[Chimera-users] [Chimera] #10638: heme not included in morph trajectory

[Elaine Meng]

Hi Francesco,
There is some progress... in the newest daily build (Apr 4) I can run the commands below to successfully show a morph of 1hho and 2hhb that includes heme and iron.  1hho only has two chains, so it is necessary to delete C,D from 2hhb before morphing.  To include heme and iron, it is necessary to delete all the other het residues that may be different between the structures.
I hope this helps,
Elaine  

Here between "----" are contents of Chimera command file, which you could save as plain text file named something.cmd and open in Chimera to execute the commands. Lines starting with # are just comments/explanation and don't do anything. 
-------------
open 2hhb
open 1hho
#
# delete 2hhb chains C,D
#
delete #0:.c-d
#
# delete het residues that may be different between the structures so that
# the HEM residues will be included in the morph (if you want to see those
# residues, open another copy of structure not used for morphing)
#
del :hoh,po4,oxy
#
# superimpose the structures; I used "mm" with defaults but it could be
# done with options, or MatchMaker GUI, or "match" command, 
# or manually with mouse
#
mm #0 #1
#
# create morph trajectory which will be model #2
#
morph start #0 frames 25
morph interpolate #1 frames 25
morph movie
~modeldisp #0,1
---------------------
Then I tried to get fancy and make a tetramer of 1hho so that the morph could be from tetramer to tetramer.  However, then only the heme/iron from A and B were included, not from C and D.  I don't know why, because they are all in the input structures!!  Here is that script in case it might be useful:
---------------------
open 2hhb
open 1hho
#
# make 1hho tetramer; #1 is original, #2 additional copy
#
sym #1
#
# combine #1,2 dimers into tetramer model #3, close #1,2
#
combine #1,2 name 1hho-tetra newchainids true close true
#
# delete het residues that may be different between the structures so that
# the HEM residues will be included in the morph (if you want to see those
# residues, open another copy of structure not used for morphing)
#
del :hoh,po4,oxy
#
# superimpose #0 and #3
#
mm #0 #3
#
# create morph trajectory which will be model #1
#
morph start #0 frames 25
morph interpolate #3 frames 25
morph movie
~modeldisp #0,3
---------------------