_________________________________________________________________________________

RNA2D3D                                           (Beta version 5.8.0, June 2011)

  1. System Installation
  2. Basic Organization of the System
  3. Nano Design Application Example

  4. Appendices (Libraries)

Reference: 
Martinez, H., Maizel, J.V. Jr., and Shapiro, B.A. "RNA2D3D: a program 
for generating, viewing, and comparing 3-dimensional models of RNA." 
J Biomol Struct Dyn. 2008 Jun;25(6):669-83.

Contacts:
Voyek Kasprzak:       kasprzaw@mail.nih.gov
Dr. Bruce A. Shapiro: shapirbr@mail.nih.gov

_________________________________________________________________________________

Please, keep in mind that this is a research software, and not an 
industrial strength package. We will attempt to assist you with installation 
problems and are interested in bug reports, but we do not have dedicated 
support resources. Thank you for your understanding.
_________________________________________________________________________________

1. SYSTEM INSTALLATION:

   NOTE: In an RNA2D3D distribution file named rna_2d3d3_vREV.tar.gz, the 
   REV part has the following parts: L - indicates RNA2D3D binaries for 
   Linux, I - Irix/SGI binaries, T - use of Tinker for MD refinements, 
   and x.y indicates the revision number.
   For example, file rna_2d3d_vLT5.6.3.tar.gz contains a compressed archive 
   of the RNA2D3D system, version 5.6.3 for Linux, and the file
   rna_2d3d_vIT5.6.tar.gz is its equivalent for the SGI/Irix platforms.

   Below, we will refer to the entire file name simply as "sysname" 
   (i.e. sysname.tar.gz)

   A) NOTE: A sub-directory named after the "sysname" will be created after 
      the commands listed in B) have been executed. 
      For example, a directory named rna_2d3d_vLT5.6.3 may be created for 
      the Linux version of the system. You can rename it as you wish.

   B) The RNA2D3D package is distributed as a compressed TAR archive file.
      You can extract it via a single call:

      tar -xzvf sysname.tar.gz

      OR

      After uncompressing it, extract the tar archive contents:
 
      gunzip sysname.tar.gz
      tar -xvf sysname.tar
      
   C) NOTE: The system installation scripts are written in C-shell syntax.
      Please, install the system and run it under C-shell (csh)!
  
      Change directory to "sysname" (cd sysname) and run the system 
      configuration and Tinker installation script (./CONFIG-RNA2D3D) to 
      build a self-contained system with all the necessary components placed 
      in the sysname directory tree.
      CONFIG-RNA2D3D creates a local ./cshrc_2d3d file based on a 
      cshrc_template and the actual user environment information, and calls
      the script to  install Tinker from its Web distribution site: 
      TINKER-FOR2D3D. This latter script differs for the Linux and Irix 
      systems (see below). 
   !!!NOTE: Temporarily (RNA2D3D versions 5.6.x and newer), we include the
      necessary Tinker 4.2 binaries, since Tinker 5.0 is incompatible.
     
   D) Following the successful installation, execute: source ./cshrc_2d3d
      This will set up environment variables needed by RNA2D3D and define 
      an alias (for example, rna_2d3d0, which can be used to invoke the 
      program.


  If you are planning to install the RNA2D3D as a program available to 
multiple users, assuming you have the administrative/root privileges, please, 
place the RNA2D3D distribution directory under a generally accessible 
directory, such as /usr/local/ and either run the CONFIG-RNA2D3D script there 
or edit the chsrc_template file to create the systems own cshrc_2d3d file. 
Placement of Tinker can be customized as well, and must be reflected in the 
cshrc_2d3d TINKER_DIR path definition.
Finally, ask the users to add the following line to their own .cshrc file:
  source /usr/local/rna_2d3d_vLT5.6/cshrc_2d3d  (your path will vary)

IMPORTANT NOTES (HELP WITH PROBLEMS):
 
a) System Libraries
   RNA2D3D has been compiled with the libraries listed below in Appendix A. 
   Most of the OpenGL libraries are shared, and they may not be installed by 
   default in your Linux environment. The following libraries are listed in 
   the Makefile (LDFLAGS):
 
   -L/usr/lib -lGLw -lGL -lGLU -lXext -lX11 -lXm -lXt -lm -lmmalloc
   
>>>In Ubuntu 10.04 LTS (also tested on one Ubuntu 9.10 system) we were able 
   to install the required libraries by executing the package installation 
   command:

   sudo apt-get install libmotif-dev     - full Open Motif development files

   This had to be augmented by an interactive Package Manager session:
   System -> Administration -> Synaptic Package Manager -> 
                                                       quick search: "mesa"

   The following Mesa packages are installed on two of our Ubuntu 10.04 
   systems (and are sufficient for RNA2D3D binaries to run):
   A:  libglu1-mesa-glx
       libglu1-mesa-dri
       libglu1-mesa

   B:  libgl-mesa-swx11
       libgl-mesa-swx11-i686
       libgl-mesa-dri
       libglu1-mesa
       libosmesa6
       mesa-common-dev


>>>In our Ubuntu 8.x Linux, we were able to install the missing
   libraries from the packages available on the Web as follows:
 
   sudo apt-get install libmotif3        - minimum needed to run the binary
   or  
   sudo apt-get install libmotif-dev     - full Open Motif development files
   
   Package libmotif-dev does not inlude the libGLw.* libraries (see 
   Appendix A) which you will have to find in order to rebuld the system 
   from the source files. Another library listed in Appendix A, which you 
   will need to download separately is the libmmalloc.a.

   
   IMPORTANT:  
   Missing or wrong libraries are the most likely cause of failures to run
   RNA2D3D after installation (Segmentation fault errors).  See Appendix A 
   for the list of libraries on the Ubuntu 8.0.4 and Red Hat Enterprise 5.5 
   used to build the system. Lack of firm standards within the Linux community 
   means that you may encounter (as we did) libraries with the correct names 
   and revision numbers, but missing contents(!). Please, use Appendix A and 
   B info as a guide. You may notice that the library sizes listed for our 
   Ubuntu and RHE set-ups differ, but they don't cause problems as far as 
   RNA2D3D is concerned.

   As a potential help to you, a sub-directory sysname/lib-Ubu contains the
   key libraries needed to run the binary image on our Ubuntu 8.0.4. test
   machine or rebuild it from the source files. A subdirectory 
   sysname/lib-RHE contains copies of the libraries sufficient to rebuild 
   RNA2D3D from source files under Red Hat Enterprise 5.5.  Compare their 
   contents against your system libraries (/usr/lib/* on Ubuntu and RHE5).

   Should the installation of the binary images not work and you would like 
   to recompile/rebuild the system, please, contact us about the source 
   files and see Appendix A and B for a list of OpenGL,  Motif (and other) 
   libraries and/or library packages that you may need to add to your Linux 
   installation before you will be able to rebuild the system yourself  
   (example from Ubuntu Users Forum). 

   If you have the source file directory, plase, see the ls -l Make*
   listing for diffrent Makefiles we used in our development environments
   Use or adopt one (copy to Makefile) and execute the make command.
   Consult appendix A in case you see errors indicating missing function
   definitions.

   If you would like to contact us requesting help with getting the system
   running send us results of the ldd rna_2d3d command which lists the
   dependencies of RNA2D3D on the system resources and may be the first 
   indication of missing libraries (see Appendix A).  Also, please, include
   as much info on the context of the failure as possible (transcript of 
   your session would be the best description).

b) The binary file directory (system/bin/)contains copies of the RNA2D3D
   binaries compiled on Ubuntu 8.0.4 with gcc compilers (rev 3.3 & 4.2)
   as well on under Red Hat Enterprise 5.5 gcc (3.4 and 4.x). 
   The default binary (rna_2d3d) is the same as the gcc 3.3 compilation, 
   as it works on all our test machines. This relies on a library
   /usr/lib/libXm.so.3 (available from sysname/lib-Ubu and lib-RHE.  
   In case of problems you may want  to copy alternative binaries in the 
   /system/bin directory to rna_2d3d an see if it makes any difference to 
   your OS set-up. The RHE-compiled binaries require library 
   /usr/lib/libXm.so.4 to be present (available from sysname/lib-RHE).  

c) We have noticed problems with the recognition of the input data paths
   (sample.dir and RNA_2D3D) when the system was invoked under bash shell.
   Till we fix it, please run it under csh (you may need to add it to your
   plain Ubuntu Linux installation via: sudo apt-get install csh

d) Tinker software
   Refinements of the structure elements and the whole structure are 
   performed by the Tinker package modules (minimize, optimize, dynamic, 
   minrigid, pdbxyz, and xyzpdb), which are downloaded - with permission 
   of prof. Jay Ponder - from the Tinker web site to the subdirectory 
   Tinker-sta.dir by "web-get" calls: 
   wget ftp://dasher.wustl.edu/pub/tinker-bin/linux/minimize.gz, etc.
   (see TINKER-FOR2D3D)

   Linux: Precompiled binaries available on the Tinker web site are 
   downloaded by the TINKER-FOR2D3D script and used here. 
   If you experience problems with any of these modules, you may have to 
   download the source files and recompile them on your machine. Please, 
   consult with the Tinker web site for instructions on building Tinker 
   command line binaries from the source files 
   (see ftp://dasher.wustl.edu/pub/tinker/doc/guide.pdf)

!!!2009 NOTE: We have experienced problems with the newly recompiled 
   Tinker 5.0 modules (PDB format incompatible with RNA2D3D parser)  Until 
   we solve the problem (update our parser), we are including in the system
   directory a subdirectory with tested Tinker 4.2 modules: Tinker42-sta.dir. 

   SGI/Irix: The script TINKER-FOR2D3D downloads the source code and builds
   the whole set of Tinker command line binaries (no Tinker GUI modules), 
   by calling scripts compile.make, library.make, and link.make stored in the 
   Tinker-sta.dir/make-sgi subdirectory. In case the calls to the Fortran 90 
   (f90)compiler which we employ in these scripts fail on your platform, 
   you may want to try f77 or g77 calls.
   (see ftp://dasher.wustl.edu/pub/tinker/doc/guide.pdf)
_________________________________________________________________________________

2. BASIC ORGANIZATION OF THE SYSTEM:

The sample input files are provided in the sample.dir subdirectory, which is 
further subdivided into subdirectories listed below, based on the file types. 

Identical organization is assumed for the RNA_2D3D subdirectory, where the 
user files are to be stored (and will be looked for by the system). Note, that
the user's work directory with the RNA_2D3D subdirectory in it does not have to
be located in the RNA2D3D system directory tree. 

BPLfiles directory contains rna_2d3d-specific base pair lists where sequence 
and all the base pairs, including pseudoknots, are listed.  Negative values 
given to base pairs denote tertiary interactions, that will be marked with 
linking lines but no attempt will be made to impose realistic geometry on them. 
For the pseudoknots for which geometry cannot be predicted automatically, the 
user may apply the tertiary (negative) designations and attempt to manually 
model them (non-trivial, but achievable). (See the sample BPL files in the
sample.dir/BPLfiles directory).

PDBfiles directory contains PDB format (AMBER, STANDARD, TINKER, MSI) files. 
These can be the rna_2d3d output files based on the predicted structures, 
or imported from external databases. If you read in a PDB file, the 3D view of 
it shows only the backbone geometry, and the 2D view the whole sequence in a 
circle. Pairing data is not parsed out of the PDB input file!

3DModels directory contains binary 2D and 3D information files. These are 
"state dumps" that can be used for saving the state of your project and 
restoring it for further work. They are also necessary as the nano-structure 
building blocks.

TPLfiles directory contains ASCII pairing lists, which specify interactions 
between building blocks assumed to be available in the 3DModels directory, 
explicitly called by their names.

