Re: [gmx-users] Regarding xpm2ps

[bipin singh]

Sir,
Thanks a lot for your help..Its working...

On Wed, Aug 24, 2011 at 18:34, Justin A. Lemkul  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  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  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 
>> 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/

Re: [gmx-users] Regarding xpm2ps

[Justin A. Lemkul]

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  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  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  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 listgmx-users@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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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Tr

Re: [gmx-users] Regarding xpm2ps

[bipin singh]

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...
On Wed, Aug 24, 2011 at 17:18, Justin A. Lemkul  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  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  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@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
> or s

Re: [gmx-users] Regarding xpm2ps

[Justin A. Lemkul]

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  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  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 listgmx-users@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
or send it to gmx-users-requ...@gromacs.org.
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 listgmx-users@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
or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists







--

Re: [gmx-users] Regarding xpm2ps

[bipin singh]

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.

On Wed, Aug 24, 2011 at 16:22, Justin A. Lemkul  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  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@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>> interface
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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
>
> 
> --
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-- 
---
Regards,
Bipin Singh
<>

gibbs.eps

Re: [gmx-users] Regarding xpm2ps

[Justin A. Lemkul]

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  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


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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


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Re: [gmx-users] Regarding xpm2ps

[bipin singh]

Hello,
I am using the below .m2p file as input for xpm2ps, but not able to
get axis range label.

; 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  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@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
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
---
Regards,
Bipin Singh
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Re: [gmx-users] Regarding xpm2ps

[Justin A. Lemkul]

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


--
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Re: [gmx-users] regarding xpm2ps?

[Martin Höfling]

Am Mittwoch 10 September 2008 13:36:15 schrieb minnale:
> Thanks Martin
> yes executing of .eps means read out the file.

I am using the following very ugly shell-script to convert to bmp format:

#!/bin/bash
cat $1 | grep -v ^"/\* Generated"| grep -v ^"/\* This"| grep -v ^"/\* title"| 
grep -v ^"/\* legend"| grep -v ^"/\* x-label"| grep -v ^"/\* y-label"| 
grep -v ^"/\* type" | xpmtoppm | ppmtobmp > $2

On the bmp, I apply tools (convert/mogrify) from the imagemagick package to 
crop & convert to png. The png then can then be read in by my 
python/scipy/numpy scripts as a matrix.

Best

Martin
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Re: [gmx-users] regarding xpm2ps?

[Justin A. Lemkul]

minnale wrote:
 


Thanks again Justin for your kind reply
I have given command like this
xpm2ps -f .xpm -o .eps -di .m2p
then it showing the following error

Fatal error:
Library file H_hbond.m2p not found in current dir nor in default 
directories.

(You can set the directories to search with the GMXLIB path variable)

Could please tell me how can I remedy this problem?


The error message is pretty explicit...does such a file exist?

-Justin


Thanks alot

On Wed, 10 Sep 2008 Justin A.Lemkul wrote :
 >
 >
 >minnale wrote:
 >>I have issued the following command
 >>xpm2s -f .xpm -o .eps
 >>If I mention option -di with m2p it showed
 >>
 >>Fatal error:
 >>Library file H_hbond.m2p not found in current dir nor in default 
directories.

 >>(You can set the directories to search with the GMXLIB path variable)
 >>
 >
 >If you specify -di you need to give xpm2ps an actual .m2p file, an 
example of which is online:

 >
 >http://www.gromacs.org/documentation/reference/online/m2p.html
 >
 >-Justin
 >
 >>Could tell me any suggestion
 >>Thanks alot
 >>
 >>
 >>On Wed, 10 Sep 2008 Justin A.Lemkul wrote :
 >>  >
 >>  >
 >>  >minnale wrote:
 >>  >>  I have converted .xpm (which generated from *g_hbond) to .eps 
by using xpm2ps command, after finished the running of this command showed

 >>  >>
 >>  >>There are 1 matrices in .xpm
 >>  >>Matrix 0 is 37501 x 1
 >>  >>Auto tick spacing failed for X-axis, guessing 2
 >>  >>Auto tick spacing for X-axis: major 2, minor 0.4
 >>  >>Auto tick spacing failed for Y-axis, guessing 0
 >>  >>Auto tick spacing for Y-axis: major 0, minor nan
 >>  >>Set the x-size of the box to 0.011
 >>  >>Set the y-size of the box to 0.011
 >>  >>
 >>  >>1.is it mean that set the box x and y sizes to 0.111 by using -bx 
and -by options.

 >>  >
 >>  >You've got problems somewhere.  Did you specify an .m2p file with 
-di?  What was your command line?

 >>  >
 >>  >>2.How can I execute this .eps for getting map?
 >>  >
 >>  >An .eps file can be opened by a number of programs - pretty much 
anything that can read a PDF (at least, on Linux and Mac), or Gimp.

