Why can't I save an Image?
You probably didn't hit the 'PrintScreen' key on your SGI after the menus go away.
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.
If you want black/white background:
1) select "View" sub-menu from the main menu.
This is the one I got (that worked on sgi,mac - was already on linux,mac):
Then, after the simple: configure; make; make install
The command '
pdb-range-ss
' easily creates custom *.ss files:
pdb-range-ss original.ss custom.ss
But remember, here the coloring is by a character (not integer!) code.
The custom.ss file created must then be used (along with any special *.color
file) in your *.ribbons file.
You must then interactively choose your new coloring scheme through the
ribbons style panel option menu:
Sequence Color.
The initial value is 'ss' to color by secondary structure.
Select choices from columns in the *.ss file to color-code
on a variety of per-residue modes. 'range' is the default column name
created by the pdb-range-ss command.
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/CNS' 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
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.
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:
(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.
*** 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).
See these hints in Help for the
Ribbon Dimensions.
Suggestions: set style/dimensions for 'helix' to be same as 'coil'.
Adjust 'Helix Shift' (on dimensions panel) - negative values can force
the ribbon to 'hide' inside of cylinders fit to helices. (try -1.5)
Please note the ribbon will not in general come out of the end circle
of your cylinder - this just doesn't make sense structurally.
However, see the command 'pdb-geom-pdb'
under Model Data preparation.
You can make a fake set of C-alphas that will mimic this bit of
cartooning. Then you must edit your *.ss file to turn 'H' into 'c'.
If you have only coils and helices, try the wavelet approximation.
For the MRC wavelet analysis, first set the ribbons style to Circle,
and set dimensions of width==depth, then toggle on. It will prompt for
input, and initiallization may take a while for large proteins.
Play with the level & watch. Still experimental.
MRC stands for Multi Resolution Curves (see
Wavelets and Molecular Structure on my web site.)
Here's a nice example from Krishna Murthy's
latest apolipoprotein structure:
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
How do I set the Background Color?
Use the Light Panel (Alt-l), then adjust the sliders.
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"
ribbons-data doesn't work?
You must get/install the latest version of Tcl/Tk - version 8.0 or higher.
(it's an old one by default on your sgi).
www.scriptics.com/software/tcltk/8.0.html
you have to make sure that the new one is in your path (type 'which wish').
'ribbons-data' expects the executable to be in '/usr/bin', so as root:
cd /usr/bin; ln -s /wherever/it/is/wish wish
How do I custom-color my Ribbon Model?
It depends: First read elsewhere - mail me if still stumped.
You must first cusomized your *.ss file. Some background:
For each residue section in the ribbons, the
'*.ss' file
determines the ribbon's secondary structure and residue colors
through a look-up table set in the
'*.color' file .
White is the default color if no look-up is set.
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'):
To create 'dotted' bonds with ribbons:
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.
How do I draw bonds off proteins? Ladders on DNA?
Currently, must get the ribbon just how you like it,
then create a special *.cyl file from Menubar File.
See the examples under
Export Ribbons Files.
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.
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".
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.
How do I make the ribbon fit the helices-as-cylinders better?
Make sure the residue ranges make sense - if you have a bent helix,
you may need to use 2 ranges. If it is curved, see wavelets below.
Set the cylinder radius to 1.0 when you create them from the ranges,
instead of the 0.15 default radius for simple bonds.
Scale and set complexity (smoothness) with the
Bond Panel as desired.
