A short primer on how to use MidasPlus


For some interesting ideas for images, check out the UCSF MidasPlus page.


Important Notes:

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1) Starting Midas

a) from the UNIX prompt
type "midas"

set window size to any you like


b) once inside Midas
notice some of the text (important later)

first, see the help on 'open' ("help open")

open a file " open 0 2hpr.pdb "

press each of the buttons on the mouse & move (then try left and center together)


c) the control panel
use the mouse in the "SideView" area to move eye position (the small square), move clipping planes, etc.

click on the line starting with "0" near the bottom of the control panel (OpenGL version; a small highlighted box in the GL version), try to rotate/move the molecule, then reactivate by clicking again

click on the small boxes under "Assignments" (OpenGL version; in the GL version, click on "Sliders") -- see how some of the boxes affect the view -- some of the same actions can also be controlled with the "SideView"


d) close the molecule & stop Midas
"close 0" (or "~open 0")

"stop"

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2) Getting/looking at molecules


Reopen the same molecule, but from the UNIX prompt
"midas 2hpr.pdb "


a) on-line help

"help" or "help command" or "help byfunction"

b) the chain command
read help first ("help chain", "help atom_spec")

"chain mainchain" displays only CA,C,N,O (backbone plus water oxygens)

now, try "chain @ca,c,n"

now, try "chain #0:15,17,46 @ca,c,n,o'


c) display/~display
read help again (quickly)

type "~display", then "display" (or use "~dis", "dis")

do "chain mainchain" again

get rid of waters "~dis :hoh" (sometimes called "wat" -- check PDB file) -- after the colon, you can either specify residue numbers or residue names

display a couple of side chains "dis #0:15,17,46"


d) show, ~show

see the help on 'show'

type "show :46,15,17@ca,c,n,o" and compare to results using the chain command as above

redisplay the entire protein ("display", "~display :hoh")


e) color

read help first....

"col yellow" -- color whole molecule yellow

"col byatom" -- color atoms according to element

"col red :15,17,46" -- color particular residues red

** See appendix for colors and associated numbers **


g) vdw command (& vdwopt)

read help on vdw

"vdw :15,17" -- draws dot surface

read help on vdwopt

"vdwopt density 3" changes the dot density

turn off with "~vdw"


h) savepos/reset

look at help for both commands find orientation you like then save it
"savepos name" (any name you like, and as many as you like)
now, move the molecule around... Then reset back to saved orientation
"reset name" (same name as above)
to get back to how the molecule looked when you first opened it:
"reset"


i) push/pop

similar to above, but without names -- see the help page....

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3) Useful utilities (modeling stuff)


a) atom picking & labeling
first, see the help on 'label'

for atom picking, hold the "Alt" key in and use the cursor -- to pick, press the left button. The name of the picked atom or atoms will appear in the command window.

This can be used in conjunction with other commands:

first, type "label " (add a space)

then, pick a couple of atoms,

then hit "enter"

the labels can be turned off (~label)


b) distance & angle measurements

the commands are either 'distance' or 'angle' -- see help

show distance between the OG of S46 & the CA of G49

"distance #0:46@og #0:49@ca"

"angle #0:46@n #0:46@ca #0:46@cb #0:46@og" shows the chi-1 of Ser46...

(shorter version of same command: "angle :46@n@ca@cb@og")

"~dist 0", "~angle 0", etc.


c) swapaa -- CPU site-directed mutagenesis

center residue 17 in the window with
" window #0:17 "
after looking at the help file for swapaa, try
" swapaa his,preserve #0:17 "


d) addgrp -- make Ser46 into P-Ser46

see the help page first

all available groups are in the appendix (with the directory location). They are text files, so you can view each of files...

to add a phospho group to a serine...

