Re: PPS97-98 - Section 1 Course Material -Reply -Reply

Deirdre Crommie (DCrommie@genetics.com)
Thu, 23 Oct 1997 14:24:02 -0500

Dear Dave,
Thanks for your reply. I seem to have a way to view pdb files now.
I couldn't configure the web browser the way you suggested because my
PowerMac Netscape Navigator window apparently isn't the same as the
Win95 netscape window. (Under my 'helper tab', I have
"Description", "MIME Type", "Suffices", then a box labeled "Handled
by...." with options for "navigatiors", "plug-ins", "applications".
I don't have an "extensions" box to type something into. The
"plug-ins" box seemed closest, but I couldn't get it to be active and
accept type directly.
Anyway, what seemed to have finally worked is that when I clicked on
the pdb test file supplied by you, Netscape recognized I didn't have
viewing capacity and directed me to install the correct "plug-in" to
view the pdb. I was directed to install "CHIME", and this seems to
work. The only thing is that I must have the RasMol application
(RasMac v2.6) open in order to get images. Is it standard to open
this application first, or should my browser be able to open the
application, and I just haven't configured it properly? I'm still a
bit shaky on how to actually obtain a pdb from the net and then look
at it in RasMac (for instance, in the test one you supplied, I just
got the picture without the "RasMol command line"(i.e., text
describing molecule's name, etc.--is this correct?-- whereas in
examples included in the RasMac folder, I did get the "command line"
along with the images). Hopefully the details of getting pdb files
will be more clear.

Other questions:
1) Which version of MAGE do you recommend loading for the PowerMac.
At the site:
http://www/faseb/org/protein/kinemages/MageSoftware.html, given by
you
there were many versions listed. Which one should I try to install?

2) Where I just started working (Genetics Institute, Cambridge, MA)
everyone uses "Quanta" to view pdb files instead of "RasMol". I have
the quanta software available to me for use on a SilconGraphics
computer. Do you think it's best for me to just transfer over to
this system. I was shying away from the sgi computer since I don't
know Unix, but people said that quanta is menu driven and probably no
more difficult than RasMol to do basics (though definitely more
complicated for full range of uses). People here are pretty busy so
I won't get a lot of help (I'm not in the structure group where all
this goes on), but I will get some direction to get started. Would
using quanta work with the class, or should I stick with what I've
begun to set up on the MAC for RasMol?

3) I'm confused about the technical list. What is the best way to
access it (I take it now I'm writing you at another location), and
how many "lists" are there in the course.

4) Are there some very busy times on the server at your end? Or was
it just a fluke that today I had a very difficult time getting
through to the technical info, whereas it has been very fast in the
past (very long waits and sometimes failure to connect 9am-1pm EST,
haven't tried since).

Thanks!!!!
Deirdre Crommie