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

Elaine Meng meng at cgl.ucsf.edu
Sun Mar 14 10:15:13 PDT 2021

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 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 

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