pymol 使用,从PDB到CCP4到电子密度图的显示.docx

/2010/04/26/display-a-mtz-file-in-pymol/Display a MTZ file in PyMOLApr 26, 2010The following will allow you to create a 2Fo-Fc map using CCP4 from a mtz file to be displayed in PyMOL.1) Start CCP4i, select ‘FFT‘ from the program list or ‘Run FFT – Create Map’ under the Map Mask Utilities2) This map will cover all the atoms in the PDB therefore must be changed (see red arrow). The F1 and PHI have also been changed from the default (see red circle) – RUNNote: if you would like to calculate a Fo-Fc map use DELFWT and PHDELWT respectively.3) Change the ending of the new map file to .ccp4 (can be either abc.map.ccp4 or abc.ccp4, but not abc.map)4) Load the map into PyMol select ‘A’, mesh, 1 sigma level and the electron density should appearIf needed, here is a previous post that will show you how to move from this point closer to a publication quality figure (also checkout the PyMOL wiki).Display Electron Density Map from the EDS in PymolJun 18, 20091) Go to the electron density server2) Save the map in CCP4 format.Note: if you save the map as an ‘XPLOR’ or ‘CNS’ file, you will need to rename the extension ‘.xplor’. This will enable you to extract the files you have just downloaded.Example: 1s - 1w5x_2fo-fc.xplor(I like to enter in the type of map (2fo-fc) as soon as I download it)-If you do not change the extension, pymol will not recognize/see the file when you are searching/browsing.3) Load pdb that corresponds to the map you downloaded into pymolExample: 1w5x.pdb4) Diplay - Background - white5) H- everything S- sticks6) Load the map that was downloaded from the electron density server into pymol.Example: File - Open - 1w5x.ccp4You will still NOT see electron density, you need to use the mesh command next (see image below).7) Mesh Displayed:If you don’t want your structure looking like clown vomit, enter the following into the command line:isomesh mesh1, 1w5x_2fofc9) mesh1 - C - grays - gray70How to display Electron Density Server results in PyMolApr 16, 20091) Go to