[gmx-users] Regarding xpm2ps
bipin singh
bipinelmat at gmail.com
Wed Aug 24 18:46:02 CEST 2011
Sir,
Thanks a lot for your help......Its working...
On Wed, Aug 24, 2011 at 18:34, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> bipin singh wrote:
>>
>> Thanks for your kind help,
>> I have tried as per your suggestion, the below command
>>
>> g_sham -f 2d_proj.xvg -xmin -5 -xmax 5 -ls gibbs.xpm
>>
>> It is running without any error , but it is not giving any xpm
>> output.......
>
> Try with "-xmin -5 -5 0 -xmax 5 5 0" - the meaning of the z-axis quantities
> here has never been clear to me since -gmax should control the range of
> z-values. Leaving them at zero should cause g_sham to calculate the
> appropriate range. Otherwise, you're limited to values of z between -5 and 5
> also, which may not be appropriate.
>
> -Justin
>
>> On Wed, Aug 24, 2011 at 17:18, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>
>>> bipin singh wrote:
>>>>
>>>> Thanks for your reply,
>>>> I am attaching the xpm file which I got from g_sham and also attaching
>>>> the eps output got from
>>>> xpm2ps.As you can see there is no axis range(PC1 and PC2) labeled in
>>>> eps
>>>> file.
>>>> As the PC1 range is from -4 to +4 and PC2 range from -5 to +4, I want
>>>> the x-axis range in eps file from -4 to +4(PC1)
>>>> and y-axis range from -5 to +4(PC2) regardless of the data values in xpm
>>>> file.
>>>> But I am unable to get using .m2p file.
>>>>
>>> The .m2p file can only be used to adjust axes if the data fit the range
>>> you
>>> want already. This was unclear from your earlier post. Now that you've
>>> said what program you used, we can solve this. g_sham allows you to set
>>> the
>>> axis manually with the -xmin and -xmax options. Re-run g_sham with these
>>> options to set the axes and you should have no problem.
>>>
>>> -Justin
>>>
>>>> On Wed, Aug 24, 2011 at 16:22, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>>>
>>>>> bipin singh wrote:
>>>>>>
>>>>>> Hello,
>>>>>> I am using the below .m2p file as input for xpm2ps, but not able to
>>>>>> get axis range label.
>>>>>>
>>>>> What axis range do you obtain? If your data do not actually span from
>>>>> -4
>>>>> to
>>>>> 4, there's not much you can do. I was assuming you had data that did
>>>>> fit
>>>>> this range. You also didn't say which tool produced the .xpm file;
>>>>> some
>>>>> programs can be forced to adjust the data range, but others can't.
>>>>>
>>>>> -Justin
>>>>>
>>>>>> ; Matrix options
>>>>>> titlefont = Helvetica ; Matrix title Postscript Font name
>>>>>> titlefontsize = 20.0 ; Matrix title Font size (pt)
>>>>>> legend = yes ; Show the legend
>>>>>> legendfont = Helvetica ; Legend name Postscript Font name
>>>>>> legendfontsize = 12.0 ; Legend name Font size (pt)
>>>>>> legendlabel ; Used when there is none in the .xpm
>>>>>> legend2label ; Id. when merging two xpm's
>>>>>> xbox = 0 ; x-size of a matrix element
>>>>>> ybox = 0 ; y-size of a matrix element
>>>>>> matrixspacing = 20.0 ; Space between 2 matrices
>>>>>> xoffset = 0.0 ; Between matrix and bounding box
>>>>>> yoffset = 0.0 ; Between matrix and bounding box
>>>>>>
>>>>>> ; X-axis options
>>>>>> x-lineat0value = no ; Draw line at matrix value==0
>>>>>> x-major = 4 ; Major tick spacing
>>>>>> x-minor = 2 ; Id. Minor ticks
>>>>>> x-firstmajor = 0 ; Offset for major tick
>>>>>> x-majorat0 = no ; Additional Major tick at first frame
>>>>>> x-majorticklen = 8.0 ; Length of major ticks
>>>>>> x-minorticklen = 4.0 ; Id. Minor ticks
>>>>>> x-label = ; Used when there is none in the .xpm
>>>>>> x-font = Helvetica ; Axis label PostScript Font
>>>>>> x-fontsize = 12 ; Axis label Font size (pt)
>>>>>> x-tickfont = Helvetica ; Tick label PostScript Font
>>>>>> x-tickfontsize = 8 ; Tick label Font size (pt)
>>>>>>
>>>>>> ;Y-axis options
>>>>>> y-lineat0value = no
>>>>>> y-major = 4
>>>>>> y-minor = 2
>>>>>> y-firstmajor = 0
>>>>>> y-majorat0 = no
>>>>>> y-majorticklen = 8.0
>>>>>> y-minorticklen = 4.0
>>>>>> y-label =
>>>>>> y-fontsize = 12
>>>>>> y-font = Helvetica
>>>>>> y-tickfontsize = 8
>>>>>> y-tickfont = Helvetica
>>>>>>
>>>>>> On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul <jalemkul at vt.edu>
>>>>>> wrote:
>>>>>>>
>>>>>>> bipin singh wrote:
>>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I have xpm matrix file, for converting this file to ps format I am
>>>>>>>> using
>>>>>>>> xpm2ps
>>>>>>>> e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range
>>>>>>>> label
>>>>>>>> mentioned for x and y-axis,
>>>>>>>> in ps file.Please let me know how to set x and y axis range label in
>>>>>>>> ps
>>>>>>>> file.
>>>>>>>> for example I want to set the x and y-axis range from -4 to +4.
>>>>>>>>
>>>>>>>>
>>>>>>> Use an .m2p file:
>>>>>>>
>>>>>>> http://manual.gromacs.org/online/m2p.html
>>>>>>>
>>>>>>> -Justin
>>>>>>>
>>>>>>> --
>>>>>>> ========================================
>>>>>>>
>>>>>>> Justin A. Lemkul
>>>>>>> Ph.D. Candidate
>>>>>>> ICTAS Doctoral Scholar
>>>>>>> MILES-IGERT Trainee
>>>>>>> Department of Biochemistry
>>>>>>> Virginia Tech
>>>>>>> Blacksburg, VA
>>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>>>
>>>>>>> ========================================
>>>>>>> --
>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>>>
>>>>> --
>>>>> ========================================
>>>>>
>>>>> Justin A. Lemkul
>>>>> Ph.D. Candidate
>>>>> ICTAS Doctoral Scholar
>>>>> MILES-IGERT Trainee
>>>>> Department of Biochemistry
>>>>> Virginia Tech
>>>>> Blacksburg, VA
>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>
>>>>> ========================================
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>> Please don't post (un)subscribe requests to the list. Use the www
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>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>
>>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
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>>> Please search the archive at
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>>>
>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
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>
--
-----------------------
Thanks and Regards,
Bipin Singh
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