Comments on: Discovery Studio Visualizer 2.5

By: Sanjay Kamat

Sanjay Kamat — Fri, 11 Jun 2010 14:00:17 +0000

Can you please tell me how you insert missing residues in a pdb file without affecting the co ordinates of the existing residues??
Thanx!!

By: Shikha

Shikha — Tue, 19 Jan 2010 19:07:55 +0000

Hi Megan,
A number of users have reported successfully installing and running the Discovery Studio Visualizer on MacOS X under Windows emulators such as VMWare and Parallels. While the DS team does not extensively test the software on these emulators, we know of no reason why the software would not run. Regards.

By: Sean

Sean — Sun, 17 Jan 2010 06:32:24 +0000

Hi Megan, PyMOL is able to run on Mac OS X, which is a great program. I would say that it is has a bit of a learning curve so if you haven't used it and get stuck feel free to drop me a line.

By: Megan

Megan — Fri, 15 Jan 2010 21:49:20 +0000

I want to use this software but am a Mac user. Any suggestions for similar software or a way to use this software without buying Windows?

By: Sean

Sean — Thu, 17 Dec 2009 17:26:05 +0000

The sentence from the post "You can download DSV for FREE after a quick registration." You need to click on the underlined/highlighted section which represents a link.

By: sri

sri — Thu, 17 Dec 2009 17:14:14 +0000

hey can u suggest me way to download this software

By: Sean

Sean — Tue, 24 Nov 2009 21:53:03 +0000

Hi Shikha,

Thanks for the reply! I can’t believe I missed that simply download feature, thanks. I played around with DSV for a couple of days before writing this post. I have been putting some more time getting familiar with the program and now believe overall it is the best program out there.

I am unsure if you have a method to compare the rendering (image quality) between DSV and PyMol, but to me DSV looks slightly worse. However, I am assuming that the image quality from DSV is fine for publication.

By: Shikha

Shikha — Tue, 10 Nov 2009 22:40:42 +0000

Hi Sean,
You can actually download PDBs automatically from File -> Open URL, type in the 4 digit code and voila!
For the surface calculation, it’s currently a little cumbersome but an option has been added in an upcoming release. The user still have to create the crystal symmetry mates before the solvent accessible surface is calculated though. For the final point, The script mentioned does not create a slab, (if it did, you would be able to move the structure or the slab to get a zoom effect). The
amount of surface shown depends on the cavity and the radius of atoms selected, you can change the radius in the script.

By: Sean

Sean — Mon, 09 Nov 2009 04:08:22 +0000

Well requesting is easy

How about a place to enter the four digit PDB ID to automatically load a structure and the option to load the maps from the electron density server?

An option to take into account crystal packing during the solvent accessibility calculation? As far as I can tell it does not, but don’t have another method to verify it.

The ability to scroll the slab (add and remove the amount of surface shown) under the scripts -> ligand interactions -> Create surface around ligand. I would like a more ‘zoomed out view’ which is different from the default script so it would be awesome to adjust that by scrolling.

By: Shikha

Shikha — Sat, 07 Nov 2009 00:10:07 +0000

Great post, Sean! Nice to see that you are exploring the DSV functionality. Color by Property is probably one of the most favorite tools which our customers like. On the small molecule side, pharmacophore perception is also very nice.
Keep me posted on any enhancement requests!