VMD-L Mailing List

From: Tyler Smith (tylersmith2_at_mail.usf.edu)
Date: Tue Jan 14 2014 - 16:01:41 CST

Hi John,

Yes, I was able to get the script working correctly. Making the atom
selections disjoint fixed the coloring issues entirely.

Thanks!

Tyler

On Tue, Jan 14, 2014 at 10:50 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Tyler,
> Did you get your problem resolved?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Fri, Jan 03, 2014 at 09:04:28PM -0600, John Stone wrote:
> > Tyler,
> > I'm out of the office this week, so I didn't get to your emails
> > until just now. Josh's suggestion is the most likely solution to
> > any cases where you see differences between the output of a ray tracer
> > and that of OpenGL ("snapshot"). When you have multiple spheres of
> > identical radii and identical coordinate, the ray tracer and OpenGL
> > can end up drawing different ones as being visible, depending on their
> > order in the list of primitives to be drawn. This is not specific just
> > to Tachyon, but is similar for other renderers as well. The solution as
> > Josh already suggested, is to avoid drawing identical sized concentric
> > spheres with different colors...
> >
> > Cheers,
> > John Stone
> >
> >
> > On Fri, Jan 03, 2014 at 08:02:57PM -0500, Tyler Smith wrote:
> > > Hi Ryan,
> > > I'm embarrassed to tell you I don't know what you mean by a
> precompiled
> > > binary, so I can't be of much help on that front. Just out of
> curiosity
> > > were you able to get multiple frames colored correctly with Tachyon
> > > Internal or just one? I should probably clarify that when I
> attempt to
> > > render multiple frames with Tachyon Internal it's not that some of
> the
> > > monomers are the wrong shade; for many of the frames all the atoms
> will be
> > > one color. As Dr. Hoy said, if you'd like to see the PSF/PDB files
> we're
> > > using or anything else you think might be relevant don't hesitate
> to ask.
> > > Thanks,
> > >
> > > Tyler
> > >
> > > On Fri, Jan 3, 2014 at 5:43 PM, Ryan Hoffman <rmhoff_at_scripps.edu>
> wrote:
> > >
> > > I get similar colors comparing TachyonInternal (.bmp) and Snapshot
> > > (.tga). I didn't exactly reproduce your workflow though -- I
> didn't run
> > > a separate script to get the snapshot. Maybe Josh's suggestion
> (not
> > > superimposing two spheres) will help.
> > >
> > > ry
> > >
> > > ________________________________________
> > > From: Hoy, Robert [rshoy_at_usf.edu]
> > > Sent: Friday, January 03, 2014 14:45
> > > To: Ryan Hoffman
> > > Cc: Smith, Tyler; vmd-l_at_ks.uiuc.edu
> > > Subject: Re: vmd-l: Issues with tachyon internal renderer
> > >
> > > Hi again, Ryan. Ah, OK, I didn't know ray tracers had this
> feature.
> > > Yep, certainly it could be some other error, or a bug - one can
> never
> > > rule that out though we've tried pretty hard to.
> > >
> > > We have duplicated this issue on both a Mac and a Linux box
> running
> > > CentOS, so I don't think it's an OS or graphics-card issue.
> > >
> > > I believe the binaries were precompiled, but am not sure ---
> Tyler?
> > >
> > > Thanks,
> > > Rob
> > >
> > > Robert Hoy
> > > Assistant Professor of Physics
> > > University of South Florida
> > > 813-974-0063
> > >
> > > On Jan 3, 2014, at 5:32 PM, Ryan Hoffman
> > > <rmhoff_at_scripps.edu<mailto:rmhoff_at_scripps.edu>> wrote:
> > >
> > > My understanding about ray tracers in general is that the
> resulting
> > > colors are due to interactions between 'material' and 'lighting'
> > > settings. So a red apple under a green light source looks black.
> But
> > > maybe this is some other kind of user error, or maybe even a bug.
> > >
> > > What system is this on? Were the binaries pre-compiled?
> > >
> > > I'll play for a few more minutes and get back to you.
> > >
> > > ry
> > > ________________________________________
