[chimerax-users] Deleting unmodelled termini

[Elaine Meng]

Hi Tiglath,
The parts of the target sequence that are not aligned with residues in the template sequence will be modeled as disordered-looking strings.  This is not an error or anything you did wrong, it is simply because there is no template for those parts.

I don't understand why you would try to delete residues in #3 before running Modeller, because before you run Modeller, there is no model #3.  The "delete" command is for parts of 3D structures, not sequences.

I also don't understand what you said about re-running Modeller after deleting residues in #3. If you re-run Modeller comparative modeling again with the same sequence alignment and same template, it will not use the comparative models you already made (it will not matter if you deleted any parts of those models).  It will just make another new set of models with the same disordered-looking parts where the target sequence is not aligned with any residues in the template sequence.

If you just mean that those parts of model #3 are ugly and you don't need them for later calculations, of course you can delete them.  Your command looks OK as far as I can tell, if those are really the correct chain IDs and residue numbers of what you wanted to delete.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 29, 2020, at 5:03 PM, mailman-bounces at cgl.ucsf.edu wrote:
> 
> From: "Moradkhan, Tiglath A" <tmoradkhan at csus.edu>
> Subject: Deleting unmodelled termini
> Date: October 29, 2020 at 4:48:14 PM PDT
> 
> Hi
> 
> I've read the delete command documentation to delete unmodelled termini and rerun Modeller, but I'm having a hard time trying to delete the C-terminal end of the models. Say that the first time Modeller wasn't able to model residues 1-67 and 209-267 because these regions don't align with the template structures. Here is the command (all the returned models are labeled as 3.1-3.4)
> 
> delete #3/A-B: 1-67,209-267
> 
> Is this right? I also tried deleting these residues before running Modeller with no success.
> 
> I'll be very glad for some help.
> 
> Thanks
> 
> Tiglath