Changes between Version 82 and Version 83 of Animation

Timestamp:

Sep 27, 2010, 1:08:50 PM (16 years ago)

Author:

Darren Weber

Comment:

--

Animation

@@ -121 +121 @@
          * production process can be streamlined over time
          * staff turnover incurs time for training
+   * The [http://www.pdb.org Protein Data Bank]
+     * The PDB has [http://www.pdb.org/pdb/static.do?p=education_discussion/educational_resources/index.html educational resources], including a "Molecules in Motion Kiosk" for animations.
+     * Automated algorithm for rotations and focus on 'special' components of PDB structures (e.g., heme in hemoglobin).
+     * Available as open-source in the [http://biojava.org/ BioJava project] (cf. [http://biopython.org BioPython], [http://www.bioperl.org BioPerl]).
+     * PDB also interested in [http://www.molsoft.com MolSoft] browser.
+       * Useful combination of text with hyper-links to molecular views in 3D viewer, using smooth animated transitions between views, transparent surfaces, etc.
+     * PDB preference is for EASY installation (e.g., java web-start).  
+     * PDB requirements for animation:
+       * By types of entities:
+         * ligand binding and binding sites
+         * conformational changes and morphing (apo/holo, active/inactive forms)
+         * enzyme catalysis
+         * molecular machines
+         * large assemblies - atom level to maps
+         * looking inside large structures
+         * molecular entities in the context of organelles and cells 
 
  * Molecular and cellular illustration resources
@@ -257 +273 @@
    * pymol installation for Ubuntu: {{{sudo apt-get install pymol apbs}}}
  * Jmol:  http://jmol.sourceforge.net/
+   * Used in the Protein Data Bank ([http://www.pdb.org PDB])
+     * [http://www.pdb.org/pdb/static.do?p=education_discussion/educational_resources/index.html Educational resources] includes a "Molecules in Motion Kiosk" for simple animations.
    * Chime (Jmol predecessor):  http://www.umass.edu/microbio/chime/
  * MGLTools at Scripps: http://mgltools.scripps.edu/