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naresh thota

how to save into pdb format from crystal viewer

Hi I tried to create CNT and it is possible to see the picture after creation. How to save that molecule co-ordinates into pdb file?

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    Tanya Faltens

    Hi Naresh,

    There are two versions of crystal viewer.  The current version provides an option to save the atom coordinates as a VTK file.  If you go to the main tool page and look in the versions tab, you will find crystal viewer version 2.3.4.  If you run that version, you can save the coordinates as a pdb file type.

    https://nanohub.org/resources/3741?rev=336

    That said, there seem to be multiple ways to specify vtk and pdb files, so you may have to take a look at the text file you download to make sure that it is readable by your pdb renderer, and possibly make edits by hand. -- I've run into problems at times with different ways of specifying geometry than were expected.

    Please respond to let us know if you are able to read the file(s).  If not, someone else in the nanoHUB community may be able to help out with translating the file into the proper format.

    Good Luck!

    Tanya

     

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