Spock FAQ

General Questions

1. What is spock?
2. Where can I get it?
3. Is spock free?

Installation/Startup Questions

1. When I try to run spock I get the message "GLwMDrawingArea: requested visual not supported", and spock does not start. What does this mean?
2. When I try to run spock under linux I get the message spock: "Symbol `_XmStrings' has different size in shared object, consider re-linking", and spock doesn't start. What does this mean?
3. When I try to run spock I get a message which says "LICENSE ERROR: Couldn't open license file". What do I do?
4. Spock's complaining "LICENSE ERROR: can not get local host name". What's wrong?
5. I get an error message "LICENSE ERROR: License key not found". Now what?
6. When I start spock, it identifies the local host as being in the "tamu.edu" domain, and I'm not. What's wrong?

General questions

1. Q: What is spock?
   
   A: Spock is a full-featured molecular graphics program developed by Jon A. Christopher while in the lab of Thomas O. Baldwin of the Department of Biochemistry and Biophysics at Texas A&M University. Spock has been designed from the ground up to be powerful, flexible and most of all, easy to use. Many of the features of spock are designed to bring molecular modeling programs into the age of the internet. Spock has the features users have come to expect from molecular graphics software including several bond and atom rendering types, and a complete array of backbone "worm" representations. Further, spock can calculate and display molecular and accessible surfaces, and color code these surfaces by properties (such as electrostatic potential).
   
   
2. Q: Where can I get spock?
   
   A: Spock may be downloaded from http://quorum.tamu.edu
   
   
3. Q: Is spock free?
   
   A: Yes and no. In order to be able to continue development on spock, we need funding. Therefore, there is a nominal fee for spock. For educational purposes, small not-for-profits, or research groups without funding, we waive the registration fee. More information may be found in the license agreement.

Installation/Startup Questions

1. Q: When I try to run spock I get the message "GLwMDrawingArea: requested visual not supported", and spock does not start. What does this mean?
   
   A: This means that your hardware doesn't support the visual attributes spock is requesting. This usually happens on non-SGI hardware such as DEC Alphas or Suns, or when trying to cross-display spock over X. You can usually work around this problem by adding the following lines to your $HOME/.Xdefaults file ($HOME/.Xresources on linux):

   *GLWidget.depthSize: 1
   *GLWidget.stencilSize: 1
   

   You may need to run "xrdb -merge $HOME/.Xdefaults" (or .Xresources) after doing so.

   Update: Spock version b160p3 and above work around this problem in software. You may wish to consider upgrading to a more recent version. If you still get this error message on a spock version later than b160p3, please let me know about it.
   
   

2. Q: When I try to run spock under linux I get the message spock: "Symbol `_XmStrings' has different size in shared object, consider re-linking", and spock doesn't start. What does this mean?
   
   A: This means you're using a version of spock which is too old. Please upgrade to v1.5.
   
   
3. Q: When I try to run spock I get a message which says "LICENSE ERROR: Couldn't open license file". What do I do?
   
   A: There are two possible causes of this problem. The first is that the SPOCK environment variable isn't set to point to the spock system directory. If the splash screen (the initial dialog that pops up when you run spock) has an hourglass instead of the spock logo, this is probably your problem. To fix this, you need to set SPOCK to point to the spock system directory. If you've installed spock into the default location, you need to:

   Bourne shell (bash, sh): export SPOCK=/usr/local/lib/spock
   C-Shell (csh,tcsh): setenv SPOCK /usr/local/lib/spock
   

   If you've installed spock somewhere other than the default directory, you need to set the SPOCK variable to point to the SYSTEM directory of the spock distribution.

   Another possible cause of this problem is that you don't have a LICENSE file. You must either generate a license to run spock from http://quorum.tamu.edu/license.html, or have contacted us for a permanent or annual gratis license as described here.
   
   

4. Q: Spock's complaining "LICENSE ERROR: can not get local host name". What's wrong?
   
   A: Spock needs to know the fully-qualified domain name (FQDN) for your machine in order to verify the license. Some machines are mis-configured so that the system hostname commands do not return information about the domain. For example, if that were the case on this machine, the hostname command would return "quorum" instead of "quorum.tamu.edu".

   There are several ways to fix this problem. The best way is to ask your system administrator to fix your system name so that hostname returns the FQDN. Alternately, you can set the "SP_DOMAIN" variable in the $SPOCK/Spockrc file so that it has the correct domain in it. Note that if you're in a subdomain, you may have to do this. For example we have a chem.tamu.edu subdomain on campus, and for machines in that subdomain, they must set SP_DOMAIN to chem.tamu.edu.

   Note: some linux boxes have real trouble with this. The best solution so far seems to be to have the FQDN listed as the first entry in /etc/hosts. For example, on this machine the first line in /etc/hosts is:

   165.91.51.79    quorum.tamu.edu quorum
   

   The program checkname may help you to diagnose this sort of problem. Checkname uses the same method of detecting the FQDN as spock's licensing code.
   
   

5. Q: I get an error message "LICENSE ERROR: License key not found". Now what?
   
   A: This means that the license file was found, but a valid license for your machine wasn't in the file. A likely cause of this is that the license string had a carriage return inserted into it because of a ill-behaved mailer or web browser. You should edit the file $SPOCK/LICENSE, and make sure that all the license keys are intact. License keys are of the form:

   9123123123:FSDK2Ljw2oe1riasjldfkj4o71iawrslkd9fjwoe5rij7l3lkSDFIewroe5rij7l3lkSDFIewr
   

   That is, a number, a colon and then an alphanumeric string. If you have something like this:

   9123123123:FSDK2Ljw2oe1riasjldfkj4o71iawrslkd9fjwoe5rij7l3lkSDFIewro
   5rij7l3lkSDFIewr
   

   Then something's inserted a carriage return into your license key and you should delete the carriage return.
   
   
6. Q: When I start spock, it identifies the local host as being in the "tamu.edu" domain, and I'm not. What's wrong?
   
   A: This indicates that your machine is configured incorrectly and it can't find the correct local domain, so it is falling back to the SP_DOMAIN variable defined in $SPOCK/Spockrc. As shipped, this variable is set to "tamu.edu". You can fix this problem by changing SP_DOMAIN in $SPOCK/Spockrc to refer to your local domain.