Hi I'm new and I just downloaded Discovery Studio Visualizer in hopes of viewing my own structure predictions but unfortunately the guide "How to view your structure predictions" is totally confusing. I have no idea what the hell it says! Can't wrap my head around it! how do I view my own structure predictions? Every single step makes absolutely no sense and I have no idea what this means: Windows: C:Program FilesBOINCslots
I use windows by the way.

Also, thank you guys all so much for being involved in this. My dad is a cancer survivor and i am very big on finding a cure to brain cancer in children in particular. My favorite approach is immunology!

Hi I'm new and I just downloaded Discovery Studio Visualizer in hopes of viewing my own structure predictions but unfortunately the guide "How to view your structure predictions" is totally confusing. I have no idea what the hell it says! Can't wrap my head around it! how do I view my own structure predictions? Every single step makes absolutely no sense and I have no idea what this means: Windows: C:Program FilesBOINCslots
I use windows by the way.

Also, thank you guys all so much for being involved in this. My dad is a cancer survivor and i am very big on finding a cure to brain cancer in children in particular. My favorite approach is immunology!

Hi

I've not looked at that guide or tried to view the predictions but I believe C:Program FilesBOINCslots should be updated to point to the new default path of c:programdataboincslots. Older versions of BOINC installed to the documents and settings folder I believe, so the slots folder could also be there...

Hope that helps,
Danny

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Hi I'm new and I just downloaded Discovery Studio Visualizer in hopes of viewing my own structure predictions but unfortunately the guide "How to view your structure predictions" is totally confusing. I have no idea what the hell it says! Can't wrap my head around it! how do I view my own structure predictions? Every single step makes absolutely no sense and I have no idea what this means: Windows: C:Program FilesBOINCslots
I use windows by the way.

Also, thank you guys all so much for being involved in this. My dad is a cancer survivor and i am very big on finding a cure to brain cancer in children in particular. My favorite approach is immunology!

Hi

I've not looked at that guide or tried to view the predictions but I believe C:Program FilesBOINCslots should be updated to point to the new default path of c:programdataboincslots. Older versions of BOINC installed to the documents and settings folder I believe, so the slots folder could also be there...

Hope that helps,
Danny

i have no idea what you just said or where to find this slots folder....

The main problem you will have is catching a task that has completed some models and has them available in it's slots folder, prior to being reported back and acknowledged, which cleans all of that out.

You can use the Windows explorer search function to find the folder named slots. It is going to be in the data directory shown at the top of your messages display in the BOINC manager.

For most of us, viewing the graphic for the task as it runs and being able to rotate and zoom around on that is sufficiently informative.

If you would really like to take some time and learn more about this stuff, I'd suggest you have a look at http://fold.it. *CAUTION* may be addictive to humans. Especially those with creative, inquisitive or curious mindset.

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Rosetta Moderator: Mod.Sense

The main problem you will have is catching a task that has completed some models and has them available in it's slots folder, prior to being reported back and acknowledged, which cleans all of that out.

You can use the Windows explorer search function to find the folder named slots. It is going to be in the data directory shown at the top of your messages display in the BOINC manager.

For most of us, viewing the graphic for the task as it runs and being able to rotate and zoom around on that is sufficiently informative.

If you would really like to take some time and learn more about this stuff, I'd suggest you have a look at http://fold.it. *CAUTION* may be addictive to humans. Especially those with creative, inquisitive or curious mindset.

ok so i found that data directory thing on the top of my messages display in the BOINC manager but i do not know how to use it in the wondows explorer search function...

Open windows explorer, click the search button, click all files and folders, enter "slots" (without the quotes) in the "all or part of the filename" blank, make sure the dropdown list is set to the drive letter that has your BOINC data directory, then click the search.

(don't tell Microsoft that Windows is totally confusing, you are looking at "ease of use resulting from innovation demanded by Microsoft customers").

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Rosetta Moderator: Mod.Sense

Once you have located the slots directory, it has subdirectories that are just numbers. There is a subdirectory for each BOINC task that has at least started execution. From the slots subdirectory, you can use the search function again. This time searching for file names with ".out", and selecting the "look in" of the slots directory. Beware, other BOINC projects may have .out files as well. You only want the ones for Rosetta. When in doubt, open the subdirectory with the task number (right click, open containing folder), if it is a Rosetta .out file, you should see some other Rosetta items in the same subdirectory such as the minirosetta_database.

So, now that you've located all of the .out files for Rosetta, you copy them all to the Rosetta project directory. Open a new Windows Explorer window. Navigate down to the directory that contains the slots directory and you should see it also contains one called "projects". Open the projects subdirectory. Here you will find a subdirectory for each of your BOINC projects. They directory names are just the project URL with slashes substituted with underscores. Open the project directory for Rosetta. Now RIGHT click each .out file and drag and drop it to the Rosetta project directory and select "Copy here" (NOT MOVE!).

OK, that's got you through step 2.

Now open a DOS window (start -> all programs -> accessories -> command prompt). CD to the drive and Rosetta project subdirectory that you found above. Enter the following DOS command:
dir *.exe

This shows all of the Rosetta programs you have. Ignore any with the word "graphics" in them. For example, on my PC I have the following...

minirosetta_2.05_windows_intelx86.exe
minirosetta_graphics_1.92_windows_intelx86.exe
minirosetta_split_terms_1.02_windows_intelx86.exe
rosetta_beta_5.98_windows_intelx86.exe

The "split_terms" is an older application version that was only out for a short time. Ignoring the graphics one. We've got two left:
minirosetta_2.05_windows_intelx86.exe
rosetta_beta_5.98_windows_intelx86.exe

These are the two currently active Rosetta applications for a 32bit Windows machine. If you look at the BOINC Manager you will most likely see that the version shown on all of your tasks is the minirosetta one. Rosetta beta has not been active for some time as well. And so we've identified the "Rosetta executable" as:
minirosetta_2.05_windows_intelx86.exe

So now you will use that in place of the word ROSETTA shown in the commands and try both options until you see messages that indicate a .pdb file was produced. This is the file that you will then point your molecular viewer to in order to rendure the models reflected in your .out file.

