I have to show electrostatic surface potential of a PDB code. I tried using APBS pymol but I don't understand why it doesn't work. I followed the tutorials available online but did't work. Can someone help me with that?
Which version of PyMOL are you using? Which operating system? In what way does it "not work"? Do you get any error message? Are there any peculiarities in your molecule? Which PDB file did you use? Did you do anything to prepare the object?
Since on my system (Mac OsX 10.14.2, PyMOL incentive version 2.2.0) a quick test running an arbitrary molecule (unliganded Fab fragment) runs fine using just the default settings in the ABPS Plugin (basically just hitting run), I need to know more about what is different in your case to find out what went wrong.
I agree with Annemarie Honegger, please also record your work. This can be done by using log_open somefile.pml. This way we could understand what you are trying to do.
I have the version 1.7 of pymol (with the latter versions I had problems with visualization in cartoon), windows 10 Pro and 64 Bit operating system. when I try to click for APBS binary location and choose apbs.exe and APBS size.py to select apbssize.py, I cannot find those and the result is an empty location which doesn't allow me to continue further more. the pdb file I am using is 3uf5. I strictly followed the tutorial available online, didn't performed other actions that are not described there. I am not an expert in this, but I don't think I have done sth wrong. I simply followed the tutorial.
The molecule is processed OK on my machine, both in the current version of PyMOL and the 1.7.4 edu version (you might want to remove some alternative localizations: I get:
Warning: multiple occupancies found: CA in ASN A 119
Warning: multiple occupancies found: CB in ASN A 119
Warning: multiple occupancies found: CG in ASN A 119
Warning: multiple occupancies found: ND2 in ASN A 119
Warning: multiple occupancies found: OD1 in ASN A 119
but that does not interfere with running pdb2pqr.
The problem seems to be in your ABPS installation or a wrong file path (you have to enter the full paths to apbs, psize.py and pdb2pqr.py
Did you install ABPS and pdb2pqr? They need to be installed separately, are not an integral part of PyMOL. You can download them from http://www.poissonboltzmann.org. Under windows ABPS should by default be located in C:\ABPS (https://apbs-pdb2pqr.readthedocs.io/en/latest/apbs/installing.html).
If it is not there, you might want have to re-install it.
Actually, The attached image is a screenshot showing you the results for 3uf5 and the ABPS file locations on a PyMOL 1.8 edu Windows installation I have access to. Obviously, the path would vary according to the Python and ABPS versions used. Check if you find something similar in the file system of your machine.
Annemarie Honegger I was able to solve the problem I had, once I used a later version of pymol. Apparently the version I used in first time isn't supported anymore. Thank you for your willingness to help! (ps: sorry for my late response)
Hi! PyMol 1.x.x and 2.x.x. are designed on different Pythons (2 and 3). Accordingly, the versions of the main program and the plugin must match. In PyMol 2.x.x. APBS plugin are originally integrated...
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