Hi Lina, Could you be more specific about what you are trying to do. E.g." I have a structure from the pdb and I would like to display the density."
If it is this option then you can automatically generate ccp4 type maps from http://eds.bmc.uu.se/eds/ assuming the structure factors have been deposited. You can them load these into pymol (file.ccp4) "Or I am determining the structure of a protein ligand complex and I wish to calculate the electron density map ." If this is the case I would suggest some further reading of the ccp4 tutorials. These come with ccp4i Hope this helps Joel _________________________________ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -----Original Message----- From: lina [mailto:lina.lastn...@gmail.com] Sent: Wednesday, 26 October 2011 1:27 a.m. To: Thomas Holder Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] about Display CCP4 Maps On Tue, Oct 25, 2011 at 7:56 PM, Thomas Holder <spel...@users.sourceforge.net> wrote: > Hi Lina, > > do you already have any electron density or reflection file (*.map, > *.mtz, > ...) or do you want to create a "fake" density from your structure? > It's not I don't have the reference electron density file. mainly wish to calculate a density map based on the structure? > clear from your question. > > Cheers, Thanks for asking. > Thomas > > On 10/25/2011 10:28 AM, lina wrote: >> >> Hi, >> >> I went through the pymolwiki and cross this page: >> >> http://www.pymolwiki.org/index.php/Display_CCP4_Maps >> >> I have some questions: >> >> 1] do I need generate the map from ccp4 >> >> (I have already installed the ccp4i, but seems not easy to know how >> to get the map) >> >> 2] For small molecular (ligand), the ccp4 is the best way to obtain >> its electron density map? >> >> Seems those questions are not so-pymol-related, but I wish if someone >> are familiar with this, can give me some advice?? >> >> Those questions might be easy, but to me at present it seems very >> confusing. >> >> Thanks with best regards, > > -- > Thomas Holder > MPI for Developmental Biology > ------------------------------------------------------------------------------ The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev _______________________________________________ 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 ------------------------------------------------------------------------------ The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev _______________________________________________ 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
