pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Burkhard,

bug fixed in SVN rev 4067. Let me know if it works for you.

Cheers,
  Thomas

On 27 Feb 2014, at 10:07, Thomas Holder <tho...@sc...> wrote:

> Hi Burkhard,
> 
> this was a very strange ATI only bug which we already could fix in our Incentive PyMOL release. The fix should soon make it into the open-source version as well.
> 
> Thomas
> 
> On 26 Feb 2014, at 02:30, end...@pr... wrote:
> 
>> Dear PyMOL Experts,
>> I did check on the mailing list and fond one email about my problem but it seems it was nor resolved:
>> (
>> http://sourceforge.net/p/pymol/mailman/message/31119931/
>> )
>> 
>> I use PyMol :  PyMOL(TM) Molecular Graphics System, Version 1.7.0.0.
>> and have the problem that the distance command does not show the 'length' label, only the yellow dashed line.
>> 
>> However, like the email in the list stated, if I use the ray command the rendered image does show the length label.
>> 
>> My graphic environment is (PyMol information):
>> Detected OpenGL version 2.0 or greater. Shaders available.
>> Detected GLSL version 4.30.
>> OpenGL graphics engine:
>> GL_VENDOR:   ATI Technologies Inc.
>> GL_RENDERER: ASUS EAH5450 Series
>> GL_VERSION:  4.3.12618 Compatibility Profile Context 13.251
>> Detected 4 CPU cores.  Enabled multithreaded rendering.
>> 
>> I also like to mention this behavior is also in PyMOL(TM) Molecular Graphics System, Version 1.6.0.0. (including pymol-code-4051-trunk). This is not the case in PyMOL(TM) Molecular Graphics System, Version 1.5.0.1., where the label is showing. All these Version I compiled on Scientific Linux 6 with the provided compilers. I also use the driver for the graphic card provided by AMD Driver Packaging Version 13.251-131206a-167201C-ATI.
>> 
>> I also tried to switch on/off the shaders (set use_shaders) without any change.
>> 
>> Thanks,
>> Burkhard
>> University Frankfurt, Germany.

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi Afshan,

as I understand you want to show isomesh for your density. Please have look at these PyMOLWiki pages:

http://pymolwiki.org/index.php/Isomesh
http://pymolwiki.org/index.php/Display_CCP4_Maps

Hope that helps.

Cheers,
  Thomas

On 20 Feb 2014, at 02:43, Afshan Begum <afs...@ya...> wrote:
> Dear User of pymol,
> 
> I want to need some guidline as i am quite new in pymol. I want to make my protein structure figure with pymol and how can i show a difference map in a figure, actually my protein contain ligand and i want to show positive density as well for that i have run my ligand with zero occupancy and keep the ligand there so now i want to show both map in my figure but i do not know how to do it . Any one help me to get it would be appreciated.
> 
> Thanks
> 
> Best Regards
> 
> AFSHAN

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi Camilo,

this should work:
PyMOL>feedback disable, opengl, warnings

Cheers,
  Thomas

On 27 Feb 2014, at 08:56, Camilo Andrés Jimenez Cruz <cam...@gm...> wrote:
> I was trying to avoid compiling pymol in windows. Is there any way to filter this at a python level? I tried tinkering with the skin text element, but pymol would freeze 
> 
> -- Camilo Jiménez
> 
> On Wed, Feb 19, 2014 at 12:07 PM, mathog <ma...@ca...> wrote:
> This patch quiets that warning.  It does nothing about the cause of the
> warning (there is a TODO
> in ortho.c, presumably when it gets done, the warning would go away).
> 
> > 8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8
> --- layer1/Ortho.c.dist 2014-02-19 08:54:36 -0800
> +++ layer1/Ortho.c      2014-02-19 08:57:03 -0800
> @@ -203,11 +203,13 @@
>   #ifndef _PYMOL_GL_DRAWARRAYS
>                /* NEED TODO FOR _PYMOL_GL_DRAWARRAYS */
>       glDrawBuffer(mode);
> +#ifdef ANNOYING_WARNINGS_ENABLE
>       if(glGetError()) {
>         PRINTFB(G, FB_OpenGL, FB_Warnings)
>           " WARNING: glDrawBuffer caused GL error\n" ENDFB(G);
>       }
>   #endif
> +#endif
>       I->ActiveGLBuffer = mode;
>     }
>   }
> 
> > 8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8
> 
> Once the patch is applied this warning remains
> 
> ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns
> err=1282
> 
> This warning shows up about 7 times when I start PyMol and load one PDB
> file.
> 
> Regards,
> 
> David Mathog
> 
> On 18-Feb-2014 17:59, Camilo Andrés Jimenez Cruz wrote:
> > I downloaded it from the link here
> > http://www.pymolwiki.org/index.php/Windows_Install
> >
> >
> > -- Camilo Jiménez
> >
> >
> > On Tue, Feb 18, 2014 at 2:17 PM, Paweł Tomaszewski
> > <cro...@gm...>wrote:
> >
> >> Hi Camilo.
> >>
> >> I've got the same error! But it seems, there's no simple solution for
> >> this. Where do you have your PyMOL from?
> >>
> >> Cheers
> >> Pawel
> >>
> >>
> >> 2014-02-18 2:08 GMT+01:00 Camilo Andrés Jimenez Cruz <
> >> cam...@gm...>:
> >>
> >>> Hi everybody
> >>>
> >>> I installed pymol 1.6.x unofficial in windows 7 home. As far as I
> >>> have
> >>> tested it works well, but the console (as in the screen that the GL
> >>> window
> >>> shows when I press escape) and the main window keep constantly
> >>> showing the
> >>> message
> >>>
> >>>  WARNING: glDrawBuffer caused GL error
> >>>
> >>> which is annoying because I can't see the help or any other output to
> >>> there.
> >>>
> >>> Any ideas on how to tackle this?
> >>>
> >>> Thanks
> >>>
> >>> -- Camilo Jiménez

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi Burkhard,

this was a very strange ATI only bug which we already could fix in our Incentive PyMOL release. The fix should soon make it into the open-source version as well.

