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vmd_make_segid_fix.tcl
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vmd_make_segid_fix.tcl
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###; Make segments name for easy analysis.
###; By: Ropón-Palacios G. <[email protected]>.
mol new step3_input.pdb type pdb waitfor all
##; Set Spike region for the ectodomain
##; example to select into analysis:
##; segid RDB RMB and name CA ---> to select all RDB
set rbd [atomselect top "protein and resid 509 to 541"] ;## for RBD region, RDB total : RDB + RBM
set rbm [atomselect top "protein and resid 437 to 508"] ;## for RBM region
set ntd [atomselect top "protein and resid 13 to 303"] ;## for NTD region, NTD total : NTD + S1
set s1 [atomselect top "protein and resid 304 to 685"] ;## for S1 region
set s2 [atomselect top "protein and resid 686 to 1273"] ;## for S2 region
$rbd set segid "RBD"
$rbm set segid "RBM"
$ntd set segid "NTD"
$s1 set segid "S1"
$s2 set segid "S2"
###; set glycosilation, ligand and other.
set md1 1
set md2 0
set md3 0
set md4 0
set md5 0
set md6 0
if { $md1 } {
set lig [atomselect top "resname UNL"]
$lig set resname "LIG"
set pocket [atomselect top "protein and same residue as within 4 of resname LIG"]
set presid [$pocket get resid]
set ofile [open "pocket_resids.dat" w]
puts $ofile "$presid"
$pocket set segid "BPO" ;## for binding pocket into RBD place.
set all [atomselect top "all"]
$all writepdb md1_renamed.pdb
quit
}
if { $md2 } {
set lig [atomselect top "resname UNL"]
$lig set resname "LIG"
set pocket [atomselect top "protein and same residue as within 4 of resname LIG"]
$pocket set segid "BPO" ;## for binding pocket into RBD place.
##; select all residue that are glycosilated
set r1 [atomselect top "protein and resid 17"]
set g1 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC BGAL BGLC AMAN BGLC AFUC"]
$r1 set segid "R1"
$g1 set segid "G1"
set r2 [atomselec top "protein and resid 616"]
set g2 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC AMAN BGLC AFUC"]
$r2 set segid "R2"
$g1 set segid "G2"
set r3 [atomselecct top "protein and resid 61"]
set g3 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r3 set segid "R3"
$g3 set segid "G3"
set r4 [atomselect top "protein and resid 74"]
set g4 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC BGAL ANE5 BGLC AMAN BGLC BGLC AFUC"]
$r4 set segid "R4"
$g4 set segid "G4"
set r5 [atoselect top "protein and resid 122"]
set g5 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r5 set segid "R5"
$g5 set segid "G5"
set r6 [atomselect top "protein and resid 149"]
set g6 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC AMAN BGLC AFUC"]
$r6 set segid "R6"
$g6 set sedig "G6"
set r7 [atomselect top "protein and resid 165"]
set g7 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC BGAL"]
$r7 set segid "R7"
$g7 set segid "G7"
set r8 [atomselect top "protein and resid 331"]
set g8 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC AMAN BGLC AFUC"]
$r8 set segid "R8"
$g8 set segid "G8"
set r9 [atomselect top "protein and resid 234"]
set g9 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN AMAN AMAN AMAN"]
$r9 set segid "R9"
$r9 set segid "G9"
set r10 [atomselect top "protein and resid 657"]
set g10 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN BGLC BGAL"]
$r10 set segid "R10"
$g10 set segid "G10"
set r11 [atomselect top "protein and resid 282"]
set g11 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC BGLC AMAN BGLC AFUC"]
$r11 set segid "R11"
$g11 set segid "G11"
set r12 [atomselect top "protein and resid 323"]
set g12 [atomselect top "resname AGAL BGAL ANE5"]
$r12 set segid "R12"
$g12 set segid "G12"
set r13 [atomselect top "protein and resid 343"]
set g13 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC AMAN BGLC AFUC"]
$r13 set segid "R13"
$g13 set segid "G13"
set r14 [atomselect top "protein and resid 603"]
set g14 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r14 set segid "R14"
$g14 set segid "G14"
set r15 [atomselect top "protein and resid 709"]
set g15 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r15 set segid "R15"
$g15 set segid "R15"
set r16 [atomselect top "protein and resid 717"]
set g16 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r16 set segid "R16"
$g16 set segid "G16"
set r17 [atomselect top "protein and resid 801"]
set g17 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r17 set segid "R17"
$g17 set segid "G17"
set r18 [atomselect top "protein and resid 1074"]
set g18 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r18 set segid "R18"
$g18 set segid "G18"
set r19 [atomselect top "protein and resid 1098"]
set g19 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC BGAL ANE5 AMAN BGLC AFUC"]
$r19 set segid "R19"
$g19 set segid "G19"
set r20 [atomselect top "protein and resid 1134"]
set g20 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC AMAN BGLC AFUC"]
$r20 set segid "R20"
$g20 set segid "G20"
set all [atomselect top "all"]
$all writepdb md2_renamed.pdb
quit
}
if { $md3 } {
set lig [atomselect top "resname UNL"]
$lig set resname "LIG"
set cryptic [atomselect top "protein and same residue as within 4 of resname LIG"]
set cresid [$cryptic get resid]
set ofile [open "cryptic_resids.dat" w]
puts $ofile "$cresid"
$cryptic set segid "CPO" ;## for cryptic pocket pocket into RBD place.
