VMD-L Mailing List

From: Robin Betz (robin_at_robinbetz.com)
Date: Fri Feb 14 2020 - 13:36:23 CST

.vmd files are just a list of commands that VMD runs.
You can open your visualization.vmd file in a text editor and look for
paths referencing files on the local computer.
"mol new" and "mol addfile" are usually the key words to look for.

Hope this helps,
Robin

On Fri, Feb 14, 2020 at 11:01 AM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> Hi John
> You are right, with GIMP, simply doing "Color -> Levels -> Auto Input
> Levels" results in some more colors being displayed, albeit not many more.
>
> As rendering of the fully shaped and colored RNA-protein cannot be done on
> the table linux box, I tried on the tesla node of the cluster, noticing
> that visualization.state.vmd cannot be transferred from computers. Is
> there a way to indicate to VMD at the cluster the new locations of the .vmd
> file and the .pdb file from which it was created?
>
> Thanks
> francesco pietra
>
>
> On Thu, Feb 13, 2020 at 7:13 PM John Stone <johns_at_ks.uiuc.edu> wrote:
>
>> Francesco,
>> It sounds to me like you're experiencing trouble that relates to
>> so-called "gamma correction" of your images. The "snapshot" rendering
>> mode in VMD takes the exact image data you're seeing on the screen
>> and writes it to a file. There is no difference in the color content
>> vs. what you saw in VMD itself, therefore I suspect an issue with your
>> image viewer.
>>
>> The renderings that VMD and Tachyon create use a linear color space
>> without any gamma correction factor (a gamma value of 1.0).
>> If you load the images that VMD or Tachyon generate into a viewer
>> program that assumes a monitor gamma of 2.2, it will have a tendency
>> to wash out your image somewhat compared to the way they are shown
>> in VMD itself (gamma 1.0).
>>
>> You can usually overcome this problem by telling the image viewer to
>> either disable automatic gamma correction, or to change its assumed
>> gamma value from 1.8 or 2.2 to 1.0, or worst case, if such controls
>> aren't available, you can tell it to apply the inverse gamma correction,
>> e.g. 0.5 and then the images should look the way they do in VMD itself.
>>
>> If you're not familiar with gamma correction or the problems it
>> creates when creating images for printed or online manuscripts,
>> this is probably a good time for you to read about it:
>> https://en.wikipedia.org/wiki/Gamma_correction
>>
>> Best regards,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Thu, Feb 13, 2020 at 06:28:10PM +0100, Francesco Pietra wrote:
>> > Hello
>> > With VMD 1.9.4a12 I am trying to obtain images, on a black
>> background, of
>> > a RNA-protein complex displayed in color by chain (new carton). As
>> you can
>> > imagine, there are so many chains. In this system, pathways of a
>> ligand
>> > are illustrated by highlighting RNA residues, as colored wdw, that
>> lie at
>> > a few Angstrom from the traveling ligand.
>> > Using Snapshot or Tachyon, the variety of colors for the new carton
>> > assembly (both RNA and proteins) in poorly reproduced, actually
>> nearly
>> > uniform color, while colors of wdw residues is correctly reproduced.
>> All
>> > that by opening the .tga file with various tools, including GIMP.
>> > Can that be a problem of using the correct tool instead of Snapshot
>> or
>> > Tachyon? Are there any better?
>> > Thanks for advice
>> > francesco pietra
>>
>> --
>> 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/
>>
>