Dear @Jean-Baptiste ,

Thank you for your interest in SAMSON!

According to your screenshot, I think the problem here is due to an unnecessary newline character in the command you past in the PowerShell terminal due to copying.

Please, note: we recommend not to build your Elements in the SAMSON Debug folders - you should use a dedicated folder to develop your SAMSON Elements

If you have -DQT5_CMAKE_INCLUDE_DIR environment variable defined in your system you can compile for Visual Studio 2017 like this:
cmake -DSAMSON_SDK_PATH="C:\Program Files\NANO-D\SDK\0.7.0" -G"Visual Studio 15 Win64" ..
else like this:
cmake -DSAMSON_SDK_PATH="C:\Program Files\NANO-D\SDK\0.7.0" -G"Visual Studio 15 Win64" -DQT5_CMAKE_INCLUDE_DIR="C:\Qt\5.9.3\msvc2017_64\lib\cmake" ..

You can copy the command from here.

You can also check whether the cmake is defined in your system by e.g. checking its version number:
cmake --version

I would also recommend to follow the updated tutorial on Building on Windows in the Developer guide.

Hi,

I think I found the problem. Some initialization functions in the constructor of my class were overriding the unserialization. I tried to make a quick fix but when I do static casts in the unserialize function, SAMSON is crashing, so I will modify my constructor and check, it will take a bit though.

Thanks for your help!

Hi Dmitriy,
My CMakeLists for the Python Bindings version is like you posted above, so I'm not linking in the debug mode. My other branches don't have any reference to Python in the CMakeLists, so they are not linking neither.

Thank you, Dmitriy. I will try later. I just tried to open pdb file in Windows, and in status bar got the message, that it "can''t open" my file. I will try to put the log here a bit later.

Installation is done.

Hi Andrea, sorry for the delay. Typization is normally performed automatically (this is a benefit of this SAMSON Element, as described in the paper Artemova, S., Jaillet, L., & Redon, S. (2016). Automatic molecular structure perception for the universal force field. Journal of computational chemistry, 37(13), 1191-1205.). The typization functions are there when you know for sure that you would like to use a different typization, but even then you should refer to the original UFF paper to make sure this is what you want.

Dear all,

Thanks for the answers. it was very helpful, we would probably then choose BSD-3 to make sure we stay compatible with SAMSON.

Best regards,

Elisa

Hello, could you please contact us by email (please reply to the registration email) so we can see what we can do?

Thanks!

The SAMSON team

Dear @Andrea ,

We have updated the Lennard-Jones Interaction Model SAMSON Element, now you can set the smaller epsilon parameter. The SAMSON Element should be updated automatically once you launch SAMSON with an Internet connection.

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.

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).

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.

Thanks!! Solved!

I think it should be possible, it will be just an additional line in the launcher script. If we will be shipping Python Scripting with the Python environment, I think we might ship the environment with a bare SAMSON installation so that to use SAMSON Elements, that depend on this environment, the user won't need to install the Python Scripting Element.

Hi Stephane,

thanks for your answer, I'll do that then.

Best

Laëtitia

Thank you @Cyril for the suggestion. We will see whether to add it as a feature in the next version of SAMSON or implement it as a SAMSON Element.

For now, you can use Python Scripting in SAMSON. To use the Python Scripting SAMSON Element you will need to have a specific version of Python installed. Please, check the Python Scripting installation instructions for SAMSON. You can also check the SAMSON Python Scripting tutorials and documentation.

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

There is an invert selection feature in SAMSON: right-click on the selection (either in the Document view or in the viewport), and in the context menu select Invert selection
0_1549532475757_InvertSelection.png

It works great ! Thanks a lot !

wonderful!
Thanks

Thanks, SAMSON SDK 7 works properly, but v6 still not (I've checked all requirements and followed installation steps from the instruction). Still, I've got working version of SDK, so thank you again)