Re: [Apbs-users] charge density plot
Biomolecular electrostatics software
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From: Nathan B. <nat...@wu...> - 2006-03-24 12:52:18
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Todd is out of town right now but is definitely the most natural person to help with this. Did you compile the Python tools when you built APBS? In the meantime, I'd encourage you to either familiarize yourself with Python or with the value.c C code so you can develop your own analysis tools for this. The type of analysis you describe is almost certainly a "custom" task and it's hard to support a lot of these from our end.=20 On the other hand, if there are things we can do to help you get going with the Python (or C) code, we'd be happy to help. Thanks, Nathan On 3/24/06, L. Michel Espinoza-Fonseca <me...@dd...> wrote: > That's the point: I'm not very familiar with Python. I tried to > execute the file vgrid.py, and what I get is "ImportError: No module > named _vgrid". I know this is something basic, but I'd really > appreciate your help! > > Thanks > Michel > > 2006/3/23, Nathan Baker <sob...@my...>: > > Do you know Python? That's the easiest way to use these tools. Through= Python, you could > > 1. Read in the charge density OpenDX file written by APBS > > 2. Set up points at the different distances you want evaluate > > 3. Evaluate through the Vgrid::value class method at the different poin= ts > > 4. Average, plot, or whatever else you want to do > > > > -- > > Assistant Professor, Dept. of Biochemistry and Molecular Biophysics > > Center for Computational Biology, Washington University in St. Louis > > Web: http://cholla.wustl.edu/ > > > > -----Original Message----- > > From: "L. Michel Espinoza-Fonseca" <me...@dd...> > > Date: Mon, 20 Mar 2006 19:17:08 > > To:"Nathan Baker" <nat...@wu...> > > Cc:apb...@li... > > Subject: Re: [Apbs-users] charge density plot > > > > Thanks for the suggestions. However, I really don't know from where to > > start... Could you give me some guidance, please? > > > > Again, thanks. > > > > Michel > > > > 2006/3/18, Nathan Baker <nat...@wu...>: > > > The best way to do that is to modify the code in tools/mesh/value.c o= r > > > tools/python/vgrid to extract values from a charge density OpenDX map= . > > > Of these two options, the Python code in tools/python/vgrid is > > > probably the easiest... > > > > > > Thanks, > > > > > > Nathan > > > > > > On 3/16/06, L. Michel Espinoza-Fonseca <me...@dd...> wrot= e: > > > > Dear all, > > > > > > > > I'm computing the charge density around a protein using APBS. I got= a > > > > very homogeneous charge surfaces, which is what I want to demonstra= te. > > > > However, I would like to know if it is possible to get a x-y plot o= f > > > > density vs distance (let's say, starting from a cutoff of 3.5-4 A), > > > > which will make my analysis get closer to more quantitative approac= h. > > > > > > > > Thanks a lot! > > > > Michel > > > > > > > > > > > > ------------------------------------------------------- > > > > This SF.Net email is sponsored by xPML, a groundbreaking scripting = language > > > > that extends applications into web and mobile media. Attend the liv= e webcast > > > > and join the prime developer group breaking into this new coding te= rritory! > > > > http://sel.as-us.falkag.net/sel?cmd________________________________= _______________ > > > > apbs-users mailing list > > > > apb...@li... > > > > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > > > > > > > > > > > > > > -- > > > Assistant Professor, Dept. of Biochemistry and Molecular Biophysics > > > Center for Computational Biology, Washington University in St. Louis > > > Web: http://cholla.wustl.edu/ > > > > > > > > > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |