#Pymol tutorial wiki how to
#Pymol tutorial wiki pdf
#Pymol tutorial wiki Patch
#Pymol tutorial wiki software

This difference density points to the ring adopting two alternate positions (see Erice 1pmq tutorial rebuilding notes).

#Pymol tutorial wiki Patch

In the 1pmq.pdb example above there is a clear patch of negative electron density next to the right-hand chlorine atom in the dichlorophenyl ring as well as a patch of positive difference density on the other side of the ring. The map is contoured at 3.0 rmsd which is quite a low value and some small patches of difference density are normal for good model. The green is used for positive difference density where the atomic model places fewer electrons than expected. The red regions mark negative difference density where the atomic model places more electrons than would be expected from the data. This map is BUSTER's version of Fo-Fc indicates regions where the current model has much more or much less electron density compared to the density expected from the data.

The red and green mesh shows the BUSTER mFo-DFc difference density map.

To override the default settings using an environment variable set BDG_BR_EDCONTOURS to your desired values. For instance to use the higher contour level used in previous versions specify -EDcontours 1.3,3.0.

You can alter the contour level that are used by buster-report with the command line argument -EDcontours.

This value is more appropriate for well order ligands and at high resolution can show 'holes in rings' that are attractive and emphasize the quality of the information.

Note that in previous versions of buster-report a level of 1.3 rmsd was used for 2mFo-DFc.

For the 1pmq.pdb example above we can see a good fit between the ligand model and the electron density with good coverage for all parts of the ligand (despite one ring being the wrong way around). The contour level of 0.7 rmsd is set to allow the visualization of weak electron density. This map is BUSTER's version of 2Fo-Fc and it shows where the data indicate electron density to be located. The map is masked to show only the density immediately next to ligand.

The grey mesh shows the BUSTER 2mFo-DFc density map that by default is contoured at 0.7 rmsd.

Otherwise standard atomic colors are used, so nitrogen atoms are blue spheres, oxygen atoms are red and chlorine atoms are green.

The molecule is displayed with bonds to carbon atoms as cyan sticks and hydrogen atoms in thin white sticks.

In buster-report if you click on the animated gif you will see a larger static image, that useful if you need a higher resolution. Note that animated gif work well in Powerpoint™ presentations. The animated gif uses a small rotation to give 3D information.

The picture is produced using PyMOL and imagemagick.

#Pymol tutorial wiki pdf

Unfortunately in the PDF version only a static view can be provided see 1pmq.pdb 880 ligand analysis PDF version.Running a BUSTER MapOnly run for 1pmq.pdb produces 1pmq.pdb buster-report Ligand Analysis page with the following picture: As an example we will use the imidazole-pyrimidine inhibitor 880 from JNK3 kinase structure 1pmq (see Erice tutorial for further information). The picture provides a view of the BUSTER electron density around the ligand.Please note that all ligand validation information is now available in the PDF, XML and TSV files produced in addition to the HTML. This new page is required because marked improvements have been made to the analysis and presentation. Brown for more information.This help page is for buster-report versions after July 2015. Have questions about PyMOL? Want to integrate it into your classroom or research project?Ĭontact Anne M.

#Pymol tutorial wiki how to

The first written and video tutorial (1 - Introduction) linked below also details how to download PyMOL for Virginia Tech Faculty, Staff, and Students with the VT site lic e nse.

#Pymol tutorial wiki software

Virginia Tech Faculty, Staff, and Students can download licensed PyMOL via VT ITPALS Software Service Center. Linked below are tutorials on PyMOL that vary from the basics of the User Interface (UI), to how to make elaborate movies with multiple structures, to advanced features on aligning, surface rendering, and more. These tutorials are available in a written or video format. PDB ID: 2BDA - Porcine P ancreatic Elastase PDB ID: 4PRG - Peroxisome Proliferated-Activated Receptor (PPAR) Gamma There are a variety of tools and ways to use PyMOL. Using PyMOL, it is possible to make high-quality images (renders) of molecules suited for publications.

PyMOL is a molecular visualization software program used for modeling and visualizing 3D structures of biomolecules (proteins, DNA, RNA, lipids, small molecules, etc.).