EM3 Version 3.00 is Now Out!
mmonnin
Centreville, VA
Major Update To EM
AMBER Core Now Recognized
New Protein Data File Structure
New EM Calculator
Even though there have been some major changes to EM internally, I always try and make upgrades as easy and simple as possible. This update is no exception. If you are already using EM, you only need to get the upgrade version. There is no need to reinstall EM using the full install zip file.
The new AMBER core is now recognized. I revamped the protein data file. I am no longer basing the protein value on the protein name. I am now using the project number. This should get rid of a lot of those unknown protein point values because the protein name on the Stanford web site doesn't match the actual protein name in the work unit data file. This is a major update to the program so I have gone from version 2 to version 3. I still have more changes to make, but this converts EM to work with this new protein data file structure and recognize the new AMBER core. The calculator has also been updated to work with this new structure also. I expect that because EM has gotten very complicated internally, there may be something I missed. Please post anything you notice that doesn't act correctly or as expected. Provide the work unit name/project number when you post.
The old protein data file will no longer be supported or updated. The old file has been removed from the site and the new one has been put up in its place. If this new method works out, I may be able to make EM update automatically and the days of posting new protein data files may be over... I hope. Only time will tell.
Thanks very much to those of you who have donated a couple of $$$ to the EM-DC.COM web site. I really appreciate the help.
Major changes to EM coming soon (10-7)
I am working on a new version of EM that uses a different protein data file structure. Stanford has had a rash of bad protein names and the points are currently determined using the protein name. I am changing that to the project number. This also means that until I release the next version I will not be updating the current protein data file. It will remain static from now on. I have kept resisting this change as a lot of code has to be modified in order to keep things working the same way it does now. I have most of the modifications in place but there are several more to go. I will try to make this next update go as smoothly as I can. I'm sure there will be a few issues, but hopefully everything will turn out better once this change is made.
Those of you who are on the Stanford beta team probably know that there is a new core coming soon. It's called AMBER and is currently being tested. I'm not sure when it will arrive, but it won't be long I'm sure. EM has already been modified to track the core, but there are several other things that remain to be changed on that.
The change in the structure of the current emprotx.dat file will probably cause a few 'ripples' because it is used all over the place and not just by EM. Some other programs use it as a reference also. There is also the csv file that EM creates that we all use for generating stats, tracking our work, and some other stuff. I am trying to keep that the same. The major problem with that is EM uses both of the files to generate information. For example, when a new work unit is downloaded and EM sees this, it looks through your data file for this work unit. If you have worked on it before, EM will grab the frame time and fill it in. This gives you instant feedback on the protein being worked on because everything is calculated from the time per frame data.
While some people never use it, when you generate information about the proteins you have worked on, EM uses both of the files, the protein data file and the csv file EM generates to keep track of things for you. I did this because the value of a protein might be different or might not have been known when a work unit was finished. Since I sometimes update the protein data file several times a day, this information can always be updated by you, or automatically by EM if you have that turned on. This method of generating information for you has a lot of advantages as you can see. Making this change will break some things, but I can also fix it by changing some code in the program. In the long run it still works out better for the person using EM for me to do it this way.
Anyway, I thought I would post this update to alert you that changes are coming soon, most likely this week. Stay tuned and pass the word in the forums. This is a major change.
Thanks Larry!
Source: EM-DC.com
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