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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, |
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