From: Ann M. <am...@tu...> - 2004-09-01 21:13:45
|
Hi, All I want to do is be able to create an electrostatic surface representation of a simple molecule. I am seriously overwhelmed by the information for compiling and setting APBS on their website. I was happy to fine a link to download a package with an installer, but when I run it it fails at the very end and tells me to try installing again. Also, is there any place that I should be installing this? I tried in the Applications folder and in the folder I made to surround PyMOL and it's user manual. I also notice that there is a binary ready to use for G5 on the website, but where do I put this to work, and where is the psize.py file. I rarely work on a UNIX platform and I have a very hard time switching from macOS to UNIX and back, since macOS is almost all point and click. Thanks for any help. Ann Ann Mullin Research Scientist Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) am...@tu... |
From: Michael G. L. <ml...@um...> - 2004-09-02 15:36:23
|
Hi, I don't have a Mac, so I can't really help you here .. I know there are quite a few people on the PyMOL list who've gotten APBS to work on Macs, though, so maybe one of them will chime in. If you don't get help here, you can probably get some more advice on the APBS mailing list. In case you didn't sign up when you downloaded APBS, the webpage is http://cholla.wustl.edu/mailman/listinfo/apbs-users Once you get APBS installed, the APBS+PyMOL plugin should just work (it doesn't really need APBS's psize.py). But .. can anyone who has installed APBS on this platform tell me where APBS puts psize.py? I'd like to list that on my webpage. Thanks, -michael -- This isn't a democracy;| _ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mlerner@umich On Wed, 1 Sep 2004, Ann Mullin wrote: > Hi, > All I want to do is be able to create an electrostatic surface > representation of a simple molecule. > > I am seriously overwhelmed by the information for compiling and setting > APBS on their website. I was happy to fine a link to download a > package with an installer, but when I run it it fails at the very end > and tells me to try installing again. Also, is there any place that I > should be installing this? I tried in the Applications folder and in > the folder I made to surround PyMOL and it's user manual. > > I also notice that there is a binary ready to use for G5 on the > website, but where do I put this to work, and where is the psize.py > file. I rarely work on a UNIX platform and I have a very hard time > switching from macOS to UNIX and back, since macOS is almost all point > and click. > > Thanks for any help. Ann > > > Ann Mullin > Research Scientist > Cell and Molecular Biology Dept. > Tulane University > New Orleans, LA 70118-5698 > 504-865-6742 (Ph) > 504-865-6785 (FAX) > am...@tu... > |
From: Alex W. S. <ale...@as...> - 2004-09-02 18:04:21
|
Michael: I followed the directions for installing from source and used Bill Scott's tweak (both links below). Everything seems to be running fine. I am a bit short of memory using my Al G4PB, but everything configured and complied with no problems. I have only used APBS with the Pymol plugin but it seems to run fine. Slow but fine. http://agave.wustl.edu/apbs/doc/html/user-guide/x122.html http://chips.csb.ki.se/pymol/msg02192.html I created the directory /usr/local/APBS. Then made all the directories the instructions called for within the APBS directory I created. The psize.py script ended up in /usr/local/APBS/src/apbs-0.3.1/tools/manip/psize.py Alex On Sep 2, 2004, at 8:36 AM, Michael George Lerner wrote: > > Hi, > > I don't have a Mac, so I can't really help you here .. I know there are > quite a few people on the PyMOL list who've gotten APBS to work on > Macs, > though, so maybe one of them will chime in. If you don't get help > here, > you can probably get some more advice on the APBS mailing list. In > case > you didn't sign up when you downloaded APBS, the webpage is > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > Once you get APBS installed, the APBS+PyMOL plugin should just work (it > doesn't really need APBS's psize.py). > > But .. can anyone who has installed APBS on this platform tell me where > APBS puts psize.py? I'd like to list that on my webpage. > > Thanks, > > -michael > > -- > This isn't a democracy;| _ |Michael Lerner > it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan > -Torrence, Bring It On| - against HTML email X | Biophysics > | / \ | mlerner@umich > > On Wed, 1 Sep 2004, Ann Mullin wrote: > >> Hi, >> All I want to do is be able to create an electrostatic surface >> representation of a simple molecule. >> >> I am seriously overwhelmed by the information for compiling and >> setting >> APBS on their website. I was happy to fine a link to download a >> package with an installer, but when I run it it fails at the very end >> and tells me to try installing again. Also, is there any place that I >> should be installing this? I tried in the Applications folder and in >> the folder I made to surround PyMOL and it's user manual. >> >> I also notice that there is a binary ready to use for G5 on the >> website, but where do I put this to work, and where is the psize.py >> file. I rarely work on a UNIX platform and I have a very hard time >> switching from macOS to UNIX and back, since macOS is almost all point >> and click. >> >> Thanks for any help. Ann >> >> >> Ann Mullin >> Research Scientist >> Cell and Molecular Biology Dept. >> Tulane University >> New Orleans, LA 70118-5698 >> 504-865-6742 (Ph) >> 504-865-6785 (FAX) >> am...@tu... >> > > > ------------------------------------------------------- > This SF.Net email is sponsored by BEA Weblogic Workshop > FREE Java Enterprise J2EE developer tools! > Get your free copy of BEA WebLogic Workshop 8.1 today. > http://ads.osdn.com/?ad_id=5047&alloc_id=10808&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Michael B. <mb...@uv...> - 2004-09-02 21:23:21
