.pymolrc

PyMOLの自作.pymolrcファイル
#2022.6.29
リガンド周りのラベリングをスッキリさせました。
#2022.8.10
AlphaFold2のplDDTスコアのカラーリングをラボォさんのtweetを参考にalias化しました。 tagをシンプルな設計に変えました。 FASTAをprintするalias作りました。 maestroっぽいセレクタのalias作りました。 そのほか細々変えました。

#set cartoon_transparency, 0.1
#set transparency, 0.4
set surface_color, white
set sphere_scale, 0.4
set label_position, (3,1,1)
set label_size, 25
# set ray_trace_mode, 1
set ray_shadow, off
bg_color silver

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'}

alias al, alignto; zoom
alias sp, split_chains enabled; alignto; zoom
alias cc, util.color_chains("(enabled and name CA)",_self=cmd)

alias pl, preset.ligand_cartoon("enabled",_self=cmd);show spheres, solvent
alias see, zoom byres organic around 8 and chain A
alias del, as nb_spheres, solvent
alias sol, as nb_spheres, solvent; hide nb_spheres
alias line, show lines, byres organic around 4 and enabled
alias hb, select ligand, organic and enabled; cmd.dist("contact","(ligand)","(byobj (ligand)) and (not (ligand))",quiet=1,mode=2,label=0,reset=1); cmd.enable("contact")


alias well, show surface, byres organic expand 5 and enabled
alias 9, create 9, byres organic expand 9 and enabled; disable !9; see
alias 5, create a5, byres organic expand 5 and enabled; disable !5; see
alias x, select sele, byres sele expand 4 and enabled

alias tag, label n. CA and sele, "%s%s" % (one_letter[resn], resi)
alias untag, hide label, sele

alias k, hide sticks, polymer.protein; show sticks, resn lys
alias c, hide sticks, polymer.protein; show sticks, resn cys
alias s, hide sticks, polymer.protein; show sticks, resn ser
alias h, hide sticks, polymer.protein; show sticks, resn his
alias t, hide sticks, polymer.protein; show sticks, resn thr
alias r, hide sticks, polymer.protein; show sticks, resn arg
alias d, hide sticks, polymer.protein; show sticks, resn asp
alias e, hide sticks, polymer.protein; show sticks, resn glu
alias n, hide sticks, polymer.protein; show sticks, resn asn
alias q, hide sticks, polymer.protein; show sticks, resn gln
alias y, hide sticks, polymer.protein; show sticks, resn tyr
alias f, hide sticks, polymer.protein; show sticks, resn phe
alias w, hide sticks, polymer.protein; show sticks, resn trp
alias g, hide sticks, polymer.protein; show sticks, resn gly
alias a, hide sticks, polymer.protein; show sticks, resn ala
alias m, hide sticks, polymer.protein; show sticks, resn met
alias p, hide sticks, polymer.protein; show sticks, resn pro
alias fasta, print(cmd.get_fastastr('enabled'))
alias plddt, spectrum b, rainbow_rev, maximum=100, minimum=25