Extensive HELP information is available either via a HELP menu or can be read 
as plain text files (see subdirectory help.dir_raw).
_________________________________________________________________________________

3. NANO DESIGN APPLICATION EXAMPLE:

The Big Picture:
a) Construct monomers (building blocks) and save them as binary 3DModels 
  (and/or ASCII PDB files).
b) Create a Topology file (see TPLfiles) to define interactions between 
   monomers.
c) Manipulate stem length and 3'tail length via "2D Monomer 3D Tectosquare" 
   tools to see global effects (change in 1 monomer is applied symmetrically 
   to all other building blocks/monomers).


Constructing Monomers:
a) Load .bpl file: 
   File -> User bpl/Sample bpl (select file: LT17.A3s.bpl) -> model A

   Note: BPL files created with different editors may cause problems
   due to carriage-return & newline combination appended at the end of
   lines (in MS Word Pad, or aothe non-Unix editors).  The quickest
   way to clean them up for use with RNA2D3D is this shell command:

   shell-prompt> sed 's|\r||' in-file.bpl > out-file.bpl



b) Modify hairpin loops by extending the 3' helicity of the supporting stem:  
   Edit -> Extend Single Strand Helicity 
   For a kissing loop 5'-GAAGCGCGCAC-3'  click on the 3' nucleotide of the 
   closing base pair (C) and the 5' most G of the palindromic sequence.  
   Results are immediately visible in the 3D window (View -> 2D A & 3D A mode)

   Stem Linker single strand (5'-AA-3') can be replaced with a PDB right angle 
   motif RA (i.e. experimental data 3D coordinates) by defining a subset in the 
   full model and its equivalent in the PDB junction structure and replacing 
   the model subset with the PDB subset.  



c) Define structure Subsets to be swapped
   - Copy model A into Model B via (Utils -> 3DM utils)
   - Read-in PDB entry into model A:  
     Sample/User PDB -> STANDARD/MSI (BIOSYM)/AMBER format -> select into model A 
     (ex: A_TURN.pdb).
   - 2D A: Level -> Subset 
    (pops up subset level control buttons on the right)
   - Define a subset by picking (button) and click on G8 (5') and U13 (3') bases 
     to highlight the subset (highlighted in green)
   - Accept definition
   - Select a subset 
     (after the button click only the subset is displayed in 3D)
   - Accept Selection

   Repeat c) for model B (where a nanostructure monomer red in from the BPLfile 
   directory is stored): 
   - define subset by picking (button)
     Click on G42 (5') and U47 (3') bases to highlight the subset

d) Do the subset substitution (from Model A):  
   Utils -> 3DM utils -> Replace a B subset with an A subset. 
   Click on Do substitution and Quit

   - Switch between models A and B via View submenu
     To view one tecto corner: 
     View -> 2D B & 3D B;  Level -> Molecule 



e) Save the monomer as a 3DM file:  
   Utils -> 3DM utils -> Save as 3DM file -> enter LT17.A3s 
 
   Note that LT17 (Long Tectosquare 17) should be used as a convention 
   (a database name for building tectosquares from multiple monomers, 
   all part of LT17).  This file is stored in the user's directory 
   sysname/RNA_2D3D.

Note: The above outlined procedure can also be used to combine PDB-based geometry 
      with the BPL-based preliminary 3D structure. An entire "PDB structure" can 
      be designated as subset A (test carefully if the 2D window shows the whole 
      sequence 1..n or, more likely for the PDB input files 1..n-1), and 
      substituted  for the "BPL subset" of identical size (1..n vs. 1..n-1 !).

