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.

Dear @Filipe

Normally it should be rendering double bonds by default, but you can change this setting in Preferences > Rendering > Structural models - check the Render multiple bonds option:
5d539e47-b05e-4872-8cc1-d1d36cb34dc5-image.png

As for the PBT format, currently, SAMSON does not have the PBT format exporter, but you can export in OBJ or glTF formats for use in Blender.

Best,
The SAMSON Team

Great contribution!

Hi @albert ,

There are several options for the colorization of structures or visual models (Ribbons is a visual model) based on chains:

The colorization using color schemes. First, select the Ribbons visual model in the Document view that you would like to colorize. Then: Biology > Colorize > Chain ID or Chain (illustrative) (i.e. in the style of D.S.Goodsell)
aedf2d1e-77e3-42cd-af72-51400ba6f73b-image.png
You can also choose "Custom..." from the list and specify the color palette. The colorization with constant colors per chain. Choose a chain in the Document view. Set the color using Visualization > Colorize.

See more in User guide - Colorizing and User guide - Visualizing.

Dear @Zilong

It’s not currently possible to export vector images. However, you can change the image resolution in the preferences:

Open the Preferences (Menu Interface > Preferences) In the Preferences, go to Interface > Captures to change capture settings, including the resolution.

Great! Thanks Tom!

Thanks Tom!

Dear @Elsaid ,

This happens because of the Wayland display server on Ubuntu. You can try specifying another display server.

If you launch SAMSON from a terminal, then you could first specify the environment variable QT_QPA_PLATFORM to use the Xorg display server (X11):
export QT_QPA_PLATFORM=xcb

Then start SAMSON in the same terminal. Note, SAMSON is installed in your home directory ~/OneAngstrom/SAMSON-Application/4.0.0/Binaries, you can try starting ./SAMSON-Launcher.sh

If this works, you can try disabling Wayland on your system, for that you will need sudo privileges:

Disable Wayland by uncommenting WaylandEnable=false in the /etc/gdm3/custom.conf Add QT_QPA_PLATFORM=xcb in your ~/.bashrc file.

You might need to restart either the OS or the terminal.

You can check whether your system uses Wayland or X11 by running the following command in the terminal:
echo $XDG_SESSION_TYPE