[Chimera-users] Display all rotamers

Eric Pettersen pett at cgl.ucsf.edu
Wed Jul 29 16:04:56 PDT 2009

In the daily build the Rotamers tool will now allow you to add  
multiple rotamers to a residue, using alt locs to distinguish them.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

> On Dec 6, 2008, at 9:35 AM, daniel.hilger at lrz.uni-muenchen.de  
> wrote:
> >
> > I´m really sorry for my imprecise question. I will concretize it. I
> > know
> > the rotamer tool, but I don´t want to replace only one rotamer into
> > another. I will have them all in the structure and in the according
> > pdb-file. With the rotamer tool, it is only allowed to choose one
> > rotamer
> > out of the rotamer list before clicking "Apply". This is my problem,
> > and I
> > didn´t found an appropriate answer in the manual and help menu.
> Hi Daniel,
> I'm sorry for misunderstanding -
> It's true that Apply only puts one copy in the structure, but if you
> don't Apply and simply keep the Rotamer list dialog and choose all of
> its lines, that displays all of the rotamers at the same time.  Maybe
> that would allow you to do what you want. The Rotamer list dialog
> allows calculating clashes and H-bonds, plus selecting the rotamer
> atoms so you can control their appearance with the Actions menu.
> The issue is that the structure can't have multiple indistinguishable
> atoms (with the same name and residue number).  We have talked about
> allowing multiple rotamers to be applied to the structure by giving
> them different "alternate location" ID codes, but that has not been
> implemented yet.  Also, some residues may have more rotamers than the
> number of possible alternate location ID codes.  Nevertheless we will
> make sure it is on one of our requested features lists.
> So currently you can't save PDB with multiple rotamers, but you can
> save/restore the session in the state where all of the rotamers are
> displayed.
> I hope this helps,
> Elaine

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