Frequently Asked Questions

Why can't I save an Image?

You probably didn't hit the `PrintScreen' key after the menus go away.

How do I save all the adjustments I've interactively set?

Hit 'Alt-z' to zero and save the three files below.
Use the `File' submenu from the `MenuBar':
Save Defaults -- to save all style and scale adjustment.
Save Materials -- to save any color adjustments
Save Orientation -- to save any viewing parameters

If you save `.matter', this will apply to all models in that directory the next time you start ribbons. If you save `YourModel.matter', this will apply to the model `YourModel'. Ditto for `.defaults' and `.orient' files.

If you think every user in your group should always use some particular settings, save, for example, `.matter' in the $RIBBONS_HOME/data directory.

How do I set the Background Color?

Use the Light Panel (alt-l), then adjust the sliders.

If you want black/white background: 1) select "View" sub-menu from the main menu.
2) select the toggle "White Background" (this is good for screen dumps to a printer) The next time it is selected, it should read: "Black Background"

How do I custom-color my Ribbon Model?

It depends: First read elsewhere - mail be if still stumped.
For each residue section in the ribbons, the `*.ss' file determines the ribbon's residue colors through a look-up table set in the `*.color' file . White is the default color if no look-up is set. Each chain may be set to a single color through the ribbons style panel. The different ribbon coloring schemes are also set with this panel.

How do I draw Hydrogen Bonds / Dashed Bonds?

Ribbons has no facilities for general H-bonding information. One command exists to write out MainChain H-bonds (the same as those computed to automatically determine secondary structure information with 'pdb-pro-ss'):

pdb-hb-cyl protein_chain.pdb mainchain_hb.cyl

The output 'mainchain_hb.cyl' is an ascii ribbons-style bond file, with the bonds from the carbonyl O to the amide H.

For general H-bonds, I have used either 'X-PLOR' or 'hbcalc'.

Usually, you would just like a few selected H-bonds for an image. It is probably fastest to just do this by hand editing. Recall, my special cylinder file format is:

x.1 y.1 z.1 x.2 y.2 z.2 rad.bond kolorIndex

To create 'dotted' bonds with ribbons:

If you just want dashed lines, use the Bond Panel Editor (alt-b), set the draw style to `lines', and adjust the complexity. If you want dashed cylinders, you must create a file with lots of short little cylinders. There is a little awk file to accomplish this. You may want to copy a version over and edit to adjust the 'DASH' variable if the pattern is not to your liking. 

   cp $RIBBONS_HOME/misc/awks/dash-cyl.awk your.awk
   awk -f your.awk < normal.cyl > dashed.cyl

How do I draw Disulphides?

Currently, must get the ribbon just how you like it, then create a special *.cyl file from Menubar File, Export Ribbons Files, SG-bond. This links ribbon to SG to SG' to ribbon'. Then include this *.cyl file in your *.bonds list. May also want to make a *.sph file of just the SG atoms for prettiness.

All my secondary structure keys don't show up?

The default "Sequence color" options in ribbons displayed on the menu are set to those in common and in order at the top of the *.ss files. These options are available to be applied to all the ribbon models at once. However, all of the *.ss keys are available on a per ribbon basis.

Examples: (1) The user has added a custom coloring scheme for two protein chains, A & B. The tops of the *.ss files are listed below: 

 Protein A (Astuff added)
 res# seq  ss sshb hb  Astuff
   15   V   c   c   O    X
	.....

 Protein B (Bstuff added)
 res# seq  ss sshb hb  Bstuff
    1   G   c   c   x	 Y
	.....
The default Sequence color options will be: "seq" "ss" "sshb" "hb" Solution: name the key in both "stuff".

(2) The user has a protein chain and a nucleic acid chain. There is more information for the protein generated by the *.ss programs, and the user has added extra information for each. 

 Protein (xtra added to mark binding site)
 res# seq  ss sshb hb   xtra
    1   G   c   c   x	 N
	.....

 DNA     (xtra added to mark binding site)
 res# seq  ss  xtra
    1   C   S   Y
	.....
The default Sequence color options will be: "seq" "ss" Solutions: Hack - add dummy "sshb" & "hb" columns to the DNA.ss file before you add the "xtra" column.

*** Note: *** In either case above, you can always set the individual *.ss color. Take the second example: Open the Ribbons Style panel, select "Ribbon Lists" (which should say "coord" by default, indicating that any changes you make to any of the widgets apply to EVERY ribbon model). You should see "coord", "Protein", & "DNA". Select "Protein", then select "xtra" with the Sequence Color widget (here you will see every field in Protein's *.ss file listed). Then select "DNA", and again select "xtra" with the Sequence Color widget (here you will see every field in the DNA's *.ss file listed).

Ribbons User Manual / UAB-CMC / carson@cmc.uab.edu