Re: [PyMOL] about Display CCP4 Maps
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
Re: [PyMOL] about Display CCP4 Maps
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 clear from your question. Cheers, 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
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
Re: [PyMOL] about Display CCP4 Maps
Lina, If you want to create an "omit" map for your ligand using CCP4i, you can find instructions here for both Fo-Fc and 2Fo-Fc maps: http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Building+and+Validation#Creating_Omit_Maps_for_Ligands_using_Refmac To display an omit map in Pymol around your ligand, you can find instructions here: http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Visualization+of+PDB+files#Visualizing_Electron_Density_Maps These last instructions are the same as those I posted on the CCP4 wiki. http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Visualization+of+PDB+files#Visualizing_Electron_Density_Maps __ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu Thomas Holder 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 clear from your question. Cheers, 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, -- 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
Re: [PyMOL] about Display CCP4 Maps
On 10/25/2011 02:27 PM, lina wrote: 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? what you want is the map_new command in PyMOL. Have a look at this example: http://pymolwiki.org/index.php/Map_set#Detailed_Example And read the help for the map_new command (there is no wiki page yet): PyMOLhelp map_new Cheers, Thomas -- 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
Re: [PyMOL] about Display CCP4 Maps
And read the help for the map_new command (there is no wiki page yet): PyMOLhelp map_new now the wiki page is there: http://pymolwiki.org/index.php/Map_new Cheers, Thomas -- 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
Re: [PyMOL] about Display CCP4 Maps
On Wednesday 26,October,2011 12:55 AM, Jason Vertrees wrote: Hi Lina, 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) The CCP4 file is a map. Once the map is loaded into PyMOL you can choose how you want to represent the data: isomesh, isosurface, slice, gradient, or the new volumes. To make a new representation for the map choose one of those from the A (Action) button. 2] For small molecular (ligand), the ccp4 is the best way to obtain its electron density map? PyMOL natively reads these maps, so you don't need ccp4i or any special plugins. At present I have problem created the map. Thanks, Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com mailto:jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