set all [atomselect top "all"]
$all writepdb md3_renamed.pdb
quit
}
if { $md4 } {
set lig [atomselect top "resname UNL"]
$lig set resname "LIG"
set cryptic [atomselect top "protein and same residue as within 4 of resname LIG"]
$cryptic set segid "CPO" ;## for cryptic pocket into RBD place.
##; select all residue that are glycosilated
set r1 [atomselect top "protein and resid 17"]
set g1 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC BGAL BGLC AMAN BGLC AFUC"]
$r1 set segid "R1"
$g1 set segid "G1"
set r2 [atomselec top "protein and resid 616"]
set g2 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC AMAN BGLC AFUC"]
$r2 set segid "R2"
$g1 set segid "G2"
set r3 [atomselecct top "protein and resid 61"]
set g3 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r3 set segid "R3"
$g3 set segid "G3"
set r4 [atomselect top "protein and resid 74"]
set g4 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC BGAL ANE5 BGLC AMAN BGLC BGLC AFUC"]
$r4 set segid "R4"
$g4 set segid "G4"
set r5 [atoselect top "protein and resid 122"]
set g5 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r5 set segid "R5"
$g5 set segid "G5"
set r6 [atomselect top "protein and resid 149"]
set g6 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC AMAN BGLC AFUC"]
$r6 set segid "R6"
$g6 set sedig "G6"
set r7 [atomselect top "protein and resid 165"]
set g7 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC BGAL"]
$r7 set segid "R7"
$g7 set segid "G7"
set r8 [atomselect top "protein and resid 331"]
set g8 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC AMAN BGLC AFUC"]
$r8 set segid "R8"
$g8 set segid "G8"
set r9 [atomselect top "protein and resid 234"]
set g9 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN AMAN AMAN AMAN"]
$r9 set segid "R9"
$r9 set segid "G9"
set r10 [atomselect top "protein and resid 657"]
set g10 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN BGLC BGAL"]
$r10 set segid "R10"
$g10 set segid "G10"
set r11 [atomselect top "protein and resid 282"]
set g11 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC BGLC AMAN BGLC AFUC"]
$r11 set segid "R11"
$g11 set segid "G11"
set r12 [atomselect top "protein and resid 323"]
set g12 [atomselect top "resname AGAL BGAL ANE5"]
$r12 set segid "R12"
$g12 set segid "G12"
set r13 [atomselect top "protein and resid 343"]
set g13 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC AMAN BGLC AFUC"]
$r13 set segid "R13"
$g13 set segid "G13"
set r14 [atomselect top "protein and resid 603"]
set g14 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r14 set segid "R14"
$g14 set segid "G14"
set r15 [atomselect top "protein and resid 709"]
set g15 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r15 set segid "R15"
$g15 set segid "R15"
set r16 [atomselect top "protein and resid 717"]
set g16 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r16 set segid "R16"
$g16 set segid "G16"
set r17 [atomselect top "protein and resid 801"]
set g17 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r17 set segid "R17"
$g17 set segid "G17"
set r18 [atomselect top "protein and resid 1074"]
set g18 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r18 set segid "R18"
$g18 set segid "G18"
set r19 [atomselect top "protein and resid 1098"]
set g19 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC BGAL ANE5 AMAN BGLC AFUC"]
$r19 set segid "R19"
$g19 set segid "G19"
set r20 [atomselect top "protein and resid 1134"]
set g20 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC AMAN BGLC AFUC"]
$r20 set segid "R20"
$g20 set segid "G20"
set all [atomselect top "all"]
$all writepdb md4_renamed.pdb
quit
}
if { $md5 } {
##; revisar los archivos generados en MD1 y MD3 para obtener los residuos
set cryptic [atomselect top "protein and resid"]
set pocket [atomselect top "protein and resid "]
$pocket set segid "BPO" ;## for binding pocket pocket into RBD place.