 >>  >
 >>  >-Justin
 >>  >
 >>  >>Could please suggest me
 >>  >>Thanks in advance.
 >>  >>
 >>  >>
 >>  >>
 >>  >>578x38_banner2.gif 


 >>  >>
 >>  >>
 >>  
 >>

 >>  >>
 >>  >>___
 >>  >>gmx-users mailing listgmx-users@gromacs.org
 >>  >>http://www.gromacs.org/mailman/listinfo/gmx-users
 >>  >>Please search the archive at http://www.gromacs.org/search before 
posting!
 >>  >>Please don't post (un)subscribe requests to the list. Use the www 
interface or send it to [EMAIL PROTECTED]

 >>  >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 >>  >
 >>  >-- 
 >>  >
 >>  >Justin A. Lemkul
 >>  >Graduate Research Assistant
 >>  >Department of Biochemistry
 >>  >Virginia Tech
 >>  >Blacksburg, VA
 >>  >jalemkul[at]vt.edu | (540) 231-9080
 >>  >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >>  >
 >>  >
 >>
 >>
 >>
 >>578x38_banner2.gif 


 >>
 >
 >-- 
 >
 >Justin A. Lemkul
 >Graduate Research Assistant
 >Department of Biochemistry
 >Virginia Tech
 >Blacksburg, VA
 >jalemkul[at]vt.edu | (540) 231-9080
 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
 >



578x38_banner2.gif 






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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: Re: [gmx-users] regarding xpm2ps?

[minnale]

  

Thanks again Justin for your kind reply
I have given command like this
xpm2ps -f .xpm -o .eps -di .m2p
then it showing the following error

Fatal error:
Library file H_hbond.m2p not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)

Could please tell me how can I remedy this problem?
Thanks alot

On Wed, 10 Sep 2008 Justin A.Lemkul wrote :
>
>
>minnale wrote:
>>I have issued the following command
>>xpm2s -f .xpm -o .eps
>>If I mention option -di with m2p it showed
>>
>>Fatal error:
>>Library file H_hbond.m2p not found in current dir nor in default directories.
>>(You can set the directories to search with the GMXLIB path variable)
>>
>
>If you specify -di you need to give xpm2ps an actual .m2p file, an example of 
>which is online:
>
>http://www.gromacs.org/documentation/reference/online/m2p.html
>
>-Justin
>
>>Could tell me any suggestion
>>Thanks alot
>>
>>
>>On Wed, 10 Sep 2008 Justin A.Lemkul wrote :
>>  >
>>  >
>>  >minnale wrote:
>>  >>  I have converted .xpm (which generated from *g_hbond) to .eps by using 
>> xpm2ps command, after finished the running of this command showed
>>  >>
>>  >>There are 1 matrices in .xpm
>>  >>Matrix 0 is 37501 x 1
>>  >>Auto tick spacing failed for X-axis, guessing 2
>>  >>Auto tick spacing for X-axis: major 2, minor 0.4
>>  >>Auto tick spacing failed for Y-axis, guessing 0
>>  >>Auto tick spacing for Y-axis: major 0, minor nan
>>  >>Set the x-size of the box to 0.011
>>  >>Set the y-size of the box to 0.011
>>  >>
>>  >>1.is it mean that set the box x and y sizes to 0.111 by using -bx and -by 
>> options.
>>  >
>>  >You've got problems somewhere.  Did you specify an .m2p file with -di?  
>> What was your command line?
>>  >
>>  >>2.How can I execute this .eps for getting map?
>>  >
>>  >An .eps file can be opened by a number of programs - pretty much anything 
>> that can read a PDF (at least, on Linux and Mac), or Gimp.
>>  >
>>  >-Justin
>>  >
>>  >>Could please suggest me
>>  >>Thanks in advance.
>>  >>
>>  >>
>>  >>
>>  >>578x38_banner2.gif 
>> >  PROTECTED]/2606998_2599290/2602379/1?PARTNER=3&OAS_QUERY=null>
>>  >>
>>  >>
>>  >>
>>  >>
>>  >>___
>>  >>gmx-users mailing listgmx-users@gromacs.org
>>  >>http://www.gromacs.org/mailman/listinfo/gmx-users
>>  >>Please search the archive at http://www.gromacs.org/search before posting!
>>  >>Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to [EMAIL PROTECTED]
>>  >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>  >
>>  >-- 
>>  >
>>  >Justin A. Lemkul
>>  >Graduate Research Assistant
>>  >Department of Biochemistry
>>  >Virginia Tech
>>  >Blacksburg, VA
>>  >jalemkul[at]vt.edu | (540) 231-9080
>>  >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>  >
>>  >
>>
>>
>>
>>578x38_banner2.gif 
>>> PROTECTED]/2606998_2599290/2602379/1?PARTNER=3&OAS_QUERY=null>
>>
>
>-- 
>
>Justin A. Lemkul
>Graduate Research Assistant
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
___
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Re: [gmx-users] regarding xpm2ps?

[Justin A. Lemkul]

minnale wrote:

I have issued the following command
xpm2s -f .xpm -o .eps
If I mention option -di with m2p it showed

Fatal error:
Library file H_hbond.m2p not found in current dir nor in default 
directories.

