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

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 15 09:44:38 PDT 2021

Great!  Thanks for sharing, your image looks nice.


> On Mar 15, 2021, at 12:53 AM, Giorgio Giardina <giorgio.giardina at uniroma1.it> wrote:
> Thank you very much Elaine!!
> it worked nicely.
> I attached the image I rendered.
> Thanks again,
> stay safe,
> Giorgio
> <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 l’insegnamento
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