Okay thank you very much Elaine ! So I have 2 questions: 1) about mol map: As I mentioned this always displays a "frozen" map selected for a particular frame in the case of multi-frame pdb (loaded trajectory) Would it be possible to update the generated map for each frame ? 2) about ball and stick representing : is it possible to reduce the resolution of the balls for a small compound selection in order that it’s 3D structure appears to be like a mystery? 😃 Thanks in advance! Le ven. 9 févr. 2024 à 17:40, Elaine Meng <meng@cgl.ucsf.edu> a écrit :
The "surface style" command always applies to the whole surface model (different parts of the same model can't have different styles). Also as shown in the usage on the help page, if you specify a surface model, the specification needs to be after the whole command "surface style": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#style>
Example: open 2gbp surface :bgc surf style #1.2 dot
I hope this helps, Elaine
On Feb 9, 2024, at 1:18 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
P.S. and for the surface style actually it works for the whole surface like demonstrated in your example, but unfortunately it does not work for the selection e.g.
surf :lig style dot
Il giorno ven 9 feb 2024 alle ore 10:04 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
MAny thanks Elaine !
Actually the molmap is a great option, and it does what I need.
I noticed that it always displays a "frozen" map selected for a particular frame in the case of multi-frame pdb. Would it be possible to update the generated map for each frame of my multi model pdb visualized as the md trajectory (open ./trajectory.pdb coordset true) ?
Yours with thanks
Enrico
Il giorno gio 8 feb 2024 alle ore 23:28 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Hello, This works fine for me:
open 1gcn surf surf style dot
However, the dot style can be very hard to see since the linewidth
(dot size) is small and you cannot increase it, and/or the surface vertices are spaced rather far apart.
Here are two ideas for making a low-resolution surface for atoms:
(A) instead of a standard molecular surface, make a gaussian surface
by using "surface" with the "resolution" option
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
- OR -
(B) try making a density map from the ligand with "molmap" ... then you can adjust the isosurface level, etc. like for other density maps <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html>
See the help links above for additional options such as to control vertex spacing of these surfaces.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 7, 2024, at 2:06 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users
I am also experimenting on the representation of the surfaces of small compounds
surface ligand gridSpacing 0.5 probeRadius 1.2 color ligand white target s transparency 90
This creates a relatively large transparent surface around the small compound. How would it be possible to reduce the volume of the surface ?
Also I did not understand how to change the style of the surface among dot/mesh etc since adding style dot did not work.
I would appreciate any further creative examples of how to change the representation of a small compound in the case when I need to make it more "coarse-graining" , hiding some precise details of the structure ?
Many thanks in advance !
Enrico
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