Dear John,

As Stephane pointed out, Adenita is for now compatible just with SAMSON 0.8.5 or 0.7.0, for Windows and Linux. But there are plans to port it to SAMSON 2020 and Mac, I expect this versions to be available during April this year.

Best regards,

Elisa

Dear @Yair-Augusto, Adenita was just updated and this problem should have been fixed. Please let me know if it persists or you find new ones.

Best regards,

Elisa

It does! Thanks a lot.

Dear @sudhir ,

For the protein-ligand simulation, you can check out the Ligand Path Finder tutorial for Ligand Path Finder Element. You can also check out the Ligand unbinding pathway search tutorial for the free Ligand Unbinding Search Element (available only on SAMSON 0.7.0).

As for saving MD trajectories, you can check out the tutorial on exporting atoms trajectories along paths which uses the Export Along Paths Element. This Element allows you to export trajectories into PDB files which you can further analyze using other software.

You can also do some analysis and post-processing in SAMSON thanks to the Python Scripting Element, you can check out the Python Scripting guide for more information, for example, the Computing RMSD sample.

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.

Hi,
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.

Dear Stephane,
Thanks for the link but I tried this too. I does not work all the time. But as I mentioned in YASARA structure, parameterization is a childs' play. How they do it is secret for me but it is kool.
If there will be something like that in SAMSON too, it will be very easy to run complex simulation affectively.

Sorry, SAMSON needs a 64-bit computer to run.

Dear Stephane,

Yes, we have atoms. The 0.8.0 solution will be the best long-term, as we are dealing with large systems and FPS drop a lot when translating or rotating, but for now I will check the ParticlePositionChanged event.

Thanks!!

Elisa

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.

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

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.

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