Re: [PyMOL] Distance or measurement labels Version 1.6 and 1.7 does not show

2014-03-03 Thread endew...@prisner.de 
Hi Thomas,

now I have the label visible immediately (w/o using ray)!

Thank you very much!

Burkhard.

On 02/28/2014 04:54 AM, Thomas Holder wrote:
 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 thomas.hol...@schrodinger.com 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, endew...@prisner.de 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.

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Re: [PyMOL] Color starting midway between adjacent chains

2014-03-03 Thread David Hall 
set_bond line_color, color_name, n. CA+CB

will color all bonds between CA and CB whatever color you put in as
color_name

If you're doing sticks instead of lines, you should use

set_bond stick_color, color_name, n. CA+CB

-David




On Mon, Mar 3, 2014 at 10:01 PM, I-Ji Jung u5205...@anu.edu.au wrote:

  Hi everyone,

  I have just started learning Pymol and PyMol seems to use a different
 colour convention than Molmol, i.e. the colour of a side chain starts half
 way between the CA and CB atoms (instead of starting at the CA). Do you
 know whether there would there be a way to start the side chain colour at
 the CA without changing the colour of the backbone?

  Any help will be greatly appreciated!

  Thank you.

  I-Ji


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