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FAQ - Frequently Asked Questions

How can i try out \sh the easiest way?

You can use Scaffold Hunters demo mode. Download the demo package provided along with the regular Scaffold Hunter releases and execute the run-demo start-script. Scaffold Hunter will then open an included data set with a pre-configured session. You do not need to configure any database connection or provide any data for analysis.

I get OutOfMemory exceptions when importing / analyzing large data

Refer to Sec. 3.3: Starting Scaffold Hunter of the manual and increase the maximum available memory for the Java virtual machine.

Scaffold Hunter crashes when saving a session of a larger dataset

If you are running into database exceptions while saving a session of a larger dataset, this might be a problem with the maximum package size or the maximum log file size of MySQL. Please refer to Sec. 2.2.1.3: Allow Large Packages and Sec. 2.2.1.4: Increase size of log file of the manual for further instructions about how to configure the MySQL server.

Scaffold Hunter crashes when deleting large datasets

This is often a database problem, when using MySQL/MariaDB. When deleting something from such a database, some content is copied over to a table, that is shared among all databases to allow roll backs of failed deletions. If this table is limited in size, you fail to delete larger datasets.

You can check if this is the case for you, by running the following SQL query on your database: SHOW GLOBAL VARIABLES LIKE 'innodb_data_file_path';

The result should look like the following:

Variable_name Value
innodb_data_file_path ibdata1:10M:autoextend:max:128M

If the string autoextend is not contained or if the string max:<some value> is contained, you should adjust the variable to the following in your MySQL/MariaDB configuration (typically my.cnf):

innodb_data_file_path = ibdata1:10M:autoextend

I cannot use all clustering options – there are no properties available for some distance measures!

Some distance measures are only applicable on molecule fingerprints. Read Chap. 5.2.2: Calculation of Properties of the manual to learn how to calculate additional properties like chemical fingerprints.

How can I prevent other users from getting access to my data?

If you conduct a study with confidential data and do not want any other user to access Scaffold Hunters data, you need to configure the mysql server accordingly. Make sure that only authorized people have read access to the schema in which Scaffold Hunters data is stored. You can also install a mysql server on your local computer and limit the access to localhost. If the performance is sufficient, you can also use the connection type HSQLDB, and save the database file on a secure place somewhere on your harddisk.

I have lost my password, how can I access my data?

As Scaffold Hunter saves your password encrypted, there is no possibility to restore your password. But it is possible to create a new password. First you need a tool to manage MySQL databases (for example: MySQL-Workbench). Start Scaffold Hunter and go to the StartDialog. Create a new user and note username and password. Open the database management tool of your choice and connect to the database using the data you used in the Connection Dialog of Scaffold Hunter. After you have connected to the database, you will probably see a long list of database tables. Select the table profiles and edit the table data. Search for the two rows showing your old and your newly created username. Copy the data of the fields password and salt from the row corresponding the new username to the fields in the row corresponding your old username. Submit your changes and exit the management tool. Now start Scaffold Hunter and login with your old username and the newly created password. Thats it.

WARNING: Be careful while editing the database. Please make a backup of the database prior to editing. Only follow the above instructions if you exactly know what you are doing.

The tooltip window annoys me!

In order to disable the Tooltip window select Session → Preferences → General Configuration from Scaffold Hunters menu bar and disable the checkbox labeled enable tooltips. Instead of disabling the tooltip, you can adjust the other tooltip settings as well. It is possible to change the maximum size of the structure image shown in the tooltip or to select the tooltip popup delay.

Where do i find the manual?

It comes with the Scaffold Hunter software in the zip file. The manual ist called manual.pdf.

faq.txt · Last modified: 2016/09/09 14:10 by till