ModView. Copyright 2000, 2001 by Valentin Ilyin and Andrej Sali.
Modview was written at The Rockefeller University.
Any selling of the original or a modified program or its parts
is prohibited without a written permission from the authors.



  ModView help. (under construction) 

        Quality Print -> just use Print button from Netscape menu.
         (Save postscript option in menu works as usual Rasmol quality)

        ModView accept majority of Rasmol coomands.
  
	Modified commands.
	
   'select' and 'restrict' -> the command is changed to include molecule number
                              (moelcules numbered from 0)

   	Examples:
>select @3            	-> all atoms in molecule 3 are selected
>select @2 11,23,234 	-> all atoms in residues 11, 23, 234 from molecule 2
			are selected
>restrict @1 34-54A	-> only atoms of residues in range from 34 to 54
			in molecule 1 chain A will be shown.

	
	New commands.

*)   'body' or 'molecule' -> to assign molecule to manipualte.
	Examples:
>body @2   	-> molecule 2 assigned.
>molecule all   -> all molecules moves together

*)    'freeze' and 'unfreeze'  -> to (un)freeze position only one molecule
	Examples:
>freeze @9
>unfreeze @8

*) 	'hide' and 'visible' -> to hide or display particular molecule or
				chain
>hide @3	-> molecule 3 will not be shown on display
>visible @3 chain A -> chain A from molecule 3 will be displayed.


*)	'plugin: color by molecule' -> use different colors to display molecules
*)	'plugin: color by common' -> color sequences and strucures according
to alignment in ali-window, common parts and insertion by differnt color.

*)	'plugin: align by common' -> fit molecules according to the alignment
in ali-window.

*)	'plugin: align by average' -> try to fit molecules using sequence and
structure information. The module is using similar to align3d algorithm. 
It does several cycles of fitting (max=20) try to maximize number of fitted
residues at certain cutoff (3.5 A), and use initial sequnce alingment as
starting point.

*) 	'plugin: main chain' -> show only main chain atoms of selected residues

*) 	'plugin: main and CB' -> show only main chain and CB atoms of selected residues

*)	'plugin: hide sliders' and 'plugin: show sliders' -> hide or show
control panel.


How to call ModView from web page.

Example 0: To have modview called automatically you have to embed it. Only one
parameter 'type' shoud be specified.
this is the only you have to include in your internet page
<EMBED  type=chemical/x-pdb> 

Example 1: But, usually people also include at least  width and height, as by default
the display can be really small. Width and height can be in persentage of
the page 
<EMBED type=chemical/x-pdb width=100% height=100%>
or in exact number of points
<EMBED type=chemical/x-pdb width=500 height=500>

When modview is loaded you can load coordinate or alignment file(s) using
skymol structure menus (click right button on mouse and dont move it).
If there is a structure you want to load automatically, you have to specify
value 'src' as local file name or internet address.
Example 2:
...
<EMBED type=chemical/x-pdb 
     src="1crn.pdb"
     width=100% height=100%>
...
or
...
<EMBED type=chemical/x-pdb 
     src="http://piano.rockefeller.edu/1crn.pdb"
     width=100% height=100%>
...

                            
To include alignment file when you initially call modview, 2 varialbes
should be set, alignment="you-alignment-file" and aliformat="PIR".
alignment file can also be your loacal file or http address.
                            
<EMBED type=chemical/x-pdb 
     alignment="a.ali"
     aliformat="PIR"
     width=100% height=100%>

modview automatically load alignment file and also look for corresponding
PDB coordinates if 4-letter code is set
in the alignment file (PIR: second field in second line, 4-letter code).
3d field used as first residue number in the alignment
4th chain ID
5th last residue number 
6th chain ID
And text on first line after >P1; goes directly to ali-window as name for
the sequence. 

To have control on modview by using Javascript object, like buttons,menus,
applets and so on, you have to specify variable 'name', any name convinient
for you can be used, but you should use the same name in Javascript objects.

<EMBED type=chemical/x-pdb
       name="modview1" 
       alignment="http://localhost/tmp/a.ali"
       aliformat="PIR"
       width=100% height=100%>
                                   
<form>
<input  type=button value=" one " 
    onclick='document.modview1.executeScript("ribbons on")'>
</form>
       
modview also has option to read initial script and excute it when it calls.
Many command can be included in one script by including them in [][].
or separate by ';' NOTE: it is better to use [] for almost all commands,
except 'plugin: *', which is better to separate by ';' .
Example:
[wireframe 20][spacefill 70];plugin: color by common;[select @1 23,24][color red]


    Alignment file.
    
    ModView uses PIR format for the alignment files, it can read many other
formats, but to similtanuously load structures only PIR format is specified yet.
You may look at Examples on main page to see how to do it, or read next.

    On first line first word after '>P1;' used to identify sequence in the
ModAlign alignment window. 

    To automatically load structures use second line in alignment file.
    
Second field in second line is 4-letter PDB code, (check the case!) 
3rd field is first residue number in the aligned sequence.
4th is chain ID of the sequence,
5th field is last residue number in the aligned sequence.
this numbers is important as usually only part of the sequences is present
in the alignment, while the whole sequnces is read from PDB structure.


>P1;5fd1
structureX:5fd1:   1 : : 106 : :ferredoxin:Azotobacter vinelandii: 1.90:0.192
AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA
EVWPNITEKKDPLPDAEDWDGVKGKLQHLER*

....



	Configuration file.

   ModView look in your home directory for file .skymol and if it present
ModView reads varibles from it.

PDBDIR to set pdb directory, where ModView will look for file(s) by pdb code,
by default it is http://pipe.rockefeller.edu/pdbdb/ 
(if .skymol file is not present or PDBDIR is not present in the file).
   All pdb files use mask pdbXXXX.ent


Example.

#  configutarion file

PDBDIR http://pipe.rockefeller.edu/pdbdb/
# for local dirs the full path should be set, like in the next line
# PDBDIR /home/valya/tmp/1/mypdbset/test/