[Chimera-users] CHARMM PBEQ calculations

[Tom Goddard]

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 at 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 at 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