Frequently Asked Questions (FAQ) about Moloc -> Moloc Home


Table of Contents
  1. What is this "a/b/c" syntax used in this FAQ?
  2. How can I get a question about moloc answered?
  3. What are the essential sections of the moloc manual?
  4. How to get on-line help?
  5. How to automatically color-code the atoms every time a new coordinate-file is read?
  6. What are recommended option-settings for beginners?
  7. How to save current option-settings, so that they become the default?
  8. How to calculate and show H-bonds?
  9. How to speed-up the calculation of H-bonds in large systems?
  10. How to change the appearance (color, spacefill, etc.) of an entry?
  11. Authors
  12. How do I get back to the moloc Homepage?

1.  What is this "a/b/c" syntax used in this FAQ?

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The following notation is used in this FAQ:

a/b/c   refers to a path down the menu-tree (where a, b and c stand for letters used in moloc's menus).

All mouse-clicks are with the right mouse-button, unless otherwise specified.

 

 

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.

 

 

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: Control of the Program,
4.0: Basic Concepts and Organization,
5.0 - 5.1: Display and Input-Output Tool,
6.0: Perform Set Manipulations,
9.3 - 9.4: Optimizer, All-Atom Force-Field,
16.0: Surfaces and Loci

A postscript version of the manual can be downloaded:

 

 

4.  How to get on-line help?

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  1. 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).

  2. 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

 

 

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".

 

 

6.  What are recommended option-settings for beginners?

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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"

 

 

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,

 

 

8.  How to calculate and show H-bonds?

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  1. 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".
  2. opt/e     wait for the calculation to finish, then click on "h".

 

 

9.  How to speed-up the calculation of H-bonds in large systems?

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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:

 

 

11.   Authors

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This document has been contributed by Stefan Fischer and Daniel Bur  (x81795).

 

 

12.   How do I get back to the moloc Homepage?

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Click to get back to the moloc Homepage.

 

 

 


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For comments or additional information, please contact Paul Gerber (x88270)
This information was last changed Thu Jan 29 16:25:38 MET 1998