Thomas

On 26 Feb 2014, at 02:30, end...@pr... wrote:

> Dear PyMOL Experts,
> I did check on the mailing list and fond one email about my problem but it seems it was nor resolved:
> (
> http://sourceforge.net/p/pymol/mailman/message/31119931/
> )
> 
> I use PyMol :  PyMOL(TM) Molecular Graphics System, Version 1.7.0.0.
> and have the problem that the distance command does not show the 'length' label, only the yellow dashed line.
> 
> However, like the email in the list stated, if I use the ray command the rendered image does show the length label.
> 
> My graphic environment is (PyMol information):
> Detected OpenGL version 2.0 or greater. Shaders available.
> Detected GLSL version 4.30.
> OpenGL graphics engine:
> GL_VENDOR:   ATI Technologies Inc.
> GL_RENDERER: ASUS EAH5450 Series
> GL_VERSION:  4.3.12618 Compatibility Profile Context 13.251
> Detected 4 CPU cores.  Enabled multithreaded rendering.
> 
> I also like to mention this behavior is also in PyMOL(TM) Molecular Graphics System, Version 1.6.0.0. (including pymol-code-4051-trunk). This is not the case in PyMOL(TM) Molecular Graphics System, Version 1.5.0.1., where the label is showing. All these Version I compiled on Scientific Linux 6 with the provided compilers. I also use the driver for the graphic card provided by AMD Driver Packaging Version 13.251-131206a-167201C-ATI.
> 
> I also tried to switch on/off the shaders (set use_shaders) without any change.
> 
> Thanks,
> Burkhard
> University Frankfurt, Germany.

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi Fei,

can you elaborate what's obscured? Is it only obscured after the windows movie maker encoding, or are the PNG files also obscured?

Both regular labels and CGO labels should work fine in 3D.

I can confirm that with use_shaders=1, labels are indeed squeezed to half-width. But ray-tracing (and use_shaders=0) should give the correct result.

Thomas

On 23 Feb 2014, at 23:24, fei wang <wf...@gm...> wrote:
> Hi all,
> 
> I am trying to make a 3D pymol movie using "cross-eye mode". I found label text in the structure bacame obscure after converting ray-traced picture to 3D movie using windows movie maker. Does any one know how to insert label in 3d movie? Is CGO text ok or using some free 3D movie maker
> 
> Thanks in Advance!
> 
> Fei Wang

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

On 27-Feb-2014 08:56, Camilo Andrés Jimenez Cruz wrote:
> I was trying to avoid compiling pymol in windows. Is there any way to
> filter this at a python level? I tried tinkering with the skin text
> element, but pymol would freeze

I don't know what PRINTFB turns into, but since the message eventually 
appears in a screen window it is possible that it passes through some 
section of Python code to get there.  If that is the case, then you 
should be able to filter it out with Python.  If not, well, then not.

Compiling PyMOL for windows wasn't that difficult.  Basically I built it 
like the Linux version using the same mingw/msys build environment I 
already had on hand for building other Linux programs.  I will post 
instructions for doing this if the current owners of PyMOL say here that 
it is OK to do so.  (I did something like that in this list once before 
and there was, um, push back, as a result.  But that was many years ago, 
before Schrodinger.)  Of course, if somebody wants a _supported_ Windows 
PyMOL version, they should still buy one of the licensed versions, 
otherwise none of the incentive bits will be present.

Regards,

David Mathog
ma...@ca...
Manager, Sequence Analysis Facility, Biology Division, Caltech

I was trying to avoid compiling pymol in windows. Is there any way to
filter this at a python level? I tried tinkering with the skin text
element, but pymol would freeze


-- Camilo Jiménez


On Wed, Feb 19, 2014 at 12:07 PM, mathog <ma...@ca...> wrote:

> This patch quiets that warning.  It does nothing about the cause of the
> warning (there is a TODO
> in ortho.c, presumably when it gets done, the warning would go away).
>
> > 8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8
> --- layer1/Ortho.c.dist 2014-02-19 08:54:36 -0800
> +++ layer1/Ortho.c      2014-02-19 08:57:03 -0800
> @@ -203,11 +203,13 @@
>   #ifndef _PYMOL_GL_DRAWARRAYS
>                /* NEED TODO FOR _PYMOL_GL_DRAWARRAYS */
>       glDrawBuffer(mode);
> +#ifdef ANNOYING_WARNINGS_ENABLE
>       if(glGetError()) {
>         PRINTFB(G, FB_OpenGL, FB_Warnings)
>           " WARNING: glDrawBuffer caused GL error\n" ENDFB(G);
>       }
>   #endif
> +#endif
>       I->ActiveGLBuffer = mode;
>     }
>   }
>
> > 8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8
>
> Once the patch is applied this warning remains
>
> ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns
> err=1282
>
> This warning shows up about 7 times when I start PyMol and load one PDB
> file.
>
> Regards,
>
> David Mathog
>
> On 18-Feb-2014 17:59, Camilo Andrés Jimenez Cruz wrote:
> > I downloaded it from the link here
> > http://www.pymolwiki.org/index.php/Windows_Install
> >
> >
> > -- Camilo Jiménez
> >
> >
> > On Tue, Feb 18, 2014 at 2:17 PM, Paweł Tomaszewski
> > <cro...@gm...>wrote:
> >
> >> Hi Camilo.
> >>
> >> I've got the same error! But it seems, there's no simple solution for
> >> this. Where do you have your PyMOL from?
> >>
> >> Cheers
> >> Pawel
> >>
> >>
> >> 2014-02-18 2:08 GMT+01:00 Camilo Andrés Jimenez Cruz <
> >> cam...@gm...>:
> >>
> >>> Hi everybody
> >>>
> >>> I installed pymol 1.6.x unofficial in windows 7 home. As far as I
> >>> have
> >>> tested it works well, but the console (as in the screen that the GL
> >>> window
> >>> shows when I press escape) and the main window keep constantly
> >>> showing the
> >>> message
> >>>
> >>>  WARNING: glDrawBuffer caused GL error
> >>>
> >>> which is annoying because I can't see the help or any other output to
> >>> there.
> >>>
> >>> Any ideas on how to tackle this?
> >>>
> >>> Thanks
> >>>
> >>> -- Camilo Jiménez
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------------
> >>> Managing the Performance of Cloud-Based Applications
> >>> Take advantage of what the Cloud has to offer - Avoid Common
> >>> Pitfalls.
> >>> Read the Whitepaper.
> >>>
> >>>
> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
> >>> _______________________________________________
> >>> PyMOL-users mailing list (PyM...@li...)
> >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>> Archives:
> >>> http://www.mail-archive.com/pym...@li...
> >>>
> >>
> >>
> >
> >
> ------------------------------------------------------------------------------
> > Managing the Performance of Cloud-Based Applications
> > Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
> > Read the Whitepaper.
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
> >
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> ------------------------------------------------------------------------------
> Managing the Performance of Cloud-Based Applications
> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
> Read the Whitepaper.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Dear PyMOL Experts,
I did check on the mailing list and fond one email about my problem but it seems it was nor resolved:
(http://sourceforge.net/p/pymol/mailman/message/31119931/)

I use PyMol :  PyMOL(TM) Molecular Graphics System, Version 1.7.0.0.
and have the problem that the distance command does not show the 'length' label, only the yellow dashed line.

