plotting of cPCA.3d_landscape

[amit]

Hello,

I used grcarma to to the analysis cPCA, which provided an output file cPCA.3d_landscape.cns. I wanted to know which software can i use to visualize the 3d landscape.

thanks

Amit

[Nicholas M. Glykos]

> I used grcarma to to the analysis cPCA, which provided an output
> file cPCA.3d_landscape.cns. I wanted to know which software can i use to
> visualize the 3d landscape.

"The carma.3d_landscape.cns can be loaded and viewed directly with VMD (you
will have to adjust the cutoff for the various isosurfaces)."


These are proper 3D maps, like this one

https://utopia.duth.gr/glykos/images/MD_310_helix.jpg

Identifying which peak corresponds to which cluster in these 3D maps is
tedious.





--


Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, https://utopia.duth.gr/glykos/

[amit]

Thanks for your prompt reply.

Do I also need to load a pdb file or any other file also to get the kind of the image which you have attached.

For instance I am attaching the .cns file i have obtained.

thanks once again.
Amit

[Nicholas M. Glykos]

> Do I also need to load a pdb file or any other file also to get the kind of
> the image which you have attached.

No other file is needed. I attach with this message an image produced by
the file you've sent. The distribution is not very complex, maybe the 2D
plots would suffice (but this depends on what you want to do).

[amit]

I am not able to create the same image sent by you. can u send me screenshot (vmd) parameters of isosurface which I need to adjust.

thanks

Amit

On Wednesday, 26 June 2019 18:17:17 UTC+2, amit wrote:

[Nicholas M. Glykos]

> I am not able to create the same image sent by you. can u send me
> screenshot (vmd) parameters of isosurface which I need to adjust.

Create a replicate of the object (so that you have two copies of the map).
Plot the first copy using wireframe, the second using solid surface.
Use the sliders to adjust the contouring levels to your satisfaction.