Re: [PyMOL] rendering missing segments

Hi Seth and Adam,

thanks a lot for the feature request and for explaining why this is useful. The sequence viewer part should not be too difficult, actually. Of course I remember the "cartoon dash" request, Seth. Working on PyMOL's cartoon code is not the easiest task (for historical reasons) but we are working on getting improvements like this in.

Cheers,
  Thomas

On 27 Sep 2014, at 10:22, H. Adam Steinberg <h.a...@gm...> wrote:

> Phenomenal idea! I fully agee! :)
> 
> On Sep 27, 2014, at 2:22 AM, Seth Harris <se...@gm...> wrote:
> 
>> Hi Thomas et al,
>> 
>> There was a recent question on the board about missing residues and the possibility of reading SEQRES headers and PyMOL being able to show the missing bits in the sequence view, perhaps with the amino acid letters grayed out to distinguish the gap. I know the reply was "PyMOL doesn't currently" do this, but it seemed to then end "full stop" rather than, "...but it's a fantastic idea". I'd like to second the idea as a great addition! When building structures or viewing and hitting gaps one always has to shuffle off to find the sequence or jump back to see how big the gap is and what type of residues are supposed to be in there. This would put it right there integrated at one's fingertips.
>> 
>> This also reminds me of something I suggested to you, Thomas, that might fit in here of having a "cartoon dash" rendering (at least for loops if not helices and strands?) such that one could borrow a loop from a homologue or build in a placeholder to provide visual continuity in a model while still clearly indicating the disordered regions, but now in a 3D ray-traced dashed line that follows the cartoon trajectory rather than the usual penciled in job.
>> 
>> I know in building a new structure I don't often have any SEQRES header in place, but if it offered advantages like this it would be easy enough to install such.
>> 
>> Thanks,
>> Seth

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.