2 Molden 3.7 for Microsoft Windows 95, 98
3 and Windows NT 4.0
Last Update: Februari 11. , 2000
4 Contents
· What is it
· Whats new in this release
· Availability
· Installation
· Where to get an X server
· Running molden
· Credits
· Additional information
· Revision History
· Legal notices
5 What is it?
The installation image contains Molden, an interactive visualization program for chemical structures, orbitals, total electron density, difference density, and electrostatic potential , ESP charges and Distributed Multipole Analysis, from Gijs Schaftenaar compiled for Microsoft Windows 95/Windows NT 4.0.
This distribution contains:
· Pre-compiled binary molden.exe
· X-Window and compiler support libraries: libX11.dll , cygwin1.dll etc.
· Mogl.exe a external helper program for molden to do OpenGL graphics
You must have Windows 95, 98 or Windows NT 4.0 SP3 to use this software.
6 Whats new in this release
· New version 3.9 from July 2003 was used
· Calculated vibration spectra
· Support for Gaussian03
· A color editor
· OpenGL within the Density mode
· Improved file manager
· Adapted Z-matrix for proteins, allows editing on aminoacid level
· Compiled for Pentium class machines. However it works also on Intel Pentium Pro/II as well as Cyrix or AMD processors equally well.
For new program features, like Gaussian 98 support, please consult the history file on the Molden Home Page.
7 Availability
The zip-file and further information can be obtained from:
http://www.cmbi.kun.nl/~schaft/molden/molden.html
7.1.1 Note:
This version does not run under Microsoft Windows 3.x (i.e. 16-Bit Windows), OS/2, Linux or Microsoft Windows NT for DEC Alpha !
8 Installation
I recommend that you download the molden_windows_nt_95.zip file from the Molden ftp-server located in the bin directory.
ftp ftp.cmbi.kun.nl
Name: anonymous
Password: your_email_address
ftp> cd pub/molgraph/molden/bin
ftp> binary
ftp> get molden_windows_nt_95.zip
ftp> quit
I am assuming you have a zip-compatible decompression program like WinZip. Unzip the molden_windows_nt_95.zip directly into the directory from which you will run molden. You may have to create it first.
PLEASE read this !!!!
1. Install into a different directory if you have previous versions of molden installed!
2. You must run molden from this directory, use molden's file manager to read in files.
3. Create a folder "tmp" and "temp" in drive C:. Otherwise you will get errors when molden tries to write temporatry files.
4. The latest PC version of molden has problems reading certain files , this is caused by an incorrect implementation of the fortran backspace function in the g77 compiler from cygnus. You can still read these files into molden by converting from DOS files to UNIX files. You can use the public domain utility RUM for this. Syntax: rum /u dosfile unixfile See more on this problem.
And of course, you will need X Windows server software. A freeware X server can be obtained from MicroImages:
http://www.microimages.com/mix
This server is somewhat limited as it does not fully support the Athena widgets (menu items when selected become invisible!). There is a fully functional demo (2 hour limit) from Starnet which is somewhat nicer:
http://www.starnet.com/product.htm
For a comprehensive list of other commercially available X servers consult Kenton Lee's page:
http://www.rahul.net/kenton/xsites.html
8.1.1 Remarks:
1. You must have some form of TCP/IP support on your Win95/NT box in order to have your X clients talking to the X Server. If you don't have a network card installed, in the very least you will need the Win95/NT dial-up network component installed (the same stuff you use to connect to an ISP).
2. Starnet's X-win32 does not work well if you have a dial-up network and you are not connected. Workaround: disable DNS, but remember to enable it back when connecting to your ISP. No such problem if you have a network card installed.
9 Running molden with the supplied test files
You have to get the test files separately from the cmbi ftp site
Be sure to use the binary transfer mode (just type binary) during ftp, this way the files will be transferred in unix-formatted files. If you use the ascii transfer mode, the files will be converted to dos-format. (See Problems).
· Start your X-Server
· Open a console window ( i.e. Start -> Programms -> Ms-Dos Prompt )
· Change to the home directory for molden ( i.e. cd c:\Program Files\molden )
· type molden.exe test/*
If all things work correctly you can put the display environment into a batch file to start up molden like in the following moldenstart.bat file:
cd C:\Program Files\molden
set PATH=%PATH%;c:\molden
set DISPLAY=localhost:0.0
startx
molden.exe
Here startx is just an example, what you have to fill in here depends on the Xserver emulator you use.