However, like the email in the list stated, if I use the ray command the rendered image does show the length label.

My graphic environment is (PyMol information):
Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 4.30.
OpenGL graphics engine:
GL_VENDOR:   ATI Technologies Inc.
GL_RENDERER: ASUS EAH5450 Series
GL_VERSION:  4.3.12618 Compatibility Profile Context 13.251
Detected 4 CPU cores.  Enabled multithreaded rendering.

I also like to mention this behavior is also in PyMOL(TM) Molecular Graphics System, Version 1.6.0.0. (including pymol-code-4051-trunk). This is not the case in PyMOL(TM) Molecular Graphics System, Version 1.5.0.1., where the label is showing. All these Version I compiled on Scientific Linux 6 with the provided compilers. I also use the driver for the graphic card provided by AMD Driver Packaging Version 13.251-131206a-167201C-ATI.

I also tried to switch on/off the shaders (set use_shaders) without any change.

Thanks,
Burkhard
University Frankfurt, Germany.

 

Hi all,

I am trying to make a 3D pymol movie using "cross-eye mode". I found label
text in the structure bacame obscure after converting ray-traced picture to
3D movie using windows movie maker. Does any one know how to insert label
in 3d movie? Is CGO text ok or using some free 3D movie maker

Thanks in Advance!

Fei Wang

Hi all

my windows installation of pymol keeps showing the WARNING: glDrawBuffer
caused GL error on windows 7
in the console

I asked here in the list and apparently there is no easy fix, and I need to
recompile pymol. I am avoiding the recompilation, so I tried tampering with
the PWM text widget, modifying the 'insert' function with no luck.

Is there any way I can forbid this warning from appearing in my console?

thanks
-- Camilo Jiménez

Dear User of pymol,

I want to need some guidline as i am quite new in pymol. I want to make my protein structure figure with pymol and how can i show a difference map in a figure, actually my protein contain ligand and i want to show positive density as well for that i have run my ligand with zero occupancy and keep the ligand there so now i want to show both map in my figure but i do not know how to do it . Any one help me to get it would be appreciated.

Thanks

 

Best Regards

AFSHAN

This patch quiets that warning.  It does nothing about the cause of the 
warning (there is a TODO
in ortho.c, presumably when it gets done, the warning would go away).

> 8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8
--- layer1/Ortho.c.dist 2014-02-19 08:54:36 -0800
+++ layer1/Ortho.c      2014-02-19 08:57:03 -0800
@@ -203,11 +203,13 @@
  #ifndef _PYMOL_GL_DRAWARRAYS
               /* NEED TODO FOR _PYMOL_GL_DRAWARRAYS */
      glDrawBuffer(mode);
+#ifdef ANNOYING_WARNINGS_ENABLE
      if(glGetError()) {
        PRINTFB(G, FB_OpenGL, FB_Warnings)
          " WARNING: glDrawBuffer caused GL error\n" ENDFB(G);
      }
  #endif
+#endif
      I->ActiveGLBuffer = mode;
    }
  }

> 8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8>8

Once the patch is applied this warning remains

ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns 
err=1282

This warning shows up about 7 times when I start PyMol and load one PDB 
file.

Regards,

David Mathog

On 18-Feb-2014 17:59, Camilo Andrés Jimenez Cruz wrote:
> I downloaded it from the link here
> http://www.pymolwiki.org/index.php/Windows_Install
> 
> 
> -- Camilo Jiménez
> 
> 
> On Tue, Feb 18, 2014 at 2:17 PM, Paweł Tomaszewski 
> <cro...@gm...>wrote:
> 
>> Hi Camilo.
>> 
>> I've got the same error! But it seems, there's no simple solution for
>> this. Where do you have your PyMOL from?
>> 
>> Cheers
>> Pawel
>> 
>> 
>> 2014-02-18 2:08 GMT+01:00 Camilo Andrés Jimenez Cruz <
>> cam...@gm...>:
>> 
>>> Hi everybody
>>> 
>>> I installed pymol 1.6.x unofficial in windows 7 home. As far as I 
>>> have
>>> tested it works well, but the console (as in the screen that the GL 
>>> window
>>> shows when I press escape) and the main window keep constantly 
>>> showing the
>>> message
>>> 
>>>  WARNING: glDrawBuffer caused GL error
>>> 
>>> which is annoying because I can't see the help or any other output to
>>> there.
>>> 
>>> Any ideas on how to tackle this?
>>> 
>>> Thanks
>>> 
>>> -- Camilo Jiménez
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> Managing the Performance of Cloud-Based Applications
>>> Take advantage of what the Cloud has to offer - Avoid Common 
>>> Pitfalls.
>>> Read the Whitepaper.
>>> 
>>> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: 
>>> http://www.mail-archive.com/pym...@li...
>>> 
>> 
>> 
> 
> ------------------------------------------------------------------------------
> Managing the Performance of Cloud-Based Applications
> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
> Read the Whitepaper.
> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
> 
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Jared, my haptic device is SensAble Phantom Omni and now it is called
Geomagic Touch. I work on integration it with PyMOL and VRPN.

So far so good, but now I have a little more complicated problem with
rotate and translate functions.

When I set camera=0 in both of them, it doesn't matter if I move the screen
with mouse or not - my cone rotations and translations are absolute to the
global origin.
But when I don't set camera=0 option translations of the cone still works
well but rotations don't.

I think this is because translate function gets coordinates that are not
absolute to the origin but it gets changes - I mean [dx, dy, dz], where
dx=|x-x0|, x is current position and x0 is previous position (the same with
dy and dz). On the other hand rotate function gets origin option params as
absolute values, here [x, y, z] are cone position. Now after turning camera
with mouse translations of the cone are relative to camera position but
origin of rotation is absolute to main coordinate system position.

