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pymolrc
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pymolrc
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#_ feedback push
#_ feedback disable,all,everything
#from pymol import cmd
import sys
set cylinder_shader_ff_workaround, 1
sys.path.append("/home/longxing/pymol_scripts/")
sys.path.append("/home/longxing/pymol_scripts/scripts")
from scripts import *
###########################################################
## Custom commands
set cartoon_flat_sheets, 0
###########################################################
#run /home/longxing/pymol_scripts/scripts/all_commands.py
run /home/longxing/pymol_scripts/scripts/tmalign.py
run /home/longxing/pymol_scripts/scripts/rawAsBfact.py
run /home/longxing/pymol_scripts/scripts/roeAsBfact.py
run /home/longxing/pymol_scripts/scripts/PDBinfo.py
aaindex.init("/home/longxing/pymol_scripts/scripts/aaindex")
# END COMMANDS
_ feedback pop
alias pbi, color gray80, chainA; color white, chainB; aaindex2b DVLA000001; spectrum b, red_green, chainB; util.cnc;
alias ipbi, color gray80, chainA; color white, chainB; aaindex2b DVLA000001; spectrum b, red_green, chainB and interface; util.cnc;
alias npbi, color gray80, chainA; color white, chainB; aaindex2b DVLA000002; spectrum b, red_green, chainB; util.cnc;
alias inpbi, color gray80, chainA; color white, chainB; aaindex2b DVLA000002; spectrum b, red_green, chainB and interfaceB; util.cnc;
alias dl, color gray80, chainA; color white, chainB; aaindex2b DVLA000003; spectrum b, green_red, chainB; util.cnc;
alias idl, color gray80, chainA; color white, chainB; aaindex2b DVLA000003; spectrum b, green_red, chainB and interfaceB; util.cnc;
alias hydro, color gray80, chainA; color white, chainB; aaindex2b NADH010101; spectrum b, green_white_yellow, chainB; util.cnc;
alias ihydro, color gray80, chainA; color white, chainB; aaindex2b NADH010101; spectrum b, green_white_yellow, chainB and interfaceB; util.cnc;
alias alpha, color gray80, chainA; color white, chainB; aaindex2b CHOP780201; spectrum b, red_green, chainB; util.cnc;
alias ialpha, color gray80, chainA; color white, chainB; aaindex2b CHOP780201; spectrum b, red_green, chainB and interfaceB; util.cnc;
alias beta, color gray80, chainA; color white, chainB; aaindex2b CHOP780202; spectrum b, red_green, chainB; util.cnc;
alias ibeta, color gray80, chainA; color white, chainB; aaindex2b CHOP780202; spectrum b, red_green, chainB and interfaceB; util.cnc;
alias stik, hide all; cmd.show("cartoon"); cmd.show("sticks","not hydro");
alias cbc, hide all; cmd.show("cartoon"); util.cbc;
alias cnc, hide all; cmd.show("cartoon"); cmd.show("sticks","not hydro"); cmd.util.cbc("all"); cmd.util.cnc("all");
alias cg, object=cmd.get_names()[0]; cmd.view('v', 'store'); util.protein_vacuum_esp(object, mode=2, quiet=0); cmd.disable(object + "_e_pot"); cmd.enable(object); cmd.view('v', 'recall');
alias surf, cmd.extract('target', 'chainA'); cmd.view('v', 'store'); util.protein_vacuum_esp('target', mode=2, quiet=0); cmd.disable('target' + "_e_pot"); cmd.enable('target'); cmd.view('v', 'recall'); cmd.zoom('interface'); cmd.create('inter_bawls','interfaceB'); cmd.show('spheres','inter_bawls'); cmd.disable('inter_bawls'); cmd.create('inter_cage',"interfaceB"); cmd.show('mesh','inter_cage'); cmd.color('magenta','inter_cage'); cmd.util.cnc('inter_cage'); cmd.disable('inter_cage');
alias bam, pdbdircyclerlite; set_cycler_command 'stix; show cartoon';
alias bbo, hide all; show sticks, name Ca+C+O+N+CA
alias hetsee, hide all; show cartoon; alignto asym*; zoom; select interfaceA, asym and chain A within 10 of (asym and chain B); select interfaceB, asym and chain B within 10 of (asym and chain A); select interfaceAA, not hydro within 3 of interfaceA; select interfaceBB, not hydro within 3 of interfaceB; show lines, interfaceAA; show lines, interfaceBB; select interfaceOri, resi and asym and interfaceAA or asym and interfaceBB; show sticks, interfaceOri; disable interface*; disable *_2_S* or *_3_S* or *_4_S* or or *_5_S*
# calculate the phi psi angle of the selected residue.
alias pp, (phi,psi)=cmd.phi_psi("sele").values()[0];abego = {phi>0 and -100<=psi<100:'G',phi<0 and psi>=100:'E',phi>0 and psi<-100:'E',phi<=0 and -75<=psi<50:'A',phi<=0 and psi<-75:'B',phi<=0 and psi>=50:'B'}[1]; print "\\n"; print "phi: %s"%(phi); print "psi: %s"%(psi); print "AGEGO: %s" % abego; print "\\n";
alias seq, one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q','ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y','ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A','GLY':'G', 'PRO':'P', 'CYS':'C'}; pyMOLSeq = []; cmd.iterate("sele and n. CA", "pyMOLSeq.append( one_letter[resn] )"); pyMOLSeq = ''.join( pyMOLSeq ); print "\\nSequence:\\n%s" % (pyMOLSeq)
#custom commands by longxing
alias sphere, show spheres,sele; useRosettaRadii