Hi Michal,
You can use the “meshmol” command to make the isosurface mesh into a fake molecule, where the the points are “atoms” and the mesh lines are “bonds” shown as sticks.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html>

Although the new “molecule model” is suppressed from appearing in the File… Save PDB dialog, you can still save it to PDB from the command line with “write” … or save it as a marker set using the File menu of the Volume Tracer tool.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html>

Either of those formats will contain the coordinates.  The marker format will do a better job of preserving the stick bonds and their radii, if that matters to you.
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 6, 2016, at 6:48 AM, Michał Kadlof <m.kadlof@cent.uw.edu.pl> wrote:
>
> Hello,
>
> I have density data in .cmap file format. I want to save a coordinates for points that are on the surface for given cutoff. I need exactly that points which are visible in mesh representation.
>
> How can I do that?
> --
> pozdrawiam serdecznie
> Michał Kadlof <m.kadlof@cent.uw.edu.pl>