Hi,
I want to draw a MoS2 monolayer similar to the one attached. I got some tips on how to do it using VMD but I do not know how to write the pdb file with the MoS2 coordinates (XYZ file). Can someone help me? Does anyone has a moS2.pbd or even a .blender file?
Other suggestions to draw this structure are also welcome,
Thank you,
Viviane
I like to use Avogadro to make molecular models. It allows you to make a unit cell and then use that unit cell to construct super cells. You can save files as .pdb or many other formats.
Check out BioBlender - http://www.bioblender.eu/ This has some great add-ons to the Blender environment specifically for molecular modeling. Otherwise, you can find some scripts to import .pdb files into Blender - http://wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/Import-Export/PDB
This is interesting too but I have not used it. - http://www.malte-reimold.de/blender/pdb2blend.html
Actually converting XYZ to PDB with VMD is pretty much straightforward, all you have to do is simply open the XYZ file in VMD and File > New Molecule, click Browse, select the XYZ file, and click Load. Then to save it in PDB just select the molecule in VMD main window, click File > Save Coordinates choose File Type and click Save.
Another even simpler solution is to use Open Babel (http://openbabel.org/wiki/Main_Page), if you're using Windows, there is a GUI version that can be easily used to convert any kind of molecule format. It is so easy to use that I don't feel like I need to explain how to use it :)
Hope that help,
Radif
http://openmopac.net/PM7_accuracy/data_solids/Molybdenum_disulfide__MoS2___ICSD_601647__Jmol.html
check this link
I am getting there with Avogadro and Blender. Thank you very much!
Once you have your PDB file, you can get it into Blender using bioBlender as previously suggested or ePMV for Blender as well (embedded Python Molecular Viewer). Since this looks like a very simple grid matrix, you could create it directly in blender with efficient particles using the correct XYZ repeats.
http://epmv.scripps.edu
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