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 The documentation for 'volmap' is a bit out of date.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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>>>>
>>>
>>
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Received on Mon Apr 25 2016 - 12:30:03 PDT
