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.

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

Sorry about the delay. Your academic email ID has been confirmed and you now have access to academic elements.

Hi Arnaud, thanks for your interest in SAMSON and sorry about this crash. We are not able to reproduce it here. Could you please try to remove the GROMACS element and add it again as follows:

Sign in on SAMSON Connect, you will arrive in My SAMSON / My Elements On the SAMSON Element called "GROMACS interaction models", you should see an "Installed" button. When you hover the mouse over it, the button turns to "Remove". Click on it. Restart SAMSON, this will uninstall the GROMACS element. Quit SAMSON. On SAMSON Connect, the button mentioned above should turn to "Add again" (this might take a minute). Click on it. It should turn to "Pending". Restart SAMSON, this will install the GROMACS element.

Please let me know if this helps. Academic accounts are the ones with academic email addresses. Is it possible for you to sign up with one?

Hi @Max
For the Python Scripting, it is necessary to specify in the OS environment variables the path to the Python executable.
If you are using Windows and Python installed by Anaconda, then you will need to append to the Path environment variable the paths to your installation of Anaconda, like that (depends on where Anaconda is installed): C:\Anaconda3;C:\Anaconda3\Scripts;
On Windows, it might be necessary to restart your system after that. All the rest should be detected automatically during the launch of SAMSON.

Also, to be able to use Python Scripting in SAMSON you will need the next Python packages installed: jupyter, qtconsole, numpy. These packages should be installed automatically if you installed Python using the Anaconda installer. You can verify your installation (https://docs.anaconda.com/anaconda/install/verify-install) and check whether the necessary packages were installed. If they are not installed (which is the case for installation using the Miniconda installer), you can install them via:
conda install jupyter qtconsole numpy

You can check the installation instructions for Python Scripting here: https://documentation.samson-connect.net/scripting-guide/python-script-installation/

Please, let us know if you still experience problems.

Hello, you get a key in two ways:

you don't create an account, and you use the one indicated on https://www.samson-connect.net: try@samson-connect.net and 38540-DEBE1-44187-A67B7-08471 you create an account, and you use your email address and the key you receive at that email address when you download the installer.

You can also have the key sent to you in the My SAMSON / Account page on SAMSON Connect:
0_1530614694842_47a485ff-97ee-4db0-8ad3-044b51b2ce42-image.png

SAMSON and many SAMSON Elements are free, yes. Note that you need to create an account if you want to choose which SAMSON Elements you add to your SAMSON.

Hope this helps,

Stephane

Hello, here is a capped nanotube for SAMSON 0.7.0.

Hope this helps.

Stephane

0_1528279139422_Capped nanotube.png

0_1528279059922_Capped nanotube.sam

Hi @Karsten ,

For every node, you create you need to invoke create function, and then if you want it to appear in the DataGraph this node needs to be added to a parent node:

auto camcopy = SAMSON::getActiveCamera()->clone(); // clone the camera camcopy->create(); // create the node document->addChild(camcopy); // add the created camera into the active document /* ... some modifications of the camcopy */ SAMSON::getActiveDocument()->setActiveCamera(camcopy); // set the active camera

Good idea, it will be in 0.8.

Hi Khoa, yes, it's always better to create nodes on the heap instead of the stack (i.e. with new). Therefore, you should use a SAMSON pointer (SBPointer) to hold it and destroy the node automatically when the variable gets out of scope.

Dear Patrice, yes, it is planned in a very near future, I didn't have time for the update yet...
Regards,
Sergei

Great video, Tom! Thanks for posting it!

Thanks for sharing, Tom!

Hi,

Did you perform other steps (preparation, minimization, equilibration) in GROMACS Wizard before running the production MD (see GROMACS Wizard tutorials)? If not, you might want to try to run them starting from the preparation step.

Could you share the input (all the input files for the step) and resulting files (the corresponding folder into which GROMACS Wizard saved the resulting files, named with a time stamp, e.g. "2024-10-23_09h55m26s-simulate-error") with us so we can try to reproduce the issue and see is the problem?

Dear @SHANLY ,

You can find the description of the UFF and IM-UFF used in SAMSON in the following papers:
UFF: https://doi.org/10.1002/jcc.24309
IM-UFF: https://doi.org/10.1016/j.jmgm.2017.08.023

And you can find information on how to perform simulations in SAMSON using the integrated force fields in the User Guide: Modeling and Simulation.

Could you please tell us more about what you would like to achieve?

Dear @David-Adrian ,

Thank you for your feedback! We will consider this for future releases. Where would you like to install it, e.g. on another drive or a USB-stick?

No, sorry, not at the moment.

Dear Rudy, sorry for the delay. You can simply merge the ligand structure into the receptor structure. Precisely, in the document view, drag the ligand node and drop it onto the receptor node (more generally, you can drag and drop nodes around to reorganize your entries).

Then, when you select the receptor and compute the normal modes, the ligand will be taken into account.

Hi Pedro,

We're sorry about the issue.

Could you please try to delete the following folders:

(IMPORTANT: make sure you don't have e.g. personal SAMSON documents in these folders that you might want to preserve.)

C:/Users/[USERNAME]/AppData/Local/OneAngstrom/
C:/Users/[USERNAME]/OneAngstrom/
C:/Users/[USERNAME]/Documents/OneAngstrom/

and try to reinstall SAMSON to see what happens?

Maybe there is a need to specify in your Windows settings that SAMSON should use specifically the NVIDIA GPU ? Please let us know.