|
RasMol and Chime FAQ (Frequently Asked Questions) - B
Part:
1
2
3
4
5
(Continued from previous part...)
Gzipping PDB files for Chime
You can skip this (rather technical) section unless you are putting a Chime-based
presentation on a web server.
All PDB files placed on servers for use by Chime should be gzipped.
(Note, however, that if the same copy of the file is to be used
for RasMol, it should not be gzipped since only unix-RasMol
can understand gzipped PDB files -- RasWin and RasMac cannot!)
Chime will automatically decompress and display
PDB files compressed with the gzip method.
Such compression reduces the sizes of PDB files by about 3.5-fold,
and reduces the time required to transfer the files through the Internet
by a similar amount. When Chime's "File, Save Molecule As" menu option
is used, the file will be saved decompressed (as plain text), even
if Chime received the file gzipped.
Gzip is a freeware program available for a wide variety of
computer platforms. Gzip originates from the Free Software Foundation, but
they do not provide the application program directly. To download gzip,
see the paragraph below for Windows or Macintosh.
Gzipping on Windows: Download
gzip.exe
(which is also available on most shareware/freeware web sites).
To gzip, for example, 1d66.pdb, open a DOS window, and type the
command "gzip 1d66.pdb". This will produce the file 1d66.pdz
which you should probably rename to 1d66.pdb (see below).
To decompress a gzipped PDB file:
If you run gzip with no parameters, just "gzip", it will reply
"For help, type: gzip -h". From the help, you will learn that to
decompress a file, the command is "gzip -d <filename>". However, the
filename must end in "z", so before decompressing, you'll need to
rename, for example, 1d66.pdb back to 1d66.pdz.
Then after you "gzip -d 1d66.pdz" it will produce 1d66.pd,
which you'll have to rename back to 1d66.pdb.
Gzipping on Macintosh: The source of the application
is
MacGzip Home Page (Spain).
Serving gzipped PDB files: In most cases, after gzipping
a PDB file for use on a web server, you will need to rename the gzipped
file back to a name ending in .pdb. This is because typically
the server will be configured to serve files ending in .pdb
as MIME type chemical/x-pdb, which directs the browser to
hand these files to the Chime plug-in for display. Unless you can
get the server administrator to reconfigure the server to serve other
types of files (for example ending .pdb.gz or .pdz) as
chemical/x-pdb, other file types won't be displayed in Chime.
If using ftp to transfer the gzipped PDB file to the
server, make sure you force binary mode! Although unzipped PDB
files are plain ASCII text, transferring a gzipped file in ASCII
mode will corrupt it. Test your gzipped PDB files by viewing in
Chime from the server after transferring them!
Is Chime Y2K complaint? Where do I get technical support for Chime?
All questions concerning support for Chime, Y2K compliance, etc.
should be directed to the source of Chime, namely MDLI at chime-feedback@mdli.com.
Eric Martz authored neither RasMol nor Chime.
Chime for SGI, linux, unix (not!)
MDLI has no plans to develop Chime for
linux or any other flavor of unix. They did provide Chime 0.9 for SGI
(still available and works fine as far as it goes) but decided not to
bring that up to version 1 or 2. MDLI is continuing to develop and
support Chime for Windows 95/98/NT and Macintosh PPC. This information
is current as of mid-1999. The source code for Chime is of course
proprietary and not available outside of MDLI. If you wish to contact
MDLI and express your interest in Chime for linux, or in having them
complete the documentation
on Chime 2 at their website, send email to
chime-feedback@mdli.com.
(Continued on next part...)
Part:
1
2
3
4
5
| 