MacInPlot

jean-yves sgro sgro at rhino.bocklabs.wisc.edu
Mon Nov 1 19:03:25 EST 1993


I just received the latest version of Tom Smith's MacInPlot 
[Macintosh ONLY] and the new features, that are so nice that
I cannot resist but post his week-end's note to me.

Tom added a Ramachandran plot option less than a month ago as well.
This program is also extraordinarily good to create quicktime
movies "on the fly" or to animate molecules right there on the
screen!

His new PDB file handling is really  nice because you can now connect
to the Protein Data Bank via anonymous ftp at  pdb.pdb.bnl.gov [130.199.144.1]
grab a file and visualize and/or animate it within minutes on your
desktop!!!!!!

To obtain his program just look into my anonymous site in /pub/MacInPlot
[see Internet addess in signature below!]

Congratulations TOM!

Here is the list of improvement just made [I just reproduce his note:]


Dear Jean,
        The latest version of MacInPlot is in your area.  
I took your advice about the preference file.  The user can
now write out a separate file...
The new stuff is...

1)      'Depth Sort(SLOW)' in the 'Drawing' menu:  Sorts all vectors so that thevectors in front are on top of all of the vectors towards the back. 
Includes ALL objects and labels in the sorting process.  NOW the depth
cueing looks good!

2)      'Preferences' in the 'Drawing' menu:  I put some of the more obscure
menu items into this preference file such as stereo and such.  The first
time the program is launched, it assigns default values.  Upon quitting, it
writes out a preference file to the system folder.  The user has the option
to write out their own preference file in a separate location if they wish
to.

3)      In the 'Preferences' in the 'Drawing' menu there is now an option called'Idiot Dialog boxes'.  This is the beginning of further changes.  This
allows a naive user to not know anything and get a drawing.  For now,
selecting this allows a user to read in a PDB file and not answer any
questions.  I determine the number of atoms in the file and set everything
else for a 'typical' conversion.  Gets rid of all of the dialog boxes in
this option.  Will be expanding this option to the Mol creating options as
well.

4)      'Depth Sort with others' in the 'Ribbon' menu:  The user now has the
option to include the ribbon drawing in the sorting routine.  For example,
you can make a ribbon drawing of hemoglobin and 'color atom' mol objects
for the heme groups.  With this option selected, the mol objects are
occluded by the ribbons which are in front of the heme groups making the
heme appear to be 'nestled' amonst the ribbons.  This enhances the depth
perception of even mono images.

5)      When 'Depth Cue' is selected, the program does not just fade the image
to black.  The program determines the color of the background and fades the
objects to that color--also known as 'fogging' out.

6)      Cleaned up and starting to re-organize the menu.
Path: rhino.bocklabs.wisc.edu!sgro
Newsgroups: bionet.virology
Distribution: world
Followup-To: 
From: sgro at rhino.bocklabs.wisc.edu (jean-yves sgro)
Organization: Inst.for Virology, Univ. of Wisconsin-Madison -USA-
Subject:MacInPlot 
Keywords:3D,protein 

I just received the latest version of Tom Smith's MacInPlot 
[Macintosh ONLY] and the new features, that are so nice that
I cannot resist but post his week-end's note to me.

Tom added a Ramachandran plot option less than a month ago as well.
This program is also extraordinarily good to create quicktime
movies "on the fly" or to animate molecules right there on the
screen!

His new PDB file handling is really  nice because you can now connect
to the Protein Data Bank via anonymous ftp at  pdb.pdb.bnl.gov [130.199.144.1]
grab a file and visualize and/or animate it within minutes on your
desktop!!!!!!

To obtain his program just look into my anonymous site in /pub/MacInPlot
[see Internet addess in signature below!]

Congratulations TOM!

Here is the list of improvement just made [I just reproduce his note:]


Dear Jean,
        The latest version of MacInPlot is in your area.  
I took your advice about the preference file.  The user can
now write out a separate file...
The new stuff is...

1)      'Depth Sort(SLOW)' in the 'Drawing' menu:  Sorts all vectors so that thevectors in front are on top of all of the vectors towards the back. 
Includes ALL objects and labels in the sorting process.  NOW the depth
cueing looks good!

2)      'Preferences' in the 'Drawing' menu:  I put some of the more obscure
menu items into this preference file such as stereo and such.  The first
time the program is launched, it assigns default values.  Upon quitting, it
writes out a preference file to the system folder.  The user has the option
to write out their own preference file in a separate location if they wish
to.

3)      In the 'Preferences' in the 'Drawing' menu there is now an option called'Idiot Dialog boxes'.  This is the beginning of further changes.  This
allows a naive user to not know anything and get a drawing.  For now,
selecting this allows a user to read in a PDB file and not answer any
questions.  I determine the number of atoms in the file and set everything
else for a 'typical' conversion.  Gets rid of all of the dialog boxes in
this option.  Will be expanding this option to the Mol creating options as
well.

