Hi Tom, First, thanks a lot to you, to Sunhwan, Elaine and to you for helping so much. Indeed the addition you mentioned solved the problem, although additionally I installed delphi which works very smoothly with chimera, but it's good in any case to have a way to work with charmm output and to have both methods available. Secondly, I have a question regarding the surface potential itself: Once the delphi run ends and I get the surface colour coded by electrostatics, (or conservation, etc.) it would be very useful to be able to know which residues is found in any specific negative or positive potential region (or conserved). But when the surface is shown, the cursor doesn't show the residue information as when the cpk representation is on (like #0 THR 684.A), and therefore is not easy to quickly find information about the residues of interest. Is there any way to overcome this limitation? It will be really useful. Best regards and have a great day, Fabian Tom Goddard said the following on 20/08/08 19:49:
Hi Fabian,
The OpenDX file you sent has a small but important error. It is missing the words "data follows" at the end of the header line that says "object 3 class array..." so Chimera never reads the data. The misleading error message comes about because the last line of the file is blank and Chimera still thinks it is reading the header. The header line
object 3 class array type double rank 0 items 378885
has to be
object 3 class array type double rank 0 items 378885 data follows
Hopefully Sunhwan can update the phi2dx.py script to include the very important "data follows". The OpenDX format is described in Appendix B of the OpenDX User's Guide:
http://opendx.npaci.edu/docs/pdf/userguide.pdf
Tom
Fabian Glaser wrote:
Dear Elaine,
I am afraid it's still giving the same error when I try to open the dx file, even when the first line is removed or # starts it. Here is the message:
Opening /media/data/WORKSPACE/PROJECTS/DanCassel/COP/step2_pbeq.dx Error reading file step2_pbeq.dx, format apbs Incorrect format: blank header line. Comments must begin with # character.
And the dx file is attached, probably I am doing something wrong....
THanks a lot,
Fabian
Elaine Meng said the following on 19/08/08 19:19:
Hi Fabian, Well, the error message says the format is wrong. Based on the message, you could try removing the blank line at the top of the file or adding # in front of it.
If that still doesn't work you could send me the file to look at, but it is probably just a simple fix such as the above. 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 19, 2008, at 7:03 AM, Fabian Glaser wrote:
Dear Sunhwan
Thanks a lot for your kind answer and for the script. The script run fine, but when I try to upload it to chimera I get an error:
Opening /media/data/WORKSPACE/PROJECTS/HaimManor/EladEliahoo/MODELS/POMBE/CHARMM-PBEQ/charmm-gui/step2_pbeq.dx
Error reading file step2_pbeq.dx, format apbs Incorrect format: blank header line. Comments must begin with # character. Done opening /media/data/WORKSPACE/PROJECTS/HaimManor/EladEliahoo/MODELS/POMBE/CHARMM-PBEQ/charmm-gui/step2_pbeq.dx
Which maybe perfectly chimera problem, so I am CCing this email also to Elaine Meng from the CHIMERA team.
Any help will be very appreciated,
Thanks a lot,
FAbian
Sunhwan Jo said the following on 19/08/08 15:25:
Dear Dr. Glaser,
I'm afraid CHIMERA is not able to read CHARMM phi80 format. But simple search guided me that CHIMERA can to read dx format file, which I have a converting script. So, please find the script in the attached file. We've been using this script to read our potential data in Pymol, so I believe this should be working fine with CHIMERA as well.
usage: python phi2dx.py step2_pbeq.phi80 > step2_pbeq.dx
Please feel free to contact me, if you have a further problem.
Thanks, Sunhwan
On Tue, Aug 19, 2008 at 4:53 AM, Fabian Glaser <fglaser@technion.ac.il> wrote:
Dearl CHARMM team,
have been trying to upload the electrostatic potential calculated by CHARMM PBEQ routine to the CHIMERA viewer, since the java viewer you use is very good but at least in my machine does not work. But despite I have been trying to upload it to chimera there seems to be some stubborn problem (or I am doing something wrong). What I am trying to do is to color the pdb by the potential in chimera so I can freely manipulate it and compare it with other calculations.
If you have any suggestion I'll be very grateful,
Best regards,
Fabian Glaser, PhD
-- Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL Web: http://bku.technion.ac.il Email: fglaser@tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396