$cryptic set segid "CPO" ;## for cryptic pocket pocket into RBD place.
set all [atomselect top "all"]
$all writepdb md5_renamed.pdb
quit
}
if { $md6 } {
##; revisar los archivos generados en MD1 y MD3 para obtener los residuos
set cryptic [atomselect top "protein and resid"] ;## adicionar los residues.
set pocket [atomselect top "protein and resid "]
$pocket set segid "BPO" ;## for binding pocket pocket into RBD place.
$cryptic set segid "CPO" ;## for cryptic pocket pocket into RBD place.
##; select all residue that are glycosilated
set r1 [atomselect top "protein and resid 17"]
set g1 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC BGAL BGLC AMAN BGLC AFUC"]
$r1 set segid "R1"
$g1 set segid "G1"
set r2 [atomselec top "protein and resid 616"]
set g2 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC AMAN BGLC AFUC"]
$r2 set segid "R2"
$g1 set segid "G2"
set r3 [atomselecct top "protein and resid 61"]
set g3 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r3 set segid "R3"
$g3 set segid "G3"
set r4 [atomselect top "protein and resid 74"]
set g4 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC BGAL ANE5 BGLC AMAN BGLC BGLC AFUC"]
$r4 set segid "R4"
$g4 set segid "G4"
set r5 [atoselect top "protein and resid 122"]
set g5 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r5 set segid "R5"
$g5 set segid "G5"
set r6 [atomselect top "protein and resid 149"]
set g6 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC AMAN BGLC AFUC"]
$r6 set segid "R6"
$g6 set sedig "G6"
set r7 [atomselect top "protein and resid 165"]
set g7 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC BGAL"]
$r7 set segid "R7"
$g7 set segid "G7"
set r8 [atomselect top "protein and resid 331"]
set g8 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC AMAN BGLC AFUC"]
$r8 set segid "R8"
$g8 set segid "G8"
set r9 [atomselect top "protein and resid 234"]
set g9 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN AMAN AMAN AMAN"]
$r9 set segid "R9"
$r9 set segid "G9"
set r10 [atomselect top "protein and resid 657"]
set g10 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN BGLC BGAL"]
$r10 set segid "R10"
$g10 set segid "G10"
set r11 [atomselect top "protein and resid 282"]
set g11 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC BGLC AMAN BGLC AFUC"]
$r11 set segid "R11"
$g11 set segid "G11"
set r12 [atomselect top "protein and resid 323"]
set g12 [atomselect top "resname AGAL BGAL ANE5"]
$r12 set segid "R12"
$g12 set segid "G12"
set r13 [atomselect top "protein and resid 343"]
set g13 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC AMAN BGLC AFUC"]
$r13 set segid "R13"
$g13 set segid "G13"
set r14 [atomselect top "protein and resid 603"]
set g14 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r14 set segid "R14"
$g14 set segid "G14"
set r15 [atomselect top "protein and resid 709"]
set g15 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r15 set segid "R15"
$g15 set segid "R15"
set r16 [atomselect top "protein and resid 717"]
set g16 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r16 set segid "R16"
$g16 set segid "G16"
set r17 [atomselect top "protein and resid 801"]
set g17 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r17 set segid "R17"
$g17 set segid "G17"
set r18 [atomselect top "protein and resid 1074"]
set g18 [atomselect top "resname BGLC BGLC BMAN AMAN AMAN AMAN AMAN"]
$r18 set segid "R18"
$g18 set segid "G18"
set r19 [atomselect top "protein and resid 1098"]
set g19 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC BGAL ANE5 AMAN BGLC AFUC"]
$r19 set segid "R19"
$g19 set segid "G19"
set r20 [atomselect top "protein and resid 1134"]
set g20 [atomselect top "resname BGLC BGLC BMAN AMAN BGLC AMAN BGLC AFUC"]
$r20 set segid "R20"
$g20 set segid "G20"
set all [atomselect top "all"]
$all writepdb md5_renamed.pdb
quit
}
puts "thanks for use."