10 Credits
These X11R6.4 libraries used to compile molden were the work of Sergey Okhapkin (sos@prospect.com.ru) and Arlindo da Silva dasilva@alum.mit.edu.
The Fortran 77 and C/C++ compilers used was the PGCC-1.03 for Win32 port from Sergey Ohapkin based on the GnuWin32 B20 project by Cygnus Solutions Inc.
And of course Molden was written by Gijs Schaftenaar.
11 Additional Information
For additional information about Molden, please consult:
http://www.cmbi.kun.nl/~schaft/molden/molden.html
The PC version of molden was initiated by Alexander Klinsky, (Institute of pharmaceutical chemistry - University of Vienna). Alexander no longer provides support for the PC version of molden. Please direct your questions to the author of molden personnally schaft@cmbi.kun.nl.
Who wishes to acknowledge the efforts of Alexander Klinsky.
12 Revision History
· July 03 - molden version 3.9
· March 97 - First b18 distribution , version 3.2
· July 97 - Revised README, new revision of version 3.2 compiled
· April 98 - Revised help file, new version 3.3, CygWin B19.1 and EGCS 1.02 compilers used, performance improvements
· August 98 - New version 3.4 from August 1998, CygWin B19.3 and PGCC 1.03 compilers used, again performance improvements on Pentium and Pentium Pro machines.
· November 99 - New version 3.6
· Februari 2000 - New version 3.6 , CygWin B20 and gcc2.95.2
· May 2001 - New version 3.7
13 Legal Notices
This is for the X11R6.4 libraries used to built and run Molden:
Copyright c 1996 X Consortium
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, dis- tribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the fol- lowing conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL- ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABIL- ITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Except as contained in this notice, the name of the X Consortium shall not be used in advertising or otherwise to promote the sale, use or other dealings in this Software without prior written authorization from the X Consortium.
X Window System is a trademark of X Consortium, Inc.
3 and Windows NT 4.0
Last Update: Februari 11. , 2000
4 Contents
· What is it
· Whats new in this release
· Availability
· Installation
· Where to get an X server
· Running molden
· Credits
· Additional information
· Revision History
· Legal notices
5 What is it?
The installation image contains Molden, an interactive visualization program for chemical structures, orbitals, total electron density, difference density, and electrostatic potential , ESP charges and Distributed Multipole Analysis, from Gijs Schaftenaar compiled for Microsoft Windows 95/Windows NT 4.0.
This distribution contains:
· Pre-compiled binary molden.exe
· X-Window and compiler support libraries: libX11.dll , cygwin1.dll etc.
· Mogl.exe a external helper program for molden to do OpenGL graphics
You must have Windows 95, 98 or Windows NT 4.0 SP3 to use this software.
6 Whats new in this release
· New version 3.9 from July 2003 was used
· Calculated vibration spectra
· Support for Gaussian03
· A color editor
· OpenGL within the Density mode
· Improved file manager
· Adapted Z-matrix for proteins, allows editing on aminoacid level
· Compiled for Pentium class machines. However it works also on Intel Pentium Pro/II as well as Cyrix or AMD processors equally well.
For new program features, like Gaussian 98 support, please consult the history file on the Molden Home Page.
7 Availability
The zip-file and further information can be obtained from:
http://www.cmbi.kun.nl/~schaft/molden/molden.html
7.1.1 Note:
This version does not run under Microsoft Windows 3.x (i.e. 16-Bit Windows), OS/2, Linux or Microsoft Windows NT for DEC Alpha !
8 Installation
I recommend that you download the molden_windows_nt_95.zip file from the Molden ftp-server located in the bin directory.
ftp ftp.cmbi.kun.nl
Name: anonymous
Password: your_email_address
ftp> cd pub/molgraph/molden/bin
ftp> binary
ftp> get molden_windows_nt_95.zip
ftp> quit
I am assuming you have a zip-compatible decompression program like WinZip. Unzip the molden_windows_nt_95.zip directly into the directory from which you will run molden. You may have to create it first.
