- What is Voxelization?
- The process of converting a geometric representation of a given model into a discrete approximation in voxel space. Each "voxel" represents a cubical cell of space that has been discretized using a user-specified voxel size, and in memory it occupies 2, 4, or 8 bits.
- What is a convex hull?
- The convex hull of a set Q of points is the smallest convex polygon P for which each point in set Q is either on the boundary of P or in its interior. For example, in the following figure the convex hull is given by CH(Q) = {po, p1, p3, p10, p12}
- What is Euclidean distance?
- It is simply the geometric distance in the multidimensional space and is computed as:
- How are the surfaces created?
- The Connolly surface which is the underlying surface of a spherical probe rolling on the van der Waals surface is calculated using the Molecular Surface Package. The program output is in the form of a polyhedral surface triangulation.
- Who do I contact if I have questions/comments/suggestions?
- Please contact davidla@purdue.edu for anything regarding this server.
- How do I calculate structural alignment RMSD values from the results?
- Click
on the check boxes next to the "Rmsd:" label and click on Calculate
RMSD. You should be able to see a green loading bar if your
structural alignment is being computed. This may take 30 seconds
depending on the size of the individual proteins in question and the
number of proteins you selected for structural alignment computation.
- What do the colors mean when I click on the cavity, protrusion, or flat options (by VisGrid)?
- The
color red indicates the largest cavity/protrusion, green indicates
second largest cavity/protrusion, and blue indicates 3rd largest
cavity/protrusion. Yellow indicates flat regions.
- How do I figure out which residues are colored using VisGrid above?
- The residue numbers of the colored atoms are displayed in the statusbar provided in the results.
- How do I render the molecular surface using Jmol?
- In the Jmol applet area, right-mouse click and select Surface menu and then the sub-menu Molecular Surface option.
- Are the 121 Zernike Invariants displayed?
- Yes. The 121 Zernike Invariants that characterize the structure are displayed in two forms: as a list of 121 numbers and as graph, where the X axis represents each of the 121 Zernike Invariants and the Y axis the value. These are shown below the molecule visualization component.
- What should I do if I get a java.security.AccessControlException on the molecule visualization component?
- Some browsers, like Safari, have very strict security settings that require additional configuration for complex applications, like JMol (the molecule visualization component used by 3d-surfer). If you get this error, it is necesssary to modify the "java.policy" file used by your browser's Java plugin. It is normally located, under the Java installation folder, in "lib/security". Add a new line that contains the following text: permission java.net.SocketPermission "dragon.bio.purdue.edu","connect,resolve";
- How can I download the structure or alignment displayed by Jmol?
- Jmol displays the information generated by VisGrid (cavity, protrusion and flat areas) and also the superimposition of structures, when the RMSD of the query against other structure is calculated. All of these can be downloaded in PDB format thanks to Jmol. In order to do so, the user needs to right click Jmol and expand the topmost option of the menu displayed. Once the corresponding sub-menu is expanded select the last option, which should display a label similar to "View structure.pdb"
- How can I download the CE alignment file corresponding to a RMSD calculation?
- When the user want to calculate the RMSD (using CE) between a query and one of the top results displayed, he can click on the RMSD checkbox displayed. After this, a new button and the RMSD numerical value will be shown; the numerical value is a link to a text file that contains the CE alignment result file.
- How can I see the relationship of different surface patches between similar proteins, such as pocket or protrusion regions?
- First, the coordinate file of the superimposed proteins can be downloaded from JMOL by clicking right mouse button on the top of the JMOL panel and selecting "cepose_xxxxx_x" tag. Also, you can download the CE alignment file by clicking the computed value of RMSD. Next, detect local features (cavity etc.) separately on the 3D-SURFER for the two proteins and record the residues involved in the features. Then, compare the location of pocket residues in the two proteins using the CE alignment file or visualize the pocket residues on the downloaded PDB format file of the superimposed structures.
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