[Chimera-users] delphi

[Elaine Meng]

Hi Darren,
Unfortunately it is an unsolved problem getting a pre-made delphi  
executable for Mac OSX that gives results that can be shown in  
Chimera.  Just to clarify for everybody, DelPhi is a program freely  
provided by another group, but without official support.

I went through several weeks of trying to get an older executable from  
the Honig site to work, installing various files myself just as you  
have.  Here is the chimera-users message where I describe running up  
against this wall:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-November/001113.html 
 >

I reported these problems to the Honig group, and some months later  
(July 2008) they updated their Mac OSX Intel executable so it does not  
require these additional libraries.  Maybe you downloaded an  
executable before that time or have a PPC Mac rather than Intel.   
Honig group DelPhi download page:
<http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:DelPhi_System_Requirements 
 >

However, although the Intel executable runs nicely and can be  
controlled by DelPhiController, something about the map format changed  
and Chimera cannot read the result.  We were unable to get information  
from the Honig lab on how the format changed, or even reverse-engineer  
the changes given our example maps.  There is nothing else we can do -  
it is a limitation recorded in our database as problem report #6228.

Possible solutions are to use DelPhi on a different type of computer,  
use one of the other Poisson-Boltzmann programs that produces files  
that Chimera understands (Grasp, APBS, UHBD):
<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html#esp 
 >

Actually in May 2008 I found one web server that will calculate an  
electrostatic potential map and let you download it (so results can be  
viewed in Chimera).  There are some complications with using it, but  
perhaps that's still easier than the alternatives.  Here is what I  
wrote in May - haven't tried it since then:
------------
webPIPSA  web server for Protein Interaction Property Similarity  
Analysis
http://pipsa.eml.org
focused on performing a calculation on multiple proteins and comparing  
them (won't let you proceed until you specify at least two), choice of  
using UHBD or APBS
input: upload PDB files or specify PDB IDs, email address for getting  
results
output: dendrogram and heat map comparing the results for the multiple  
proteins, optional download of zip file with intermediate results  
(includes map files and corresponding PDBs)
  - my first attempt with two structures and align "none" and use UHBD  
failed...I guess you are only supposed to use "none" if the proteins  
are already superimposed, which they weren't because I didn't care  
about the comparison
  - second attempt with align option "sup2pdbs" and use UHBD was  
successful.  In Chimera, should probably only view the maps along with  
the corresponding PDBs from the intermediate results since they may  
have been transformed (in the superposition step)
-----------

Good luck,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html



On Dec 30, 2008, at 12:41 PM, Darren Thompson wrote:

> I installed the ibm compiler libraries on Mac OSX tiger, but delphi  
> still does not see them
>
> Applications            System Folder           mach.sym
> Applications (Mac OS 9) TheVolumeSettingsFolder mach_kernel
> Desktop (Mac OS 9)      Trash                   opt
> Desktop DB              Users                   private
> Desktop DF              Volumes                 sbin
> Desktop Folder          automount               sw
> Developer               bin                     tmp
> Documents               cores                   usr
> Library                 dev                     var
> Network                 etc
> System                  mach
>
> the opt folder (ibm) is there.
>
> I did a symbolic link to the Mac OSX executable in the /usr/local/ 
> release1.1/exe directory to /usr/bin/delphi, downloaded the example  
> files from delphi's website,
> [psb-232-45:release1.1/examples/example_1] darren% delphi param_1
> dyld: Library not loaded: /opt/ibmcmp/lib/libxlf90.dylib
>   Referenced from: /usr/bin/delphi
>   Reason: image not found
> Trace/BPT trap
>
> when I try directly
> [psb-232-45:local/release1.1/exe] darren% ./delphiMacOSX
> dyld: Library not loaded: /opt/ibmcmp/lib/libxlf90.dylib
>   Referenced from: /usr/local/release1.1/exe/./delphiMacOSX
>   Reason: image not found
> Trace/BPT trap
>
> Does it matter that it's looking for /libxlf90.dylib and I have / 
> libxlf90.A.dylib?
>
> Have some xmas charity
> Help a newb
>
> Darren Thompson
> Graduate Student
> UCSC
> 1156 High St.
> Santa Cruz, CA 95064
> 831-459-3390  voice
> 831-459-2395 fax
> http://people.ucsc.edu/~ministry