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Examples below describe the use of PyMol plugin and PyMol ver. 0.98 with bacterial enzymes haloalkane dehalogenases.
the active site is located among Asp108, Trp109, Asn38, His272; CL ion is bound between Trp109 and Asn38
select Phe151, Asn38, and Trp109 using the command "select start, i. 151 or i. 38 or i. 109"
check the name of your selection "(start)"
call CAVER plug-in
set correct binary (caver.exe) location
click on the radio button "Use average point from centers of given selections" and write "(start)" to Selection list:
remove CL ions (using the command "select ions, resname CL ; remove ions"), note: CAVER allows to ignore WAT, HOH, H2O residues, but not ligands and counterions
run CAVER
compare your results with saved pyMol session (1mj5.pse - pyMol 0.98 zipped)
the active site is located among Asp117, Trp118, Asn52, His283; IOD (iodine) ion is bound between Trp118 and Asn52
select Asp117, Trp118, Asn52, and Phe179 using the command "select start, i. 117 or i. 118 or i. 52 or i. 179"), selection si named "(start)"
call CAVER plug-in
set correct binary (caver.exe) location
click on the radio button "Use average point from centers of given selections" and write "(start)" to Selection list:
remove IOD ions using command "select ions, resname IOD ; remove ions"
run CAVER
compare your results with saved pyMol session (1cqw.pse - pyMol 0.98 zipped)
the active site is located among Asp124, Trp125, Glu56, His289, Trp175
select Asp124, Trp125, and Trp175 using command "select start, i. 124 or i. 125 or i. 175"
call CAVER plug-in
set correct binary (caver.exe) location
click on the radio button "Use average point from centers of given selections" and write "(start)" to Selection list:
run CAVER
compare your results with saved pyMol session (2had.pse - pyMol 0.98 zipped)
active site of LinB is connected with the solvent by two tunnels
remove CL ions (using the command "select ions, resname CL ; remove ions")
select Phe151, Asn38, and Trp109 using the command "select start, i. 151 or i. 38 or i. 109" and check the name of your selection "(start)"
call CAVER plug-in
check grid resolution, (0.8 A was used for this example)
check correct binary (caver.exe) location
click on the radio button "Use average point from centers of given selections" and write "(start)" to Selection list:
click on "Show starting point" button - X, Y, Z coordinates of the starting point are recalculated and shown as "crisscross", note: position of the starting point can be tuned by three scrolls
check "Ignore water (HOH, WAT, H2O)"
click "Run CAVER" button
plugin shows the 1st tunnel, i.e. the easiest way from the active site to the solvent
in order to find the 2nd tunnel, gorge must be closed (corked), X24 is located in the gorge, to see radius of maximally inscribed ball here, right-click on X24 point and choose atom->labels->vdw radius (1.26 A)
select X24 tunnel point "select cork, name X24"
write "origin (cork)" and "center (cork)"
to cork this position, use Build->Fragment->Cyclopentyl from the pyMOL main menu, cyclopentane appears at the same position as X24
join protein with cyclopentane cork using command "select 1MJ5_corked, 1MJ5 or cyclopentane" (in case you want to save the first tunnel remane it "set_name tunnel, 1_tunnel)
call CAVER plugin
check that selection "(start)" exists
set "Selection to use:" "(1MJ5_corked)"
set "use average point.." to "(start)"
check "Remove water"
run CAVER
an alternative tunnel appears
compare your results with saved pyMol session (1mj5_2.pse - pyMol 0.98 zipped)
1MJ5 as analyzed by CAVER capable to find more tunnels (3 tunnels shown)
active site of P450Cam is connected with several tunnels with solvent
select CAMphore by click, create object and rename it as CAM, delete selection atoms
call CAVER (0.99.2 - Beta) plug-in
check grid resolution, (0.8 A was used for this example)
check correct binary (caver.exe) location
set selection to use as "1akd"
set number of tunnels to "5"
click on the radio button "Use average point from centers of given selections" and write "CAM" to Selection list:
click on "Show starting point" button - X, Y, Z coordinates of the starting point are recalculated and shown as "crisscross"
check "Ignore water (HOH, WAT, H2O)"
click "Run CAVER" button
after calculation (several minutes) plugin shows the 5 tunnels
Download file Examples.tar.gz
tar xfvz Examples.tar.gz
cd Examples/DhlA
caver --enable-output-trajectory
cd "C:\CAVER\Examples\DhlA"
caver --enable-output-trajectory
Compare results with file in RESULT/result.dat