|
On Sep 2, 2004, at 2:03 PM, Alex W. Smith wrote: > Michael: > I followed the directions for installing from source and used Bill > Scott's tweak (both links below). Everything seems to be running > fine. I am a bit short of memory using my Al G4PB, but everything > configured and complied with no problems. I have only used APBS with > the Pymol plugin but it seems to run fine. Slow but fine. Hi Alex, and anyone else who might have a suggestion here; I am also trying to use APBS for electrostatics in PyMOL. Running a G4 AlBook, 10.3.5, Apple's X11, latest fink, XCodeTools 1.0 (I havent upgraded to 1.5 yet). But I got the personal attention of my Unix guru for a while today and made some progress installing from source. He helped me get maloc installed in /usr/local by using ./configure --prefix=/usr/local Then I started on APBS, by following Bill Scott's tips, summarized here: 1. start up zsh (to make use of its recursive globbing capability) 2. ./configure 3a. perl -pi -e 's|\-L/usr/local/|\-lcc_dynamic \-L/usr/local/|g' **/Makefile 3b. make 3c. make install I got the following errors that stopped the make: g77 -g -O2 -g -O2 -o apbs main.o routines.o -L/Users/mbovee/lib/powerpc-apple-darwin7.5.0 ../src/aaa_lib/.libs/libapbs.a -L/Users/mbovee/Desktop/apbs-0.3.1/lib /usr/local/lib/powerpc-apple-darwin7.5.0/libmaloc.a /usr/local/lib/powerpc-apple-darwin7.5.0/libblas.a /usr/local/lib/powerpc-apple-darwin7.5.0/libvf2c.a -lm /usr/bin/ld: warning -L: directory name (/Users/mbovee/lib/powerpc-apple-darwin7.5.0) does not exist /usr/bin/ld: warning -L: directory name (/Users/mbovee/Desktop/apbs-0.3.1/lib) does not exist /usr/bin/ld: Undefined symbols: restFP saveFP collect2: ld returned 1 exit status make[1]: *** [apbs] Error 1 make: *** [all-recursive] Error 1 doing a little more checking on these undefined symbols, I find: $ nm *.a |grep restFP U restFP U restFP $ nm *.a |grep saveFP U saveFP U saveFP Can anyone tell me where these symbols are defined, or what I screwed up? Maybe I should just start over and let the scripts install everything in my homedir automatically... --Michael |
From: Luca J. <luc...@ma...> - 2004-09-02 21:52:11
|
> /usr/bin/ld: Undefined symbols: > restFP > saveFP > collect2: ld returned 1 exit status Hi Michael, these symbols are in: /usr/lib/libgcc.a try linking with -lgcc ! -Luca -------------------------------------------------------- Luca Jovine, Ph.D. Brookdale Department of Molecular, Cell & Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 One Gustave L. Levy Place, New York, NY 10029-6574, USA Voice: +1.212.241-8620 FAX: +1.360.926-1823 E-Mail: luc...@ma... - luc...@ms... W3: http://www.mssm.edu/students/jovinl02 -------------------------------------------------------- |
From: Ann M. <am...@tu...> - 2004-09-02 19:56:04
|
I have X11 and developer tools. I can get maloc installed, but when I configure apbs, I get: checking build system type... powerpc-apple-darwin7.5.0 checking host system type... powerpc-apple-darwin7.5.0 ... ... checking if Fortran 77 compiler accepts -nofor_main... no checking how f77 mangles function names... configure: error: failed to compile fortran test program I also notice that the same place that has APBS has this site that computes electrostatics from a PDB file and returns a PQR file. This would be lovely for people like me to use for the calculations. Now how can I use the PQR file to create an electrostatic surface with pymol? Ann Ann Mullin Research Scientist Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) am...@tu... On Sep 1, 2004, at 5:26 PM, Alex W. Smith wrote: > Ann: > > The first question is do you have the Apple X11 and Developer tools > installed. If you don't you will have to get them installed before > you do anything. If you have them installed then the directions below > should help out. > > I just got through doing all this for my G4 AlPB. Turns out I need > more memory but everything works fine. It may seem like a lot at > first but installing from source (especially on a OS X box) is > probably the best bet. I tried the binary for G4 and had some library > problems. Below are two links that helped me a lot. The first is > directions for installing from source. Be sure to get the MALOC (link > is on the first webpage) tar file as well as the APBS. Start out with > the Installation directories. Be sure to list the directory name > properly (i.e. change export FETK_SRC=/home/soft/src to the > directories you want to install to. > Then just move both tar files to the /home/soft/src (or whatever you > call it) directory. Then just follow the directions for MALOC. > > For APBS, just follow the directions for unpacking APBS. Then follow > Bill Scott's tweak (http://chips.csb.ki.se/pymol/msg02192.html). It > should not take that long to compile them both. > > Once APBS is installed you can use the plugin to find the