Dear @Emmanuel ,

Thanks for reporting this issue! It's now fixed, and the fix will be available with SAMSON 2020 R2, which will be deployed in a few days.

Dear @Emmanuel ,

Thanks for reporting this issue! It's now fixed, and the fix will be available with SAMSON 2020 R2, which will be deployed in a few days.

Thanks for reporting this bug! It's now fixed, and the fix will be available with SAMSON 2020 R2, which will be deployed this monday (may 11, 2020).

Hi Clement,

To listen to the document closed signal I connect my nodes to a custom signal like this:

SB_FOR(SBNode* node, atomIndexer) node->connectBaseSignalToSlot(this, SB_SLOT(&SENormalModesAnalysisApp::onBaseEvent));

Then, in my onBaseEvent function I catch the NodeEraseBegin event which corresponds to the signal emitted when the document is closed or the nodes erased.

void SENormalModesAnalysisApp::onBaseEvent(SBBaseEvent* event) { if (event->getType() == SBBaseEvent::NodeEraseBegin) { //disconnet the connected nodes SB_FOR(SBNode* node, atomIndexer) {node->disconnectBaseSignalFromSlot(this, SB_SLOT(&SENormalModesAnalysisApp::onBaseEvent)); } //....// }

Remember to disconnect the connected nodes.
Hope I answered your question,
Yassine

Hello Arturo,

thanks for your interest in SAMSON!
The AutoDock Vina element has been deprecated as it was offering limited functionality (only one ligand at a time). It is still possible to use the AutoDock Vina Extended element for free for 30 days (no credit card needed) and it can do more, including pre-minimization of ligands and docking entire libraries.
Can you please ask your teacher to contact us at contact@samson-connect.net so we can find the best solution to provide access to all students?

Thanks,
Stephane

Adenita needs older versions of SAMSON because it hasn’t been updated yet (you can see this on the element page). You need to reinstall SAMSON and check the box “Install older versions” to install 0.8.5. Also, please check the requirements on the element page.

Thank you @Rahad !
Do you mean the minimization step in the AutoDock Vina Extended module? What error does it show?

As for ligand libraries, AutoDock Vina Extended module supports libraries with ligands in formats that can be opened in SAMSON, including .pdb, .mol2, .sdf, .xyz, etc, but not .mol and .pdbqt for now. You do not need to import all the ligands in SAMSON, you just need to provide the path to the folder with a ligand library.

Hi,
Sorry for the issue the file was not shipped with the SDK.
See : https://documentation.samson-connect.net/developers/latest/page_installation.html
To launch SAMSON just execute SAMSON-Core after doing the step inside the previous link.

If the file is absent you can create SAMSON-Core.command with the following content

#!/bin/sh

echo "saving context"
SAVED_DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH
SAVED_DYLD_FRAMEWORK_PATH=$DYLD_FRAMEWORK_PATH
SAVED_DYLD_FALLBACK_LIBRARY_PATH=$DYLD_FALLBACK_LIBRARY_PATH

echo "launching SAMSON-Core"
script_dir=$(cd "$(dirname "$0")";pwd)
cd "$script_dir"

echo "You need to add ~/Qt5.12.5/5.12.5/clang_64/lib folder in your DYLD_FRAMEWORK_PATH or edit this file"

#export DYLD_FRAMEWORK_PATH=~/Qt5.12.5/5.12.5/clang_64/lib or the one corresponding to your setup
export DYLD_LIBRARY_PATH=$script_dir
export DYLD_FALLBACK_LIBRARY_PATH=$script_dir

./SAMSON-Core #available flags --disablenetwork /--import /--logconsole /--logfile "file" /--logdefaultfile

echo "restoring context"
export DYLD_LIBRARY_PATH=$SAVED_DYLD_LIBRARY_PATH
export DYLD_FRAMEWORK_PATH=$SAVED_DYLD_FRAMEWORK_PATH
export DYLD_FALLBACK_LIBRARY_PATH=$SAVED_DYLD_FALLBACK_LIBRARY_PATH

then execute chmod +x SAMSON-Core.command
then execute chmod +x SAMSON-Core

Jocelyn

I have a structure I would like to alter a bit using Adenita, but whenever I try to select it, it becomes non-responsive and crashes. I've tried using a .json file and a .pdb file and neither is capable of having parts selected. I tried on two different computers, one with a quad-core and one with a 6-core and it still crashed. Is there a way I can perform this on my build? Or is this a software issue that others experienced?