"addgrp phos3O,1.43,109.5,180 #0:46@og@cb@ca "


e) rotation

now, let's move it around to relieve bad contacts...

first, you need to assign some rotations

"rotation :46@ca :46@cb :46@og :46@p1" -- can try picking to enter this command

"rotation :46@og :46@p1"

("rotation :46@cb :46@og :46@p1 :46@o2" would activate the same torsion)

rotate the bonds using the corresponding "bondrot" boxes under "Assignments" (OpenGL version; in the GL version, click on the "Sliders" in the control panel, then move the sliders for the two assigned rotations).


f) watch/watchopt

see the help for 'watch' first -- similar to BUMP in Insight
to turn on - type "watch"
after turning on, move the two rotations set above to
watch the various bad contacts light up.

to turn off - type "~watch"

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At this point, go ahead and quit this session ("stop")... and open a new molecule


"midas 1poh.moved", display only the backbone "chain mainchain",
then display a couple of sidechains (change the colors if you like)


4) Rendering programs within Midas

a) "ribbonjr" -- for this command, see the 'man' page at the UNIX prompt, not the help page.

first, type "ribbonjr"...not very striking...in this case, there is no secondary structure listing in the PDB file (click on the image to exit).

type "ksdssp" to update this information (see the man page).

now type "ribbonjr"


useful options for ribbonjr (including file generation)

-F -- full screen

-b R,G,B(,R,G,B(,R,G,B)) -- background color (0 - 1)

-e 'command' -- execute UNIX command (e.g., scrsave on SGI's)

-x file -- change appearance of ribbon

-p -- don't wait for mouse click to exit; often used with the -e option

-a -- show only mainchain (even if other atoms are displayed in Midas)

-A # -- # is the scale factor of the VDW radius of displayed atoms

-B # -- # is the scale factor for bonds

-r # -- # is the refinement level (smoothness of spheres, see second example below)


try these:

"ribbonjr -F -b 0,1,0 -A 0.2 -B 0.1" (green background, small ball & sticks)

"ribbonjr -F -b 1,0,0,0,0,1 -A 1 -r 5" (red to blue fade with CPK-style atoms)

"ribbonjr -F -b 1,0,0 -x xs.rect (red background, different ribbon shape)

"ribbonjr -F -b 1,1,1 -e 'scrsave rib.rgb' -p"

(white background and generates an RGB image that can be viewed with "ipaste rib.rgb" from the UNIX prompt on SGI's)


b) conic/neon -- as with ribbonjr, more info is available on the 'man' page.
Both use the same program, but do different things. 'neon' makes a stick or ball & stick model, and 'conic' makes a CPK model (VDW-radius spheres). As a result, options shown below are usable for both. For the sake of speed, just display a small portion of the molecule:
"show #0:45-55",
then for fun, add a distance
"distance #0:46@og #0:49@n"
then try both "neon" and "conic".
"~distance 0"
removes the distance monitoring.


options at the command line include:

-F -- full screen

-c file -- read more options from a configuration file

-o outfile -- write out an image file

-s -- display the image (used only when an image is also written out to a file)

the configuration file has a number of options, including

background R G B (R G B (R G B)) -- background (as above)

eye R G B -- add a point light source of a specified color at the viewing position

output outfile -- write an image file (same as the -o command-line option above)


for example, try
"conic -c cfig1" (just a plain white background)

"conic -c cfig2" (same except adds 'eye' light source)

"conic -c fade" (fades the background)

** "conic -c cfig3"

(combination of the above, plus writes an RGB file called fade.rgb which can be viewed with 'ipaste' at the UNIX prompt on SGI's)

** the configuration file cfig3 is appropriate for version 2.1 of MidasPlus (1997 release); for version 2.0 use cfig3.old. The newer version writes TIFF files by default, and an additional line is needed to specify the SGI RGB format instead.

you can try using 'neon' instead of conic in the commands above


In addition, 'neon' uses its own file called 'neon.dat' which sets up a number of parameters. In this file, a number of options can be varied (like the backbone and sidechain stick thicknesses, depth cuing, the color of the distance dashes, and whether they are dashes at all). The location of the default file (which has the default parameters) is /usr/local/midas/resource/neon.dat, and can be copied to your own directory for customization. For now, just to see the possible differences try:

"neon -F -c fade"

copy the file neon.dat into the directory you started Midas from,

then redo the above neon command to see the differences...


c) 'rainbow'

rainbow is a 'perl' script that gradually colors the molecule from one end to the other - which is primarily useful when trying to either trace the chain, or trying to figure out what a particular atom is when things are too crowded for the atom picking.