binary, > which will be in the apbs/bin directory. > > > Don't let the source code install scare you. They are easy enough to > beat after a bit. > Hope this helps. > > Alex > > http://agave.wustl.edu/apbs/doc/html/user-guide/x122.html > http://chips.csb.ki.se/pymol/msg02192.html > > > > > On Sep 1, 2004, at 2:12 PM, Ann Mullin wrote: > >> Hi, >> All I want to do is be able to create an electrostatic surface >> representation of a simple molecule. >> >> I am seriously overwhelmed by the information for compiling and >> setting APBS on their website. I was happy to fine a link to >> download a package with an installer, but when I run it it fails at >> the very end and tells me to try installing again. Also, is there >> any place that I should be installing this? I tried in the >> Applications folder and in the folder I made to surround PyMOL and >> it's user manual. >> >> I also notice that there is a binary ready to use for G5 on the >> website, but where do I put this to work, and where is the psize.py >> file. I rarely work on a UNIX platform and I have a very hard time >> switching from macOS to UNIX and back, since macOS is almost all >> point and click. >> >> Thanks for any help. Ann >> >> >> Ann Mullin >> Research Scientist >> Cell and Molecular Biology Dept. >> Tulane University >> New Orleans, LA 70118-5698 >> 504-865-6742 (Ph) >> 504-865-6785 (FAX) >> am...@tu... > |
From: Michael G. L. <ml...@um...> - 2004-09-02 21:14:07
|
> I also notice that the same place that has APBS has this site that > computes electrostatics from a PDB file and returns a PQR file. This > would be lovely for people like me to use for the calculations. Now > how can I use the PQR file to create an electrostatic surface with > pymol? A PQR file is like a PDB file, but it includes charge and radius information that is used by programs like APBS to generate electrostatic potential surfaces. PyMOL can generate PQR files (e.g. via the APBS Plugin), as can the PDB2PQR web portal that you found on the APBS website. If you can't get APBS installed locally, you may be able to use the APBS web portal (https://gridport.npaci.edu/apbs/) to run the APBS calculations. I don't think that's as convenient as APBS+PyMOL, but it's definately an option if you can't get APBS installed. Hopefully, some Mac-savvy person will be able to help you with the Fortran problems. -michael > > Ann > > Ann Mullin > Research Scientist > Cell and Molecular Biology Dept. > Tulane University > New Orleans, LA 70118-5698 > 504-865-6742 (Ph) > 504-865-6785 (FAX) > am...@tu... > On Sep 1, 2004, at 5:26 PM, Alex W. Smith wrote: > > > Ann: > > > > The first question is do you have the Apple X11 and Developer tools > > installed. If you don't you will have to get them installed before > > you do anything. If you have them installed then the directions below > > should help out. > > > > I just got through doing all this for my G4 AlPB. Turns out I need > > more memory but everything works fine. It may seem like a lot at > > first but installing from source (especially on a OS X box) is > > probably the best bet. I tried the binary for G4 and had some library > > problems. Below are two links that helped me a lot. The first is > > directions for installing from source. Be sure to get the MALOC (link > > is on the first webpage) tar file as well as the APBS. Start out with > > the Installation directories. Be sure to list the directory name > > properly (i.e. change export FETK_SRC=/home/soft/src to the > > directories you want to install to. > > Then just move both tar files to the /home/soft/src (or whatever you > > call it) directory. Then just follow the directions for MALOC. > > > > For APBS, just follow the directions for unpacking APBS. Then follow > > Bill Scott's tweak (http://chips.csb.ki.se/pymol/msg02192.html). It > > should not take that long to compile them both. > > > > Once APBS is installed you can use the plugin to find the binary, > > which will be in the apbs/bin directory. > > > > > > Don't let the source code install scare you. They are easy enough to > > beat after a bit. > > Hope this helps. > > > > Alex > > > > http://agave.wustl.edu/apbs/doc/html/user-guide/x122.html > > http://chips.csb.ki.se/pymol/msg02192.html > > > > > > > > > > On Sep 1, 2004, at 2:12 PM, Ann Mullin wrote: > > > >> Hi, > >> All I want to do is be able to create an electrostatic surface > >> representation of a simple molecule. > >> > >> I am seriously overwhelmed by the information for compiling and > >> setting APBS on their website. I was happy to fine a link to > >> download a package with an installer, but when I run it it fails at > >> the very end and tells me to try installing again. Also, is there > >> any place that I should be installing this? I tried in the > >> Applications folder and in the folder I made to surround PyMOL and > >> it's user manual. > >> > >> I also notice that there is a binary ready to use for G5 on the > >> website, but where do I put this to work, and where is the psize.py > >> file. I rarely work on a UNIX platform and I have a very hard time > >> switching from macOS to UNIX and back, since macOS is almost all > >> point and click. > >> > >> Thanks for any help. Ann > >> > >> > >> Ann Mullin > >> Research Scientist > >> Cell and Molecular Biology Dept. > >> Tulane University > >> New Orleans, LA 70118-5698 > >> 504-865-6742 (Ph) > >> 504-865-6785 (FAX) > >> am...@tu... > > |