4)      'Depth Sort with others' in the 'Ribbon' menu:  The user now has the
option to include the ribbon drawing in the sorting routine.  For example,
you can make a ribbon drawing of hemoglobin and 'color atom' mol objects
for the heme groups.  With this option selected, the mol objects are
occluded by the ribbons which are in front of the heme groups making the
heme appear to be 'nestled' amonst the ribbons.  This enhances the depth
perception of even mono images.

5)      When 'Depth Cue' is selected, the program does not just fade the image
to black.  The program determines the color of the background and fades the
objects to that color--also known as 'fogging' out.

6)      Cleaned up and starting to re-organize the menu.

7)      Wrote a conversion for the new style O plot files (5.9).

8) Stupid mistake... When the user wants to write over a file 
with the same name, before it hit an error.  Now I detect the
error, and delete the old file first -- hence writing over the
file after the user has been warned about it first.


Future....
1) Show neigbors.  Draw lines and distances to nearest neighbors.
Distances will be set in preference file

2)  Do rendered barrels and ribbons.

3)  More idiot options.

4)  Mouse directed rotations.

5)  Set light source and reflections for current ribbon diagrams
(have algorithm mentally written, just no time to debug it)

What do you think?  Thanks for the bionet stuff.

Talk to you later,
Tom

Dear Jean,
        The latest version of MacInPlot is in your area.  
I took your advice about the preference file.  The user can
now write out a separate file...
The new stuff is...

1)      'Depth Sort(SLOW)' in the 'Drawing' menu:  Sorts all vectors so that thevectors in front are on top of all of the vectors towards the back. 
Includes ALL objects and labels in the sorting process.  NOW the depth
cueing looks good!

2)      'Preferences' in the 'Drawing' menu:  I put some of the more obscure
menu items into this preference file such as stereo and such.  The first
time the program is launched, it assigns default values.  Upon quitting, it
writes out a preference file to the system folder.  The user has the option
to write out their own preference file in a separate location if they wish
to.

3)      In the 'Preferences' in the 'Drawing' menu there is now an option called'Idiot Dialog boxes'.  This is the beginning of further changes.  This
allows a naive user to not know anything and get a drawing.  For now,
selecting this allows a user to read in a PDB file and not answer any
questions.  I determine the number of atoms in the file and set everything
else for a 'typical' conversion.  Gets rid of all of the dialog boxes in
this option.  Will be expanding this option to the Mol creating options as
well.

4)      'Depth Sort with others' in the 'Ribbon' menu:  The user now has the
option to include the ribbon drawing in the sorting routine.  For example,
you can make a ribbon drawing of hemoglobin and 'color atom' mol objects
for the heme groups.  With this option selected, the mol objects are
occluded by the ribbons which are in front of the heme groups making the
heme appear to be 'nestled' amonst the ribbons.  This enhances the depth
perception of even mono images.

5)      When 'Depth Cue' is selected, the program does not just fade the image
to black.  The program determines the color of the background and fades the
objects to that color--also known as 'fogging' out.

6)      Cleaned up and starting to re-organize the menu.

7)      Wrote a conversion for the new style O plot files (5.9).

8) Stupid mistake... When the user wants to write over a file 
with the same name, before it hit an error.  Now I detect the
error, and delete the old file first -- hence writing over the
file after the user has been warned about it first.


Future....
1) Show neigbors.  Draw lines and distances to nearest neighbors.
Distances will be set in preference file

2)  Do rendered barrels and ribbons.

3)  More idiot options.

4)  Mouse directed rotations.

5)  Set light source and reflections for current ribbon diagrams
(have algorithm mentally written, just no time to debug it)

What do you think?  Thanks for the bionet stuff.

Talk to you later,
Tom
this option.  Will be expanding this option to the Mol creating options as
well.

4)      'Depth Sort with others' in the 'Ribbon' menu:  The user now has the
option to include the ribbon drawing in the sorting routine.  For example,
you can make a ribbon drawing of hemoglobin and 'color atom' mol objects
for the heme groups.  With this option selected, the mol objects are
occluded by the ribbons which are in front of the heme groups making the
heme appear to be 'nestled' amonst the ribbons.  This enhances the depth
perception of even mono images.

5)      When 'Depth Cue' is selected, the program does not just fade the image
to black.  The program determines the color of the background and fades the
objects to that color--also known as 'fogging' out.

6)      Cleaned up and starting to re-organize the menu.

7)      Wrote a conversion for the new style O plot files (5.9).

8) Stupid mistake... When the user wants to write over a file 
with the same name, before it hit an error.  Now I detect the
error, and delete the old file first -- hence writing over the
file after the user has been warned about it first.


Future....
1) Show neigbors.  Draw lines and distances to nearest neighbors.
Distances will be set in preference file

2)  Do rendered barrels and ribbons.

3)  More idiot options.

4)  Mouse directed rotations.

5)  Set light source and reflections for current ribbon diagrams
(have algorithm mentally written, just no time to debug it)

What do you think?  Thanks for the bionet stuff.

Talk to you later,
Tom



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