[PyMOL] Bonds

2003-06-27 Thread Tsjerk Wassenaar
Hi all! I've written a script to position all atoms into a simulation box, but the connectivity stays, thus generating a beautiful image of bonds all across the box. Though not too clear. Is there a way to update the connectivity directly (other than saving the coordinates and reloading)?

[PyMOL] ray-tracing clip's off C-terminus

2003-06-27 Thread Casey M . Finnerty
I am making C-alpha ribbon traces with two different sets of coordinates. Each time, when I type ray to render, the resulting image has the C-terminal C-alpha clipped off. The missing carbon is visible in the non-ray traced image, however. Please send suggestions to fix this asap.

[PyMOL] convert avs to phi ?

2003-06-27 Thread Stefan Bäckström
Hello.. I have my electrostatic potential in avs format, and I wonder if anyone knows how to convert it into phi format in order to read it into pymol ?? Best wishes, Stefan Bäckström UCMP Umeå University Sweden