[Chimera-users] render by attribute displacement of a NMA

Giorgio Giardina giorgio.giardina at uniroma1.it
Mon Mar 15 00:53:45 PDT 2021

Thank you very much Elaine!!

it worked nicely.
I attached the image I rendered.

Thanks again,
stay safe,
[image: NMA-worms-displacement.png]

On Sun, 14 Mar 2021 at 18:15, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Giorgio,
> I don't know exactly what's in your file, but if it opens as multiple
> models (e.g. #0.1, #0.2, #0.3 similar to when you open an NMR structure
> such as 1g1p, or as #0, #1, #2 ...):
> (1) first check: are the structures shown as a ribbon?  (like spaghetti,
> all same radius)  If Chimera can show it as the spaghetti-like ribbon, it
> can show it as a worm.  If not (only dots) it cannot show it as a worm.
> (2) show the sequence of any one, doesn't matter which one since they all
> have the same sequence (menu: Favorites... Sequence, choose which model)
> (3) in the sequence window menu,
>   (a) choose Structure... Associations, and in the resulting dialog make
> all of the structures associate with that same single sequence
>   (b) choose Headers... RMSD:ca to show the histogram of RMSD values
> (4) choose which model you want to represent as worm, hide all of the
> others (e.g. with Model Panel "S" checkboxes)
> (4) in Render by Attribute, choose attributes of residues, then choose
> attribute: mavRMSDca, use Worms tab, etc.
> Click the Help buttons on tools to see their detailed instructions.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Mar 13, 2021, at 9:07 AM, Giorgio Giardina <
> giorgio.giardina at uniroma1.it> wrote:
> >
> > Hy,
> >
> > I have a pdb file containing the models (only CA atoms) describing the
> lowest mode from a NMA.
> > I can easily generate a movie using the morphing tool, but I would like
> to visualize the mode as an image, using the render by attribute tool and
> with the displacement of each CA as value of the worm radius.
> > How can I generate this attribute?
> >
> > Thanks in advance for you rhelp!
> > Giorgio
> >

Giorgio Giardina, Ph.D.
Dep. of Biochemical Sciences (CU027) - Room T2
SAPIENZA - University of Rome
Tel. +39.06.49910713 | Lab: http://www.macinmec.it/giorgio-giardina/  |
Art: http://www.giorgio-giardina.com/
Art. 33 della Costituzione: *L’arte e la scienza sono libere e libero ne è

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