VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 19 2006 - 15:30:13 CDT

Samuel,
  When you re-run Tachyon, you would do it outside of VMD
(i.e. don't re-export the .dat file using the Render menu of VMD)
by running a command such as this simple example:
  /usr/local/lib/vmd/tachyon_LINUX -mediumshade plot.dat -o mypic.tga

  John

On Fri, May 19, 2006 at 04:15:12PM -0400, Samuel Flores wrote:
> Hi Axel,
>
> I don't understand. I create the image using Tachyon, and then modify
> plot.dat. However when I rerun Tachyon it just overwrites plot.dat with the
> default parameters. Can you tell me more explicitly how to invoke Tachyon
> the second time such that my modified parameters are used rather than
> overwritten?
>
> Thanks
>
> Sam
>
> On Thu, 11 May 2006, Samuel Flores wrote:
>
> SF> Hi Guys,
> SF>
> SF> I am using vmd to make some high resolution images. So far they have
> been
> SF> very nice but now I need to increase the resolution. I see that
> SF> TachyonInternal uses the screen display to set the resolution of the
> TARGA
> SF> output. I have read that I can override this with a higher resolution
> by
> SF> modifying the scene file. But where is this file?
>
> sam,
>
> please use the regular (external) tachyon renderer this will
> create a .dat file that will be the input to tachyon. you can
> edit the file, which has the keyword Resolution in the second line.
> now you need to manually re-run tachyon (easiest by adapting
> the command line from the render menu). you may want to try out
> playing with the availble parameters (-fullshade, -aasamples)
> to see whether you like those image more...
>
> regards,
> axel.
>
> SF>
> SF> I was able to modify the parameters for POV3 to get satisfactory output,
> but
> SF> now want to import to adobe illustrator, which only takes TGA, tiff,
> jpg,
> SF> etc.
>
> povray should actually be able to create TGA and TIFF files, IIRC
> please check out the manpage/online help for the corresponding
> flag (i though +FT should create .tga format files...), see:
>
> F[x] = write output file (in format x)
> FC - Compressed Targa with 24 or 32 bpp
> FN[n] - PNG (n bits/color, n = 5 to 16, default is 8)
> FP - PPM
> FS - System specific
> FT - Uncompressed Targa with 24 or 32 bpp
>
>
> SF> Can anyone help with advice on increasing the TachyonInternal resolution
> or
> SF> translating the .pov?
> SF>
> SF> Sam
> SF>
> SF> Samuel Flores
> SF> Graduate Student
> SF> Gerstein Lab
> SF>
> SF> Office:
> SF> Bass 437
> SF> 266 Whitney Avenue
> SF> New Haven, CT 06520
> SF> 203.432.5405
> SF>
> SF> Home:
> SF> 28 Pearl Street
> SF> New Haven, CT 06511
> SF> cell: 203.747.2682
> SF>
> SF> -----Original Message-----
> SF> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
> Of
> SF> Ting Wang
> SF> Sent: Thursday, May 11, 2006 2:47 PM
> SF> To: vmd-l_at_ks.uiuc.edu
> SF> Subject: vmd-l: bug in membrane plugin
> SF>
> SF>
> SF> Dear VMD users,
> SF>
> SF> It seems there is a bug in the Membrane Plugin.
> SF>
> SF> When the membrane size is larger than 50A x 50A, the commond "membrane
> -l
> SF> popc ..." will generate lipid molecules with serious clash. Some
> atom-atom
> SF> distances are even smaller than 0.2A.Energy minimization can not get
> over
> SF> it, actually minimiztion can not run.
> SF>
> SF> Did anybody else notice this? Can this bug be fixed?
> SF>
> SF> Thank you very much!
> SF>
> SF> Ting
> SF>
> SF>
>
> --
> =======================================================================
> 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.
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078