(You can set the directories to search with the GMXLIB path variable)

Could tell me any suggestion
Thanks alot



If you specify -di you need to give xpm2ps an actual .m2p file, an example of 
which is online:


http://www.gromacs.org/documentation/reference/online/m2p.html

-Justin



On Wed, 10 Sep 2008 Justin A.Lemkul wrote :
 >
 >
 >minnale wrote:
 >>  I have converted .xpm (which generated from *g_hbond) to .eps by 
using xpm2ps command, after finished the running of this command showed

 >>
 >>There are 1 matrices in .xpm
 >>Matrix 0 is 37501 x 1
 >>Auto tick spacing failed for X-axis, guessing 2
 >>Auto tick spacing for X-axis: major 2, minor 0.4
 >>Auto tick spacing failed for Y-axis, guessing 0
 >>Auto tick spacing for Y-axis: major 0, minor nan
 >>Set the x-size of the box to 0.011
 >>Set the y-size of the box to 0.011
 >>
 >>1.is it mean that set the box x and y sizes to 0.111 by using -bx and 
-by options.

 >
 >You've got problems somewhere.  Did you specify an .m2p file with 
-di?  What was your command line?

 >
 >>2.How can I execute this .eps for getting map?
 >
 >An .eps file can be opened by a number of programs - pretty much 
anything that can read a PDF (at least, on Linux and Mac), or Gimp.

 >
 >-Justin
 >
 >>Could please suggest me
 >>Thanks in advance.
 >>
 >>
 >>
 >>578x38_banner2.gif 


 >>
 >>
 >>
 >>
 >>___
 >>gmx-users mailing listgmx-users@gromacs.org
 >>http://www.gromacs.org/mailman/listinfo/gmx-users
 >>Please search the archive at http://www.gromacs.org/search before 
posting!
 >>Please don't post (un)subscribe requests to the list. Use the www 
interface or send it to [EMAIL PROTECTED]

 >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 >
 >-- 
 >
 >Justin A. Lemkul
 >Graduate Research Assistant
 >Department of Biochemistry
 >Virginia Tech
 >Blacksburg, VA
 >jalemkul[at]vt.edu | (540) 231-9080
 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
 >



578x38_banner2.gif 






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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: Re: [gmx-users] regarding xpm2ps?

[minnale]

I have issued the following command
xpm2s -f .xpm -o .eps
If I mention option -di with m2p it showed 

Fatal error:
Library file H_hbond.m2p not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)

Could tell me any suggestion 
Thanks alot


On Wed, 10 Sep 2008 Justin A.Lemkul wrote :
>
>
>minnale wrote:
>>  I have converted .xpm (which generated from *g_hbond) to .eps by using 
>> xpm2ps command, after finished the running of this command showed
>>
>>There are 1 matrices in .xpm
>>Matrix 0 is 37501 x 1
>>Auto tick spacing failed for X-axis, guessing 2
>>Auto tick spacing for X-axis: major 2, minor 0.4
>>Auto tick spacing failed for Y-axis, guessing 0
>>Auto tick spacing for Y-axis: major 0, minor nan
>>Set the x-size of the box to 0.011
>>Set the y-size of the box to 0.011
>>
>>1.is it mean that set the box x and y sizes to 0.111 by using -bx and -by 
>>options.
>
>You've got problems somewhere.  Did you specify an .m2p file with -di?  What 
>was your command line?
>
>>2.How can I execute this .eps for getting map?
>
>An .eps file can be opened by a number of programs - pretty much anything that 
>can read a PDF (at least, on Linux and Mac), or Gimp.
>
>-Justin
>
>>Could please suggest me
>>Thanks in advance.
>>
>>
>>
>>578x38_banner2.gif 
>>> PROTECTED]/2606998_2599290/2602379/1?PARTNER=3&OAS_QUERY=null>
>>
>>
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before posting!
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>
>-- 
>
>Justin A. Lemkul
>Graduate Research Assistant
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
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Re: [gmx-users] regarding xpm2ps?

[Justin A. Lemkul]

minnale wrote:
 
I have converted .xpm (which generated from *g_hbond) to .eps by using 
xpm2ps command, after finished the running of this command showed


There are 1 matrices in .xpm
Matrix 0 is 37501 x 1
Auto tick spacing failed for X-axis, guessing 2
Auto tick spacing for X-axis: major 2, minor 0.4
Auto tick spacing failed for Y-axis, guessing 0
Auto tick spacing for Y-axis: major 0, minor nan
Set the x-size of the box to 0.011
Set the y-size of the box to 0.011

1.is it mean that set the box x and y sizes to 0.111 by using -bx and 
-by options.


You've got problems somewhere.  Did you specify an .m2p file with -di?  What was 
your command line?



2.How can I execute this .eps for getting map?


An .eps file can be opened by a number of programs - pretty much anything that 
can read a PDF (at least, on Linux and Mac), or Gimp.


-Justin


Could please suggest me
Thanks in advance.



578x38_banner2.gif 






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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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