VMD-L Mailing List

From: John Keller (jwkeller_at_alaska.edu)
Date: Sun Mar 29 2020 - 02:55:42 CDT

 

 

Sent from Mail for Windows 10

 

From: John Keller
Sent: Saturday, March 28, 2020 10:47 PM
To: Chris Neale
Subject: RE: Re: vmd-l: CIF file reader

 

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

 

 

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From: Chris Neale
Sent: Saturday, March 28, 2020 8:29 PM
To: John Stone; FX; Giacomo Fiorin; vmd-L
Subject: Re: vmd-l: CIF file reader

 

Dear FX:

 

I was just trying to view a CIF (for the first time) this week (cholesterol crystal structure) and was disappointed that VMD could not view it: http://scripts.iucr.org/cgi-bin/paper?S0108768101018729

 

I can't help with the implementation, but I thought perhaps it was worth commenting that I would be interested in using that feature, given that more interest might help it to happen. I tried a conversion tool I found with a google search (https://mmcif.pdbj.org/converter/index.php?l=en) but that would only handle mmCIF format.

 

Thank you, and good luck,

Chris.

 

 

 

 

On Sat, Mar 28, 2020 at 9:43 PM John Stone <johns@ks.uiuc.edu> wrote:

Hi,
  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. 
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. 

Best,
  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
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/