[Chimera-users] pocket cavity file produced by rdock

Fabian Glaser fabian.glaser at gmail.com
Sun Mar 2 00:38:11 PST 2014


Dear Tom,

It worked!!

Yes I moved the molecule prior to docking, the pocket is in the place it should.

Thanks a lot!!

I will offer the rdock people to add the script to their site, if it is Ok with you.

Best regards and thanks again,

Fabian

On Feb 27, 2014, at 11:03 PM, Tom Goddard wrote:

> Hi Fabian,
> 
>   As I said in the bug report you submitted yesterday
> 
> 	http://plato.cgl.ucsf.edu/trac/chimera/ticket/12875
> 
> "The ".grd" file suffix is recognized by Chimera as a UHBD electrostatic potential binary file. But your file is a text file as can be seen in any text editor. A look at the rdock documentation mentions it uses InsightII grid format
>http://www.ysbl.york.ac.uk/rDock/documents/rDock_reference_guide.html
> 
> and that format is described here
> 
>http://hincklab.uthscsa.edu/html/soft_packs/msi_docs/insight980/insight/Utilities.fcs.html
> 
> and appears to match your file header which looks like
> 
> RBT FFT GRID
> (1F15.10)
> 
> 20.500 17.500 18.500 90.000 90.000 90.000
> 
> 41 35 37
> 
> 1 -33 8 -35 0 -5 32
> 
> 0.0000000000
> 0.0000000000
> 
> ...
> 
> Chimera does not read Insight II grid file format. It is not much different from some other text grid file formats like DX format, or CNS format, or XPLOR format, which Chimera reads. You might be able to convert to one of those formats in a text editor. It would also be possible to write your own Chimera file reader in Python if it was worth your effort."
> 
> 
> 
> I've attached a Python script insightgrid.py that will open your grid in Chimera using Chimera command
> 
> 	runscript ~/Desktop/insightgrid.py ~/Desktop/2C6U_rdock_mdmix_R4_cav1.grd
> 
> The grid does not align with the standard 2C6U PDB file as shown in the attached image but maybe you used a shifted or rotated version of that PDB.
> 
> 	Tom
> 
> 
> 
> 
> <2c6u_insight_grid.jpg>
> 
> 
> 
> 
> <insightgrid.py>
> 
> 
> 
> 
> On Feb 26, 2014, at 4:09 AM, Fabian Glaser  wrote:
> 
>> Hi all,
>> 
>> I am trying to upload and examine the cavity file produced by the rbcavity program from rdock, an open source docking program. There are both a binary form and a regular file "RBT FFT GRID" but I am not able to upload or visualize them.
>> 
>> Can you please help me to do it?
>> 
>> Files are attached.
>> 
>> Thanks a lot,
>> 
>> Fabian
>> 
>> <2C6U_rdock_mdmix_R4_cav1.grd><2C6U_rdock_mdmix_R4.as>_______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




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