All operations described in this chapter assume that your machine holds an active internet connection. Without one, the features here will not be available to you.
The MembraneEditor inherits an embedded mode for searching and downloading a Protein from the Protein Data Bank by using your internet connection. The Editor can link to the RCSB site ( http://www.rcsb.org ) via http and ftp protocol and retrieve the required data.
If your internet connection uses a proxy, make sure to make the connection settings first.
In order to search, open the 'Search Dialog' from the menubar.
There is also a button available in the upper right corner of the Local Database View.
The Search Dialog
You can search a PDB file using different kinds of terms. These can be for example, its whole or partial pdb code, a species, an author or any word that you think is related to the protein you're looking for. You can refine your search by entering multiple search terms, separated by whitespace. You will get a match for an entry that contains each of your search strings at least once. You can enter your terms in the box at the upper right side. Run the search by pressing [Enter] or the 'Search' button.
The Search Box
You can also choose from your previously entered search terms located in the dropdown menu of the textfield.
All matches found during search will be listed in the table on the left. You can sort your matches by clicking the header of a column.Eventually, there might be additional alignment data available for some of the matching proteins in the OPM or the PDBTM. In this case, some extra hints in the second (PDBTM) and the third (OPM) column will be visible.
When you select a match from the list, a preview image should appear on the right side. This image is extracted from the specified rcsb page. This site can be opened in your OS Browser by pressing the button located beneath the image.
You can change your directory for incoming files if you want. Just enter the path into the "Incoming Folder" textfield or press to use a file chooser for it.
You can download the selected file by double-clicking the match or by pressing the 'Download PDB' button. In case an OPM entry exists for your selected protein, you may want to download this instead by using the 'Download OPM' button. If 'add to Database' is selected, your file will be added to the local database when the download has finished.
In order to search, the program uses an index file located in the settings folder. This file can be updated by pressing the 'Update PDB' button. That file is quite large (>15mb), so please be patient.
The same technique is applied for the PDBTM and OPM. You can update their index files by using the 'Update PDBTM' and 'Update OPM' buttons. But in contrast to the PDB index file, CmME is already packaged with the OPM and PDB_TM index file.
Due to the fast and rising growth of the Protein Data Bank and the delayed update process of OPM and PDBTM, it is recommended that you use the update functions once in a while. The name of the file and the date of its last update is shown below the buttons. Holding the mouse over the file names shows the exact path to the files.
If you use the semi-automatic protein placement feature of CmME, please cite the according publications:
Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H, Shindyalov I, Bourne P (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235-242.
Tusnády GE, Dosztányi Z, Simon I. (2005) PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res. 33(Database issue), D275-278.
Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006) OPM: Orientations of Proteins in Membranes database. Bioinformatics 22, 623-625.
The topologies of transmembrane proteins follow MPtopo:
Jayasinghe S, Hristova K, and White SH (2001) MPtopo: A database of membrane protein topology Protein Science 10: 455-458.
Sommer B, Dingersen D, Gamroth C, Schneider SE, Rubert S, Krüger J, Dietz, K-D: CELLmicrocosmos 2.2 MembraneEditor (2011): A Modular Interactive Shape-Based Software Approach To Solve Heterogeneous Membrane Packing Problems. J. Chem. Inf. Model. 51(5), pageX-pageY.