| Detailed description |
|
|
System:
Mac OSX 10.10.5
Climber: latest
I used the CDPK1 (calcium dependent protein kinase, with and without Ca2+) structures for morphing. Climber could not reach the final conformation, i.e. the ending state from climber does not look like one of the protein structures that I loaded.
You can see the starting and ending structures on protopedia.
http://proteopedia.org/wiki/index.php/CDPK
Here is what I did:
$ cd ~/climber-work
$ mkdir CDPK-2
$ cd CDPK-2
$ curl -o 3KU2_orig.pdb https://files.rcsb.org/download/3KU2.pdb
$ curl -o 3HX4_orig.pdb https://files.rcsb.org/download/3HX4.pdb
$ export CLIMBERDIR=~/climber-work/Climber
$ awk '/ATOM/ {print}' < 3KU2_orig.pdb > 3KU2.pdb
$ awk '/ATOM/ {print}' < 3HX4_orig.pdb > 3HX4.pdb
$ ${CLIMBERDIR}/sh/rms.sh 3KU2 3HX4 > morphx.al1
$ ${CLIMBERDIR}/sh/morphx.sh 3KU2 3HX4 50
Climber created 114 files.
I imported them into PyMOL and the last structure does not look at all like 3HX4. I attached a png of the final structure.
Note that the two conformations of this protein are quite different (that's what makes it interesting). This may be beyond the capabilities of Climber.
|
|
