***Phil likes to give me some credit for this-but he wrote this mainly in response to me asking him a lot of questions and things he didn't know we worked out together.-Bill
POV4GRASP is a great little program that allows you to convert grasp molecular surfaces files into povray output. Povray allows you to control every aspect of your figure-which makes it a very powerful graphics rendering program. The pov4grasp home page is: http://pov4grasp.free.fr/index.php
According to the authors, the best way to make a "Good GRASP molecular surface" is to do the following when setting up GRASP.
Now you can construct high quality molecular surface with much more triangles. Before using any construction method (such as Build Molecular Surface or the Surf_Charge_PB_Interpolate macro), you have to set the minimum surface resolution required.
Try at least 1.5 or 2, and increase this value until you obtain a surface of about 200,000 triangles for instance.
Now your set to use GRASP
About half of the trivial operations in GRASP can be done using the pulldown menu. Press the right button and rummage around for the desired option. However in order to do anything more elaborate you will have to use the GRASP command line language, which is unparalleled in it's terseness. This tutorial is some sort of attempt to give you an idea of how to do simple things in GRASP, and handle some of the command-line syntax.
In what follows, anything that looks like Read->PDB File->Show List is a menu traversal (PDB File option within the Read menu, Show List option within the PDB File menu). Menu selections/traversal are handled using the right mouse button.
GRASP pops up with a graphics window and a small terminal window. Arbitrary text typed into the terminal window will be ignored, just to frustrate you.. There's a trick to getting command text accepted, and we'll talk about that later (for the impatient: type the FIRST character of the command over the graphics window, type the rest of the command in the text window once it pops up).
Read your PDB file using the menus. Click the right mouse
to bring up the menu. Traverse the menu Read->PDB File->Show
List, select your PDB file. GRASP displays it as CPK. You can
hide the CPK using:
Display->Hide->Atoms
and restore then using:
Display->Show->Atoms->YES!
and you can show the bond representation by:
Display->Show->Bonds->YES!
(and Display->Hide->Bonds to get rid of them)
You can manipulate the molecule (rotation) using the left mouse button. GRASP also responds to the dials on the SGI.
To display surface curvature, first build the molecular surface, then Calculate->Surface Curvature->All Surfaces->All Atoms. The coloring scheme can be tweaked by moving the mouse arrow over the coloring bar and using the left and middle mouse buttons to change the values associated with that color.
One of the basic tricks is to understand that you can color the residues any way you feel inclined, and then color the surface using the atom color. In order to do this ;ast step you need to issue the command vc=a (vertex color = atom color). To issue this command, put your mouse over the graphics window and type the first letter of the command "v". The text window will pop up and let you type the rest of the command "c=a". GRASP executes the command "vc=a". Although this seems like the dumbest user interface idea known to mankind, this is actually how GRASP handles user text input. If GRASP seems not to respond to things you type at the textport, you've probably forgotten to type the first character in the graphics window. Note that you don't type the "v" twice - GRASP copies it from the graphics buffer to the text buffer.
Coloring: the command c=N (N is an integer) causes the atoms to be colored according to color N (see below for the definitions). The related commands vc=n, bc=m, kc=n, ic=n set the colors for surfaces bonds, backbone boxes and pair-wise interactions. Setting the color to zero makes the object disappear. vc=a colors the surface from the atom color.
Subsetting atoms: the command a=string selects only those atoms that match "string". E.G. a=oe1 selects atoms "oe1" or "OE1", a=oe? selects "oe1", "OE1", "oe2" and "OE2". a=ba selects backbone atoms. a=sch selects non-backbone atoms (a=-ba does the same thing). an=n selects a range of atom numbers e.g. an=(1,500) selects the first 500 atoms. For obvious raasons this is not the most useful command.
Subsetting residues: the command r=string selects only those residues that match "string". E.G. r=lys selects residues "lys" or "LYS". r=crg selects residues that are formally charged (Lys, Arg, Glu, Asp). r=hyd selects hydrophobic residues. r=pol selects polar resides. You can always negate the selections (r=-hyd, r=-pol). rn=num selects the residue number E.G. rn=245 and can also include a range E.G. rn=(245,247). You can also specify a chain via ch=a.
You create atom colorings by combining these commands with a comma as a separator:
ch=a,c=2 colors all of chain A red (color 2) r=hyd,c=3 colors all hydrophobic residues green (color 3) vc=a map the color changes to the surface
Other commands that we have little or no use for include:
| Command | Meaning |
|---|---|
| q | Assigned charge |
| R | Assigned radius |
| p | Assigned potential |
| x | PDB x coordinate |
| y | PDB y coordinate |
| z | PDB z coordinate |
| X | Screen x coordinate |
| Y | Screen y coordinate |
| Z | Screen z coordinate |
| m | Molecule number |
| S | Acc. surface area |
| d | Distance |
| cd | Assigned color |
| vn | Vertex number |
| C | Surface curvature |
| s | Surface number |
| Index | Color | Red | Green | Blue |
|---|---|---|---|---|
| 1 | White | 255 | 255 | 255 |
| 2 | Red | 255 | 0 | 0 |
| 3 | Green | 0 | 255 | 0 |
| 4 | Blue | 0 | 0 | 255 |
| 5 | Magenta | 255 | 0 | 255 |
| 6 | Cyan | 0 | 255 | 255 |
| 7 | Yellow | 255 | 255 | 0 |
| 8 | Gray | 125 | 125 | 125 |
| 9 | Orange | 200 | 100 | 50 |
The next 9 colors are accessed by the space bar, and so on, and so on. User colors can be defined in the range 10-89. Colors 91-99 are always reset to the values above for 1-9 irrespective of defcol.dat.