PLEASE read this !!!!
1. Install into a different directory if you have previous versions of molden installed!
2. You must run molden from this directory, use molden's file manager to read in files.
3. Create a folder "tmp" and "temp" in drive C:. Otherwise you will get errors when molden tries to write temporatry files.
4. The latest PC version of molden has problems reading certain files , this is caused by an incorrect implementation of the fortran backspace function in the g77 compiler from cygnus. You can still read these files into molden by converting from DOS files to UNIX files. You can use the public domain utility RUM for this. Syntax: rum /u dosfile unixfile See more on this problem.
And of course, you will need X Windows server software. A freeware X server can be obtained from MicroImages:
http://www.microimages.com/mix
This server is somewhat limited as it does not fully support the Athena widgets (menu items when selected become invisible!). There is a fully functional demo (2 hour limit) from Starnet which is somewhat nicer:
http://www.starnet.com/product.htm
For a comprehensive list of other commercially available X servers consult Kenton Lee's page:
http://www.rahul.net/kenton/xsites.html
8.1.1 Remarks:
1. You must have some form of TCP/IP support on your Win95/NT box in order to have your X clients talking to the X Server. If you don't have a network card installed, in the very least you will need the Win95/NT dial-up network component installed (the same stuff you use to connect to an ISP).
2. Starnet's X-win32 does not work well if you have a dial-up network and you are not connected. Workaround: disable DNS, but remember to enable it back when connecting to your ISP. No such problem if you have a network card installed.
9 Running molden with the supplied test files
You have to get the test files separately from the cmbi ftp site
Be sure to use the binary transfer mode (just type binary) during ftp, this way the files will be transferred in unix-formatted files. If you use the ascii transfer mode, the files will be converted to dos-format. (See Problems).
· Start your X-Server
· Open a console window ( i.e. Start -> Programms -> Ms-Dos Prompt )
· Change to the home directory for molden ( i.e. cd c:\Program Files\molden )
· type molden.exe test/*
If all things work correctly you can put the display environment into a batch file to start up molden like in the following moldenstart.bat file:
cd C:\Program Files\molden
set PATH=%PATH%;c:\molden
set DISPLAY=localhost:0.0
startx
molden.exe
Here startx is just an example, what you have to fill in here depends on the Xserver emulator you use.
10 Credits
These X11R6.4 libraries used to compile molden were the work of Sergey Okhapkin (sos@prospect.com.ru) and Arlindo da Silva dasilva@alum.mit.edu.
The Fortran 77 and C/C++ compilers used was the PGCC-1.03 for Win32 port from Sergey Ohapkin based on the GnuWin32 B20 project by Cygnus Solutions Inc.
And of course Molden was written by Gijs Schaftenaar.
11 Additional Information
For additional information about Molden, please consult:
http://www.cmbi.kun.nl/~schaft/molden/molden.html
The PC version of molden was initiated by Alexander Klinsky, (Institute of pharmaceutical chemistry - University of Vienna). Alexander no longer provides support for the PC version of molden. Please direct your questions to the author of molden personnally schaft@cmbi.kun.nl.
Who wishes to acknowledge the efforts of Alexander Klinsky.
12 Revision History
· July 03 - molden version 3.9
· March 97 - First b18 distribution , version 3.2
· July 97 - Revised README, new revision of version 3.2 compiled
· April 98 - Revised help file, new version 3.3, CygWin B19.1 and EGCS 1.02 compilers used, performance improvements
· August 98 - New version 3.4 from August 1998, CygWin B19.3 and PGCC 1.03 compilers used, again performance improvements on Pentium and Pentium Pro machines.
· November 99 - New version 3.6
· Februari 2000 - New version 3.6 , CygWin B20 and gcc2.95.2
· May 2001 - New version 3.7
13 Legal Notices
This is for the X11R6.4 libraries used to built and run Molden:
Copyright c 1996 X Consortium
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, dis- tribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the fol- lowing conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL- ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABIL- ITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Except as contained in this notice, the name of the X Consortium shall not be used in advertising or otherwise to promote the sale, use or other dealings in this Software without prior written authorization from the X Consortium.
X Window System is a trademark of X Consortium, Inc.
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