[Chimera-users] Electrostatic Potential Visualization

Tue Aug 25 09:12:09 PDT 2015

Hello Minju,
In the APBS dialog, you must specify the PDB2PQR output — NOT your original structure — as the input Molecule.  The APBS manual page and the tutorial both say this, but still it is a common problem…
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-July/011258.html>
Best,
Elaine

> On Aug 24, 2015, at 10:46 AM, Chun, Minju <minju.chun at pnnl.gov> wrote:
> 
> Hello,
> 
> Thanks for the quick reply!
> 
> I have run it through PDB2PQR where it added hydrogens and optimized the protein.
> 
> I still have the same error though, so I was wondering if there was something else wrong.
> 
> Thanks,
> 
> Minju Chun
> 
> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
> Sent: Monday, August 24, 2015 10:44 AM
> To: Chun, Minju
> Cc: chimera-users at cgl.ucsf.edu BB
> Subject: Re: [Chimera-users] Electrostatic Potential Visualization
> 
> Helo Minju,
> As I already said in (C) below, and also done if you follow the tutorial "Electrostatic Potential: Poisson-Boltzmann” section, you have to run PDB2PQR before you run APBS.
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
> 
> Best,
> Elaine
> 
>> On Aug 24, 2015, at 9:04 AM, Chun, Minju <minju.chun at pnnl.gov> wrote:
>> 
>> Hello,
>> 
>> Thank you very much for all the help!
>> 
>> One quick question, after deciding on the APBS route, even after I run the protein through APBS it says:
>> 
>> Charges are missing for some atoms.
>> Please run Add Charge or PDB2PQR.
>> 
>> Do you have a workaround for this?
>> 
>> Thank you,
>> 
>> Minju Chun
>> 
>> -----Original Message-----
>> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
>> Sent: Friday, August 21, 2015 10:43 AM
>> To: Chun, Minju
>> Cc: chimera-users at cgl.ucsf.edu
>> Subject: Re: [Chimera-users] Electrostatic Potential Visualization
>> 
>> Hello Minju,
>> All of those things are possible: opening electrostatic potential files from other programs, or using Chimera to calculate and display electrostatic potential, and they are covered in the "Surface Properties" image tutorial:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.h
>> tml>
>> 
>> (You can also see the tutorials from the Chimera menu: Help... Tutorials).  You don't have to install any separate plug-in, just make sure you have a fairly recent version of Chimera (current release is 1.10.2). The tutorial has step-by-step instructions, but I'll outline three possibilities here:
>> 
>> (A) If you have already calculated electrostatic potential (ESP) with some other program, it should be very easy.  All you have to do is open your structure, display a surface for the structure, and open the electrostatic potential file.  The electrostatic potential file formats that Chimera knows about, and how they should be named (*.dx etc.) are listed here:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp>
>> 
>> When you open one of those file types, the Surface Color dialog should open automatically, and then you can use it to color the surface already displayed for your structure according to the data in the ESP file.  Remember you have to display the surface before you can color it!
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/s
>> urfcolor.html>
>> 
>> (B) The second easiest is to use Chimera to calculate and display Coulombic electrostatic potential, as in the "Electrostatic Potential: Coulombic" section of the tutorial. It is a simpler approach than APBS, but often shows very similar results for display purposes.  You would open your structure, display a surface, and then use Coulombic Surface Coloring (in menu under Tools... Surface/Binding Analysis).
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/c
>> oulombic.html>
>> 
>> (C) The APBS approach has more steps because you first need to run PDB2PQR to add charges to your structure, and then you need to use the result from PDB2PQR as input to the APBS calculation.  Both of these tools are in the Chimera menu under Tools.. Surface/Binding Analysis.  When the APBS calculation is done it will open the resulting *.dx ESP file, and then it is the same as (A) above.  This is the "Electrostatic Potential: Poisson-Boltzmann" section of the tutorial.  You can also click the Help button on each tool to open its manual page:
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pq
>> r.html> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.h
>> tml>
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department 
>> of Pharmaceutical Chemistry University of California, San Francisco
>> 
>> On Aug 21, 2015, at 8:05 AM, Chun, Minju <minju.chun at pnnl.gov> wrote:
>> 
>>> Hello,
>>> I am an intern working with Chimera, and I was wondering if I was missing a plug-in that calculated electrostatic potential.
>>> 
>>> I attempted to load a dx and cube file to emulate electrostatic potential, but there seemed to be a problem finding/reading the files(perhaps I'm doing this wrong too). I thought that if I calculated electrostatic potential directly with Chimera, I could see electrostatic potential.
>>> 
>>> It says on your website that Chimera can calculate the electrostatic potential with APBS:
>>> "electrostatic potential calculated with Adaptive Poisson-Boltzmann 
>>> Solver (APBS); the APBS tool in Chimera runs this program via web service provided by the NBCR"
>>> 
>>> Do you have a tutorial that goes in more detail in how to calculate potential with APBS?
>>> Thank you,
>>> Minju Chun
>> 
>> 
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