[PyMOL] new to pymol

2015-08-28 Thread Chi Celestine 

Hi,
I am very new in pymol and will like to know how know the display in the lower 
command line works. However, i can see how to make it active. I have pymol 
v1.7.6.4
Thanks
Celestine


--
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] creation of a sphere

2015-08-28 Thread David Hall 
What version of PyMol are you using?

 On Aug 27, 2015, at 7:50 AM, Christian Trindler 
 christian.trind...@unibas.ch wrote:
 
 Hello,
  
 I’ve been trying to make a pseudoatom/sphere simply by typing:
 pseudoatom name
 into the command line of Pymol, but it only gives me the following error 
 message instead of the pseudoatom:
  
 Traceback (most recent call last):
   File C:\Program Files (x86)\DeLano 
 Scientific\PyMOL/modules\pymol\parser.py, line 370, in parse
 exec(com2[nest]+\n,pymol_names,pymol_names)
   File string, line 1
  pseudoatom name
   ^
 SyntaxError: invalid syntax
  
 What is the error? What do I have to change?
  
 Thanks for your help,
 Christian
  
 --
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net


--
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

[PyMOL] creation of a sphere

2015-08-28 Thread Christian Trindler 
Hello,

I've been trying to make a pseudoatom/sphere simply by typing:
pseudoatom name
into the command line of Pymol, but it only gives me the following error 
message instead of the pseudoatom:

Traceback (most recent call last):
  File C:\Program Files (x86)\DeLano 
Scientific\PyMOL/modules\pymol\parser.py, line 370, in parse
exec(com2[nest]+\n,pymol_names,pymol_names)
  File string, line 1
 pseudoatom name
  ^
SyntaxError: invalid syntax

What is the error? What do I have to change?

Thanks for your help,
Christian

--
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] new to pymol

2015-08-28 Thread Osvaldo Martin 
Hi Celestine,

Welcome to the PyMOL community!

I am not sure what is your problem, could you please provide more details?

Cheers,
Osvaldo.





On Fri, Aug 28, 2015 at 6:00 AM, Chi Celestine 
chi.celest...@phys.chem.ethz.ch wrote:


 Hi,
 I am very new in pymol and will like to know how know the display in the
 lower command line works. However, i can see how to make it active. I have
 pymol v1.7.6.4
 Thanks
 Celestine



 --
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

--
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

[PyMOL] how to copy color?

2015-08-28 Thread Albert 
Hello:

I've colored object1 in various color in different regions. I am just 
wondering how can we copy the color scheme for object1 to object2? 
Object 2 is the same protein with object1 but with different conformations.

Thank you very much

Albert

--
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] how to copy color?

2015-08-28 Thread Thomas Holder 
Hi Albert,

Such a property transfer can be done with iterate and alter:

stored.colors = {}
iterate obj1, stored.colors[chain,resi,name] = color
alter obj2, color = stored.colors.get((chain,resi,name), color)
recolor

Hope that helps.

Cheers,
  Thomas

On 28 Aug 2015, at 10:03, Albert mailmd2...@gmail.com wrote:

 Hello:
 
 I've colored object1 in various color in different regions. I am just 
 wondering how can we copy the color scheme for object1 to object2? 
 Object 2 is the same protein with object1 but with different conformations.
 
 Thank you very much
 
 Albert

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net