[Chimera-users] pocket cavity file produced by rdock

Tom Goddard goddard at sonic.net
Thu Feb 27 13:03:11 PST 2014


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








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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20140227/d0e7b20d/attachment-0003.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 2c6u_insight_grid.jpg
Type: image/jpg
Size: 54476 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20140227/d0e7b20d/attachment-0001.jpg>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20140227/d0e7b20d/attachment-0004.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: insightgrid.py
Type: text/x-python-script
Size: 1758 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20140227/d0e7b20d/attachment-0001.bin>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20140227/d0e7b20d/attachment-0005.html>


More information about the Chimera-users mailing list