Thanks for your reply.
> That's not an OpenDX file at all. What command did you use in cpptraj to
> generate the .dx file?
That makes sense then. I used the following command:
volmap test_volmap 0.5 0.5 0.5 .* centermask .*
But the doc clearly says:
> volmap filename dx dy dz <mask> [xplor] [radscale <factor>] [ [[buffer
> <buffer>] [centermask <mask>]] | [center <x,y,z>] [size <x,y,z>] ]
> [peakcut <cutoff>] [peakfile <xyzfile>]
> filename The name of the output file with the grid density. By default
> it is written in the OpenDX file format
Also, I get an error if I try to use the xplor key word (but then again,
maybe I'm doing somethig wrong):
volmap test_volmap 0.5 0.5 0.5 xplor @* centermask @*
VOLMAP: Grid spacing will be 0.50x0.50x0.50 Angstroms
Grid centered around @* with 3.00 Ang. clearance
Density will wrtten to test_volmap
Error: [volmap] Not all arguments handled: [ xplor ]
Le 25/04/2016 12:14, Jason Swails a écrit :
> On Mon, Apr 25, 2016 at 4:44 AM, Jean-Patrick Francoia <
> jeanpatrick.francoia.gmail.com> wrote:
>
>> Hi,
>>
>> I generated an opendx file with the volmap command of cpptraj. VMD and
>> Chimera are supposed to be able to read it, but it doesn't work.
>> Chimera's error log says:
>>
>> Error reading file test_volmap.dx, format apbs
>> Missing "object 1 class gridpositions counts <l> <m> <n>" header line
>>
>> Can I assume the opendx file outputed by volmap is not properly
>> formatted ? Here is the head of the dx file:
>>
>> # VOLMAP_00000
>> 1.000 1.000 1.000 0.0000
>> 2.000 1.000 1.000 0.0000
>> 3.000 1.000 1.000 0.0000
>> 4.000 1.000 1.000 0.0000
>> 5.000 1.000 1.000 0.0000
>> 6.000 1.000 1.000 0.0000
>> 7.000 1.000 1.000 0.0000
>> 8.000 1.000 1.000 0.0000
>> 9.000 1.000 1.000 0.0000
>>
> That's not an OpenDX file at all. What command did you use in cpptraj to
> generate the .dx file?
>
>
>> Could you tell me how I can visualize this map ?
>>
> It needs to be either an OpenDX or XPLOR grid file rather than a raw data
> file with space-separated numbers.
>
> HTH,
> Jason
>
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Received on Mon Apr 25 2016 - 04:00:06 PDT