Constructing Tectosquares:
Once you have created four monomers (stored in the 3DModels directory) to be used
as building blocks, create/edit the topology file for a nanostructure to be built
out of these blocks. 
This file is in the directory sample.dir(RNA_2D3D)/TPLfiles and it specifies, for 
example, that the first building block (name listed) interacts with the second, 
starting at the base positions listed: 1:68-2:22. Interactions are automatically 
extended to include all contiguous complementary bases. Refer to the sample 
file LT17:

MONO	1   LT17.A3s   1  1:68-2:22  	0:0-0:0 
MONO	2   LT17.B1s   1  2:68-3:22  	0:0-0:0
MONO	3   LT17.C8s   1  3:68-4:22 	0:0-0:0
MONO	4   LT17.D6s   1 *4:68-1:22    	0:0-0:0      <- * denotes connectivity 
                                                          left open


Superstructures can be designed in this same way - see the sample file LT17-LT20,
in which four tectosqares (LT17 through LT20) are given connectivity information,
and the individual tectosquares connect with each other via 3' tails (single-stranded
ares) forming helices in the final model:

MONO	1   LT17.A3s   1  1:68-2:22  	1:87-7:92  
MONO	2   LT17.B1s   1  2:68-3:22  	0:0-0:0
MONO	3   LT17.C8s   1  3:68-4:22 	0:0-0:0
MONO	4   LT17.D6s   1 *4:68-1:22    	0:0-0:0
MONO	5   LT18.A8ps  2  5:68-6:22  	0:0-0:0 
MONO	6   LT18.B5ps  2  6:68-7:22  	6:92-12:87
MONO	7   LT18.C3ps  2  7:68-8:22  	0:0-0:0
MONO	8   LT18.D7ps  2 *8:68-5:22    	0:0-0:0
MONO	9   LT19.A4s   3  9:68-10:22  	0:0-0:0
MONO	10  LT19.B7s   3  10:68-11:22  	0:0-0:0
MONO	11  LT19.C2s   3  11:68-12:22   11:92-13:87
MONO	12  LT19.D5s   3 *12:68-9:22    0:0-0:0
MONO	13  LT20.A2ps  4  13:68-14:22  	0:0-0:0
MONO	14  LT20.B6ps  4  14:68-15:22  	0:0-0:0
MONO	15  LT20.C4ps  4  15:68-16:22  	0:0-0:0
MONO	16  LT20.D1ps  4 *16:68-13:22  *16:92-2:87
 
Note: the above examples are based on Chworos et al.,Science 306, 2004.

_________________________________________________________________________________
_________________________________________________________________________________

APPENDIX A: The listing below and the subdirectories within your RNA2D3D
            distribution (sysname/lib-Ubu and sysname/RHE) are meant as
            a reference and a potential source of libraries missing in your
            Linux environment.

  Please, notice the libGLw.so and libXm.so dependencies listed below (**)
  Also, keep in mind that libGL.so may be tied to your graphics card driver
  (as is the case with nvidia driver used on our RHE boxes), and you have to 
  be careful not to replace it (overwrite it) with an incompatible library!
_________________________________________________________________________________

Key Libraries used to build RNA2D3D under Ubuntu 8.0.4 Linux 
(*) - denote static libraries which you don't need for the system to run 
(compiled binaries).
 
!!! In our experience the correct libGL.so.1 is crucial crucial !!!

Under our Red Hat Enterprise 5.5 this library was updated at the time the 
latest nVidia card driver was installed and reflected the driver revision 
number (e.g. libGL.so.1 -> libGL.so.256.35). This update was crucial for 
the test call glxinfo to return correct values, and for other applictions 
to work (VMD and PyMOL, for example)

................................................................................
A sample listing of libraries found in Ubuntu Linux 
(available from sysname/lib-Ubu directory):

In /usr/lib:

 2978364 2008-04-05 18:06 libGL.a
      10 2009-07-17 16:35 libGL.so -> libGL.so.1
      19 2009-07-17 16:35 libGL.so.1 -> libGL.so.1.5.070002
 2427064 2008-04-05 18:06 libGL.so.1.5.070002

      11 2009-08-19 16:37 libGLU.so -> libGLU.so.1
      20 2008-11-10 06:30 libGLU.so.1 -> libGLU.so.1.3.070002
  532568 2008-04-05 18:06 libGLU.so.1.3.070002

