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Electron Microscope v3.0.0 (update)

L

LPerry

The Weatherman
Joined
Apr 4, 2001
Messages
2,454

Major Update To EM
AMBER Core Now Recognized
New Protein Data File Structure
New EM Calculator update

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. 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.

Enjoy! :D

Get the latest version here: http://www.em-dc.com

latestem.jpg
 
Very nice work Larry.

One small bug found.
p586_BBA5/POL3 is a new amber core protein.
From my log file.
[07:30:25] Assembly optimizations on if available.
[07:30:25] Entering M.D.
[07:30:39] Completed 0 out of 50000 steps (0)
[07:46:34] Writing checkpoint files
[07:57:07] Writing local files
[07:57:07] Completed 500 out of 50000 steps (1)
[08:02:23] Writing checkpoint files
[08:18:13] Writing checkpoint files
[08:23:29] Writing local files
[08:23:29] Completed 1000 out of 50000 steps (2)
etc, etc.
Every time it write the checkpoint the time taken to finish alters.
I get either 8 hours or 24 hours.

Luck............ :D
u=Tigerbiten.gif
 
Tigerbiten, check the other thread about the new amber core. Larry has an explanation about this there.

 
Cheers Larry, thanks for the great work you put into this program :)
 
The "trigger" file I have used for years is being updated at every checkpoint now... DOH!
Thank you Stanford for staying consistant! NOT! :mad:

I'm working on a fix... ;)
 
Make a copy of any file in the folder EM is running in.
Rename the file to Show.Me ... EM will show up in less than 30 seconds...

Or, shut down EM and use the -nostealth flag to start the program...
 
After the first couple of frames it settled down and is now showing the correct time to finnish.
215 points in 26:22 hours at 2.1 Ghz.

Luck............ :D
u=Tigerbiten.gif
 
I've posted an update to EM V 3.0.2
Hopefully this fixes the Unk proteins issue and the Linux tracking issues.

Let me know if you are still having issues with these things after trying this new version.
 
Thanks Larry! In the time I started writing this you released 3.0.3 which fixed the problem with changing number of clients viewed. You sir are [H]ard! :eek:

And I hope you make good use of the PayPal contribution I made. Thanks for making EMIII and thanks for keeping it going. It must be a heck of a lot of work, so thanks.

So guys, you made your PayPal contribution yet?

Edit: EMII -> EMIII
 
I'd like to say thanks for a great program.

I'm still having a few issues with the UNK point values. It seems like they aren't even in the protein data file. Here is an example:

Unk 215 p729_gsgs_md (739) 36/26/32 [152]
Click to expand...

So i searched the protein data file for "739" and there is nothing to be found. I have this problem with multiple proteins. They are:

Unk 215 p729_gsgs_md (729) 27/31/67 [152]
Unk 356 p251_gnra_dd_erf_e0.5_c18 (251) 2/397/19 [114]
Unk 215 p730_gsgs_sd_h2o (740) 3/19/8 [152]
Unk 393 p638_L939_K12M_ext (638) 57/41/35 [143]
Unk 356 p260_gnra_dd_erf_e0.5_c18 (260) 1/843/10 [114]
Unk 602 p925_n910pf (925) 85/62/7 [151]
Unk 132 p1014_a21nat_289_dd19 (1014) 4/53/0 [149]
Unk 385 p559_BBA5_N (559) 108/10/7 [113]
Unk 1000 p266_ch3cn (266) 0/113/0 [114]
Unk 245 p731_BBA5_md (731) 24/3/65 [152]
 
Take the list of your current proteins that are not in the list over to the official fah forums and post them in the web site issues section of the forum. Stanford has had a lot of 'F'in up with their site information lately... slap em around a little... might do them some good. ;)
 
Looks like that worked. After I got up this morning and checked for new work units I found a bunch of new ones listed. Just in time too! EM was happily tracking a Tinker work unit that was not listed in the EM protein data file... but, a few seconds after I updated the file with the new stuff... 239 point value appeared. :)

BTW, I posted a little update to EM that appears to take care of the last Unk point issue when navigating through views or new skins in EM. V 3.0.3 is available. :D
 
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