[Chimera-users] Chimera secondary-school use

[Thomas Goddard]

Follow up on "[Chimera-users] first time use of chimera".

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From: "Rich Kaufman" <richkaufmanpv at hotmail.com>
To: goddard at cgl.ucsf.edu
Subject: Chimera, afterthought
Date: Tue, 19 Sep 2006 11:38:26 -0500

Dear Tom,

Just to mention a few more details, I am trying to
use electron density maps we generated in the lab
using a Spider processing of cryo-EM photos .I will
be  downloading PDB's from the RCSB to dock with
these.

After properly hand docking the PDB, I will then load
the density map and the hand-aligned PDB into a
Normal Mode Flexible Fitting package ( NMFF ) for
fine-tuning of the fit, to give a higher resolution picture
of the electron density map.

I've been working on this project for about three months.
I had never heard of any of these things prior to that. It's
been an amazing learning curve for me....quite interesting.


Sincerely,

Rich Kaufman, ( background....mainly physics; teacher
of high school chemistry and physics )

P.S.  One goal of this project is to enable me to use
these techniques at the secondary education level.
I don't know if that's doable....suggestions welcomed.

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Date: Tue, 19 Sep 2006 10:00:38 -0700 (PDT)
From: Thomas Goddard <goddard at cgl.ucsf.edu>
To: richkaufmanpv at hotmail.com
Subject: Re: Chimera, afterthought

Hi Rich,

  Oh!  I sent my previous email before I read this one about what you are
actually doing.  You're doing some fancy stuff.

  If you hand-align a PDB model in the SPIDER map you can then do a local
position optimization within Chimera using menu entry

	Tools / Volume Data / Fit Models in Maps

This moves the model using a rigid rotation and translation to maximize
the map values at selected atom positions.  Here's a page describing how
to use it:

	http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmodel

The bottom of the following tutorial also gives step by step instructions
for placing a PDB model in a map:

	http://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/07-VolumeData/tutorial/chaperonin.html

In fact, most of the tutorials on the following page do this kind of fitting:

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

The normal mode fitting you will do is fancier, allowing the model to
deform to fit into the map.

  The following page explains alot of the Chimera features for working with
density maps.

	http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html

  The myosin animation on the following web page shows fitting a model into
a map:

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

Finally, here are some databases that show some cryo-EM maps of viruses
and other systems.

	http://viperdb.scripps.edu/tnumlist.php?N=all

	http://www.ebi.ac.uk/msd-srv/emsearch/AccEMServ?criterion=Retrieve+All&value1=&andor=and&value2=&Submit=Submit+Query

  I'm sure this is more than you wanted to know!

	Tom