.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