初步整理的一些较常用的命令，时间有限，未能注释。后续会进一步注释。
http://pymolwiki.org/index.php/Main_Page
Pymol> log_open log-file-name.pml
Pymol> log_close
Creat a file to record the commands
Pymol> load 2vlo.pdb
Pymol> load 2vlo.pdb, test
Pymol> show representation
Pymol> hide representation
Representation: cartoon, ribbon, dots,spheres, surface, mesh
Pymol> label all, chains
Pymol> hide ribbon, chain f+g+h+i+j
Or
Pymol> select test, chain f+g+h+i+j
Pymol> hide ribbon, test
Pymol> select selection-name,selection-expression
Pymol> color color-name
Pymol> color color-name, selection-expression
Pymol> color red, ss h
Pymol> color yellow, ss s
Pymol> color green, ss l+""
selection-expression
selector + identifier
symbol: chemical-symbol-list, e.
Pymol> select polar, symbol o+n
name: atom-name-list, n.
Pymol> select carbons, name ca+cb+cg+cd
resn: residue-name-list, r.
Pymol> select aas, resn asp+glu+asn+gln
resi: residue-identifier-list, l.
Pymol> select mults10, resi 1+10+100
residue-identifier-range
Pymol> select nterm, resi 1-10
alt: alternate-conformation-identifier-list,alt
Pymol> select altconf, alt a+b
chain: chain-identifier-list, c.
Pymol> select firstch, chain a
segi: segment-identifier-lis, s.
Pymol> select ligand, segi lig
flag: flag-nummer, f.
Pymol> select f1, flag 0
numeric_type: type-nummer, nt.
Pymol> select type1, nt. 5
text_type: type-string, tt.
Pymol> select subset, tt. HA+HC
id: external-index-number, id
Pymol> select idno, id 23
index: internal-index-number, idx.
Pymol> select intid, index 23
ss: secondary-structure-type, ss
Pymol> select allstrs, ssh+s+l+""
Pymol> select chain a and resi 100 andca
Pymol> select a/100/ca
/objectname/segiidentifier/chainidentifier/resiidentifier/nameidentifier
/objectname/segiidentifier/chainidentifier/resiidentifier
/objectname/segiidentifier/chainidentifier
/objectname/segiidentifier
resiidentifier/nameidentifier
chainidentifier/resiidentifier/nameidentifier
segiidentifier/chainidentifier/resiidentifier/nameidentifier
objectname/segiidentifier/chainidentifier/resiidentifier/nameidentifier
Cartoon:
Pymol> cartoon type, (selection)
automatic, loop, tube, oval, rectangle,arrow, dumbbell, skip
Pymol> set cartoon_flat_sheets, 1
Pymol> set cartoon_flat_sheets, 0
Pymol> set cartoon_smooth_loops, 1
Pymol> set cartoon_smooth_loops, 0
Pymol> set cartoon_oval_width, 0.2
Pymol> set cartoon_oval_length, 1.5
Pymol> set cartoon_rect_width, 0.5
Pymol> set cartoon_rect_length, 1.5
Pymol> set cartoon_loop_radius, 0.2
Pymol> set cartoon_fancy_helices, 1
Pymol> set cartoon_fancy_sheets, 1
Pymol> set cartoon_dumbbell_width, 0.1
Pymol> set cartoon_dumbbell_length, 2
Pymol> set cartoon_dumbbell, 0.2
Pymol> set cartoon_transparency, 0.5
Pymol> set cartoon_refine, 20
Pymol> set cartoon_color, green
fft HKLIN protein.mtz XYZIN protein.pdbMAPOUT 2fofc.ccp4
LABIN F1=FWT PHI=PHWT
GRID SAMPLE 5
END
Pymol> load glucosyltransferase.pdb, pro
Pymol> load 2fofc.ccp4
Wizard -- Density
Pymol> remove resn HOH
Pymol> select upg, chain b
Pymol> as cartoon, pro
Pymol> as stick, upg
Pymol> orient, upg
Pymol> isomesh upg-d, 2fofc, 2.0, upg, carve=1.5
Pymol> set stick_radius, 0.2
Pymol> set mesh_radius, 0.01
Pymol> isomesh name, map, level[,(selection) [,buffer [,state [,carve ]]]]
load pdb file:pdb1lza # Load in a PDB file (lysozyme)
util.cbaw #Set normal CPK colours and render as sticks so we
cansee the coordinates through the mesh
show sticks, pdb1lza
setnormalize_ccp4_maps, 1 # Load in the electrondensity map (CCP4 format)
load 1lza.ccp4 #This was obtained fromthe Uppsala Electron Density
serverhttp://fsrv1.bmc.uu.se/eds/
#First we make sure that map normalisation is turned
on- this means that we can contour at sigma levels
(ratherthan absolute values)
isomesh mesh,1lza.ccp4, 2.0 # Contour the map at 2.0 sigma across the wholecell
color green, mesh
select res,////87 # Select one residue -ASP 87
isosurface surf,1lza, 1, res, carve=2 # Createan isosurface at 1.0 sigma, just in the vicinity
ofthis residue
#(onlyin a region with 2 angstrom of the selected
residue)
set transparency,0.5 #Make the isosurface semitransparent
move z, -20 #Zoom out a bit so we can see it better
Movie:
Load the file 1L0T_sidechains
mset 1 x120 #Reserve space for 120 frames
setray_trace_frames, 0 # Make sure thatray-tracing is turned off for movie
generation-otherwise, this would take a LONG time
util.mroll(1,120,1) #Use a built in utility function to generate a full 360-degree rotation roundthe y-axis, over 120 frames
mplay #Play the movie
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