To preserve session_record, copy it while GRASP is running or kill the program with ^C. The file looks like this:
GRASP HISTORY FILE Wed Sep 18 11:35:40 2002 DRAW DRAW Menu Cascade Begin menu :GRASP | Build menu :This Structure.. | Molecular Surface menu :Which Atoms | All Atoms Menu Cascade End DRAW ROT: Z= 15.945408 ROT: Y= 2.886174 ROT: Z= -15.945408 DRAW ROT: Z= 15.945408 ROT: Y= 5.096077 ROT: Z= -15.945408 DRAW ROT: Z= 40.426113 ROT: Y= 20.299999 ROT: Z= -40.426113 DRAW ROT: Z= 38.893940 ROT: Y= 22.961708 ROT: Z= -38.893940 DRAW ROT: Z= 31.195120 ROT: Y= 24.579870 ROT: Z= -31.195120 DRAW ROT: Z= 30.524588 ROT: Y= 10.335376 ROT: Z= -30.524588 DRAW ROT: Z= 33.281906 ROT: Y= 7.000000 ROT: Z= -33.281906 DRAW ROT: Z= 33.743591 ROT: Y= 0.700000 ROT: Z= -33.743591 DRAWThe ROT lines describe the molecular orientation. Note that these are absolute angles not relative ones so if you are looking for a specific orientation you can chop out all the intermediate ones. Notice also than any menu action is also included in the file, and GRASP can recreate that action from this description.
To create a macro from the session file you need to add Macro Name: mymacro at the top of the file and Macro End as the last line in the file. Chop out the header lines that say "GRASP HISTORY FILE" and give the date - you don't want those. Then you can edit out what you want in the macro and what you don't want in there. To get GRASP to run the macro, do:
grasp -rx grasp.macro(assuming you called the file grasp.macro) and GRASP will execute the contents of the file. Watching it do the intermediate rotations is fun at first, but it's a lot faster if you get rid of unnecessary ROT and DRAW lines once you start tweaking the macro.
Example GRASP Macro File:
Macro Name: mymacro Thu Apr 17 18:33:38 2003 DRAW DRAW DRAW Menu Cascade Begin menu :GRASP | Miscellaneous menu :MISCELLANEOUS | Toggle cross hairs on and off Menu Cascade End DRAW Menu Cascade Begin menu :GRASP | Read menu :Read Submenu | PDB File menu :Enter/List | Show List menu :PDB LIST | aligned_integrin.pdb Menu Cascade End DRAW Menu Cascade Begin menu :GRASP | Display menu :Display Action | Hide ALL Menu Cascade End DRAW Menu Cascade Begin menu :GRASP | Display menu :Display Action | Menu Cascade End Menu Cascade Begin menu :GRASP | Build menu :This Structure.. | Molecular Surface menu :Which Atoms | All Atoms Menu Cascade End DRAW Menu Cascade Begin menu :GRASP | Display menu :Display Action | Show menu :STRUCTURE | Molecular Surface menu :Default Settings? | YES! Menu Cascade End DRAW ROT: Z= 180.000000 ROT: Y= 1.400000 ROT: Z= -180.000000 DRAW line :c=6; rn=18; a=sch line :c=6; rn=21; a=sch line :c=6; rn=93; a=sch line :c=6; rn=111; a=sch line :c=6; rn=156; a=sch line :c=6; rn=159; a=sch line :c=6; rn=122; a=sch line :c=6; rn=120; a=sch line :c=6; rn=121; a=sch line :c=6; rn=154; a=sch line :c=6; rn=179; a=sch line :c=6; rn=221; a=sch line :c=6; rn=219; a=sch line :c=6; rn=245; a=sch line :c=6; rn=249; a=sch line :c=6; rn=224; a=sch line :c=6; rn=278; a=sch line :c=6; rn=275; a=sch line :c=6; rn=272; a=sch line :c=6; rn=273; a=sch line :c=6; rn=271; a=sch line :c=6; rn=301; a=sch line :c=6; rn=309; a=sch line :c=6; rn=299; a=sch line :c=6; rn=399; a=sch line :c=6; rn=400; a=sch line :c=6; rn=401; a=sch line :c=6; rn=427; a=sch line :vc=a DRAW ROT: Z= 1.974936 ROT: Y= 0.700000 ROT: Z= -1.974936 DRAW Macro End
| ^A | Toggle active subset rotations |
| ^B | Toggle color scale widgets |
| ^C | Change current map (^C over textport kills program) |
| ^F | Toggle full screen view |
| ^L | Fix/free light source |
| ^M | Toggle texport depth (RETURN also does this) |
| ^O | Toggle GRASP boundary box display |
| ^P | Bring up color palette (see above) |
| ^Q | Quit |
| ^U | Toggle unhooking of dials |
| ^V | Repair surface |
| ^X | Toggle cross hairs |
| ^Z | Launch Unix shell |