PostScipt files produced by Molecular Modeling Systems
- From: jkl;at;ccl.net
- Subject: PostScipt files produced by Molecular Modeling
- Date: Wed, 11 Sep 91 15:06:48 EDT
I produced PostScript Files made by plot commands of Insight, Quanta and
(note, that I listed them alphabetically) from Biosym, Polygen and Tripos
respectively. All were latest versions for Iris 4D70. I wanted to include
them in the TeX paper I am writing. TeX (and all other programs
which import PostScript pictures into documents) require the EPS file
(Encapsulated PostScript File).
None of the packages mentioned produce the EPS file.
It is usually easy to produce the EPS file from any PostScript
file, assuming that the PostScript files are written with basic
adherence to generic PostScript rules (yes, I mean it). There are
several basis rules:
1. Use Adobe-2.0 standard
2. Use Header comments (e.g. %%BoundingBox: llx llu urx ury)
3. Never ever use initxxxx commands (i.e., initgraphics, initclip,
4. Do not use anything from statusdict
5. Do not leave anything on the stack
My preliminary analysis of PostScript files produced by all the 3 packages
is that their Postscript may not make them that much proud.
The Biosym postscript %%BoundingBox dimensions are just dimensions of
the whole page instead of the actual picture. I have to print the picture,
take the ruler and find the bounding box myself. I have to measure
the binding box myself in inches and then multiply them by 72.
| urx |
| llx *** ^ |
|<--->*** | |
| *** | |
| ^ ury|
| |lly | |
| | | |
Then I have to edit the Biosym PostScript file by adding %%Boundingbox
header comment and deleting initgraphics command at the top of PostScipt file.
Then I have to change the beginning of the file from:
And it works then. I think that Biosym files are the ones which you can
convert to EPS file format at a resonable expense of your time.
HOWEVER !!! You cannot legally use them. They contain a record
%%Creator: RRT. Copyright (C) 1989 BIOSYM
at the top, which says that you cannot reproduce pictures made by
Biosym Software (do not laugh --- this is exactly what it says). I am not sure
if BIOSYM is serious about it and waits until we publish enough pictures
and then they will sue us all, or maybe they have this big red rubber stamp
and they put "Copyrighted" on anything.
The Postscript files produced by Sybyl by Tripos Assoc. are, to say mildly,
strange. They include the header:
Which means: "Hi, we are Encapsulated Postscript", and the first sight
they are not, since they:
1. do not include %%BoundingBox header comment
2. they include: initclip and initmatrix. Deleting these commands
ruins your picture. Keeping them in, prevents you from scaling and
positioning the picture in your document
They make nice pictures, but the only way you can include them in your
document is by using scissors. Moreover, they are not copyrighted.
The QUANTA does not plot what is on the screen, but gives you a limitted
menu of what you can print (i.e., no maps, no fancy stuff, just simple
molecular images). For this reason it is of limitted utility to me.
However, they are easily converted to EPS files:
1. Change first line to: %!PS-Adobe-2.0 EPSF-1.2
2. find a BoundingBox by measuring a picture as
described above and put as the second line a header comment, e.g.:
%%BoundingBox: 0 0 612 792
3. Delete initgraphics command at the top of the file.
After doing this the pictures scale and can be moved on the document page.
DOES ANYBODY KNOWS HOW TO MAKE THIS EASIER ?
CAN WE GET SOME COMMITMENT FROM SOFTWARE VENDORS THAT THEY WILL MAKE OUR
LIFE EASIER IN A NEAR FUTURE BY FIXING THEIR ACT WITH POSTSCRIPT ?
Ohio Supercomputer Center
1224 Kinnear Rd
Columbus, OH 43212-1163