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Pymol 命令整理 V1.0

已有 6334 次阅读 2013-11-25 14:19 |个人分类:科研笔记|系统分类:科研笔记| Pymol

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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