In this situation I have two origins: origin of rotations that is equal to
position of the cone and some global PyMOL origin where everything begins.

I hope it's clear so far ;)

Now, is it possible to change the origin of rotation not with values that
are absolute to the global origin but with changes relative to it's
previous position. Or maybe I should ask: "Is it possible to CHANGE origin
of rotation, not to SET it?".

I know it's a little complicated to explain what I mean using words, but I
hope I succeeded here ;)

Cheers,
Paweł




2014-02-18 20:24 GMT+01:00 Sampson, Jared <Jar...@ny...>:

>  Hi Pawel -
>
>  Glad you were able to make it work.  Also, that haptic device (I guess
> the new version is the Geomagic Touch?) looks pretty neat.
>
>  I'm now realizing that when you asked "how to make a rotation of the CGO
> about axis that is NOT of the global pymol coordinate system but goes
> through the CGO itself" you probably didn't necessarily mean a rotation
> about the cone's primary axis, because that doesn't really do a whole lot
> unless your object isn't radially symmetric!
>
>  For correctness' sake, however, I need to amend my previous response.
>  It turns out I chose unfortunate values for the cone base and tip
> positions in my example, which resulted in the cone axis going through the
> global coordinate origin.  My previous attempt fails for cones that don't
> point at or away from the origin.  Whoops!
>
>  Thomas'  suggestion about the origin argument fixes it, though.  So for
> my example, I'd also need either the tip or the base position:
>
>  # print the values to use later
> print "tip_xyz = %s" % tip_xyz   # need this, too!
> print "axis = %s" % cone_axis
>
>
>  and then rotate the cone with, e.g.:
>
>  rotate [3,3,3], 10, object=cone, camera=0, origin=[4,5,6]
>
>
>  or everything with, e.g.:
>
>   rotate [3,3,3], 10, origin=[4,5,6]
>
>
>  Cheers,
> Jared
>
>  --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> 550 First Avenue
> New York, NY 10016
> 212-263-7898
> http://kong.med.nyu.edu/
>
>
>
>
>
>
>  On Feb 18, 2014, at 2:04 PM, Paweł Tomaszewski <cro...@gm...>
>  wrote:
>
>  Jared, Thomas thank you guys!
>
> Now everything works great :)
> The solution was pretty simple and I don't know why it took me so long...
> I have a X,Y and Z coordinates from my SensAble Pantom haptic device and
> quaternions to do rotations of cone.
>
>  The problem was, that in 'translate' function I didn't use 'camera=0'
> option, what in did in 'rotate'. Moreover I should set 'origin=[X,Y,Z]'
> option as well as 'camera=0' in rotate option.
>
>  Now it work smoothly and pretty nice ;)
>
>  Thank you
> Paweł
>
>
>
> 2014-02-18 19:40 GMT+01:00 Sampson, Jared <Jar...@ny...>:
>
>> Hi Pawel -
>>
>>  If you can determine the primary axis of the cone from the tip and the
>> center of the circle at the base, you can give `rotate` an arbitrary
>> [x,y,z] float vector as its first argument instead of x, y or z.  For
>> example, if you generate your cone using something like the following
>> Python script:
>>
>>  ### cone_cgo.py ###
>>
>>   from pymol.cgo import *
>> from pymol import cmd
>>
>>  # set up the cone
>> base_xyz = [1.0, 2.0, 3.0]
>> tip_xyz = [4.0, 5.0, 6.0]
>> base_radius = 1.0
>> tip_radius = 0.0
>> base_color = [0.9, 0.0, 0.0]
>> tip_color = [0.0, 0.0, 0.9]
>>
>>  # calculate the cone axis
>> cone_axis = [ tip_xyz[0]-base_xyz[0],
>>               tip_xyz[1]-base_xyz[1],
>>               tip_xyz[2]-base_xyz[2] ]
>>
>>  # print the axis to use later
>> print cone_axis
>>
>>  # generate the cone CGO text
>> obj = [CONE, base_xyz[0], base_xyz[1], base_xyz[2], tip_xyz[0],
>> tip_xyz[1], tip_xyz[2], base_radius, tip_radius, base_color[0],
>> base_color[1], base_color[2], tip_color[0], tip_color[1], tip_color[2], 1,
>> 1]
>>
>>  # load it
>> cmd.load_cgo(obj, 'cone')
>>
>>  # generate a pseudoatom for reference
>> cmd.pseudoatom('point', pos=[2,5,4])
>> cmd.show_as('nb_spheres', 'point')
>>
>>   ### end cone_cgo.py ###
>>
>>
>>  and load it via `run cone_cgo.py`, then you can rotate the cone on its
>> axis using, e.g.:
>>
>>  rotate [3,3,3], 10, object=cone, camera=0
>>
>>
>>  Even with a radially symmetric cone surface, if you look closely, you
>> can see the individual polygons changing at the cone base.  You can also
>> rotate the scene around the cone axis with, e.g.:
>>
>>   rotate [3,3,3], 10
>>
>>
>>  Hope that helps.
>>
>>  Cheers,
>> Jared
>>
>> --
>> Jared Sampson
>> Xiangpeng Kong Lab
>> NYU Langone Medical Center
>> 550 First Avenue
>> New York, NY 10016
>> 212-263-7898
>> http://kong.med.nyu.edu/
>>
>>
>>
>>
>>
>>
>>   On Feb 17, 2014, at 2:40 PM, Paweł Tomaszewski <cro...@gm...>
>> wrote:
>>
>>    Thank you Thomas
>> Using camera=0 caused my cone not to do rotations related to the camera
>> position.
>> Cone still rotates not about itself, but about axis of global coordinate
>> system.
>> Do you have any other ideas?
>>
>>  Cheers,
>>    Paweł
>>
>>
>> 2014-02-06 17:00 GMT+01:00 Thomas Holder <tho...@sc...>:
>>
>>> Hi Pawel,
>>>
>>> have you tried using the camera=0 argument?
>>>
>>> cmd.rotate(axis, angle, object='yourcone', camera=0)
>>>
>>> Cheers,
>>>   Thomas
>>>
>>>
>>  On 05 Feb 2014, at 15:46, Павел Томашевский <cro...@gm...> wrote:
>>>
>>> > Hello
>>> > I've made a cone CGO (something like a pointer) and now I need to make
>>> a rotation of the cone. I have got yaw, pitch and roll angle values, but
>>> when I do 'rotate' command it rotates about axis of the global coordinate
>>> system.
>>> >
>>> > My question is, how to make a rotation of the CGO about axis that is
>>> NOT of the global pymol coordinate system but goes through the CGO itself?
>>> >
>>> > I hope it's clear what I mean ;)
>>> >
>>> > Thank you
>>> > Pawel
>>>
>>>
>>>  --
>>> Thomas Holder
>>> PyMOL Developer
>>> Schrödinger, Inc.
>>>
>>>
>>
>> ------------------------------------------------------------------------------
>> Managing the Performance of Cloud-Based Applications
>> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
>> Read the Whitepaper.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk_______________________________________________
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>>
>>
>>  ------------------------------------------------------------
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>> organization accepts no liability for any damage caused by any virus
>> transmitted by this email.
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>>
>
>
> ------------------------------------------------------------------------------
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> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
> Read the Whitepaper.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk_______________________________________________
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>
>  ------------------------------------------------------------
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I downloaded it from the link here
http://www.pymolwiki.org/index.php/Windows_Install


