[Chimera-users] further levels of detail in low-res surface of a single chain Multiscale model

[Thomas Goddard]

Hi Ute,

  Here are two ideas about how to get nucleic acid depictions with bases
and backbone as distinct blobs.  Both use the Multiscale tool.

  One idea is just use a resolution of 1 angstrom in the multiscale tool.
Also adjust two other multiscale surfacing parameters by pressing the
"..." checkbutton to the right of the Resolution field in the multiscale
dialog.  Change "Threshold atom density" to 0.01 to get a fatter surface.
And change smoothing iterations to 5 to get a smoother surface.  Here
is the result on PDB 100d:

	http://www.cgl.ucsf.edu/home/goddard/temp/100d-1A-5i.png

  A second approach is to make each base be a separate surface, and have
the backbone be a separate surface.  The trick to doing this is to give
each base a separate PDB chain id.  The multiscale tool makes a surface
for each separate chain.  You can do this by just editting the PDB file
changing the chain ids for each base.  That is pretty tedious work so I
made a script that can do that in Chimera.  It is available on the Chimera
experimental feature page along with pictures of the resulting Multiscale
surfaces:

	http://www.cgl.ucsf.edu/chimera/experimental/experimental.html

  A third idea (not using multiscale) is to use the Chimera Nucleotides
tools (menu entry Tools / Depiction / Nucleotides).  It can depict bases
as discs or rectangular slabs.  Here is an example from the Chimera
image gallery

	http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/pret.html

and here is a tutorial about how that image was made.

	http://www.cgl.ucsf.edu/Outreach/Workshops/UCI-2005/02-PubPres/Publish_Tutorial.html


  Tom