Re: [PyMOL] Possible (minor) bug

2012-12-03 Thread Thomas Holder
Hi Joel, thanks for the report. This will be fixed in the next PyMOL release. Cheers, Thomas Joel Tyndall wrote, On 12/03/12 02:53: Hi Jason/all, Possible bug. When measuring distances around coordinated metals, I then wanted to change the colour of the resulting dashed line. The colour

[PyMOL] setting the cutoff radius that determines when atoms are bonded

2012-12-03 Thread Rye Terrell
I have a silicon bulk system. Pymol indicates that a handful of the atoms are bonded to each other. Many bonds are not indicated. Is there some value I can adjust that will make pymol indicate that more atoms are bonded? I usually do this by setting some cutoff radius, but googling around has

Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded

2012-12-03 Thread Jason Vertrees
Hi Rye, How about connect_cutoff in Å? There's also connect_mode (http://www.pymolwiki.org/index.php/Connect_mode). If you send me a copy of your file I can look at it. Cheers, -- Jason On Mon, Dec 3, 2012 at 4:03 PM, Rye Terrell ryeterr...@ryeterrell.net wrote: I have a silicon bulk system.