For kinemage, go for MAGE_4.3.sea and see how you get on.
Quanta is reasonably easy to use and if you some help on it then I can
let you have the brief and simple notes I use to tutor our Msc molecular
modelling and bioinformatics students. I don't think quanta can be used
for chemical mime in the same way as rasmol can. If you've got access
to the SG then you could of use the SG version of Rasmol/netscape for
which the chemical mime works fine. We certainly won't be using the
advanced features that quanta provides in the course.
To use the technical list simply mail to
pps97-98-technical@mail.cryst.bbk.ac.uk instead (in fact if you have
more questions about chemical mime etc then perhaps you should switch to
this list). The technical list works in just the same way as the
general list. These are the only two lists so far we add more as and
when they are needed.
There is no real busy time for our server, I guess the problems you've
had are the heavy load on the connecting computers between yours and
ours, 9am-1pm EST means a lot of people getting into work and starting
to surf, increasing the net traffic.
Hopefully thats answered most of your questions, any more problems then
please don't hesitate to get back to us,
Cheers,
Dave H.
Deirdre Crommie wrote:
> 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