Hi James, Just because it has red, white and blue blotches does not mean it is showing ESP!! I don't think the different filenames in the DelPhi log are a problem - I believe temp files are generated from the ones you specify and used in the calculation for technical reasons. However, I do not know the reason for the error and not getting any output. You could try using Help... Report a Bug in the Chimera menu - give more details, such as all the error messages obtained and what it says at the end of the DelPhi log file. The main difficulty with DelPhi and any ESP calculation program is that atom names need to match those in the DelPhi charge parameter files. If you want to use all the hydrogens, you have to either edit all the names in the DelPhi charge parameter file or write out your PDB beforehand and edit all of its atom names to match those in the DelPhi charge parameter file. I have found this to be well nigh impossible. In general many hydrogen names not match and your molecule gets a very large net negative charge. Chimera tries to name hydrogens according to current PDB standards, but these old DelPhi parameter files use a different set of names. Instead, I would just used the DelPhi parameter files "default.crg" and "default.siz" which ignore hydrogens and just plop positives on nonhydrogen atoms in Lys, Arg (maybe His and N-term, I forget) and negatives on nonhydrogen atoms in Asp, Glu (maybe C-term). It is impossible to tell what "half all red" and "half all blue" means. It depends on what levels you have specified to be displayed as red and blue. Maybe the APBS map is fine - try changing the values set to red and blue to larger magnitudes. If APBS writes some sort of log file I would look at that, see if there is a reasonable net charge. Again most of the trickiness is in getting the right charges assigned to the atoms. You could use the PDB2PQR server to get an input file for APBS (if you didn't try that already). <http://nbcr.sdsc.edu/pdb2pqr/> Another possibility is to use the webPIPSA server as mentioned in previous messages, e.g. http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/003006.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 27, 2008, at 7:58 PM, James Fethiere wrote:
Hi Elaine,
Nice that you found what I did 6kkm away!!! thanks. However, I must say that it does look artificial. I'm just desperate to get the electrostatic look as nice as possible (just like the pictures in http://www.cgl.ucsf.edu/chimera/tutorials/maps08/exercises.html#esp) and found that was the closest I could get. One example I'm trying is on 1DH3
On this note, I did try the delphicontroller to get the true potentials but cannot get it to work. I have installed delphi on windows-XP and called it from within chimera with tool/ surfaceanalysis/delphicontroller. I entered the path for the executable and charge and radii files. When I run delphi, I get an error with no output file generated and some strange parameters in the log file:
in(pdb, file="tmph4vkzc") This does not correspond to the chimera model I have chosen in(siz, file="tmplk_go0") same here; not the file specified in(crg, file="tmpbg7nlz") same thing AC = true CS = true PF = 60 SC = 1.2 PR = 1.4 FC = true LG = false LP = false PX = false PY = false PZ = false BC = 4 ID = 2 ED = 80 GC = 0.0 IS = 0.0 IR = 0.0 NI = 0
P.S. I did addH before starting Delphi! Any idea of what is going wrong?
I also tried to run APBS and got a potential file. But when I read it in chimera, I get strange looking surfaces with half all red and half all blue!!! here again I could use some guidance.
Thanks for your help.
James -- James Fethiere, Ph.D. Institut de Recherche en Immunologie et Cancerologie Pavillon Marcelle Coutu, University de Montreal 2900 edouard-montpetit Montreal, Qc H3t 1J4 Tel: 514-343-6111 ext. 0918/0919 Fax: 514-343-5839 james.fethiere@umontreal.ca