SOC workstation

This is an admin maintenance guide for the SOC workstation.

Access to the Station: To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl

Available software

On the workstation we have the following software installed:

Software installed on the SOC workstation (last updated 30.01.2025)

Software	Intended purpose	License
7-zip	Compressing and decompressing .zip files	n.a.
Avogardo	Small molecule modelling	n.a.
ChemOffice	Drawing molecules (chemdraw) or saving as .sdf	RU
GOLD	Precise molecular docking with a genetic algorithm (GA) for pose sampling	Academic, RU-broad from solid state chemistry
Mogul	Torsion angle checking against the CSD	Academic, RU-broad from solid state chemistry
Conquest	Software to search the CSD	Academic, RU-broad from solid state chemistry
MOE	Primary use of the workstation, all-round software for LBDD and SBDD such as: QSAR, Pharmacophores, homology modelling, (template-based) docking, protein-ligand modelling, fragment-growing, library enumeration, visualization.	Rutjes group exclusive, 1 license
Wincoot	Inspecting electron density maps (EDMs) of biomolecules WARNING! Downloading precomputed EDM .mtz files from the PDB is no longer possible	Academic
YASARA Structure (currently no license)	Homology Modelling, Protein-ligand modelling, molecular dynamics (MD), Visualization program	Academic, wtitulaer personal

If you require different software, please send a message to socmoe-access@science.ru.nl. For other software available to the SOC please check Molecular software

Maintenance (admin only)

Important to note is that for any problem that should arise, Hakim can be contacted in principle. It also good to note that we no longer know the BIOS password (can be overwritten with a physical jumper) but for now this should not be an issue.

The idea is that all software updates / maintenance can be performed from the admin account unless stated differently on this page. Here follows a list of common practices per software that the PC runs that should be checked from time-to-time.

Hardware checks

Disk checks (2/year)

Disk checks should be performed twice per year for each disk (raid 1 mirror setup). This can be done by using the desktop folder maintenance and running the listed commands in a Windows cmd administrator shell. Check the 'SMART overall-health self-assessment test result:' it should say PASSED and if not Hakim should be contacted with the info also found after running this command. Similarly, the Intel rapid storage app (accessible through the popup icon in the footer) should have green indications that everything is working as it should.

CCleaner

Should run automatically but if changes needed, these need to be reconfigured per user.

Windows updates (2/year)

Run windows 10 updates twice per year and book a slot for this.

Software updating

The idea is to conservatively update the system. Should updates still be needed, here are recommendations.

Teamviewer

Teamviewer is managed from the admin account with the gear icon (requiring the Settings password). When update is needed, ensure to make screenshots of all settings prior to updating. The most important settings to keep:

• At advanced settings, Disable local input and Enable blackscreen
• Ensure Full Access is selected
• Deactivate random password
• Personal password is the Access password for SOCMOE that allows users to enter a remote session without needing to fill in another password.

Transfer of access

Important is that 'Licentiebeheer ILS' knows who is in charge of the station. Our current contact is Wietske (RU) who emails on if license for Teamviewer needs to be continued after which Samuel handels the payment.

Guidelines for adding new users

Terms of use

Users who apply for the use of the machine must all accept it terms of conditions (the standard email with the same file). @Willem, could include which software can be used by whom.

New user Teamviewer (remote access)

Using the online [login.teamviewer.com TeamViewer] with your own user login (requires being added as an admin previously). Then do the following:

• Admin makes a new user with the specified email address (preferably RU or science) with a password
• Admin removes everything at the Advanced settings apart from the 'log sessions' setting
• Admin sets permission to user
• User receives email and makes the account
• Now that the user is actually active, the share can be assigned to the user with a Read-only permission.

Furthermore, it is important here the setting 'Incoming LAN connections' is set to 'accept' since otherwise people on the RU-network will not be able to connect remotely.

Booking

Currently on Hakim's google drive. @Willem, let Hakim know once you take it offline and inform others on new one.

Mailing list

Mailman lists from CnCz, mailed by Hakim (some link to login with a password) For socmoe-announce you only need Membership Management. For adding, Mass Subscriptions Basically put people in, put people out.

SOC-MOE-access list

MOE downloads/licenses

At CCG, Download Request Request type => Existing customers Use the exact correct email address. Make sure the Daemon version / license manager version is good. 3 tokens/pc Increment part of the license file specifies the teaching licenses. Every year we should automatically get the new license after the payment is done. Then a new license.dat can be made and sent to CnCz. Check in April with Samuel if payment is done cause license is only issued once payment has been received. 31 May 2025 we need to buy another 3 years with annual payment and Samuel fixes the payment. Mauricio gets in touch and asks to renew. Emails come from MOE License Management Text goes into license.dat

The license.dat also goes into the moexxx/ folder. Since the current license goes up to MOE2025.01 we can just copy the previous license.dat file.

Caveats on installed software

Office is unofficial.

Knime (guidelines caveat mentioned there as well). Should always be ran as MSS user since the file system space would be registered to admin Wincoot only used from MSS.

Always install software from the admin account

Firefox & Chrome should update itself in the admin account. Extensions need to be updated in both accounts. Once a year check Notepad++. Knime instead of updating uninstall and reinstall. Chemdraw licensed to socmoe-access@science.ru.nl (Otherwise ask Dani).

Suggestions from Hakim

- Purge non Rutjes / non-active users - Add the black screen not active remote access part / UPDATE - Maybe remove the Linux part from the guidelines - Consider removing the shutdown part through group policy changes from MSS just keep the restart - Consider overwriting the power button. - How to find the current Teamviewer users