VMD-L Mailing List

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Wed Aug 06 2003 - 00:53:22 CDT

Hi John,

Thank you for your reply.
I was more or less asking if I want to write my own code to extract from a
trajectory that for a reduced group of atoms, what is the way to read the
binary dcd file and then read only the coordonates corresponding to the
selected group of atoms I want.

-what is the order in which the information is written in the dcd file
-how do I deal with the binary encription of the coordinates ?

Thank you,
Ioana

On Tue, 5 Aug 2003, John Stone wrote:

>
> Ioana,
> What I was trying to suggest in my previous email, is that
> you're having problems _because_ you're forwarding your
> display to a different machine. Try running it on the console
> of the machine and you'll probably be ok. I believe the 'dgl'
> error you got is caused by forwarding the display connection.
>
> Regarding getting Z coords, you can use the 'atomselect' command
> in VMD to retrieve coordinates as in an example along these lines:
> set sel [atomselect top "all"]
> $sel get z
>
> You may also wish to set the active frame and other things but
> the concept is similar. This is all documented in the VMD
> User's Guide.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Aug 05, 2003 at 08:32:21PM -0700, Ioana Cozmuta wrote:
> > Hi John,
> >
> > I am running the vmd on another machine by forwarding the graphical
> > display on my station. Moreover I understood that the machine (it is a
> > mass storage) moves files biger than a certain size on tape automatically
> > so when the files are used they are read from the tape. Do you think that
> > this delay causes the trouble I've got?
> >
> > I am using this opportunity to ask another question:
> > I want to retrieve the z coordinate of a couple of atoms from the NAMD
> > generated dcd (trajectory) file. What is the way to do this (I wrote out
> > the trajectory in binary format)?
> >
> > Thank you,
> > Ioana
> >
> >
> >
> > On Tue, 5 Aug 2003, John Stone wrote:
> >
> > >
> > > Ioana,
> > > That looks like a low level error in dmconvert. The "dgl" error
> > > sounds like it may require that you be running it locally on the
> > > console of the SGI, since "dgl" is the SGI way of doing their
> > > proprietary graphics stuff, potentially employing hardware
> > > video codecs etc. Did you run all this on the console of
> > > your SGI?
> > >
> > > Thanks,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Tue, Aug 05, 2003 at 04:04:15PM -0700, Ioana Cozmuta wrote:
> > > > Hi,
> > > >
> > > > I am trying to make an mpeg (dmconvert) movie using the vmdmovie menue but
> > > > I get the following error.
> > > >
> > > > Converting frames from rgb format to ppm... Converting frames to SGI
> > > > MPEG-1 video format dmconvert -v -f mpeg1v -p video,rate=24 -n
> > > > /u2/ioana/calibr_meas/1K/diff_1K/movieK.####.ppm,start=0,end=9,step=1
> > > > /u2/ioana/calibr_meas/1K/diff_1K/movieK.####.ppm
> > > > /u2/ioana/calibr_meas/1K/diff_1K/movieK.mpg
> > > > bgerror failed to handle background error.
> > > > Original error: -------- Scanning input ... dgl error (read): <bad
> > > > errno = 0>
> > > > Error in bgerror: invoked "break" outside of a loop
> > > >
> > > > Does anyone have any idea what is causing this error?
> > > >
> > > > Thank you,
> > > > Ioana
> > >
> > > --
> > > 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
> > >
>
> --
> 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
>