####################################################
# Saving by command line, and directory location

opening via shortcut
opening at file location

pwd	where am i?
ls	what is in this directory?
cd	move into directory ('cd ..' to go backwards)

save whatever.pdb, whatever

####################################################
# proximity selection https://pymolwiki.org/index.php/Selection_Algebra


#select residues around binding site
rein
fetch 1nqu
bg_color white
util.cbc
colour black, org
util.cnc
remove solvent + inorganic
select ligA, bm. first org
select close, br. polymer near_to 5 of ligA
show sticks, close & sc. + close & n. CA + close & r. PRO & n. N

# removing atoms outside of a distance
rein
fetch 5npp
bg_color white
util.cbc
remove solvent + c. D
remove br. polymer.nucleic gap 15
remove br. polymer.protein gap 15
 
# binding site surface visualisation 1
rein
fetch 1nqu
bg_color white
util.cbc
colour black, org
util.cnc
remove solvent + inorganic
select ligA, bm. first org
select close, br. polymer near_to 5 of ligA
show surface, close
set transparency, 0.3

# binding site surface visualisation 2
rein
fetch 1nqu
bg_color white
util.cbc
colour black, org
util.cnc
remove solvent + inorganic
select ligA, bm. first org
select prot, polymer
set surface_carve_cutoff, 4.5
set surface_carve_selection, ligA
set surface_carve_normal_cutoff, -0.1
show surface, prot within 8 of ligA
set two_sided_lighting
set transparency, 0.5
orient ligA
zoom ligA, 2
select close, br. polymer near_to 5 of ligA
show sticks, close & sc. + close & n. CA + close & r. PRO & n. N
set surface_color, white
distance hbond, ligA, prot, mode=2
color magenta, hbond


####################################################
# Crystal lattice expansion and contacts.

reinitialize 
fetch 1wl9, async=0
alter 1wl9, segi='rpdb'
remove solvent + inorganic
bg_color white

symexp sym, 1wl9, (1wl9), 4
alter sym*, segi='crys'
color grey90
color black, 1wl9
show sticks

select loop, 1wl9 & ps. LYRPGTSI
color green, loop
alter loop, segi='loop'

select near, br. 1wl9 near_to 5 of loop
color cyan, near
alter near, segi='near'

select crys, br. loop around 5 & ! 1wl9
color hotpink, crys
alter crys, segi='crys'

orient loop
zoom loop, 10
util.cnc

select removeme, br. loop gap 15
remove removeme & ! 1wl9
deselect


####################################################
# getting data from pymol (Make a ramachandran plot)

rein
fetch 3chb

chain=D
residues=$(grep " D " 3chb.pdb | grep ATOM | grep ' CA ' | wc -l )
echo "fetch 3chb, async=0
f=open('phipsi.txt','w')" > phipsi.pml

for i in $(seq 1 $residues) ; do 
sele1=$i
sele2=$(($i + 1))
sele3=$(($sele2 + 1))
echo "
select sele1, c. D & i. $sele1
select sele2, c. D & i. $sele2
select sele3, c. D & i. $sele3" >> phipsi.pml 
echo '
phi=cmd.get_dihedral("'sele1' & n. C", "'sele2' & n. N", "'sele2' & n. CA", "'sele2' & n. C")
psi=cmd.get_dihedral("'sele2' & n. N", "'sele2' & n. CA", "'sele2' & n. C", "'sele3' & n. N") 
f.write("'$sele2-phi' %s\n" % phi)
f.write("'$sele2-psi' %s\n" % psi)' >> phipsi.pml 
done
echo "f.close()" >> phipsi.pml 
pymoll -qc phipsi.pml 

grep phi phipsi.txt | awk '{print $2}' > a.tx
grep psi phipsi.txt | awk '{print $2}' > b.tx
dos2unix a.tx
dos2unix b.tx
paste -d',' a.tx b.tx > phipsi.csv
excel phipsi.csv

###########

Simple stuff
echo " 
f=open('outfile.tx','w')
cnt=cmd.centerofmass("'"i. '$comres'"'") " >> fetch.pml
echo 'f.write("'oricapcom' %s\n" % cnt)' >> fetch.pml
echo "f.close()

Simple stuff

f=open('outfile.tx','w')
cnt=cmd.centerofmass("'"i. '$comres'"'") 
echo 'f.write("'oricapcom' %s\n" % cnt)
echo "f.close()



####################################################
# automatic secondary structure detection

dss
rebuild

####################################################
# show electron density

wget https://edmaps.rcsb.org/maps/3ueq_2fofc.dsn6
wget https://edmaps.rcsb.org/maps/3ueq_fofc.dsn6

fetch 3ueq_A, type=pdb, async=0
load 3ueq_2fofc.dsn6
load 3ueq_fofc.dsn6
select search-seq, 3ueq_A & ps. WILSN
orient search-seq
color black, search-seq
bg_color white
util.cnc
deselect
as sticks, polymer
isomesh 3ueq-2fofc_1.5, 3ueq_2fofc, 1.5
color blue, 3ueq-2fofc_1.5
isomesh 3ueq-fofc_3, 3ueq_fofc, 3
isomesh 3ueq-fofc_-3, 3ueq_fofc, -3
color green, 3ueq-fofc_3
color red, 3ueq-fofc_-3
map_trim 3ueq*, search-seq, 4
orient search-seq
deselect
mset 1 -360
mview store, 1
turn y, -180
mview store, 180
turn y, -180
mview store, 360
mplay