   27878 2009-08-19 16:53 libGLw.a                       (*)
      15 2009-07-17 17:13 libGLw.so.1 -> libGLw.so.1.0.0
   20204 2008-05-27 13:02 libGLw.so.1.0.0

!!! NOTE:  Under Ubuntu libGLw.so.1 -> libGLw.so.1.0.0 expects libXm.so.3 (**)

 3080238 2007-04-30 05:42 libXm.a
      14 2009-08-25 17:37 libXm.so -> libXm.so.3.0.2
      14 2009-06-11 17:31 libXm.so.3 -> libXm.so.3.0.2    Needed by libGLw.so
 2349356 2007-04-30 05:42 libXm.so.3.0.2                  
      14 2009-07-17 15:56 libXm.so.2 -> libXm.so.2.0.1    
 1282384 2007-10-12 18:37 libXm.so.2.0.1                 

 
  429164 2007-05-21 08:27 libXt.a
      14 2009-07-17 15:45 libXt.so -> libXt.so.6.0.0
      14 2009-07-17 15:45 libXt.so.6 -> libXt.so.6.0.0
  326564 2007-05-21 08:27 libXt.so.6.0.0

   74970 2007-07-24 04:00 libXext.a
      16 2009-07-17 15:26 libXext.so -> libXext.so.6.4.0
      16 2008-11-10 06:30 libXext.so.6 -> libXext.so.6.4.0
   56156 2007-07-24 04:00 libXext.so.6.4.0

 1487004 2008-03-11 16:33 libX11.a
      15 2009-07-17 15:45 libX11.so -> libX11.so.6.2.0
      15 2009-07-17 15:45 libX11.so.6 -> libX11.so.6.2.0
  944876 2008-03-11 16:33 libX11.so.6.2.0

   11000 2009-08-19 12:13 libmmalloc.a                   (*)

 492842 2008-09-12 10:33 libm.a
     14 2009-07-17 15:26 libm.so -> /lib/libm.so.6
     11 2010-05-26 16:13 /lib/libm.so.6 -> libm-2.7.so
 145232 2010-05-21 14:12 /lib/libm-2.7.so
................................................................................

In /usr/lib/i686/cmov/ (in Ubuntu):

      19 2009-07-17 16:35 libGL.so.1 -> libGL.so.1.5.070002
 2414776 2008-04-05 18:06 libGL.so.1.5.070002

  149328 2009-08-17 21:04 libm-2.7.so
      11 2009-08-31 09:03 libm.so.6 -> libm-2.7.so

 1364388 2009-08-17 21:04 libc-2.7.so
      11 2009-08-31 09:03 libc.so.6 -> libc-2.7.so

................................................................................

!!! IMPORTANT !!!: In Red Hat Enterprise - we noticed missing definitions 
in the header file /usr/include/GL/GLwDrawA.h  - please copy the equivalent 
file from the sysname/lib-RHE subdirectory to your /usr/include/GL/

A sample listing of libraries found in Red Hat Enterprise 5.5 Linux 
(available from sysname/lib-RHE directory):
In /usr/lib:

    7946 2010-08-18 16:04 GLwDrawA.h-Ubu
    2126 2010-08-18 16:04 GLwMDrawA.h-Ubu-RHE

     654 2010-08-18 16:20 libGL.la
      10 2010-08-18 18:04 libGL.so -> libGL.so.1
      15 2010-08-18 18:04 libGL.so.1 -> libGL.so.256.35
  765460 2010-08-18 16:21 libGL.so.256.35            - comes with nvidia driver

      11 2010-08-18 18:04 libGLU.so -> libGLU.so.1
      20 2010-08-18 18:04 libGLU.so.1 -> libGLU.so.1.3.060501
  524008 2010-08-18 16:23 libGLU.so.1.3.060501