> > > From: Hoy, Robert [rshoy_at_usf.edu<mailto:rshoy_at_usf.edu>]
> > > Sent: Friday, January 03, 2014 14:27
> > > To: Smith, Tyler
> > > Cc: Ryan Hoffman; vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
> > > Subject: Re: vmd-l: Issues with tachyon internal renderer
> > >
> > > Hi, Ryan. It's not a lighting issue -- the colors are completely
> > > different, and "right" in Snapshot" but "wrong" in Tachyon.
> Besides the
> > > TCL scripts, would you also like us to send you some PSF/PDB
> files, or
> > > anything else?
> > >
> > > Thanks a lot for your help!
> > >
> > > Rob
> > >
> > > Robert Hoy
> > > Assistant Professor of Physics
> > > University of South Florida
> > > 813-974-0063
> > >
> > > On Jan 3, 2014, at 5:24 PM, Tyler Smith
> > > <tylersmith2_at_mail.usf.edu<mailto:tylersmith2_at_mail.usf.edu
> ><mailto:tylersmith2_at_mail.usf.edu>>
> > > wrote:
> > >
> > > sure
> > >
> > > On Fri, Jan 3, 2014 at 5:07 PM, Ryan Hoffman
> > > <rmhoff_at_scripps.edu<mailto:rmhoff_at_scripps.edu><mailto:
> rmhoff_at_scripps.edu>>
> > > wrote:
> > > Can we see some of the resulting Tcl script? Maybe a lighting
> issue?
> > > ry
> > > ________________________________________
> > > From:
> > > owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu><mailto:
> owner-vmd-l_at_ks.uiuc.edu>
> > > [owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu><mailto:
> owner-vmd-l_at_ks.uiuc.edu>]
> > > On Behalf Of Tyler Smith
> > > [tylersmith2_at_mail.usf.edu<mailto:tylersmith2_at_mail.usf.edu
> ><mailto:tylersmith2_at_mail.usf.edu>]
> > > Sent: Friday, January 03, 2014 12:19
> > > To:
> > > vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu><mailto:
> vmd-l_at_ks.uiuc.edu>
> > > Cc: Robert Hoy
> > > Subject: vmd-l: Issues with tachyon internal renderer
> > >
> > > Hi All,
> > > I'm attempting to create a movie in vmd that shows how the
> local
> > > crystallization of a system of polymers evolves with time during
> > > quenching. A metric for local crystallization called the CCE
> norm was
> > > used to assign every monomer in the system a crystalline
> structure (
> > > HCP, FCC, fivefold, unordered). Psf files were used to convey
> > > information about the crystalline structure using dummy
> variables; for
> > > example, all monomers with mass < .2 correspond to monomers with
> FCC
> > > ordering and are colored red. Every psf file gives local
> crystalline
> > > structure for one timestep in the quench, so in order to create a
> movie
> > > of evolving crystalline structure a new pair of psf and pdb files
> needs
> > > to be loaded in for every frame. As far as i know vmd can't
> internally
> > > create movies with multiple psf files, so I decided to render a
> series
> > > of bitmap images using vmd and then string them together using
> another
> > > program.
> > >
> > > A c++ program was used to create a long .tcl script that
> loads in
> > > the pdb and modified psf, colors the monomers accordingly,
> renders an
> > > image and then repeats for the next pair of files. This process
> worked
> > > well using the snapshot renderer, but I would prefer to generate
> higher
> > > quality images using Tachyon Internal. When the Tachyon Internal
> > > renderer is employed images are rendered but they are not colored
> > > correctly.
> > >
> > > Does anyone have any ideas as to why snapshot works and
> TachyonInternal
> > > doesn't? I'll attach the c++ scripts used to generate the .tcl
> scripts
> > >
> > > Also if there is an easier way to create movies with multiple
> psf
> > > files and custom coloring please let me know.
> > >
> > > Thanks,
> > >
> > > Tyler
> > >
> > > ________________________________
> > >
> > > <snapshot.tcl><TachyonInternal.tcl>
> >
> > --
> > 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/
>
> --
> 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/
>