-- Camilo Jiménez


On Tue, Feb 18, 2014 at 2:17 PM, Paweł Tomaszewski <cro...@gm...>wrote:

> Hi Camilo.
>
> I've got the same error! But it seems, there's no simple solution for
> this. Where do you have your PyMOL from?
>
> Cheers
> Pawel
>
>
> 2014-02-18 2:08 GMT+01:00 Camilo Andrés Jimenez Cruz <
> cam...@gm...>:
>
>> Hi everybody
>>
>> I installed pymol 1.6.x unofficial in windows 7 home. As far as I have
>> tested it works well, but the console (as in the screen that the GL window
>> shows when I press escape) and the main window keep constantly showing the
>> message
>>
>>  WARNING: glDrawBuffer caused GL error
>>
>> which is annoying because I can't see the help or any other output to
>> there.
>>
>> Any ideas on how to tackle this?
>>
>> Thanks
>>
>> -- Camilo Jiménez
>>
>>
>> ------------------------------------------------------------------------------
>> Managing the Performance of Cloud-Based Applications
>> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
>> Read the Whitepaper.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>

Hi Sampsa -

The long list of ids crashes for me as well.  Instead of listing each id separately, you can use ranges to define your selections.

select paska, id 36-58
select isopaska, id 36-350

If you need to use non-continuous ids, you can use Boolean logic to join the ranges:

select isopaska_without_id_59, id 36-58 or id 60-350 

Cheers, 
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/






On Feb 18, 2014, at 1:50 PM, Sampsa Riikonen <sam...@ik...>
 wrote:

> Hi,
> 
> I am trying to select a large number of atoms, using a pymol script.  
> The first script file looks like this:
> -----------
> select paska, id 
> 36+37+38+39+40+41+42+43+44+45+46+47+48+49+50+51+52+53+54+55+56+57+58
> ------------
> The second one like this:
> ------------
> select isopaska, id 
> 36+37+38+39+40+41+42+43+44+45+46+47+48+49+50+51+52+53+54+55+56+57+58+59+60+61+62+63+64+65+66+67+68+69+70+71+72+73+74+75+76+77+78+79+80+81+82+83+84+85+86+87+88+89+90+91+92+93+94+95+96+97+98+99+100+101+102+103+104+105+106+107+108+109+110+111+112+113+114+115+116+117+118+119+120+121+122+123+124+125+126+127+128+129+130+131+132+133+134+135+136+137+138+139+140+141+142+143+144+145+146+147+148+149+150+151+152+153+154+155+156+157+158+159+160+161+162+163+164+165+166+167+168+169+170+171+172+173+174+175+176+177+178+179+180+181+182+183+184+185+186+187+188+189+190+191+192+193+194+195+196+197+198+199+200+201+202+203+204+205+206+207+208+209+210+211+212+213+214+215+216+217+218+219+220+221+222+223+224+225+226+227+228+229+230+231+232+233+234+235+236+237+238+239+240+241+242+243+244+245+246+247+248+249+250+251+252+253+254+255+256+257+258+259+260+261+262+263+264+265+266+267+268+269+270+271+272+273+274+275+276+277+278+279+280+281+282+283+284+285+286+287+288+289+290+291+292+293+294+295+296+297+298+299+300+301+302+303+304+305+306+307+308+309+310+311+312+313+314+315+316+317+318+319+320+321+322+323+324+325+326+327+328+329+330+331+332+333+334+335+336+337+338+339+340+341+342+343+344+345+346+347+348+349+350
> -------------
> 
> When running the first script, it works ok, however, if I run the second 
> one, pymol crashes:
> ---------------
> 
> *** buffer overflow detected ***: python2.7 terminated
> ======= Backtrace: =========
> /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f171c6ce08c]
> /lib/x86_64-linux-gnu/libc.so.6(+0x111020)[0x7f171c6cd020]
> ...
> ---------------
> 
> How can I select a laarge number of atoms based on their numbers?
> 
> Regards,
> 
> Sampsa
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Managing the Performance of Cloud-Based Applications
> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
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=================================

Hi Pawel -

Glad you were able to make it work.  Also, that haptic device (I guess the new version is the Geomagic Touch?) looks pretty neat.

I'm now realizing that when you asked "how to make a rotation of the CGO about axis that is NOT of the global pymol coordinate system but goes through the CGO itself" you probably didn't necessarily mean a rotation about the cone's primary axis, because that doesn't really do a whole lot unless your object isn't radially symmetric!

For correctness' sake, however, I need to amend my previous response.  It turns out I chose unfortunate values for the cone base and tip positions in my example, which resulted in the cone axis going through the global coordinate origin.  My previous attempt fails for cones that don't point at or away from the origin.  Whoops!

Thomas'  suggestion about the origin argument fixes it, though.  So for my example, I'd also need either the tip or the base position:

# print the values to use later
print "tip_xyz = %s" % tip_xyz   # need this, too!
print "axis = %s" % cone_axis

and then rotate the cone with, e.g.:

rotate [3,3,3], 10, object=cone, camera=0, origin=[4,5,6]

or everything with, e.g.:

rotate [3,3,3], 10, origin=[4,5,6]

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/






On Feb 18, 2014, at 2:04 PM, Paweł Tomaszewski <cro...@gm...<mailto:cro...@gm...>>
 wrote:

Jared, Thomas thank you guys!