First, display the whole molecule ("dis"), then type

"rainbow"


d) 'label3d'

(hard to use, but nice pictures) This is a delegate program which Midas passes commands to and receives commands from. It creates 3-dimensional labels (actually graphical objects) that can be rendered in 'ribbonjr' and 'neon'. 3-D labels are especially useful in complicated stereo views. The 'man' pages have examples (type "man label3d" to see a complete description).


e) 'noeshow'

is a 'perl' script that can be used to show NMR-derived distance and torsion angle constraints as well as hydrogens within a cutoff distance of a given hydrogen.

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5) Other neat stuff


a) alias
The 'alias' command allows lengthy commands with options to be aliased to a single word.

To alias a command, type "alias newcommand command".

To expand the alias (see the original command), type "alias newcommand".


b) other colors (cedit & colordef)

If you can't find a particular color, you can define one. First, use 'cedit' from the UNIX prompt (SGI's only). After getting the color you like, divide each of the numbers for red, green, and blue by 255.

in Midas, type

"colordef colorname R G B"
where R,G, and B are numbers between 0 and 1, obtained as described above. Then colorname can be used in coloring commands just like red, yellow, etc.


c) set, ~set

allow for customization of the display; the possible settings are given in the help page.

try the following:

"~set control"

"set control"

"set file"

"~set file"


d) record/source (records or sources files with commands)

Midas has the ability to record and play back commands from a text file. This becomes handy when there are a number of repeated commands, or a string of commands that is easier to edit with a text editor than typing in each command one at a time.

The file is simply a text file listing of Midas commands, and therefore can easily be written either with the 'record' command or by writing one with an editor of your choice. The file is then played back with the 'source file' command.

For an interesting display, try this:

"source midas-commands"
Jot or vi the file if you want to see which commands are being executed.


e) command recall and editing

These allow you to recall previous commands and edit them (e.g. if you mistype something). Some of the more useful ones are:

ctrl-p -- previous command

ctrl-n -- next command (after using ctrl-p)

crtl-f -- forward space without erasing

ctrl-b -- backspace without erasing

crtl-h -- backspace and delete

crtl-u -- delete the whole line

**in editing, all typing is inserted.

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6) More than one molecule


a) opening & viewing.
Everything is the same as above, but with multiple model numbers. At this point, with 1poh.moved already displayed as model 0,
type "open 1 2hpr.pdb"

Since the two molecules have somewhat different coordinates, the new structure may be out of the viewing window. This can be quickly remedied with the command "window".

Notice that now, two lines near the bottom of the control panel are occupied, one for each "model" (OpenGL; in the GL version there are two highlighted numbered boxes), and that both molecules rotate/translate in unison. By clicking on its line (or box), you can deselect or select a particular molecule for motion, that is, toggle it between movable and immovable states. This can also be accomplished with the commands 'select' and '~select' . However, for most of the display-oriented commands such as 'display' or 'color,' the selection of molecules has no effect.

All of the previously described commands apply, except that if you want to perform a particular function on just one of the molecules, the specification must indicate so. For example,

"col yellow :46" colors all residue 46's yellow, whereas

"col red #1:46" only colors residue 46 in molecule #1


b) overlaying molecules by using the 'match' command

typing "match" will match all the atoms in one molecule with all the atoms in the other. As you can see, this doesn't work well when one model as a lot of extra atoms (e.g. waters).


More useful versions would be:

"match #0:2-85 mainchain #1:2-85 mainchain" which aligns most of the backbones

"match #0:2-44,55-85@ca,c,n #1:2-44,55-85@ca,c,n" which matches selected parts of the backbones

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7) saving information -- check the help pages
a) "write filename.pdb" or "pdbrun cat > filename.pdb" (new PDB file with USER records)

b) "save session_name" (save views, etc.. for later work)

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8) Stuff outside of Midas worth knowing about -- check the 'man' pages


a) ksdssp, conic, neon & ribbonjr can be used outside of Midas
If you want all the colors, orientation and other aspects that you saw when viewing the molecule in Midas, then a PDB file should be written (using 'pdbrun' or 'write'). The USER records appended to the coordinates specify things like atom colors.


b) dms, esp & their options

'dms' calculates a molecular surface and reports the surface area

'esp' calculates the electrostatic potential on the molecular surface


c) image tools (on SGI's)

'ilabel' adds text labels to RGB images

'itops' converts a color RGB image to postscript for printing

'imgcopy' converts among image file formats

'imginfo' gives information on an image file (size, format, etc.)

