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Molekel - Message forums

New User Problem

Submitted by Christopher Barry; posted on Friday, February 16, 2007

Hello, I just installed the latest binary of molekel_5 and am not able to get many features to work. I opened a molecule (pdb) and cannot generate any surfaces. I can get the menu to open but all features are faded out. Is this because I have not installed some necessary accessory application? Thanks

Re: New User Problem

Submitted by Ugo Varetto; posted on Monday, March 05, 2007

The type of surfaces that can be generated depends on the data read from the file. * SAS/VdW surfaces can be generated for molecules read from any file format (including PDBs). * SES (Connolly) can be generated as point clouds and as regular surfaces by specifying the path to M.F. Sanner's msms executable. * Surfaces from grid data can be generated from Gaussian .cube files only (and ADF tape 41 file if you compile a version from the code in the vault). * Surfaces from electron density data can be generated only if the proper information is specified in the file; Gaussian, GAMESS and Molden formats may contain this information. To generate a surface a molecule needs of course to be selected first.

Re: New User Problem

Submitted by B Plank; posted on Tuesday, May 15, 2007

"Surfaces from grid data can be generated from Gaussian .cube files only (and ADF tape 41 file if you compile a version from the code in the vault)." Can you please let me know how to compile a version from the code in the vault? I would like to visualize the orbitals from adf *t41 files. Thanks

Re: New User Problem

Submitted by Ugo Varetto; posted on Friday, June 08, 2007

Version 5.1.1 released on May 11 has some support for ADF tape41 files.

Re: New User Problem

Submitted by yang Si-Ya; posted on Sunday, September 06, 2009

Hi, I cann't change atoms color used molekel 5.4 or 5.3 I request to adjust each atom colors for a *xyz format file in accordance with my preforence. Best resgards. Yang si-ya

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