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4.1 Electron Microscope
Edit: In response to the feedback from murky , yes, the link is broken. The best information we have been able to receive is that TheWeatherman hopes to bring back the site and support of EMIII. So, we wait ... :) ~sorto'
Feedback received on this FAQ entry:
Edit: Note that EMIII support may be spotty. At this time, as far as we know, TheWeatherMan is busy with other ventures but hopes to return in the future. He is missed!
2.) Unzip EMIII either into where you have your F@H files, or as I do, make a new folder named EMIII and place EMIII files into that folder.
3.) Next, make a Desktop shortcut by right clicking on the EMIII.exe file (looks like a little microscope), then SendTo/Desktop as a shortcut.
4.) Now double-click the icon on desktop. The option window will open. Now before setup, move the EMIII and option window off to the side of desktop so center of desktop is clear, the reason will become clear in a bit.
5.) In the options window, Click the "Browse to folder" icon I have highlighted in red, which allows you to search for and point to the FAH client(s) that you want EMIII to track.
6.) Now browse to your F@H folder where the client files are and select the FAH Client. A warning message may popup in the center of your desktop (this is why we moved things in step 4) warning about the client being wrong, just accept.
7.) Now you should be back to the Options window, Place a name you choose in the "Box Name" area, then hit "Add a Box". Now check the box in upper section where I have the red arrow and click "Save Editing".
8.) In General Settings, I have selected these options. Once you check the settings you want, close the window, EMIII saves the settings automatically.
9.) Once you have completed one Work Unit, the page below will show in the options menu, giving you the options to make a HTML stats page.
These are my settings:
•Time Per Frame
•Frames (Change default 100 to 400)
•W/U Total Time
•Save XYZ File
10.) If you would like to install the BBR Team Helix skin for EMIII, download the skin here.
Unzip and put the files in the EMIII skin file.
Go to the EMIII options menu and then the Skins Settings page.
Click on the BBRskin and the skin will change.
Your EMIII should look like below:
I hope you find this guide helpful!
If you find anything in the guide that is incorrect or out of date, please let us know.
If you have more advanced installation questions, please ask them in the forum.
Edit: At this time, if you have not already downloaded EMIII, you will be unable to do so. We hope that we will see TheWeatherMan in the future, but suggest that, in the meantime, a suitable substitute for EMIII might be FahMon.
You can download FahMon here.
You can clear it all out by starting EM with the -clear flag.
2) Click on the Microscope in the upper left hand corner to bring up the options window.
3) At the bottom of that window there is an option to 'Use Extra Launch Commands'.
3) Enter the commands/switches here that you want to use and check the box.
EM only uses the flags on the local system on which EM is installed and only when you let EM start the client (which is configured in the third options screen by checking 'Launch F@H on Start-up').
To find out more about which switches you can use and what they do, use this link.
What are the current switches and what do they do?
download Electron Microscope III and extract it in its own separate directory. Start up EMIII and you will see a microscope icon in the top left hand corner. Click on that icon and a new window named Options will open up. Near the bottom there will be three lines; CPU Info, Box Name, and Box Path. To the end Box Path you will see a computer icon. Click on it and a new window will open up allowing you to find your FAH console file. Locate the file and add it to EMIII by pressing the Add a Box button. Once the Box Path is set, you can configure the Box Name and CPU Info. Once configured, select the Save Editing button to save your new information. Repeat the process over again by clicking on the small computer icon again but add the second FAH console file from your second directory. Thats it! You are ready to have Electron Microscope III track your new dual processor computer.
Edit: Hopefully, TheWeatherMan will return in the future- I know that we would all be pleased! At this time, in his absence, EMIII can not be downloaded from the location indicated.
here. You can unzip them anywhere you want. I put them in my EMIII folder so I can have them handy. Look for the skin that you want, shut down EMIII, and copy/paste the contents of the folder to Skins\Default (within the EMIII folder).
When you restart EMIII your skin should be there.
If its not, go to options and click the arrows until you get to the skin settings screen. If you have more than option click it and it should load automatically.
Edit: Note that as TheWeatherMan is not currently available to support this site, the EMIII skins are not available at this time. Perhaps when he comes back... :-)
Skin Info Page
or directly: HERE
If you create a skin for your team he can host it for you on the EM web site.
Have Fun! :D
Edit: At this time TheWeatherMan is not available to help with skins, and the EMIII web site is unavailable. I am sure that he will let us know if he is able to resume his EMIII activities!
Added support for the new core, GBGromacs. This core is a variant on the main Gromacs core Core_78, differing in its incorporation of a fast, "implicit solvent" model (as used in Core_65). It complements Core_78 nicely, increasing the spectrum of tools available.
If you updated to 3.0.3 recently (10/18/04) , you also need to grab the new protein file. It was changed after the 3.0.3 update due to some problems at Stanford.
Fixed a problem with a Windows PC running EMIII being able to read Linux files via Samba.
Had a very quick Half Life.
Because the new AMBER core writes a file I have been using to trigger the completion of a frame at every checkpoint, I have modified EM to use a different file for this trigger. The issue with the Linux boxes still hasn't been resolved yet. Next release should see a fix for that.
AMBER core 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.
AMBER core now recognized. Beta test.
A long time ago we stopped having proteins that took less than 60 seconds per frame so I made an adjustment to the code which tried to keep EM from sounding a false alarm if something seemed to be happening a little more quickly than it probably should. Until lately, this hasn't been an issue. But with the release of some proteins with 500 frames, each frame sometimes breaks the 60 second barrier on a fast machine. This caused EM to appear hung up. It actually saw each frame complete, it just didn't consider the time valid so it reset the watch. Now, unless the frame time goes under 10 seconds, this won't happen.
EM wasn't shutting down the FAH 5 Client when it was told to do so by the user. That issue is fixed.
Shame on you, you haven't updated!
Enjoy the latest and greatest! :D
Special Thanks to The Weatherman for all the efforts!
Get the latest version here: »www.em-dc.com
Edit: Note that you will not be able to download EMIII at this time. This FAQ is informational if you have already installed and updated EMIII to this point.
If your EMIII looks like the above image, it could be your font size is too large.
EM can not adjust to large font settings. Many set the font sizes larger, 125% or more and use super hi res screens.
Setting the fonts to standard/normal default setting will fix this issue.
XP can be modified two ways, font size and DPI.
Right click the windows background screen and select properties. Select "settings", then the Advanced button.
Make sure the DPI setting is 96...
The information was provided by TheWeatherMan from the following threads: Thread 1 ... Thread 2
1) A check is in the box next to the path in the options menu.
2) A check is in the boxes used to control the start/stop of the client.
3) The client has to be named FAH500-Console.exe
The information provided in this FAQ was taken from this thread by TheWeatherMan.
EM should download the file automatically if you have the "Check for new EM updates" box in the options menu checked.
If it doesn't do it automatically, or you don't want to have the option checked, you will have to install it manually.
To do this, follow these steps:
First, you must download the Electron Microscope III Protein Data file from here. Remember to click on the Downloads link on the left to get there.
Close EMIII, unzip the file and put the emprotz.dat file where your EMIII files are.
When you restart EMIII it should show the correct points, if it doesn't, TheWeatherMan hasn't added that protein yet.
You will also get the Unk when Stanford releases a new core that TheWeatherMan hasn't seen yet (rare occurrence).
Edit: Note that at this point, Team Helix members howieh and RayW are doing an excellent job keeping EMIII current by posting new emprotz.data files as needed in the Team Helix forum.
Watch for their new files in the Team Helix forum.