CCL: molecular modeling - animation

 Sent to CCL by: Ben Sattelle [ben.sattelle|*|postgrad.manchester.ac.uk]
2. I have a docked complexes contains ligands and proteins. With this, I may want to create a movie showing docking of a ligand into the active site and save it in file. 
 hi, this may or may not be useful. below is a howto for converting a CHARMM
 trajectory into an animated *.gif file. requires, VMD, PyMol & convert
 (imagemagik tool, comes with cygwin). ben.
 1)
 load *.pdb file into VMD
 load *.dcd trajectory into VMD
 goto File->Save Coordinates
 select molecule
 choose 'Frames' for animation (say 10-50 in total for testing, see later)
 leaving 'stride' set to 1 worked for me
 under 'File type' select 'pdb' and then 'Save'
 you should now have a stack of structures in one (pdb) file
 2)
 use this sed oneliner on the file to substitute END for ENDMDL globally,
 $ sed -e 's/END/ENDMDL/' infile.pdb > outfile.pdb
 outfile.pdb can now be read by PyMol
 3)
 read outfile.pdb into PyMol and setup as you wish
 e.g. select fmn, resn fmn
     set stick_radius=0.15
     select T57, resid 57
     select A58, resid 58
     select water, resn TIP3
 4)
 issue the following at the PyMol command line
mset 1 -50 /* ... if you have 50 frames, see mset in PyMol manual 
 */
 set ray_trace_frames=1    /* ... looks pretty! */
 set cache_frames=0	  /* ... save memory */
 mclear			  /* ... clear memory */
 mpng animationame         /* ... go! */
 this may take some time, go for a cup of coffee!
processing 50 frames requires a few minutes on my pc, setting ray_trace_frames=0 
 should save time
if you can't find the output (*.png files) in the cwd have a look in C:\Program 
 Files\DeLano Scientific\PyMOL
 5)
 cd to directory containing *.png files, use convert
 $ convert -delay 20 *.png animation.gif
 the -delay flag sets the time between frames (ms), other outfile formats are
 supported also, man convert
 the *.gif animations function within powerpoint (in presentation mode) and web
 browsers!