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**APPENDIX**

Colors:

Because Midas assigns numbers to colors (primarily for shading/mixing of colors), a number of named colors are available.

The named colors and their associated numbers are: 

	# ---    color
	--------------
	0  ---   white
	1  ---   green
	8  ---   cyan
	16 ---   blue
	24 ---   magenta
	32 ---   red
	48 ---   yellow
	64 ---   black

An additional named color is gray. This system allows for gradual color changes (for example, "color 1-48 #0" will color the atoms in model 0 from green to yellow according to B-factor, with the other colors appearing the order above).

Groups that can be added:
from /usr/local/midas/resource/midas/groups/* 


   1-naphthyl      GLN             SER             h
   2-naphthyl      GLN.old         SER.old         i
   3-pyridine      GLU             SMe             iBu
   A               GLU.old         SO2CH3          iPr
   A.old           GLY             SO2F            ibu
   ALA             GLY.old         SO2NH2          indole
   ALA.old         H               SO2NHR          ipr
   ARG             HIS             SO2NR2          leu.con
   ARG.old         HIS.old         T               me
   ASN             HYP             T.old           myTRP
   ASN.old         I               THR             n
   ASP             ILE             THR.old         nbz
   ASP.old         ILE.old         TRP             nhcoch3
   BR              LEU             TRP.old         nn
   Bu              LEU.old         TYR             no2
   Bz              LYS             TYR.old         o
   C               LYS.old         U               obu
   C3H5Me2         MET             UNK             obz
   CC              MET.old         VAL             oc11
   CH2-2-THF       Me              VAL.old         oh
   CH2CN           N               br              ome
   CH2COCH3        NBz             bu              oph
   CH2CONH2        NHCOCH3         bz              opr
   CH2COO-         NN              c2h5me2         oxt
   CH2OCH3         NO2             carbon          p
   CHOHCH3         NPR             cc              ph
   CL              O               ch2-2-thf       phenol
   CN              OBu             ch2cn           phos
   COCH2PO3        OBz             ch2coch3        phos3O
   COCH3           OC11            ch2conh2        pr
   COLD            OH              ch2coo-         s
   CONH2           OMe             ch2och3         s-ph
   COO-            OPh             chohch3         sBu
   COPh            OPr             cl              sbu
   CYS             OXT             cn              sme
   CYS.old         P               coch2po3        so2ch3
   CYX             PHE             coch3           so2f
   Et              PHE.old         conh2           so2nh2
   EtCl            PRO             coo-            so2nhr
   EtOMe           PRO.old         coph            so2nr2
   F               Ph              et              tBu
   G               Pr              etcl            tbu
   G.old           S               etome           tempo
   GD              S-Ph            f


Other stuff (from man -k midas -- each has its own man page):


density (1) - Midas delegate for displaying formatted XPLOR electron density data

discern (1) - Midas delegate for visualizing multi-dimensional data

fixses (1) - update pre-MidasPlus 2.0 session files

gd (1) - a MidasPlus delegate which serves as an interface between MidasPlus and Peter Goodford's GRID program [1].

gentpl (1) - generate a MIDAS template from a Protein Data Bank coordinate file

label3d (1) - Midas delegate for displaying 3-D labels

makems (1) - Midas delegate for convenient generation of molecular surfaces

midas (1) - MidasPlus molecular interactive display program

midas.tty (1) - terminal based version of MidasPlus display program

midasman (1) - access midas manual pages

midasmaninst (1) - install manual page

mrotate (1) - Midas delegate for interpolating between orientations

pdb2group (1) - generate Midas group file from Protein Data Bank (PDB) file

pdbopen (1) - Midas delegate for browsing and opening PDB entries

ps2illustrator (1) - convert midas copy file (PostScript) to Adobe Illustrator format

run2ses (1) - convert a PDBRUN file into a Midas session

stereops2illustrator (1) - convert a stereo midas copy file (PostScript) to Adobe Illustrator format

viewdock (1) - Midas delegate for browsing DOCK output

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meng@cgl.ucsf.edu / July 1997