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ModView version 0.903 for Linux is
available for download!
New options:
- new command 'pload xxxx' to load coordinates from PDB,
where 'xxxx' is 4 letter PDB code.
This command can be included in any script and can be applied many times,
like
...
script="pload 1d2r; pload 1rnt; ... "
...
- new command 'alionline' which allows to read set of sequences from a HTML form
in CGI script, this variable should be included in EMBED object, when calling modview like
...
alionline=$myformalignment
aliformat="PIR"
...
An example, how to make HTML form and call ModView is in examples
Several bugs fixed.
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ModView version 0.902 for Linux is
available for download!
New options:
- ModView is able to load any local or remote coordinate file
automatically reading it from the alignment. The name of the file has
to be specified on second line, in the second field of the PIR alignment
exactly instead of pdb code. ModView checks this field and
a) if the name is 4 letter long it considered as a standart pdb code
and look for the file in PDB dir.
b) the name 'model' is reserved for ModBase.
c) any other name is considered as user's local or remote file and
ModView looks for this file.
- ModView can superpose structures by the alignment only for selected
sequences. Button [Alignment] on the Control Panel. If there is no selection it will
superpose all structures.
- ModView can read multiple copies of the same coordinate file.
- ModView is also is used as structural interface in IceDB
- ModView will NOT open the control and script window automatically,
instead, there is new variable SCRIPT in configuration file (~/.skymol),
where you can put any initial script you wish. In order to have the control
and script window, the next line has to be added to ~/.skymol file
SCRIPT plugin: show sliders; plugin: show ali
or
SCRIPT plugin: show sliders; plugin: show ali;[select @0][color red]
or any other script you want to be executed at initial point.
The script command from HTML file in EMBED object is also works and
will be executed second.
Bugs fixed:
- Multiple alignment with CLUSTALW works.
- Sort button works.
and some other internal bugs fixed.
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ModView version 0.901 for Linux is
available for download!
This is new redesigned version.
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ModView version 0.894 for Linux is
available for download!
New Features in version 0.894:
- New menu option in Ali window:
- Align -> CLUSTALW alignment
I introduce 'bridge technology' to communicate between ModView
and other programs. This menu option provides multiple sequence
alignment by external CLUSTALW. In order to use this option you
have to have CLUSTALW executable on your computer, you can
download and install CLUSTALW for example from
CLUSTALW link .
ModView works good with version 1.82 of CLUSTALW, older version
may have some problems. You also have to create scratch directory
for CLUSTALW files on your computer and set two variables
in ~/.skymol file in your home directory, which may look like this:
> more ~/.skymol
...
SCRATCH /usr/tmp/sss/
CLUSTALWEXE /home/valya/bin/clustalw
...
make sure the SCRATCH variable is pointed to existing directory and
also have '/' character at the end.
CLUSTALWEXE should be full path to the executable.
- Some bugs fixed.
When you load additional coordinate file by menu
ModView now add a button to Control Window.
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ModView version 0.892 is now
available for download!
New Features in version 0.892:
- New commands:
- plugin: show ali
- plugin: hide ali
- plugin: show sliders
- plugin: hide sliders
are added. These commands can be used both from command line and at the initial call (for
example:script="plugin:hide ali" - if one desires to have specific combination of windows at first call
to ModView)
- Include checking between alignment sequence and corresponding PDB sequence (they should be 100% identical)
- Sort menu is added for sorting sequence by ID, tree group, length or tree order
- New input/output options:
- load alignment from either file or from html link
- load PDB coordinates by PDB code
- save ali to file
- save alingment as postscript file
are added to File Menu
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ModView version 0.889 for SGI is
available for download!
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ModView upgrade version 0.879 is
available for download.
Upgrade Features in upgrade version 0.879:
- Alignment fit works correctly for multiple proteins
- Colors work properly for 'crazy' proteins (with non-sequencial residue numbering)
- Able to use different color scheme in alignment window
- Include cross checking between the sequence from
alignment and the sequence from pdb structure
- Include error message window
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ModView version 0.875 is available for
download.
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ModView is developed and maintained by Valentin Ilyin in the laboratory of
Andrej Sali ,Laboratories of Molecular Biophysics, Pels Family Center for
Biochemistry and Structural Biology, The Rockefeller University, 1230 York Ave, New York, NY 10021.
ModView is copyright © 2001. Any selling of the original, modified or parts
of the program is prohibited without a written permission from the authors.
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