Search found 162 matches

by bjoern
11.05.2017, 09:27
Forum: Cm2.2 MembraneEditor (CmME)
Topic: Tutorial: Import and work with custom lipid PDBs in CmME
Replies: 0
Views: 18316

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...
by bjoern
11.05.2017, 08:49
Forum: Cm2.2 MembraneEditor (CmME)
Topic: Bug Report MembraneEditor 2.2.2_2
Replies: 3
Views: 19734

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...
by bjoern
01.05.2017, 23:16
Forum: Cm2.2 MembraneEditor (CmME)
Topic: Bug Report MembraneEditor 2.2.2_2
Replies: 3
Views: 19734

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...
by bjoern
08.03.2016, 00:36
Forum: CmCM Cell Modelling
Topic: VizBi 2016 Blender Workshop
Replies: 0
Views: 20471

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...
by bjoern
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: 32930

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...
by bjoern
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: 42506

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...
by bjoern
11.03.2015, 19:02
Forum: Cm2.2 MembraneEditor (CmME)
Topic: Scripts for Vesicle analysis
Replies: 2
Views: 33589

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...
by bjoern
12.01.2015, 14:58
Forum: Membrane Packing Algorithms Archive
Topic: DimensionLister [java]
Replies: 0
Views: 19635

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
by bjoern
12.01.2015, 14:45
Forum: Membrane Packing Algorithms Archive
Topic: MembraneBoxifier [java]
Replies: 0
Views: 16775

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...
by bjoern
12.01.2015, 14:36
Forum: Membrane Packing Algorithms Archive
Topic: MyMembraneAlgorithm [java]
Replies: 0
Views: 15855

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...
by bjoern
12.01.2015, 14:20
Forum: Membrane Packing Algorithms Archive
Topic: Advanced Random Placing Parallel (ARPP) [jar]
Replies: 0
Views: 17841

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...
by bjoern
12.01.2015, 13:59
Forum: Cm2 MembraneEditor
Topic: Questions
Replies: 10
Views: 54529

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...
by bjoern
12.01.2015, 13:54
Forum: Cm2 MembraneEditor
Topic: Questions
Replies: 10
Views: 54529

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...
by bjoern
12.01.2015, 08:59
Forum: Membrane Packing Algorithms Archive
Topic: The GMX-Plugin [jar]
Replies: 0
Views: 18578

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...
by bjoern
18.12.2014, 14:56
Forum: Cm2.2 MembraneEditor (CmME)
Topic: Scripts for Vesicle analysis
Replies: 2
Views: 33589

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...