   27878 2010-08-18 17:16 libGLw.a      (*)
      11 2010-08-18 18:04 libGLw.so -> libGLw.so.1
      15 2010-08-18 18:04 libGLw.so.1 -> libGLw.so.1.0.0
   17144 2010-08-18 16:16 libGLw.so.1.0.0

!!!NOTE: Under Red Hat Enterprise libGLw.so expects libXm.so -> libXm.so.4.0.1 (**)

 3377306 2010-08-18 16:13 libXm.a
      10 2010-08-18 18:04 libXm.so -> libXm.so.4
      14 2010-08-18 18:04 libXm.so.4 -> libXm.so.4.0.1  - needed by RHE-compiled
 2637260 2010-08-18 16:12 libXm.so.4.0.1                  binaries to run
      14 2010-08-18 18:04 libXm.so.3 -> libXm.so.3.0.2  - needed by Ubuntu-compiled
 2542860 2010-08-18 16:12 libXm.so.3.0.2                  binaries to run

      15 2010-08-18 18:04 libX11.so -> libX11.so.6.2.0
      15 2010-08-18 18:04 libX11.so.6 -> libX11.so.6.2.0
 1062076 2010-08-18 17:12 libX11.so.6.2.0

      16 2010-08-18 18:04 libXext.so -> libXext.so.6.4.0
      16 2010-08-18 18:04 libXext.so.6 -> libXext.so.6.4.0
   62200 2010-08-18 17:15 libXext.so.6.4.0

      14 2010-08-18 18:04 libXt.so -> libXt.so.6.0.0
      14 2010-08-18 18:04 libXt.so.6 -> libXt.so.6.0.0
  359364 2010-08-18 16:27 libXt.so.6.0.0

   11000 2010-08-18 16:04 libmmalloc.a  (*) - same as in Ubuntu

      19     Jul 29 15:19 libm.so -> /lib/libm.so.6
      11     Jul 29 15:18 libm.so.6 -> libm-2.5.so
  216544     Jul 16 05:21 libm-2.5.so
-------------------------------------------------------------------------------

A listing of library dependencies for RNA2D3D via the command ldd:

1) Compiled on Ubuntu Linux (see above):

ldd ./bin/rna_2d3d
	linux-gate.so.1 =>  (0xb7f9f000)
	libGL.so.1 => /usr/lib/i686/cmov/libGL.so.1 (0xb7d2d000)
	libGLU.so.1 => /usr/lib/libGLU.so.1 (0xb7caa000)
	libXext.so.6 => /usr/lib/libXext.so.6 (0xb7c9b000)
	libX11.so.6 => /usr/lib/libX11.so.6 (0xb7bb4000)
	libXm.so.3 => /usr/lib/libXm.so.3 (0xb7974000)    (**)- see above
	libXt.so.6 => /usr/lib/libXt.so.6 (0xb7923000)
	libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb78fe000)
	libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb77af000)
	libpthread.so.0 => /lib/tls/i686/cmov/libpthread.so.0 (0xb7796000)
	libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0xb76a3000)
	libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb7698000)
	libXau.so.6 => /usr/lib/libXau.so.6 (0xb7695000)
	libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0xb7693000)
	libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb767a000)
	libdl.so.2 => /lib/tls/i686/cmov/libdl.so.2 (0xb7676000)
	libXmu.so.6 => /usr/lib/libXmu.so.6 (0xb7660000)
	libSM.so.6 => /usr/lib/libSM.so.6 (0xb7658000)
	libICE.so.6 => /usr/lib/libICE.so.6 (0xb7640000)
	libXp.so.6 => /usr/lib/libXp.so.6 (0xb7638000)
	/lib/ld-linux.so.2 (0xb7fa0000)
	libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0xb7632000)

