Author Topic: Plotting COSMO cavity  (Read 1073 times)

guo.chen

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Plotting COSMO cavity
« on: November 10, 2016, 01:17:40 am »
Hi all,

I was wondering whether there is a way to export the COSMO cavity information on a grid and view it using some molecular viewer.

Thanks,
Guo Chen

uwe

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Re: Plotting COSMO cavity
« Reply #1 on: November 10, 2016, 05:06:13 pm »
Hi,

did you try TmoleX? It visualizes the COSMO cavity. Start TmoleX (on your local desktop), generate a new project (if you start TmoleX for the first time) and use the File -> 'Open Job/Control File' menu to read in the control file from the directory your job has been running. Then switch to 'Results' and click on the 'View .cosmo File' button.

This will open the COSMOview program, which, by the way, can also be started as an own application (is part of the TmoleX installation).

To see the individual surface patches rather than the nice smooth picture, you have to change the settings. Click on the settings button in the tool bar, switch to 'COSMO cavities' and set 'Segments' instead of 'Wireframe' in the upper part of the settings window. Apply and/or save the settings and then click on the 'Display Segments' button (the icon that looks like a wireframe cavity).

Regards,

Uwe

guo.chen

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Re: Plotting COSMO cavity
« Reply #2 on: November 10, 2016, 08:40:30 pm »
Hi Uwe,

Thank you for the help.

The 'View .cosmo File' button seems to only recognize the .cosmo file extension. It is gray when there is no .cosmo file in the working directory. I tried to rename the out.ccf file to out.comso and modify the control file accordingly. I was then able to click on the 'View .cosmo File' botton, but no molecule or COSMO cavity show up in the COSMOview dialog. I tried both TmoleX 4.1 and 4.2 on a Ubuntu Linux machine. I wonder whether I should put some additional keywords in control in order to generate a .cosmo file that can be read by COSMOview?

Thanks,
Guo

uwe

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Re: Plotting COSMO cavity
« Reply #3 on: November 10, 2016, 10:20:35 pm »
Hi Guo,

the ccf files are 'compressed' cosmo files, binary alike, to keep their size small. Initially made to build up large databases. In TmoleX you can set the file format of the output in the 'Molecular Attributes' section - but here the default is .cosmo anyway.

On the command line, just define the cosmo file name with:

$cosmo_out  file=name.cosmo

If the file name has a .cosmo extension, it will be of that type.

Regards,

Uwe

guo.chen

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Re: Plotting COSMO cavity
« Reply #4 on: November 11, 2016, 01:46:42 am »
Thanks. It works now.

Best,
Guo