The electron density we usually display with an atomic model is based on experimental diffraction data (usually x-ray). The purpose of the density map is usually to validate the model, i.e. show it is consistent with the map calculated using experimental data. Even for many structures that are at the PDB (deposited before 2009?) the data is not available, so you cannot make an experimental density map. Likewise for NMR structures, but they have experimental data of a different kind.
If you got the pdb file from a colleague who solved the structure, you can ask him for the data or for a map. If the structure is a theoretical model that you built, then the usual reason for showing a density map (to validate the structure) doesn't exist. You can calculate a purely theoretical electron density map from any pdb file using for example CCP4's SFALL and FFT programs (actually sfall by itself run in mapout mode, I think). But before you do this you should think about what you want the map for, and if a theoretical map serves your purpose. And if you display the model with theoretical electron density, you should make it very clear that the map is calculated from the model, otherwise most people will take it as evidence tat you have solved the structure by crystallography. HTH, eab Mehdi Talebzadeh Farooji wrote: > Dear All, > > I am trying to create a electron density map for the pdb file which is not > deposited in RCSB bank, however I do > not find any option on http://eds.bmc.uu.se/eds/. Is there any way to get > density map for the pdb files which are > not deposited in pdb data bank? > > All the best, > > Mehdi > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_sfd2d_oct > > > > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