2) Compiled on RHE 5.5 Linux (see above):

ldd ./bin/rna_2d3d
linux-gate.so.1 =>  (0xffffe000)
	libGLw.so.1 => /usr/lib/libGLw.so.1 (0xf7f65000)
	libGL.so.1 => /usr/lib/libGL.so.1 (0xf7e9a000)
	libGLU.so.1 => /usr/lib/libGLU.so.1 (0xf7e1a000)
	libXext.so.6 => /usr/lib/libXext.so.6 (0x00c70000)
	libX11.so.6 => /usr/lib/libX11.so.6 (0x00ab7000)
	libXm.so.4 => /usr/lib/libXm.so.4 (0xf7b95000)    (**)- see above
	libXt.so.6 => /usr/lib/libXt.so.6 (0x0723d000)
	libm.so.6 => /lib/libm.so.6 (0x008f1000)
	libc.so.6 => /lib/libc.so.6 (0x00775000)
	libnvidia-tls.so.256.35 => /usr/lib/tls/libnvidia-tls.so.256.35 (0xf7b92000)
	libnvidia-glcore.so.256.35 => /usr/lib/libnvidia-glcore.so.256.35 (0xf6662000)
	libdl.so.2 => /lib/libdl.so.2 (0x008ea000)
	libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x0091c000)
	libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00aa1000)
	libXau.so.6 => /usr/lib/libXau.so.6 (0x00bbc000)
	libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00aaf000)
	libXmu.so.6 => /usr/lib/libXmu.so.6 (0xf664a000)
	libXp.so.6 => /usr/lib/libXp.so.6 (0xf6641000)
	libXft.so.2 => /usr/lib/libXft.so.2 (0x006cd000)
	libXrender.so.1 => /usr/lib/libXrender.so.1 (0x00a96000)
	libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0x0066c000)
	libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0x005ea000)
	libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x00d49000)
	libpng12.so.0 => /usr/lib/libpng12.so.0 (0x00bd3000)
	libSM.so.6 => /usr/lib/libSM.so.6 (0x00c82000)
	libICE.so.6 => /usr/lib/libICE.so.6 (0x00c8d000)
	/lib/ld-linux.so.2 (0x00756000)
	libexpat.so.0 => /lib/libexpat.so.0 (0x00c4d000)
	libz.so.1 => /usr/lib/libz.so.1 (0x00bfb000)

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Appendix B:
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From: Ubuntu Forums > Ubuntu Forum Community > Other Community Discussions >
 Development & Programming > Programming Talk > Where is Motif?

---------------------------------------------------------------------------------
Q: I am an Ubuntu newbie wanting the Motif header files for C/C++ programming. 
Where/how can I find these and, if there is some form of search facility, 
what search key to use? (Sep. 2008)

=================================================================================
KEY INFO IN RESPONSE:

edb@lapedb:~$ apt-cache search motif | grep dev

freeglut3-dev - OpenGL Utility Toolkit development files
libglut3-dev - development libraries and headers for GLUT
libxt-dev - X11 toolkit intrinsics library (development headers)
libzephyr-dev - The original "Instant Message" system development libraries
tk8.4-dev - Tk toolkit for Tcl and X11, v8.4 - development files
lesstif2-dev - development library and header files for LessTif 2.1
libvibrant6-dev - NCBI libraries for graphic biology applications (development)
libwxgtk2.4-contrib-dev - wxWindows Cross-platform C++ GUI toolkit (devel.libs)
libwxgtk2.4-dbg - wxWindows Cross-platform C++ GUI toolkit (GTK+ development)
libwxgtk2.4-dev - wxWindows Cross-platform C++ GUI toolkit (GTK+ development)
libxbae-dev - Xbae Matrix Widget development package
tk-dev - The Tk toolkit for Tcl and X11 (default version) - development files
tk8.3-dev - Tk toolkit for Tcl and X11, v8.3 - development files
tk8.5-dev - Tk toolkit for Tcl and X11, v8.5 - development files
xmhtml1-dev - A Motif widget for display HTML 3.2
libmotif-dev - Open Motif - development files


So you probably want to install the last one:
sudo apt-get install libmotif-dev


To see what files are in an installed package:
dpkg -L libmotif-dev

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This document has been written by Voytek Kasprzak, kasprzaw@mail.nih.gov
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