[Chimera-users] Chimera application questions

Yanhe Zhao yanhezhao1990 at gmail.com
Mon Jul 2 10:17:28 PDT 2018

Awesome, thanks!  I will try.

Elaine Meng <meng at cgl.ucsf.edu> 于 2018年7月2日周一 11:41写道:

> Hi Yanhe,
> (1) Combine is for merging multiple models (usually multiple input files)
> into one model.  If all four of your copies are already in one model (one
> input file) it makes no difference.  Maybe you meant you just wanted to
> remove the other copies when saving a file.  If you already have all the
> atoms you want to keep selected, just use menu: File… Save PDB, and in the
> resulting dialog, turn on the option “Save selected atoms only”
> (2) PDB is not a map format; it contains coordinates of points, usually
> atoms.  I see in SASDB that some entries have PDB files that are fully
> modeled proteins, and others are just a set of balls that fit the shape of
> the envelope.  Since you said “lines-like” the one you have is probably
> just a set of balls.  Chimera doesn’t know they aren’t really a protein, so
> it is trying to show a ribbon.  Try commands to turn off ribbon and show
> all points as spheres:
> ~ribbon
> display
> repr sphere
> Then it should look like a bunch of balls that show the shape of the SAS
> data.  Either way (full protein or set of balls) you can use the “molmap”
> command to simulate a density map from the points, for example:
> molmap #0 8
> … meaning to create a map from the “atoms” (the balls are fake atoms) in
> model #0 using resolution 8.  I don’t know what resolution value is best,
> but in the Volume Viewer dialog that automatically appears when you create
> the map, you can change from “surface” to “mesh” display and judge for
> yourself.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Jun 30, 2018, at 7:37 PM, Yanhe Zhao <yanhezhao1990 at gmail.com> wrote:
> >
> > To whom may concern,
> > This is Yanhe Zhao from UT Southwestern Medical Center. I have to
> question when use Chimera as below, hopefully someone could do me a favor
> to answer it.
> > 1, my crystal structure have four copies in one Asymmetrical structural
> unit. When I try to combine two of them by selection and combine command,
> always combine all of them. I pretty sure that I only select two of them;
> > 2, I got one PDB from SASDB, how can I show it as a density map like
> CryoEM? When I open, it's shown as lines-like map so as to which couldn't
> be used for docking.
> > I really appreciate it if someone could do me this favor. Thanks a lot.
> >
> > Best,
> > Yanhe
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