Setting the isovalue to 1e-05 made the trick !
Thank you very much to all of you
Le 25/04/2016 21:41, Daniel Roe a écrit :
> It will help if you could provide your exact cpptraj input, and maybe
> some details about your system.
>
> That said, you can adjust the isovalue in VMD to view different
> contouring levels. ~1e-05 seems good to me.
>
> -Dan
>
> On Mon, Apr 25, 2016 at 1:26 PM, Jean-Patrick Francoia
> <jeanpatrick.francoia.gmail.com> wrote:
>> Ok, now it works. I can open the file in VMD or chimera.
>> I just have a little problem now: nothing appears when I open the file .dx.
>>
>> I looked inside the file, and I only see very small numbers. I attached my
>> dx file. Could you have a look and tell me if something went wrong please ?
>>
>> Sincerely
>>
>>
>> Le 25/04/2016 16:41, Daniel Roe a écrit :
>>> Hi,
>>>
>>> The documentation for 'volmap' is a bit out of date. The format of the
>>> output file can be chosen by given your output file a different
>>> extension: for OpenDX use '.dx', for Xplor use '.xplor', etc (similar
>>> to output from 'grid').
>>>
>>> -Dan
>>>
>>> On Mon, Apr 25, 2016 at 7:12 AM, Jean-Patrick Francoia
>>> <jeanpatrick.francoia.gmail.com> wrote:
>>>> I'm using:
>>>>
>>>> CPPTRAJ: Trajectory Analysis. V15.00
>>>>
>>>> Le 25/04/2016 14:53, Jason Swails a écrit :
>>>>> What version of cpptraj are you using?
>>>>>
>>>>> On Mon, Apr 25, 2016 at 6:54 AM, Jean-Patrick Francoia <
>>>>> jeanpatrick.francoia.gmail.com> wrote:
>>>>>
>>>>>> 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 - 14:00:03 PDT
