Hi Mohan Raj, > i am new to pymol. i dont know how the coordinates are made in pdb file.
This is not really related to Pymol. Maybe you should go to www.rcsb.org/pdb and have a look around. > cold someone tell me? how do we arrive at the coordinates from crystal > structure. Do you mean from a crystal structure, or from a crystal? Structure implies that the coordinates have been solved already from the crystal. Solving them from a crystal is is a field by itself (if you neglect the obtaining/growing of the crystals :)). > cold we change the coordinated of the existing pdb file? Coordinates are just numbers, so of course they can be changed. Just have a look at a pdb file. For some reason I presume you're using Windows, don't blame me if I'm wrong, but in that case you might want to use wordpad or so (notepad may not be suited when the files were written under linux). If you happen to work under linux anyway, then you should know how to view files. > also cold any one tell me how to introduce a substrate? eg when i am viewing > the structure of a lipase how could i introduce the substrate in to pymol. > thanking you in advance. Pymol is also not really the tool of choice for that. If you want to do docking, find a docking program. I think you might want to do some more general background reading in structural biology. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ 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