Now everything works great :)
The solution was pretty simple and I don't know why it took me so long...
I have a X,Y and Z coordinates from my SensAble Pantom haptic device and quaternions to do rotations of cone.

The problem was, that in 'translate' function I didn't use 'camera=0' option, what in did in 'rotate'. Moreover I should set 'origin=[X,Y,Z]' option as well as 'camera=0' in rotate option.

Now it work smoothly and pretty nice ;)

Thank you
Paweł



2014-02-18 19:40 GMT+01:00 Sampson, Jared <Jar...@ny...<mailto:Jar...@ny...>>:
Hi Pawel -

If you can determine the primary axis of the cone from the tip and the center of the circle at the base, you can give `rotate` an arbitrary [x,y,z] float vector as its first argument instead of x, y or z.  For example, if you generate your cone using something like the following Python script:

### cone_cgo.py ###

from pymol.cgo import *
from pymol import cmd

# set up the cone
base_xyz = [1.0, 2.0, 3.0]
tip_xyz = [4.0, 5.0, 6.0]
base_radius = 1.0
tip_radius = 0.0
base_color = [0.9, 0.0, 0.0]
tip_color = [0.0, 0.0, 0.9]

# calculate the cone axis
cone_axis = [ tip_xyz[0]-base_xyz[0],
              tip_xyz[1]-base_xyz[1],
              tip_xyz[2]-base_xyz[2] ]

# print the axis to use later
print cone_axis

# generate the cone CGO text
obj = [CONE, base_xyz[0], base_xyz[1], base_xyz[2], tip_xyz[0], tip_xyz[1], tip_xyz[2], base_radius, tip_radius, base_color[0], base_color[1], base_color[2], tip_color[0], tip_color[1], tip_color[2], 1, 1]

# load it
cmd.load_cgo(obj, 'cone')

# generate a pseudoatom for reference
cmd.pseudoatom('point', pos=[2,5,4])
cmd.show_as('nb_spheres', 'point')

### end cone_cgo.py ###

and load it via `run cone_cgo.py`, then you can rotate the cone on its axis using, e.g.:

rotate [3,3,3], 10, object=cone, camera=0

Even with a radially symmetric cone surface, if you look closely, you can see the individual polygons changing at the cone base.  You can also rotate the scene around the cone axis with, e.g.:

rotate [3,3,3], 10

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/






On Feb 17, 2014, at 2:40 PM, Paweł Tomaszewski <cro...@gm...<mailto:cro...@gm...>> wrote:

Thank you Thomas
Using camera=0 caused my cone not to do rotations related to the camera position.
Cone still rotates not about itself, but about axis of global coordinate system.
Do you have any other ideas?

Cheers,
   Paweł


2014-02-06 17:00 GMT+01:00 Thomas Holder <tho...@sc...<mailto:tho...@sc...>>:
Hi Pawel,

have you tried using the camera=0 argument?

cmd.rotate(axis, angle, object='yourcone', camera=0)

Cheers,
  Thomas

On 05 Feb 2014, at 15:46, Павел Томашевский <cro...@gm...<mailto:cro...@gm...>> wrote:

> Hello
> I've made a cone CGO (something like a pointer) and now I need to make a rotation of the cone. I have got yaw, pitch and roll angle values, but when I do 'rotate' command it rotates about axis of the global coordinate system.
>
> My question is, how to make a rotation of the CGO about axis that is NOT of the global pymol coordinate system but goes through the CGO itself?
>
> I hope it's clear what I mean ;)
>
> Thank you
> Pawel


--
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


------------------------------------------------------------------------------
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Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
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=================================

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=================================

Hi Camilo.

I've got the same error! But it seems, there's no simple solution for this.
Where do you have your PyMOL from?

Cheers
Pawel


2014-02-18 2:08 GMT+01:00 Camilo Andrés Jimenez Cruz <
cam...@gm...>:

> Hi everybody
>
> I installed pymol 1.6.x unofficial in windows 7 home. As far as I have
> tested it works well, but the console (as in the screen that the GL window
> shows when I press escape) and the main window keep constantly showing the
> message
>
>  WARNING: glDrawBuffer caused GL error
>
> which is annoying because I can't see the help or any other output to
> there.
>
> Any ideas on how to tackle this?
>
> Thanks
>
> -- Camilo Jiménez
>
>
> ------------------------------------------------------------------------------
> Managing the Performance of Cloud-Based Applications
> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
> Read the Whitepaper.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Jared, Thomas thank you guys!

Now everything works great :)
The solution was pretty simple and I don't know why it took me so long...
I have a X,Y and Z coordinates from my SensAble Pantom haptic device and
quaternions to do rotations of cone.

The problem was, that in 'translate' function I didn't use 'camera=0'
option, what in did in 'rotate'. Moreover I should set 'origin=[X,Y,Z]'
option as well as 'camera=0' in rotate option.

Now it work smoothly and pretty nice ;)

Thank you
Paweł



2014-02-18 19:40 GMT+01:00 Sampson, Jared <Jar...@ny...>:

>  Hi Pawel -
>
>  If you can determine the primary axis of the cone from the tip and the
> center of the circle at the base, you can give `rotate` an arbitrary
> [x,y,z] float vector as its first argument instead of x, y or z.  For
> example, if you generate your cone using something like the following
> Python script:
>
>  ### cone_cgo.py ###
>
>   from pymol.cgo import *
> from pymol import cmd
>
>  # set up the cone
> base_xyz = [1.0, 2.0, 3.0]
> tip_xyz = [4.0, 5.0, 6.0]
> base_radius = 1.0
> tip_radius = 0.0
> base_color = [0.9, 0.0, 0.0]
> tip_color = [0.0, 0.0, 0.9]
>
>  # calculate the cone axis
> cone_axis = [ tip_xyz[0]-base_xyz[0],
>               tip_xyz[1]-base_xyz[1],
>               tip_xyz[2]-base_xyz[2] ]
>
>  # print the axis to use later
> print cone_axis
>
>  # generate the cone CGO text
> obj = [CONE, base_xyz[0], base_xyz[1], base_xyz[2], tip_xyz[0],
> tip_xyz[1], tip_xyz[2], base_radius, tip_radius, base_color[0],
> base_color[1], base_color[2], tip_color[0], tip_color[1], tip_color[2], 1,
> 1]
>
>  # load it
> cmd.load_cgo(obj, 'cone')
>
>  # generate a pseudoatom for reference
> cmd.pseudoatom('point', pos=[2,5,4])
> cmd.show_as('nb_spheres', 'point')
>
>   ### end cone_cgo.py ###
>
>
>  and load it via `run cone_cgo.py`, then you can rotate the cone on its
> axis using, e.g.:
>
>  rotate [3,3,3], 10, object=cone, camera=0
>
>
>  Even with a radially symmetric cone surface, if you look closely, you
> can see the individual polygons changing at the cone base.  You can also
> rotate the scene around the cone axis with, e.g.:
>
>   rotate [3,3,3], 10
>
>
>  Hope that helps.
>
>  Cheers,
> Jared
>
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> 550 First Avenue
> New York, NY 10016
> 212-263-7898
> http://kong.med.nyu.edu/
>
>
>
>
>
>
>  On Feb 17, 2014, at 2:40 PM, Paweł Tomaszewski <cro...@gm...>
> wrote:
>
>  Thank you Thomas
> Using camera=0 caused my cone not to do rotations related to the camera
> position.
> Cone still rotates not about itself, but about axis of global coordinate
> system.
> Do you have any other ideas?
>
>  Cheers,
>    Paweł
>
>
> 2014-02-06 17:00 GMT+01:00 Thomas Holder <tho...@sc...>:
>
>> Hi Pawel,
>>
>> have you tried using the camera=0 argument?
>>
>> cmd.rotate(axis, angle, object='yourcone', camera=0)
>>
>> Cheers,
>>   Thomas
>>
>>
>  On 05 Feb 2014, at 15:46, Павел Томашевский <cro...@gm...> wrote:
>>
>> > Hello
>> > I've made a cone CGO (something like a pointer) and now I need to make
>> a rotation of the cone. I have got yaw, pitch and roll angle values, but
>> when I do 'rotate' command it rotates about axis of the global coordinate
>> system.
>> >
>> > My question is, how to make a rotation of the CGO about axis that is
>> NOT of the global pymol coordinate system but goes through the CGO itself?
>> >
>> > I hope it's clear what I mean ;)
>> >
>> > Thank you
>> > Pawel
>>
>>
>>  --
>> Thomas Holder
>> PyMOL Developer
>> Schrödinger, Inc.
>>
>>
>
> ------------------------------------------------------------------------------
> Managing the Performance of Cloud-Based Applications
> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
> Read the Whitepaper.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk_______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>
>  ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain information that is proprietary,
> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
> have received this email in error please notify the sender by return email
> and delete the original message. Please note, the recipient should check
> this email and any attachments for the presence of viruses. The
> organization accepts no liability for any damage caused by any virus
> transmitted by this email.
> =================================
>

Hi,

I am trying to select a large number of atoms, using a pymol script.  
The first script file looks like this:
-----------
select paska, id 
36+37+38+39+40+41+42+43+44+45+46+47+48+49+50+51+52+53+54+55+56+57+58
------------
The second one like this:
------------
select isopaska, id 
36+37+38+39+40+41+42+43+44+45+46+47+48+49+50+51+52+53+54+55+56+57+58+59+60+61+62+63+64+65+66+67+68+69+70+71+72+73+74+75+76+77+78+79+80+81+82+83+84+85+86+87+88+89+90+91+92+93+94+95+96+97+98+99+100+101+102+103+104+105+106+107+108+109+110+111+112+113+114+115+116+117+118+119+120+121+122+123+124+125+126+127+128+129+130+131+132+133+134+135+136+137+138+139+140+141+142+143+144+145+146+147+148+149+150+151+152+153+154+155+156+157+158+159+160+161+162+163+164+165+166+167+168+169+170+171+172+173+174+175+176+177+178+179+180+181+182+183+184+185+186+187+188+189+190+191+192+193+194+195+196+197+198+199+200+201+202+203+204+205+206+207+208+209+210+211+212+213+214+215+216+217+218+219+220+221+222+223+224+225+226+227+228+229+230+231+232+233+234+235+236+237+238+239+240+241+242+243+244+245+246+247+248+249+250+251+252+253+254+255+256+257+258+259+260+261+262+263+264+265+266+267+268+269+270+271+272+273+274+275+276+277+278+279+280+281+282+283+284+285+286+287+288+289+290+291+292+293+294+295+296+297+298+299+300+301+302+303+304+305+306+307+308+309+310+311+312+313+314+315+316+317+318+319+320+321+322+323+324+325+326+327+328+329+330+331+332+333+334+335+336+337+338+339+340+341+342+343+344+345+346+347+348+349+350
-------------

When running the first script, it works ok, however, if I run the second 
one, pymol crashes:
---------------

*** buffer overflow detected ***: python2.7 terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f171c6ce08c]
/lib/x86_64-linux-gnu/libc.so.6(+0x111020)[0x7f171c6cd020]
...
---------------

How can I select a laarge number of atoms based on their numbers?

Regards,

Sampsa

Hi Pawel -

If you can determine the primary axis of the cone from the tip and the center of the circle at the base, you can give `rotate` an arbitrary [x,y,z] float vector as its first argument instead of x, y or z.  For example, if you generate your cone using something like the following Python script:

### cone_cgo.py ###

from pymol.cgo import *
from pymol import cmd

# set up the cone
base_xyz = [1.0, 2.0, 3.0]
tip_xyz = [4.0, 5.0, 6.0]
base_radius = 1.0
tip_radius = 0.0
base_color = [0.9, 0.0, 0.0]
tip_color = [0.0, 0.0, 0.9]

# calculate the cone axis
cone_axis = [ tip_xyz[0]-base_xyz[0],
              tip_xyz[1]-base_xyz[1],
              tip_xyz[2]-base_xyz[2] ]

# print the axis to use later
print cone_axis

# generate the cone CGO text
obj = [CONE, base_xyz[0], base_xyz[1], base_xyz[2], tip_xyz[0], tip_xyz[1], tip_xyz[2], base_radius, tip_radius, base_color[0], base_color[1], base_color[2], tip_color[0], tip_color[1], tip_color[2], 1, 1]

# load it
cmd.load_cgo(obj, 'cone')

# generate a pseudoatom for reference
cmd.pseudoatom('point', pos=[2,5,4])
cmd.show_as('nb_spheres', 'point')

### end cone_cgo.py ###

and load it via `run cone_cgo.py`, then you can rotate the cone on its axis using, e.g.:

rotate [3,3,3], 10, object=cone, camera=0

Even with a radially symmetric cone surface, if you look closely, you can see the individual polygons changing at the cone base.  You can also rotate the scene around the cone axis with, e.g.:

rotate [3,3,3], 10

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/






On Feb 17, 2014, at 2:40 PM, Paweł Tomaszewski <cro...@gm...<mailto:cro...@gm...>> wrote:

Thank you Thomas
Using camera=0 caused my cone not to do rotations related to the camera position.
Cone still rotates not about itself, but about axis of global coordinate system.
Do you have any other ideas?

