> 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) > amul...@tulane.edu > 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) > >> amul...@tulane.edu > >
