VMD-L Mailing List

From: Francesca Mocci (francy_at_mvcch3.unica.it)
Date: Wed Nov 12 2003 - 05:47:26 CST

Dear John,

thanks a lot for the prompt reply.
Unfortunately the problem remained.

> Rather than using the "readedm" Tcl script, please use the
>built-in X-PLOR EDM reader plugin in VMD, it is much much faster
>than the Tcl script, and handles several cases that the Tcl script
>doesn't handle. Select "EDM" as the file type.
>
After selecting the EDM file type and trying to load my map file in the
vmd console
I read:

found 1 datasets
ERROR) Error reading volumetric data set 1

It should be noted that in my edm files there are empty lines between
two raws belonging to the same XY plane:
Here is my edm file , from the first line to the first empty line:

> This line is ignored
> 1
> rdparm generated grid density
> 60 -29 30 60 -29 30 60 -29 30
> 30.000 30.000 30.000 90.000 90.000 90.000
> ZYX
> -29
> 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
> 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
> 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
> 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
> 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
> 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
> 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
> 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
> 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
> 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
>
> 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
> 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000

If all the empty lines are deleted the readedm.tcl script is able to
read the file and
is possible to display the isosurface,
Note that the edm reader plugin is not able to read also this modified
file.

Thanks for your attention,
Francesca

>Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
>On Tue, Nov 11, 2003 at 04:11:11PM +0100, Francesca Mocci wrote:
>
>
>>Hello!
>>
>>I have an xplor map file (produced with the program ptraj of the
>>amber7 package)
>>and I want to display it with vmd.1.8.1
>>I downloaded the readedm.txt file from
>>http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/readedm/readedm.txt
>>I changed its name in readedm.tcl
>>and I followed the suggestion for the usage written in the readedm file:
>>
>>vmd > source readedm.tcl
>>vmd > mol load pdb my_structure.pdb
>>vmd > readedm my_edm.map
>>
>>and the following error occurred:
>>mol volume: size of data does not match specified sizes
>>
>>this is the output in the vmd console:
>>
>>
>>
>>>EDM Reader, opening Light/2na_light.map
>>> rdparm generated grid density
>>>Grid dimensions: X: 60, Y: 60, Z: 60
>>>Grid elements: 216000
>>>Grid orientation: a: 30.000, b: 30.000, c: 30.000,
>>> alpha: 90.000, beta: 90.000, gamma: 90.000
>>> xOrigin, yOrigin, zOrigin: -14.5, -14.5, -14.5
>>> xVec: 30.0 0 0
>>> yVec: -1.53102359078e-10 30.0 0
>>> zVec: -1.53102359078e-10 -1.53102359079e-10 30.0
>>> ZYX
>>> # of grids in 1 slide: 3600
>>> # of grids in 1 line: 6
>>> # of lines in 1 slide: 600.0
>>> 215964
>>>0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
>>>mol volume: size of data does not match specified sizes
>>>
>>>
>>It is quite clear that my edm format is not ok for readedm,
>>and I tried to change it in several way but with no results..
>>
>>Did anybody solved this problem for xplor map file
>>obtained by means of the program ptraj?
>>If not, it can be usefull for me
>>to have a look at an xplor map file that is accepted by vmd
>>in order to convert mine.
>>
>>Thanks for your attention,
>>Francesca
>>
>>
>>
>>
>
>
>