Re: [PyMOL] How to move/turn CGO

2013-08-12 Thread David Hall
For a definition of TTT , see http://pymolwiki.org/index.php/Object_Matrix You'll notice that set_object_ttt takes a 16-member list that corresponds to this matrix. -David On Aug 12, 2013, at 11:48 AM, Павел Томашевский wrote: > Thank you Thomas, translate and rotate works great, but I'm not

Re: [PyMOL] How to move/turn CGO

2013-08-12 Thread Павел Томашевский
Thank you Thomas, translate and rotate works great, but I'm not sure what set_object_ttt function does. I'm also looking for a function that can set absolute coordinates of my cgo cone, not relative to current position like translate/rotate. Is there such a function? 2013/8/12 Thomas Holder >

Re: [PyMOL] varying label positions

2013-08-12 Thread Gregory Ryslik
Hi Thomas, This was perfect, thanks for your help! Kind regards, Greg On 8/12/2013 5:37 AM, Thomas Holder wrote: > Hi Gregory, > > we are working on improved label placement right now. So far, > label_position is just an object-level and not an atom-level setting. > However, you can actually drag

Re: [PyMOL] Bind reset to a key?

2013-08-12 Thread Thomas Holder
Hi Boris, the second argument must be a function reference, not a function call. Basically means: no parenthesis. So this works: cmd.set_key('ALT-r', cmd.reset) Cheers, Thomas Boris Kheyfets wrote, On 08/12/13 10:49: > Hello PyMOL users, > > I need to bind reset to a key. > I tried both PyMO

Re: [PyMOL] varying label positions

2013-08-12 Thread Thomas Holder
Hi Gregory, we are working on improved label placement right now. So far, label_position is just an object-level and not an atom-level setting. However, you can actually drag each label individually in edit mode. This is independant of the label_position setting and cannot be done with a script. E

Re: [PyMOL] How to move/turn CGO

2013-08-12 Thread Thomas Holder
Hi Pawel, > Currently I'm working on some plugin for PyMOL and I need your help. > I need to draw an object (CGO) and create some function that will move > this object or simply change its coordinates. > I've done my job with the first part, that is drawing a sphere on a > screen using > cmd.

Re: [PyMOL] ColorByRMSD autoscaling colors?

2013-08-12 Thread Thomas Holder
Hi Alicia, these are rounding errors. If you print the pairwise distances, which are stored in the b-factor column by the ColorByRMSD script, you will see some numbers which are not zero but close to zero (order of 1e-6). As soon as there is any real difference between the two conformations, the c

Re: [PyMOL] PyMol can't show molecule as line

2013-08-12 Thread Thomas Holder
Hi Junjun, you probably have a cheap graphics card with limited shader support. This should help: PyMOL> set cylinder_shader_ff_workaround And eventually: PyMOL> unset line_as_cylinders Can you please also send me the output of: PyMOL> print cmd.get_renderer() See also: http://pymolwiki.org/i

[PyMOL] Bind reset to a key?

2013-08-12 Thread Boris Kheyfets
Hello PyMOL users, I need to bind reset to a key. I tried both PyMOL API way: cmd.set_key('ALT-r', cmd.reset()) and PyMOL commad way: cmd.set_key('ALT-r', cmd.do("reset") But it doesn't work. I bind various things to keys, so I'm certain of the procedure. How could I bind reset to a key?