From: Maximilian Ebert (m.ebert_at_umontreal.ca)
Date: Tue Feb 26 2013 - 16:35:54 CST

Hi John,

Thank you for your prompt answer. I am using mol load and mol delete to empty my RAM. The trajectory file is too large to load it completely. So I split it into smaller pieces to calculate the bfactor for the complete simulation. I load a 2GB DCD pull out the information of all frames, store them in an array, go to next fragment trajectory, do the same and finally calculate the bfactor.

If there is a better way to handle large files in VMD I am always happy to know about it. (I saw Read Big DCD Files but I thought this way the calculations would be faster)

Anyhow I will change my code from mol load to mol new just in case you will remove the load command. Maybe you should mention in http://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html that load is deprecated.

Thank you very much,

Dipl.-Ing. Maximilian Ebert

Étudiant au doctorat en biochimie
Laboratoire du Dr. Joelle Pelletier
Université de Montréal

m.ebert_at_umontreal.ca

On 2013-02-26, at 5:16 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Max,
> At present there's not a way to silence the console output, but I wouldn't
> have expected you to get massive console output from just loading 20 files.
> Are you loading each of the trajectories into a separate molecule for
> a particular reason? You should be using the newer "mol new" and "mol addfile"
> syntax when loading files, as the old "mol load" syntax is now deprecated
> and will be removed from the program eventually.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Feb 26, 2013 at 04:52:38PM -0500, Maximilian Ebert wrote:
>> Hi list,
>>
>> I wrote a Tcl script to calculate the bfactor from a trajectory which was split into many pieces because the trajectory itself is too large to load as one file. It is working but now I want to execute it with less output. Since I load more than 20 trajectories I don't want to see the output of:
>>
>> mol load psf $psffile dcd $item
>>
>> Is there a possibility to suppress it in the console? In addition, I wanted to know if someone knows why the Tcl console GUI is so slow compared to the console window? I am using Mac OS X 10.8.2 and vmd 1.9.1.
>>
>> Thank you very much,
>>
>> Max
>
> --
> 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
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