OS: Windows 10
Ver: SAMSON 0.8.5

Hello @Prokop ,

To connect two atoms with a bond, use the Add editor: press on the first atom and draw a bond to the second one and then release. Please see the gif below:
0_1583572262919_Connecting with a bond.gif

Dear @Tadija
This just means that SAMSON was not able to get the name of the GPU but it should have detected it properly. Does SAMSON work properly for you or you experience some problems with graphics?

Dear Sudhir, calculation time depends on the exhaustiveness (the higher the slower, but the more exhaustive the search is), the number of rotatable bonds in the ligands (each rotatable bond adds a search dimension) and the number of cores on your computer (the module takes all cores minus one, so your computer remains responsive). This seems normal.

Hello Emmanuel! We were actually talking about you just a few hours ago because we saw your posts about your VR class! It's awesome!

You can actually already move molecules with one hand if you use the "Move" mode (which moves stuff) instead of the "Navigate" mode (which moves yourself).

We decided to use both hands for navigation because we wanted the user to be able to scale as well as rotate / translate the view (7 degrees of freedom), and our tests have shown that this is what is familiar to many people (who use two fingers for scaling on phones). Using both hands and spreading arms / bringing arms closer changes your scale relatively to the molecules. When you move both hands without changing the distance between them you can rotate, translate, etc. Changing the scale in an intuitive way was really important to us to address many different scales as in the virus demo. In the frame below, the user height is around 0.1 microns:

0_1571932063809_35c2d463-2005-4034-8590-7d01aed44b7a-image.png

while in this frame (inside the virus) the user height is about 1 nanometer:
0_1571932649700_8f1fb7ac-5a84-4d25-8cf0-e90e2fd9775a-image.png
(sorry for the video compression blur).

To move molecules instead of yourself, you use the thumbpad in "Move mode" (the two other thumbpad modes are "Add" and "Erase"), and you choose the selection filter that corresponds to what you want to move. This way, you can move a molecule with a single hand (or two molecules with two hands).

For example, in the Selection menu, choose the selection filter called "Structural models" as in the figure below:
0_1571931319443_3aac795a-8757-4f3c-b47f-a644a8b09d68-image.png

Depending on your structures, you might want to select other levels (e.g. molecules, chains, etc., or the default "atoms and bonds").

Then, using the thumbpad, you can rotate / translate when you press on the thumbpad. This is demonstrated e.g. in this video where the user manipulates two carbon nanotubes at the same time to stick them together during interactive simulation. Each hand independently moves each nanotube.
0_1571931699541_991a4089-53fb-46fc-aac5-9d1ea04e8fa7-image.png.

You can have different modes in each hand (e.g. Add on the left hand, Move on the right hand, etc.).

I hope this helps. I'll be happy to talk more about it, as well as about extensions and applications.

Best,

Stephane Redon

Dear @sudhir ,

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.

Dear @Jeremy

You have two ways of programming (e.g. this preparation step) in SAMSON:

Using SAMSON SDK which allows you to develop your own SAMSON Element using SAMSON API, C++, and Qt. For that, you need to register on SAMSON Connect as a developer which is free and one-click.

Using Python Scripting Element, which allows you to access most of the SAMSON API to process and automatize tasks. See the Python Scripting guide, you can check out tutorials there and the Python Scripting samples.

In the 1st case, you have more functionality and control over processes. The 2nd one is faster to develop and try, and you can further use the developed scripts for your tasks.

For the simulation in which you are interested in, you can use GROMACS Wizard Element (see the GROMACS Wizard tutorial), which allows you to easily run simulations using GROMACS (it comes with the Element) including various temperature ranges. There is yet no possibility to run simulations automatically, but you can launch many simulations in a queue using jobs. In future releases, it will be possible to run them on the cloud. You can freely try this Element for 30-days.

The size of the system for simulation is limited by your computer performance (RAM, CPU, GPU) and the max computation time you are willing to spend. In SAMSON it is possible to load systems with tens of thousands of atoms (depending on the performance of your computer).