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
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_Syst...
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@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
Hi Darren and others, I forgot to mention a recent development that might interest you: We recently added a Coulombic Surface Coloring tool (under Tools... Surface/Binding Analysis, not yet documented). This is for people who want to color by electrostatic potential but can't or prefer not to run any of the continuum electrostatics programs (DelPhi, APBS, UHBD) - it associates the atoms with partial charges from AMBER, calculates a Coulombic potential, and allows you to color the molecular surface by those values. The Coulombic potential is cruder than what you get from Poisson-Boltzmann calculations, but our comparisons on a handful of structures showed the same qualitative results (bluest and reddest patches generally in the same places). This is only available in the daily builds, not the recent production release. Users should also be aware it is still being improved upon and various behaviors may change. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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 4:55 PM, Elaine Meng wrote:
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@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
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Darren Thompson -
Elaine Meng