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1.  What is this "a/b/c" syntax used in this FAQ?
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The following notation is used in this FAQ:
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a/b/c refers to a path down the menu-tree
(where a, b and c
stand for letters used in moloc's menus).
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All mouse-clicks are with the right mouse-button, unless otherwise specified.
 
 
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2.  How can I get a question about moloc answered?
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If, after looking over this FAQ, you still do not
have a satisfactory answer,
contact either
Paul Gerber (x81795)
or anyone in the Molecular Design group.
We would be happy to answer your question
or direct you to the person most competent to do so.
 
 
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3.  What are the essential sections of the moloc manual?
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Before looking for answers in this FAQ,
please make sure that you have read the following
sections of the moloc manual:
3.3 - 3.5:
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Control of the Program,
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4.0:
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Basic Concepts and Organization,
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5.0 - 5.1:
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Display and Input-Output Tool,
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6.0:
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Perform Set Manipulations,
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9.3 - 9.4:
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Optimizer, All-Atom Force-Field,
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16.0:
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Surfaces and Loci
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A postscript version of the manual can be downloaded:
 
 
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4.  How to get on-line help?
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- In moloc:
CTRL-click with the right mouse-button onto the menu-letter of
the function for which you need info. The help will be written into the
text-port (i.e. the window from which moloc was started).
- On the Web: The moloc manual and
many others are on-line under
http://rbaw01.bas.roche.com:8080/manuals/manuals.html
The manual can be searched by entering a keyword into
http://rbaw01.bas.roche.com:8080/prpc/index.html
 
 
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5.  How to automatically color-code the atoms every time a new coordinate-file is read?
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Atom-markers are colored dots placed on non-C atoms (N = blue, O = red, S = yellow, etc.):
.../g/o set "marker" = "all" , click "ok".
 
 
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6.  What are recommended option-settings for beginners?
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- .../g/o set :
- "view" = "read"
- "marker" = "all"
- "label" = "none"
Hint: click-&-hold the right mouse-button in the right column
of the options-table to see other possible answers.
- .../:/h set "toggled help" = "y"
Hint: Click
to get a robust version of the .Moloc file in your web browser.
Then click the browser's File menu and Save as Text to your home directory as ".Moloc"
 
 
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7.  How to save current option-settings, so that they become the default?
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.../:/s type ".Moloc" as the filename, hit ENTER.
This creates in the current directory a file called ".Moloc", which holds
a list of all option-settings.
Every time moloc is started, it looks first
in the current directory and then in your home directory for a ".Moloc" file.
The first ".Moloc" file the program finds is used.
Hint: If you want the ".Moloc" file just created to be read
even when moloc is started from another directory,
copy this file into your home directory,
 
 
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8.  How to calculate and show H-bonds?
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- Set the status of the relevant entries to "active" (active means that
the atoms of these entries will be used in the calculation) :
.../a put an "A" in front of each entry that should be active,
then click "x".
- opt/e wait for the calculation to finish, then click on "h".
 
 
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9.  How to speed-up the calculation of H-bonds in large systems?
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- Fix the atoms of some large entries:
opt/s select some entries, whose atoms will
be considered as fixed upon leaving the selection-tool.
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Note: it is not necessary to set "ignore H-bonds between fixed atoms"="y"
under the opt/m options. A large speed improvement due to the fixing
occurs even when this option remains in its default setting of "n".
OR (recommended only for viewing, not if geometries are to be optimized)
- Turn off the computation of the "van der Waals" interactions:
opt/w set "1-n interactions" = 0.0 , "1-4 interactions" = 0.0
 
 
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10.  How to change the appearance (color, spacefill, etc.) of an entry?
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.../e select in the pop-up menu
the entry to be changed, then do one of the following:
- Coloring the entry:
Click "c", click on a color and click "x".
- Getting a spacefill representation of the entry:
- Click "b", adjust the rulers with the left
mouse-button (for ex. "atom radius" = 100), right-click anywhere, click "x".
- .../:/b click on "cover".
Note: choosing "cover" instead of the default "overblend" will slow down moloc's screen display.
- See section 3.1 of the manual for more entry-dependent display options. To exit this menu, click "x".
 
 
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11.   Authors
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This document has been contributed by Stefan Fischer and Daniel Bur 
(x81795).
 
 
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12.   How do I get back to the moloc Homepage?
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Click
to get back to the moloc Homepage.