > Thanks Giacomo,
> > >
> > > > In summary, it's a good idea to work with John on getting the
> plugin
> > to be a part of VMD. But in my opinion you shouldn't feel obliged
> to
> > rewrite a big chunk of code just to work around the lack of a now
> > established standard.
> > >
> > > I???m not gonna rewrite the code because it???s not my code,
> it???s
> > the CIF-handling headers that I need that are C++11.
> > > I still wish there was a way to get the plugin in official VMD
> builds,
> > since most people use the official builds.
> > >
> > > FX
> >
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > [2]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone:
> 217-244-3349
> > [3]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
> >
> > --
> > Giacomo Fiorin
> > Associate Professor of Research, Temple University, Philadelphia, PA
> > Research collaborator, National Institutes of Health, Bethesda, MD
> > [4]http://goo.gl/Q3TBQU
> > [5]https://github.com/giacomofiorin
> >
> > References
> >
> > Visible links
> > 1. mailto:johns_at_ks.uiuc.edu
> > 2. http://www.ks.uiuc.edu/~johns/
> > 3. http://www.ks.uiuc.edu/Research/vmd/
> > 4. http://goo.gl/Q3TBQU
> > 5. https://github.com/giacomofiorin
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
>