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Rosetta Moderator: Mod.Sense

Open windows explorer, click the search button, click all files and folders, enter "slots" (without the quotes) in the "all or part of the filename" blank, make sure the dropdown list is set to the drive letter that has your BOINC data directory, then click the search.

(don't tell Microsoft that Windows is totally confusing, you are looking at "ease of use resulting from innovation demanded by Microsoft customers").

ugh... believe it or not the furthest i got was opening windows explorer... i use vista so... mayb that makes a difference? i managed to find two BOINC thingies, one that lead to boinc manager and a folder. the folder was empty

Go to "C:Documents and SettingsAll UsersApplication DataBOINCslots" You will see a number of folders there with names like 0,1,2,3 and so on. In these folders you will see the .out files. You might have to turn off "Hide system files/folders" and "Hide known extension types". You might want to make copies of the .out files to another folder.

PS This goes for XP, I don't think Vista is a lot different.

There's no 'Documents and Settings' folder in Vista or Win7 - it's replaced by C:ProgramData and C:Users ;)

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P.S. Catalyst, the slots folder will probably be in c:ProgramDataBOINC

HTH
Danny

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ok thanks guys i finally figured it our... now my only problem is that when i bring it into my molecule viewing program i end up with a text file and can't convert it into a structure... T_T

any ideas on how i can change it from .out to .pdb ?

Once you have located the slots directory, it has subdirectories that are just numbers. There is a subdirectory for each BOINC task that has at least started execution. From the slots subdirectory, you can use the search function again. This time searching for file names with ".out", and selecting the "look in" of the slots directory. Beware, other BOINC projects may have .out files as well. You only want the ones for Rosetta. When in doubt, open the subdirectory with the task number (right click, open containing folder), if it is a Rosetta .out file, you should see some other Rosetta items in the same subdirectory such as the minirosetta_database.

So, now that you've located all of the .out files for Rosetta, you copy them all to the Rosetta project directory. Open a new Windows Explorer window. Navigate down to the directory that contains the slots directory and you should see it also contains one called "projects". Open the projects subdirectory. Here you will find a subdirectory for each of your BOINC projects. They directory names are just the project URL with slashes substituted with underscores. Open the project directory for Rosetta. Now RIGHT click each .out file and drag and drop it to the Rosetta project directory and select "Copy here" (NOT MOVE!).

OK, that's got you through step 2.

Now open a DOS window (start -> all programs -> accessories -> command prompt). CD to the drive and Rosetta project subdirectory that you found above. Enter the following DOS command:
dir *.exe

This shows all of the Rosetta programs you have. Ignore any with the word "graphics" in them. For example, on my PC I have the following...

minirosetta_2.05_windows_intelx86.exe
minirosetta_graphics_1.92_windows_intelx86.exe
minirosetta_split_terms_1.02_windows_intelx86.exe
rosetta_beta_5.98_windows_intelx86.exe

The "split_terms" is an older application version that was only out for a short time. Ignoring the graphics one. We've got two left:
minirosetta_2.05_windows_intelx86.exe
rosetta_beta_5.98_windows_intelx86.exe

These are the two currently active Rosetta applications for a 32bit Windows machine. If you look at the BOINC Manager you will most likely see that the version shown on all of your tasks is the minirosetta one. Rosetta beta has not been active for some time as well. And so we've identified the "Rosetta executable" as:
minirosetta_2.05_windows_intelx86.exe

So now you will use that in place of the word ROSETTA shown in the commands and try both options until you see messages that indicate a .pdb file was produced. This is the file that you will then point your molecular viewer to in order to rendure the models reflected in your .out file.

i finally did it! now my only problem is changing it from .our to .pdb
how do i do that?

P.S. Catalyst, the slots folder will probably be in c:ProgramDataBOINC

HTH
Danny

thanks for the help! i figured it out but i still have the problem of changing the .out file to a .pdb file. do u know how to do that?

Step 3 of the instructions is what translates the .out to a .pdb for the viewer to use. Did step 3 produce any output for you?

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Rosetta Moderator: Mod.Sense

Step 3 of the instructions is what translates the .out to a .pdb for the viewer to use. Did step 3 produce any output for you?

...uh...step 3 didn't make any sense to me. i don't even know what is a text editor. i have found a program that is just called "edit" but it made no sense to me.

Edit: wait, now i found out that notepad is a text editor. so... what next? how do i make a .bat batch file? is this my rosetta executable: chk_s_1WWZA_7_0001_FastRelax_chk1_fa ? Is the result file and the executable the same thing?

Step 3 of the instructions is what translates the .out to a .pdb for the viewer to use. Did step 3 produce any output for you?

...uh...step 3 didn't make any sense to me. i don't even know what is a text editor. i have found a program that is just called "edit" but it made no sense to me.

Edit: wait, now i found out that notepad is a text editor. so... what next? how do i make a .bat batch file? is this my rosetta executable: chk_s_1WWZA_7_0001_FastRelax_chk1_fa ? Is the result file and the executable the same thing?

Edit: nvm. now, looking at your instructions on step 3, i got as far as cd to a drive. how do i do that?