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From: lina <lin...@gm...> - 2011-10-25 08:28:25
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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, |
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From: Thomas H. <sp...@us...> - 2011-10-25 11:57:07
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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 |
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From: Roger R. <rro...@co...> - 2011-10-25 12:51:10
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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <meta content="text/html;charset=us-ascii" http-equiv="Content-Type"> <title></title> </head> <body bgcolor="#ffffff" text="#000000"> <font face="Verdana">Lina,<br> <br> 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:<br> <br> <a class="moz-txt-link-freetext" href="http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Building+and+Validation#Creating_Omit_Maps_for_Ligands_using_Refmac">http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Building+and+Validation#Creating_Omit_Maps_for_Ligands_using_Refmac</a><br> </font><br> To display an omit map in Pymol around your ligand, you can find instructions here:<br> <br> <a class="moz-txt-link-freetext" href="http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Visualization+of+PDB+files#Visualizing_Electron_Density_Maps">http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Visualization+of+PDB+files#Visualizing_Electron_Density_Maps</a><br> <br> These last instructions are the same as those I posted on the CCP4 wiki.<br> <br> <a class="moz-txt-link-freetext" href="http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Visualization+of+PDB+files#Visualizing_Electron_Density_Maps">http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Visualization+of+PDB+files#Visualizing_Electron_Density_Maps</a><br> <br> ______________________________________<br> Roger S. Rowlett<br> Gordon & Dorothy Kline Professor<br> Department of Chemistry<br> Colgate University<br> 13 Oak Drive<br> Hamilton, NY 13346<br> <br> tel: (315)-228-7245<br> ofc: (315)-228-7395<br> fax: (315)-228-7935<br> email: <a class="moz-txt-link-abbreviated" href="mailto:rro...@co...">rro...@co...</a><br> <br> Thomas Holder wrote: <blockquote cite="mid:4EA...@us..." type="cite"> <pre wrap="">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: </pre> <blockquote type="cite"> <pre wrap="">Hi, I went through the pymolwiki and cross this page: <a class="moz-txt-link-freetext" href="http://www.pymolwiki.org/index.php/Display_CCP4_Maps">http://www.pymolwiki.org/index.php/Display_CCP4_Maps</a> 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, </pre> </blockquote> <pre wrap=""><!----> </pre> </blockquote> </body> </html> |
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From: Thomas H. <sp...@us...> - 2011-10-25 12:54:21
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On 10/25/2011 02:27 PM, lina wrote: > On Tue, Oct 25, 2011 at 7:56 PM, Thomas Holder > <sp...@us...> 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): PyMOL>help map_new Cheers, Thomas -- Thomas Holder MPI for Developmental Biology |
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From: Thomas H. <sp...@us...> - 2011-10-25 13:26:27
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> And read the help for the map_new command (there is no wiki page yet): > PyMOL>help map_new now the wiki page is there: http://pymolwiki.org/index.php/Map_new Cheers, Thomas -- Thomas Holder MPI for Developmental Biology |
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From: lina <lin...@gm...> - 2011-10-25 12:27:40
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On Tue, Oct 25, 2011 at 7:56 PM, Thomas Holder <sp...@us...> 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 > |
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From: Joel T. <joe...@ot...> - 2011-10-26 06:41:08
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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:lin...@gm...] Sent: Wednesday, 26 October 2011 1:27 a.m. To: Thomas Holder Cc: pym...@li... Subject: Re: [PyMOL] about Display CCP4 Maps On Tue, Oct 25, 2011 at 7:56 PM, Thomas Holder <sp...@us...> 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 (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
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From: Jason V. <jas...@sc...> - 2011-10-25 17:24:40
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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. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
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From: lina <lin...@gm...> - 2011-10-26 04:54:03
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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) Jas...@sc... <mailto:Jas...@sc...> > (o) +1 (603) 374-7120 |
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