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selector_manager [2014/03/10 14:35] nuno |
selector_manager [2014/03/11 11:35] (current) nuno [1. Introduction] |
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===== 1. Introduction ===== | ===== 1. Introduction ===== | ||
+ | ### | ||
+ | VMD is an exceptional program to visualize molecular structures. The main drawback of this software is the learning curve that turns it hard to use by non-expert users. | ||
+ | One of the major difficulties that non-expert users have while handling VMD regards the selection of atoms. This is done through a series of keywords that the user must dominate in order to for example visualize and/or hide particular parts of the molecule, do specific transformations on the atoms of that selectin, etc. | ||
- | Molecular docking is becoming an important part in the process of developing new drugs. There is much docking software that has been successfully used in a myriad of keystone problems, however, as commonly happens with most of the scientific software, the programs are often complex and a deep knowledge is required for the common user to carry out standard steps. | + | ### |
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- | This is an obstacle and a cornerstone issue for the research teams in the fields of Chemistry and the Life Sciences, who are interested in conducting this kind of calculations but do not have enough programming skills. | + | In order to overcome this issues we have developed "Selection Manager". This plug-in allows to do common selections on molecules without requiring any prior knowledge regarding the keywords available on VMD. It makes the selection of atoms simpler and easy for non-expert users. In addition it still allows the insertion of advanced commands but alerts the user for any error that might exist on the syntax. |
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- | To overcome these limitations, we have designed vsLab (Virtual Screening LABoratory), an easy-to-use graphical interface for the well known molecular docking software AutoGrid/AutoDock that has been included into VMD as a plug-in. This program allows almost anyone to use AutoDock and AutoGrid for simple docking or for virtual screening campaigns without requiring any deep knowledge about these techniques. | + | |
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- | The potential associated to this software makes it an attractive choice not only for educational purposes, but also for more advanced users that can use vsLab to increase workflow and productivity of everyday tasks. | + | |
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===== 2. ScreenShots ===== | ===== 2. ScreenShots ===== | ||
- | {{gallery>software:vslab?*&150x150&lightbox}} | + | {{::2014-03-10_02.49.15_pm.png?direct&150|}} {{:software:screen_shot_2014-03-10_at_14.51.33.png?direct&150|}} {{::screen_shot_2014-03-10_at_14.52.55.png?direct&150|}} {{:software:screen_shot_2014-03-10_at_15.03.23.png?direct&150|}} |
===== 3. Download ===== | ===== 3. Download ===== | ||
- | In order to run the vsÇab plug-in, the Visual Molecular dynamics software (VMD) must be installed. It can be found at http://www.ks.uiuc.edu/Research/vmd/ . | + | In order to run the"Selector Manager" plug-in, the Visual Molecular dynamics software (VMD) must be installed. It can be found at http://www.ks.uiuc.edu/Research/vmd/ . |
<note tip> | <note tip> | ||
- | * VsLab Plug-in : **v1.1** {{:software:vslab:vslab1.1.zip| }} | + | * Selector Manager Plug-in : **v1.0** {{:software:selectionmanager.zip| }} |
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===== 4. Installation ===== | ===== 4. Installation ===== | ||
### | ### | ||
- | VsLab can only be installed in LINUX and MAC operating systems, due to the limitations of the autodock software. Installation in Windows will be available whenever possible. | + | The selector manager plug-in can be installed in any operating systems where VMD works. |
+ | In order to work the user has to add the following lines to the .vmdrc that can be found on the home directory: | ||
### | ### | ||
+ | #### selectionMAnager | ||
+ | lappend auto_path /home/users/nunocerqueira/selectionManager | ||
+ | vmd_install_extension selV "::selV::start" "PortoBioComp/Selection Manager" | ||
+ | ## END | ||
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+ | Note: /home/users/nunocerqueira/selectionManager is the directory where the plug-in has been installed. | ||
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