Follow up on "[Chimera-users] first time use of chimera". ------------------ From: "Rich Kaufman" <richkaufmanpv@hotmail.com> To: goddard@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. --------------------- Date: Tue, 19 Sep 2006 10:00:38 -0700 (PDT) From: Thomas Goddard <goddard@cgl.ucsf.edu> To: richkaufmanpv@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#fitmode... 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/tuto... 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&value... I'm sure this is more than you wanted to know! Tom