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Re: [PyMOL] about Display CCP4 Maps
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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> |