Cheers,
   Paweł


2014-02-06 17:00 GMT+01:00 Thomas Holder <tho...@sc...<mailto:tho...@sc...>>:
Hi Pawel,

have you tried using the camera=0 argument?

cmd.rotate(axis, angle, object='yourcone', camera=0)

Cheers,
  Thomas

On 05 Feb 2014, at 15:46, Павел Томашевский <cro...@gm...<mailto:cro...@gm...>> wrote:

> Hello
> I've made a cone CGO (something like a pointer) and now I need to make a rotation of the cone. I have got yaw, pitch and roll angle values, but when I do 'rotate' command it rotates about axis of the global coordinate system.
>
> My question is, how to make a rotation of the CGO about axis that is NOT of the global pymol coordinate system but goes through the CGO itself?
>
> I hope it's clear what I mean ;)
>
> Thank you
> Pawel


--
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


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Hi Pawel,

you should read

PyMOL> help(cmd.rotate)

This would tell you that the rotate function has a "origin" argument.

Hope that helps.

Cheers,
  Thomas

On 17 Feb 2014, at 14:40, Paweł Tomaszewski <cro...@gm...> wrote:

> Thank you Thomas
> Using camera=0 caused my cone not to do rotations related to the camera position. 
> Cone still rotates not about itself, but about axis of global coordinate system.
> Do you have any other ideas?
> 
> Cheers, 
>    Paweł
> 
> 
> 2014-02-06 17:00 GMT+01:00 Thomas Holder <tho...@sc...>:
> Hi Pawel,
> 
> have you tried using the camera=0 argument?
> 
> cmd.rotate(axis, angle, object='yourcone', camera=0)
> 
> Cheers,
>   Thomas
>  
> On 05 Feb 2014, at 15:46, Павел Томашевский <cro...@gm...> wrote:
> 
> > Hello
> > I've made a cone CGO (something like a pointer) and now I need to make a rotation of the cone. I have got yaw, pitch and roll angle values, but when I do 'rotate' command it rotates about axis of the global coordinate system.
> >
> > My question is, how to make a rotation of the CGO about axis that is NOT of the global pymol coordinate system but goes through the CGO itself?
> >
> > I hope it's clear what I mean ;)
> >
> > Thank you
> > Pawel

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi everybody

I installed pymol 1.6.x unofficial in windows 7 home. As far as I have
tested it works well, but the console (as in the screen that the GL window
shows when I press escape) and the main window keep constantly showing the
message

 WARNING: glDrawBuffer caused GL error

which is annoying because I can't see the help or any other output to there.

Any ideas on how to tackle this?

Thanks

-- Camilo Jiménez

Hi Thomas,
I am using the build that comes with Fedora. One could think they
skipped the plugin when compiled, as the error I get is:

load something.cube
 ObjectMolecule: plugin 'cube' cannot open 'kim-dense.cube'.


Nevertheless,  it does load it correctly when I use "Open" from the gui.

Thanks!

Raul

On Mon, Feb 17, 2014 at 11:41 PM, Thomas Holder
<tho...@sc...> wrote:
> Hi Raul,
>
> there should be no difference between loading from the GUI or using the "load" (not "Load") command.
>
> The cube file needs to have a ".cube" extension.
>
> Cheers,
>   Thomas
>
> On 16 Feb 2014, at 19:45, Raúl Mera Adasme <rm...@gm...> wrote:
>> Hi all,
>>
>> I am trying to code a little script that needs to load Guassian cube
>> files (to later create some isusurfaces). The cube format is
>> supported, and one can easily use the TK interface (file->open) to
>> load the file into PyMOL. I have been looking for the command to do it
>> automatically in a script, but have not found it. "Load" is unable to
>> open the files.
>>
>> Any ideas?
>>
>> Cheers,
>>
>> Raul
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.
>

Hi Raul,

there should be no difference between loading from the GUI or using the "load" (not "Load") command.

The cube file needs to have a ".cube" extension.

Cheers,
  Thomas

On 16 Feb 2014, at 19:45, Raúl Mera Adasme <rm...@gm...> wrote:
> Hi all,
> 
> I am trying to code a little script that needs to load Guassian cube
> files (to later create some isusurfaces). The cube format is
> supported, and one can easily use the TK interface (file->open) to
> load the file into PyMOL. I have been looking for the command to do it
> automatically in a script, but have not found it. "Load" is unable to
> open the files.
> 
> Any ideas?
> 
> Cheers,
> 
> Raul

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Thank you Thomas
Using camera=0 caused my cone not to do rotations related to the camera
position.
Cone still rotates not about itself, but about axis of global coordinate
system.
Do you have any other ideas?

Cheers,
   Paweł


2014-02-06 17:00 GMT+01:00 Thomas Holder <tho...@sc...>:

> Hi Pawel,
>
> have you tried using the camera=0 argument?
>
> cmd.rotate(axis, angle, object='yourcone', camera=0)
>
> Cheers,
>   Thomas
>
>
 On 05 Feb 2014, at 15:46, Павел Томашевский <cro...@gm...> wrote:
>
> > Hello
> > I've made a cone CGO (something like a pointer) and now I need to make a
> rotation of the cone. I have got yaw, pitch and roll angle values, but when
> I do 'rotate' command it rotates about axis of the global coordinate system.
> >
> > My question is, how to make a rotation of the CGO about axis that is NOT
> of the global pymol coordinate system but goes through the CGO itself?
> >
> > I hope it's clear what I mean ;)
> >
> > Thank you
> > Pawel
>
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.
>
>