Search found 162 matches
- 11.05.2017, 09:27
- Forum: Cm2.2 MembraneEditor (CmME)
- Topic: Tutorial: Import and work with custom lipid PDBs in CmME
- Replies: 0
- Views: 18329
Tutorial: Import and work with custom lipid PDBs in CmME
CmME comes already with a number of lipid files. If you want to create a membrane for illustrative purposes, then it is normally sufficient to use the delivered lipid files. But, in case you want to prepare a simulation, e.g. with GROMACS, you will usually want to use your own files, as you need PDB...
- 11.05.2017, 08:49
- Forum: Cm2.2 MembraneEditor (CmME)
- Topic: Bug Report MembraneEditor 2.2.2_2
- Replies: 3
- Views: 19746
Re: Bug Report MembraneEditor 2.2.2_2
Phil: Just a note, my webstart start stopped loading in the cm2 file, but I just ran the executable jar and everything worked, no idea what happened. Please use Java 8 if you are using the Web Start Version. Especially for Mac OS X we strongly recommend to use Java 8, as the previous version 1.6 an...
- 01.05.2017, 23:16
- Forum: Cm2.2 MembraneEditor (CmME)
- Topic: Bug Report MembraneEditor 2.2.2_2
- Replies: 3
- Views: 19746
Bug Report MembraneEditor 2.2.2_2
The biggest improvement of version 2.2.2_2 is the removal of the old Java 3D 1.5.2 backbone from Sun and the use of Jogamp's Java 3D continuation 1.6.0 final from http://jogamp.org. The big improvement should be here that the self-executables and also (hopefully in the future) web start will not wor...
- 08.03.2016, 00:36
- Forum: CmCM Cell Modelling
- Topic: VizBi 2016 Blender Workshop
- Replies: 0
- Views: 20480
VizBi 2016 Blender Workshop
This forum is intended for the two Blender workshops at VizBi 2016 of Chris Hammang and Björn Sommer. Session I Blender_Tutorial_VizBi2016__session1__1_2.pdf Image for the morning session from http://ccdb.ucsd.edu/sand/main?mpid=3487&event=displayRaw CCDB3487.jpg Resources Blender Camera Animati...
- 05.04.2015, 03:19
- Forum: Cm2.2 MembraneEditor (CmME)
- Topic: When will there be the release? Where is the Source Code?
- Replies: 3
- Views: 32938
Re: When will there be the release? Where is the Source Code
first official release version of CmME. It is planned for 2011... Is it....??? :D Yes, my friend, it was published in 2011. If you would click on the link http://Cm2.CELLmicrocosmos.org - instead of posting your commercial info here - you would have known :mrgreen: (by the way, sorry for removing y...
- 11.03.2015, 19:31
- Forum: Stereoscopic Camera Plugin for Blender
- Topic: Stereoscopic Camera Plugin for Blender 2.6X to 2.7X
- Replies: 0
- Views: 42520
Stereoscopic Camera Plugin for Blender 2.6X to 2.7X
The Stereoscopic Camera Plugin was developed by noeol.de. I updated only to version 1.6.8 (see below). However, the original website does not provide the old versions anymore. This is a problem, because many old Blender files are only compatible to the specific Blender version they were created with...
- 11.03.2015, 19:02
- Forum: Cm2.2 MembraneEditor (CmME)
- Topic: Scripts for Vesicle analysis
- Replies: 2
- Views: 33590
Re: Scripts for Vesicle analysis
Everytime I attempt to make a micelle utilizing the Vesicle Builder I get a mistake message (java.lang.NullPointer Exception). Lipids were allocated to EC. By allotting lipids to IC they are added to the basic circle, however the procedure pends in the beginning including lipids stage and I can not...
- 12.01.2015, 14:58
- Forum: Membrane Packing Algorithms Archive
- Topic: DimensionLister [java]
- Replies: 0
- Views: 19645
DimensionLister [java]
DimensionLister This algorithm uses the basic functionality of the MembraneEditor to compute the area per lipid. This is not accurate, it can only be used to give hints! Please use APL@Voro to compute the correct area per lipid: http://www.aplvoro.org DimensionLister.java developer: Björn Sommer
- 12.01.2015, 14:45
- Forum: Membrane Packing Algorithms Archive
- Topic: MembraneBoxifier [java]
- Replies: 0
- Views: 16784
MembraneBoxifier [java]
MembraneBoxifier This small tool can be used to transfrom lipids to bounding boxes. For this purpose, the maximal distances of the different atoms are taken into account to create the 8 edges of a box. With this algorithm, you can do two things: Change the shapes of a previously generated membranes...
- 12.01.2015, 14:36
- Forum: Membrane Packing Algorithms Archive
- Topic: MyMembraneAlgorithm [java]
- Replies: 0
- Views: 15872
MyMembraneAlgorithm [java]
MyMembraneAlgorithm.java This very basic algorithm is used for this introduction: http://cellmicrocosmos.org/index.php/developer/introduction It is a good way to start with the development of Membrane Packing Algirithms. This algorithm has to be used with the standalone version of the MembraneEdito...
- 12.01.2015, 14:20
- Forum: Membrane Packing Algorithms Archive
- Topic: Advanced Random Placing Parallel (ARPP) [jar]
- Replies: 0
- Views: 17851
Advanced Random Placing Parallel (ARPP) [jar]
Advanced Random Placing Parallel (ARPP) This is the alpha version of a small Membrane Packing Algorithm using Java Threading for computation. It is based on the Random Placing Algorithm, but using only bounding boxes for the computation. Developers: Martin Holland, Leroy Rügemer (based on a algorit...
- 12.01.2015, 13:59
- Forum: Cm2 MembraneEditor
- Topic: Questions
- Replies: 10
- Views: 54537
Re: Questions
So it will be not so easy, because these files will usually not contain any information about the atoms - only some coordinates representing positions and shapes. So I fear, you cannot just create a PDB file from this STL file by writing a script. Sure and that is not what I want to do. Does the gr...
- 12.01.2015, 13:54
- Forum: Cm2 MembraneEditor
- Topic: Questions
- Replies: 10
- Views: 54537
Re: Questions
Hi, its me again :wink: Would it be possible to get upper and lower leaflet as individual chains in the generated .pdb-file? Of course I you could separately generate both layers but that would double the time. I am asking this because there is always a defined space between both layers and since I...
- 12.01.2015, 08:59
- Forum: Membrane Packing Algorithms Archive
- Topic: The GMX-Plugin [jar]
- Replies: 0
- Views: 18585
The GMX-Plugin [jar]
The GMX-Plugin The GMX-Plugin is an interface between GROMACS 4.X and the MembraneEditor 2.2.2. It uses the force field ffGMX45a3 and special lipid topologies which can also be downloaded here. Learn here how to import this algorithm into the WebStart or Standalone version: http://cellmicrocosmos.o...
- 18.12.2014, 14:56
- Forum: Cm2.2 MembraneEditor (CmME)
- Topic: Scripts for Vesicle analysis
- Replies: 2
- Views: 33590
Re: Scripts for Vesicle analysis
The VesicleBuilder plugin for the MembraneEditor you will find here: http://www.cellmicrocosmos.org/Cmforum/viewtopic.php?f=35&t=676&p=1398 During Manuel's internship, I improved the VesicleBuilder step-by-step (thanks go to Manuel for his valuable comments! ;). The new beta version of the r...