Thread: Re: [apbs-users] Retrieval of the charge of a particular residues after the visualization of the el
Biomolecular electrostatics software
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From: Baker, N. <Nat...@pn...> - 2012-10-09 13:24:38
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Hello -- We do not have the simple mechanism that you describe but you should be able to extract the box dimensions for each residue via a simple script. In particular, the psize.py script provided with APBS (http://apbs.svn.sourceforge.net/viewvc/apbs/trunk/tools/manip/) may help with your analysis — it could be run on a series of PDB or PQR files that contain each residue of the protein. Good luck, -- Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me From: Wing <whh...@gm...<mailto:whh...@gm...>> Date: Sunday, October 7, 2012 8:21 PM To: APBS-USERS mailing list <apb...@go...<mailto:apb...@go...>> Cc: Wing <whh...@gm...<mailto:whh...@gm...>> Subject: Re: [apbs-users] Retrieval of the charge of a particular residues after the visualization of the electrostatic potential Hi Keith, Thanks a lot for your kind info! I am interested in 2) the electrostatic potential at a particular location. I have just visited the page explaining the "mergedx2 utility", and I have seen an example command line for -b flag: ./mergedx2 -b -3.13 -2.0 -2.14 31.0 25.4 22.1 file1.dx file2.dx file3.dx May I ask 2 silly questions? (i) where can I find the "xmin ymin zmin xmax ymax zmax" for a particular residue in a visualization? Or would it be possible to specify a residue position say "65th amino acid residues" in the command line? (ii) for "file1.dx file2.dx file3.dx", does it mean the file name of my visualization of electrostatic potential? Sorry for bothering again ... Best regards, Wing On Sunday, October 7, 2012 7:48:39 PM UTC+2, Keith Callenberg wrote: Hi Wing, Are you interested in 1) the components of the total energy that are due to particular atoms in the system or 2) the electrostatic potential at particular locations in the system? If you are interested in 1: I don't use the PyMol interface, so I can't speak for whether this functionality is part of that interface, but in order to get the energy that is associated with particular atoms, you need to use the "calcenergy comps" keyword. See http://www.poissonboltzmann.org/apbs/user-guide/running-apbs/input-files/elec-input-file-section/elec-keywords/calcenergy. If the APBS interface in PyMol does not have this set in its APBS input file, you'll need to add it and re-run the calculation from the command-line. If you are interested in 2: Extracting the electrostatic potential for a particular region of the system can be done in a few different ways. One way is using the mergedx2 utility provided in the share/tools/mesh directory. You can use the -b bounds flag to set the part of the system you are interested in. This will give you a new dx file with only the potential values for that region. See http://www.poissonboltzmann.org/apbs/user-guide/apbs-tools/mesh-tools/mergedx2 for more details. Keith On Sun, Oct 7, 2012 at 4:58 AM, Wing <whho...@gmail.com<javascript:>> wrote: > Dear all, > > I am a beginning for using APBS, sorry if I have asked a silly question ... > > I work with a protein that the charge of one of its particular surface is > critical for binding of its ligand, and the charge of this surface can be > determined by a residues at position X. Now amongst the 19 remaining amino > acids, I would like to find out in which amino acid mutation can lead to the > most significant reversion of charge (e.g. positive to negative charge) of > the surface. But rather than just using the APBS tool to visualize the > electrostatic potential after each of the 19 mutations, I will need to > present my the charge value of position X "quantitatively" (in unit of > either "mV" or " dimensionless units of kb T ec-1". ) > > May I ask, after the visualization, would there be any way that I can > retrieval the charge of a residues at a particular position after the > visualization of electrostatic potential of my protein (I am using PyMol in > Mac)? > > Many thanks for your kind reply in advance! > > Yours faithfully, > > Wing > > ------------------------------------------------------------------------------ > Don't let slow site performance ruin your business. Deploy New Relic APM > Deploy New Relic app performance management and know exactly > what is happening inside your Ruby, Python, PHP, Java, and .NET app > Try New Relic at no cost today and get our sweet Data Nerd shirt too! > http://p.sf.net/sfu/newrelic-dev2dev > _______________________________________________ > apbs-users mailing list > apbs-...@lists.sourceforge.net<javascript:> > https://lists.sourceforge.net/lists/listinfo/apbs-users > -- Keith M. Callenberg Ph.D. Candidate, Computational Biology Carnegie Mellon University-University of Pittsburgh kmc112@{pitt,cmu}.edu http://www.pitt.edu/~kmc112/ |