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Contact Module in Maestro - contact cutoff ratio

11/30/2012

1 Comment

 
In Maestro when visualizing a structure file, you can  select Tools -> Measurements -> Contacts panel in order to see Good contacts and Bad&Ugly contacts. When contacts are displayed, good contacts are green by default, bad ones are orange, and ugly ones are red. These criteria whether a contact is defined as good, bad or ugly are based on the following formula:

C = D12 / ( R1 + R2 )

where D12 is the distance between atomic centers 1 and 2, and R1 and R2 are the radii of atomic centers 1 and 2. C is defined as the "contact cutoff ratio" in Maestro and has default values of 0.85 for "Bad" contacts and 0.70 for "Ugly" contacts. C must be monotonically increasing for each of the contact types, that is C(ugly) < C(bad) < C(good). These three values then provide 4 ranges. Distances greater than C(good) are not marked, less than C(good) but greater than C(bad) are marked as "good", etc.

This answer was provided by the Schrodinger help team.

Zoe

1 Comment

libstdc++.so.6: version `GLIBCXX_3.4.11' not found

11/23/2012

1 Comment

 
While trying to use some of Desmond tools I got the following error:

/opt/desmond2012/maestro-v93023/lib/Linux-x86_64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib/pymodules/python2.7/matplotlib/ft2font.so)

The solution is to instal the GNU C compiler and GNU C++ compiler for x86_64.
To install the gcc and g++ compilers, you will need the build-essential package. This will also install GNU make.
build-essential contains a list of packages which are essential for building Ubuntu packages including gcc compiler, make and other required tools.

$ sudo apt-get update
$ sudo apt-get upgrade
$ sudo apt-get install build-essential
$ gcc -v
$ make -v

Then,
$ cd /opt/desmond2012/maestro-v93023/lib/Linux-x86_64
$ sudo mv libgcc_s.so.1 libgcc_s.so.1.back
$ sudo ln -s /lib/libgcc_s.so.1 libgcc_s.so.1
$ sudo rm libstdc++.so.6 (this was already a symbolic link)

and finally create a symbolic link
$ sudo ln -s  /usr/lib/gcc/x86_64-linux-gnu/4.6.1/libstdc++.so libstdc++.so.6

Hope that helps!
Evi

1 Comment

Desmond Installation Problem

5/28/2012

1 Comment

 
In some cases, when installing Desmond software, the following error message can appear:

556: Illegal number: unknownunknown

You can use the following procedure to replace the original platform file with the updated one. You must have write permissions to your SCHRODINGER directory to perform this update.

  1. Back up the original platform file:

    mv $SCHRODINGER/platform $SCHRODINGER/platform.orig
  2. Right-click on the following link and choose to save it as a file (Save Link As):

    ftp://ftp.schrodinger.com/support/hidden/TS/platform_118130

    You should save it to your SCHRODINGER (installation) directory with the name platform. If you have a problem saving the file, then save it to another directory and move it to $SCHRODINGER/platform.
Now that the platform file has been replaced in your SCHRODINGER installation directory, try to start Maesto or run machid once again.

(source: http://www.schrodinger.com/kb/1528)

Harris


1 Comment

    Alexis, Maria, Dimitra, Ioannis,  Michalis, Danai, Panos, George, Aspa, Zoe

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