(Category) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory :
Running VMD Publish and Sync
Details on getting VMD to work.
Subcategories:

Answers in this category:
(Answer) I just found out about BioCoRE, VMD, and the Theoretical Biophysics website. Why doesn't VMD start?
(Answer) Is there a way I can get away without having to grant permission EVERY TIME I want to run VMD?
(Answer) How do I know that the security certificate was imported correctly?
(Answer) Apparently Netscape doesn't think I have the security certificate, but I went through the process. What went wrong?
(Answer) VMD WAS working fine through the collaboratory, and then it quit. What happened?
(Answer) How do I publish a session?
(Answer) How do I retrieve a previously saved session?
(Answer) How do I load a pdb file from the BioFs?
(Answer) When I try to load a session from the Message Board using Internet Explorer, it doesn't work.
(Answer) If someone else publishes a session while I am using VMD, how can I view it?
(Answer) How do I get the "VMD Sessions" window to appear if I'm running Windows 95/98?

(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
I just found out about BioCoRE, VMD, and the Theoretical Biophysics website. Why doesn't VMD start?
If you are new to our site, there is a good chance that you haven't yet downloaded and installed VMD. This is necessary before you can actually run VMD via your web browser. Go to http://www.ks.uiuc.edu/Research/vmd and download vmd, and then you will have much better luck.
If you DO have VMD on your system and you still aren't having any luck, check out the other questions in this area and one of them will probably help you out.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
Is there a way I can get away without having to grant permission EVERY TIME I want to run VMD?
Note: You do NOT have to reimport the certificate every time that you want to run VMD. You should only have to do that once.
But, your web browser will continually pop up the box asking you each time whether or not you want to grant permission to actually start the program on the hard disk (which happens to be VMD in this case).
You can get around this by clicking the button in that box that says: Remember My Decision. Then, it will remember that you said yes and you won't have to answer the question every single time.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
How do I know that the security certificate was imported correctly?
The process of importing the security certificate to run VMD is probably the most tricky part to getting everything working correctly.
To see if you have certificate, go to the page for running VMD, and tell it to import the certificate. If you already have it, a little box will pop up telling you that you already have the certificate. If Netscape doesn't think you have the certificate, it will once again lead you through the import process.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
Apparently Netscape doesn't think I have the security certificate, but I went through the process. What went wrong?
There are a number of things that might have happened:
1) If you JUST imported the certificate, you will need to reload the page to get VMD to actually run. Do this with a shift-reload.
2) When you click your way through the boxes, you MUST choose the option to trust software programmers from the BioCoRE site. If you do not choose this option it won't work.
3) When you started Netscape, if you got the warning that "Netscape has detected a lock file which may indicate that another user is running Netscape, etc..." this same warning box also mentions that "You may continue to use Netscape, but you will be unable to user the disk cache, global history, or YOUR PERSONAL CERTIFICATES. The security certificate that you get from us is considered one of your personal certificates, so it won't be in effect for this 'warned' netscape.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
VMD WAS working fine through the collaboratory, and then it quit. What happened?
1) When you started Netscape, if you got the warning that "Netscape has detected a lock file which may indicate that another user is running Netscape, etc..." this same warning box also mentions that "You may continue to use Netscape, but you will be unable to user the disk cache, global history, or YOUR PERSONAL CERTIFICATES. The security certificate that you get from us is considered one of your personal certificates, so it won't be in effect for this 'warned' netscape.
2) If you (or anyone with access to the files) have been "messing with" the netscape files, you could have just possibly messed something up in Netscape. Under unix, these files would be located in ~/.netscape and in Windows they are hidden better, but still accessible.
3) Something might have happened to VMD. Try going to a command prompt and typing 'vmd' and see if VMD starts. If not, you have a problem external to the collaboratory.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
How do I publish a session?
When you start VMD from BioCoRE, and you have loaded a molecule in a specific representation, etc, you can then save that state to BioCoRE so other group members can view it.
Once you have the molecule in the representation and orientation that you wish to save, fill in a name and description in the appropriate boxes in the Saved State Window, and click on the "Save state" button. Yur sesson will be saved to BioCoRE.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
How do I retrieve a previously saved session?
If you've started VMD from BioCoRE, select a session from the "Saves sessions" box within the "VMD Sessions" window. A description of this session will appear in the "Description" box. To load it, click on the "Load session from BioCoRE"
In BioCoRE, you can go to the VMD states page in the Message Board by selecting the "List of saved VMD states" link on the VMD page, or selecting "Saved VMD sessions" from the "Show" box in the Message Board. This will give you a list of the saved sessions for this project. Clicking on one of them gives you the script used for saving this session, and you can also see the description given. Click on "START VMD SESSION" link at the top of the page, and VMD will start with that state.
NOTE: Starting a VMD session from the Message Board will not work when using Internet Explorer. We are working on this problem.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
How do I load a pdb file from the BioFs?
To load a pdb file from the BioFs, (BioCoRE's file system), click on the "Load file from BioFs" button in the "VMD Sessions" window. This will bring up a list of all the pdb files in the BioFs for that project. Select the one you wish to load and click "Load".
NOTE: It is important that you save sessions that use files from the BioFs or the RCSB so that all members have access to the files when they wish to load the sessions. If you publish a state that uses a local file, others may not be able to view it.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
When I try to load a session from the Message Board using Internet Explorer, it doesn't work.
Yes, this is a known bug and we are working on it. We apologize for the inconvenience.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
If someone else publishes a session while I am using VMD, how can I view it?
Currently, VMD does not automatically update other users' "VMD Sessions" windows when one publishes a session. To update your window, click on the "Refresh session list" button. This will add any sessions that have been published since you started VMD.
(Answer) (Category) BioCoRE Collaboratory FAQ : (Category) Using the Collaboratory : (Category) Running VMD Publish and Sync :
How do I get the "VMD Sessions" window to appear if I'm running Windows 95/98?
First, running on a version of Windows that old isn't officially supported. We suggest that you upgrade.
1.) If the folder C:\Temp does not exist on your computer, please create the folder.
2.) Start VMD from BioCoRE. This will not start VMD with "VMD Sessions" window, but it will write a file called "tmp.bat" to the C:\Temp folder.
3.) Double-click on C:\Temp\tmp.bat. This will run the file and it should start VMD with the "VMD Sessions" window, allowing you to load and save sessions.
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