Difference between revisions of "3Dstrut"
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{|class = infobox | {|class = infobox | ||
|- | |- | ||
| − | ! | + | !Type |
|Plugin | |Plugin | ||
|- | |- | ||
!Download | !Download | ||
| − | |https://github.com/ | + | |https://github.com/raghuyennamalli/3Dstrut |
|- | |- | ||
!Author | !Author | ||
| − | | | + | |Tony Kamenick, Stuart Ballard |
|- | |- | ||
!Other authors | !Other authors | ||
| − | | | + | |George N Phillips Jr. |
|- | |- | ||
| − | ! | + | !Other contributors |
| − | |Shashank Ravichandran, Gautham Krishna, [[User:Ragothaman|Ragothaman Yennamalli]] | + | |Shashank Ravichandran, Yatindrapravanan Narasimhan, Gautham Krishna, [[User:Ragothaman|Ragothaman Yennamalli]] |
|} | |} | ||
| − | 3Dstrut is an external plugin for the molecular visualization program PyMOL. The plugin generates struts at optimal positions and thus enables 3D printing of any structure visualized using PyMOL. This software is distributed freely for Windows | + | 3Dstrut is an external plugin for the molecular visualization program PyMOL. The plugin generates struts at optimal positions and thus enables 3D printing of any structure which can be visualized using PyMOL. This software is distributed freely for Windows and MacOS platforms. |
| + | |||
| + | == Website == | ||
| + | https://github.com/raghuyennamalli/3Dstrut | ||
== Version history == | == Version history == | ||
| − | Version | + | Version 2.0 |
== Installation == | == Installation == | ||
| − | + | The following steps are applicable to both windows and MacOS systems | |
| + | |||
| + | I. Download the ‘.zip’ file and save it in your home directory. Once you unzip the file, you should see a directory named ‘3D_strut_plugin’ containing three files: | ||
| + | |||
| + | __init__.py, struts.py, build_struts.py | ||
| + | |||
| + | |||
| + | II. Open PyMOL and go to Plugin → Plugin manager. | ||
| + | |||
| + | III. Select the ‘Install new Plugin’ tab and click on the choose button, a window will popup. | ||
| + | |||
| + | IV. Navigate to where you extracted the ‘.zip’ file and select the ‘__init__.py’ file. Click open. | ||
| + | |||
| + | V. Make sure that the path in the ‘Select Plugin directory’ popup box is similar to the one in the figure below and then click ok. | ||
| + | |||
| + | VI. A new window will pop up with the message ‘Plugin “3D_Strut_plugin” has been installed.” and a new menu named “3-D printer” will be added to the menu bar. If you do not see the new menu immediately, close the plugin manager window quit and re-open PyMOL. | ||
| + | |||
| + | == Tutorial == | ||
| + | |||
| + | * Open a PDB file of your choice | ||
| + | |||
| + | * Navigate to 3D Printer → Build Struts (CA) | ||
| + | |||
| + | * A popup will ask you to enter a value for the maximum length a strut. Click OK to proceed to next step/popup | ||
| + | |||
| + | * Then, enter the value for the minimum distance between struts | ||
| + | |||
| + | * If you want to build struts for everything opened in PyMOL, type “all”. Otherwise, if you want only one chain to be built, select that particular chain, make a new object, and hide the rest of the protein. In this case, you will type “visible” | ||
| + | |||
| + | * You should be able to see the structs for the model in white color | ||
| + | |||
| + | * You should look for spots where building one more strut would make the printed model structurally stable. For example, in this case this loop will be unstable after printing and will crumble during processing of the model | ||
| + | |||
| + | * For the additional struts to be built, change the selection mode from “Residues” to “Atoms” | ||
| + | |||
| + | * Pick the two atoms | ||
| + | |||
| + | * And press F1. (In some keyboards the “fn” button needs to be pressed while pressing F1) | ||
| + | |||
| + | * You can see view the same tutorial with screenshots here: https://github.com/raghuyennamalli/3Dstrut/blob/main/Readme.pdf | ||
| + | |||
| + | |||
| + | [[Category:Plugins]] | ||
Latest revision as of 06:21, 1 September 2021
| Type | Plugin |
|---|---|
| Download | https://github.com/raghuyennamalli/3Dstrut |
| Author | Tony Kamenick, Stuart Ballard |
| Other authors | George N Phillips Jr. |
| Other contributors | Shashank Ravichandran, Yatindrapravanan Narasimhan, Gautham Krishna, Ragothaman Yennamalli |
3Dstrut is an external plugin for the molecular visualization program PyMOL. The plugin generates struts at optimal positions and thus enables 3D printing of any structure which can be visualized using PyMOL. This software is distributed freely for Windows and MacOS platforms.
Website
https://github.com/raghuyennamalli/3Dstrut
Version history
Version 2.0
Installation
The following steps are applicable to both windows and MacOS systems
I. Download the ‘.zip’ file and save it in your home directory. Once you unzip the file, you should see a directory named ‘3D_strut_plugin’ containing three files:
__init__.py, struts.py, build_struts.py
II. Open PyMOL and go to Plugin → Plugin manager.
III. Select the ‘Install new Plugin’ tab and click on the choose button, a window will popup.
IV. Navigate to where you extracted the ‘.zip’ file and select the ‘__init__.py’ file. Click open.
V. Make sure that the path in the ‘Select Plugin directory’ popup box is similar to the one in the figure below and then click ok.
VI. A new window will pop up with the message ‘Plugin “3D_Strut_plugin” has been installed.” and a new menu named “3-D printer” will be added to the menu bar. If you do not see the new menu immediately, close the plugin manager window quit and re-open PyMOL.
Tutorial
- Open a PDB file of your choice
- Navigate to 3D Printer → Build Struts (CA)
- A popup will ask you to enter a value for the maximum length a strut. Click OK to proceed to next step/popup
- Then, enter the value for the minimum distance between struts
- If you want to build struts for everything opened in PyMOL, type “all”. Otherwise, if you want only one chain to be built, select that particular chain, make a new object, and hide the rest of the protein. In this case, you will type “visible”
- You should be able to see the structs for the model in white color
- You should look for spots where building one more strut would make the printed model structurally stable. For example, in this case this loop will be unstable after printing and will crumble during processing of the model
- For the additional struts to be built, change the selection mode from “Residues” to “Atoms”
- Pick the two atoms
- And press F1. (In some keyboards the “fn” button needs to be pressed while pressing F1)
- You can see view the same tutorial with screenshots here: https://github.com/raghuyennamalli/3Dstrut/blob/main/Readme.pdf