VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 12 2007 - 01:15:22 CDT

Hi,
  We don't have a build of catdcd for windows currently, but it should be
possible to make one. The read speed of the trajectory will go much
faster if you select the "load all at once" checkbox in the molecule
file browser window when loading. This will make the file load anywhere
from 5 to 20 times faster. Also, be sure not to try and load more
frames than your computer actually has RAM for, as this will also
slow things down unnecessarily.

For the plugins such as ClustalW, you'll need to
read the source files or contact the authors of Multiseq, as it is
mainly a plugin intended to be called by Multiseq.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 07, 2007 at 10:32:50AM -0800, lily jin wrote:
> John,
>
> I installed VMD1.8.5 and the plugins released on 11/15/2006.
> I should be able to read the dcd now, but it takes forever to read the thousands of frames. Did you mean I can use catdcd under Windows? I didn't find catdcd under windows.
> By the way, how can I use the TCl plugins, like Clustalw ect. ? I didn't find the instruction.
> Thank you!
>
> Lily
>
>
>
> ----- Original Message ----
> From: John Stone <johns_at_ks.uiuc.edu>
> To: lily jin <lily1907_at_yahoo.com>
> Cc: vmd_at_ks.uiuc.edu
> Sent: Tuesday, March 6, 2007 4:08:01 PM
> Subject: Re: vmd-l: DCD for windows
>
>
> Lily,
> If you run the most recent version of VMD, you should be able to
> load sections of the DCD file into VMD and write them back out into
> separate smaller DCD files. Alternately, you could shuffle things
> around and use catdcd to do this a bit more conveniently.
>
> John
>
> On Tue, Mar 06, 2007 at 02:58:34PM -0800, lily jin wrote:
> > The original dcd file is over 17G. I usually use catdcd.LINUX to convert it in to a dcd file that windows version VMD can read and pickup 1/10 of the trajectries so that it is less than 1G.
> > This time I was required to trnasfer all my data from the cluster machine to release some space and I didn't get time to do the conversion. I loaded all the original dcd files on my windows machine and I don't know how I can deal with them:(
> > Thank you for helping!
> >
> >
> > Lily
> >
> >
> >
> > ----- Original Message ----
> > From: John Stone <johns_at_ks.uiuc.edu>
> > To: lily jin <lily1907_at_yahoo.com>
> > Cc: NAMD-L <namd-l_at_ks.uiuc.edu>; VMD-L <vmd-l_at_ks.uiuc.edu>
> > Sent: Tuesday, March 6, 2007 3:20:27 PM
> > Subject: Re: vmd-l: DCD for windows
> >
> >
> > Hi,
> > You need to be sure that you correctly transfer the DCD files in
> > binary mode, otherwise they will be corrupted by the transfer process.
> > Some windows file transfer programs assume that any unrecognized file
> > extension is a text file, and will damage the contents of the DCD file,
> > so you'll need to make absolutely sure that this is not occuring during
> > your transfer. If the DCD file is larger than 2GB, you may also need to
> > make sure that you're running one fo the most recent versions of VMD since
> > older versions of the Windows version of the DCD plugin were not able
> > to read very large files due to limitations in the Windows C library
> > stdio implementation.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Mar 06, 2007 at 01:25:40PM -0800, lily jin wrote:
> > > Hi,
> > >
> > > I trnasfered the dcd files generated by NAMD from the cluster to my local machine. However, they cannot be open under my windows system with VMD. Can anyone give me a solution to convert them on my machine? Thank you!
> > >
> > > Lily
> > >
> > >
> > >
> > > ____________________________________________________________________________________
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> > --
> > 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
> >
> >
> >
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> 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
>
>
>
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-- 
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