Hi Elaine, using both of your suggestions, I have an alias that does pretty much what I originally wanted, I’m posting it here in case it is useful to anyone else: #pbond. Places black stick pseudobond between two selected atoms. #Usage: pbond alias ^pbond dist sel; setattr p label "" sel; setattr p drawMode 1 sel; setattr p radius 0.03 sel Cheers, Oli.
On Nov 6, 2015, at 4:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, You can find out the attribute names from the balloon help over the pseudobond attributes dialog opened from the Pseudobond Panel. So if I have a pseudobond selected and mouse over the “bond style” listing in the “Component PseudoBond Attributes” section of that dialog, it tells me the attribute name is “drawMode” with possible values 0,1,2 and what those values mean.
So you could use
setattr p drawMode 1
… to change all pseudobonds to stick, or if you just want only the ones with end atoms selected
setattr p drawMode 1 sel
I hope this helps, Elaine
P.S. this kind of attribute name lookup is mentioned in the docs here (it’s also linked to “attribute name” in the “setattr” manpage) <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#attrnames>
On Nov 6, 2015, at 12:49 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Elaine, stupid question, but do you know how to change the pseudobond style to stick from the command line? I have tried "setattr p bond style stick” and variations thereof to no avail.
Cheers, Oliver.
On Nov 6, 2015, at 1:28 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
That is supposed to be two double quotation marks straight from the keyboard, although they seem to have been fancified into open and close quotation marks, at least in my mail viewer. Two plain old single quotation marks would also work. Elaine
On Nov 6, 2015, at 10:25 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
setattr p label “” sel