[Chimera-users] 3D dashed pseudobond styles?

Oliver Clarke olibclarke at gmail.com
Sat Nov 7 09:22:29 PST 2015


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 at 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 at 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 at 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 at cgl.ucsf.edu> wrote:
>>> 
>>>> setattr p label “” sel
>>> 
>> 
>> 
> 




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