The sample script for this task can be found below. You can either copy it inside of the Python Scripting console in SAMSON, or save it as a .py file and open this file in SAMSON when you need to execute this script.
This example shows how to select bonds which center lies in between of two planes: z_min and z_max
If you want to select bonds which center lies on a specific plane, just set z_min=z_max
# Get an indexer of all bonds in the active document. Here we use SAMSON Node Specification Language to get only bonds
allBondsIndexer = SAMSON.getNodes('node.type bond')
# two planes: 1.7A and 2.3A
z_min = Quantity.angstrom(1.7)
z_max = Quantity.angstrom(2.3)
for bond in allBondsIndexer: # a loop over an indexer
# compute the z-axis center of the bond
bondCenterZ = (bond.leftAtom.getZ() + bond.rightAtom.getZ()) / 2.0
# check whether the bond lies in between of desired planes
if bondCenterZ >= z_min and bondCenterZ <= z_max:
# select the bond by setting the selectionFlag to True
bond.selectionFlag = True
allBondsIndexer.clear() # clear an indexer
Thank you for the suggestion, @Cyril !
Yes, for now, it is possible only with an importer for crystallographic .cif files. There is a possibility to replicate crystals thanks to the Crystal Creator App, but it does not expand them periodically with bond connections. We will see what we can do.
Hello @Kava ! Thank you for your interest in SAMSON. As far as we know, no one is currently working on the STL exporter. But this would be a really nice feature. For the efficiency and speed reasons, the Gaussian surface is generated on GPU. Therefore, we don't have direct access to resulting shapes and it won't be that easy to export these shapes. We will see what we can do.
Another possibility is to program the Gaussian surface on CPU yourself and export the resulting shape in the STL file (see Documentation for developers).
Rendering of spheres is fast, it is done on GPU, rendering of disks should not make it much faster. It is the Document view, which makes it slower for bigger systems, but it will be faster in the next SAMSON version.
If you want to see the flat visualization of atoms, you can modify the rendering preferences via changing the lightning preferences in SAMSON (see User guide: Visualizing. Lightning section). Basically, in the SAMSON preferences (Ctrl/Cmd+K) go to Rendering > Lightning: set the light intensity for first and second lights to zero; set the ambient light to 1 and the Fresnel intensity to 0.
Actually interactive fitting only VMD is providing and that is also very limited. VMD chops off your actual EM map according to the provided pdb model instead of fitting it into the density.
So, as I want to fit multiple structures in the map, I can not do it. I was trying to fit my multi-chain PDB in the same map but it failed.
Chimera do not provide interactive fitting and it fits the protein poorly in the map. Therefore, it is hard to get a proper knowledge of the conformation of any of these tools.
Rest tools are more programming centric, making them hard to be used by biologists having limited programming skills like me.
To simulate a protein-membrane complex you can use the GROMACS Wizard Element, using this Element you can easily prepare your system for GROMACS simulation, minimize and equilibrate the structure, and simulate your system using GROMACS. See the GROMACS Wizard tutorial for more information.
To save only the last frame in the trajectory into a PDB file, you can select a path corresponding to this trajectory and set the step to the last one in the Inspector (click Ctrl/Cmd + I to open the Inspector in SAMSON), this will update the structural model - it will correspond to the step you chose. Now you can select the structural model in the Document view and save only the selection as a PDB file, for that in the menu go to Selection > Save selection as and select the PDB format in the types of files.
As for now, there is no direct way to save a .gro file from within SAMSON.
The GROMACS Wizard Element saves the temporary files, including some gro files in a specific scratch folder in your user's directory, the path is different for different OS (Windows, Linux, Mac OS). You can either try looking for the Scratch/GROMACS on your system or check out the path to SAMSON's scratch folder by launching SAMSON-Core-Console executable version and checking for a line with SBGPath::getScratchPath() in the beginning of the console output. On Windows it will be something like: C:\Users\user\AppData\Local\OneAngstrom\SAMSON\DATA\0.8.3\Scratch.