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LBEM-CH / focus

High Throughput Electron Microscopy Image Processing Software
http://www.focus-em.org
GNU General Public License v2.0
35 stars 14 forks source link

2D crystal image analysis on preliminary negative stain images? #219

Closed acdrennan closed 6 years ago

acdrennan commented 6 years ago

I am attempting to use FOCUS to analyze preliminary negative stain 2D crystals. I know FOCUS is built to analyze cryo images... can it be used for negative stain images as well?

I've been using the YouTube video "FOCUS 2D crystals 1" to help me navigate the program, and although I can import my .tif images, it seems that perhaps they are recognized as a stack. The reason I think this is that when I double-click on an imported image, there is no "import 2D image" folder under the "process" tab; instead, there is an "unpack stack" folder.

Note also that in the video, the 2D images are described as "2D image", while mine are described as "Average". I am using a CCD camera.

If focus will not support my analysis, is there a another program that might work?

sthennin commented 6 years ago

Yes, for neg. stain, you simply have to invert the contrast when creating the final map. Everything else stays the same.

Did you run FOCUS in the "2D Electron Crystallography" mode? If not, you can change the mode if you click top left onto the "Project" button, and then click on the second button top left in that window, labeled "Change Project Mode". Depending on the project mode, different scripts will appear. If you are in single particle mode, then some of the scripts are different. The Prepare scripts should be called

If you have different scripts there, then which version do you run? It might be outdated? Where did you get FOCUS from?

Import should be with the script “Import 2D Image” from the “Prepare" section. Then you could continue with the “2DXtal” section scripts.

acdrennan commented 6 years ago

I did run FOCUS in the 2D Electron Crystallography Mode. I am running Focus 1.1.0, and I believe it is set up to update every evening. I got focus from SBGrid, as my IT department will not allow me to run it from the source.

sthennin commented 6 years ago

SBGrid updates from our nightly builds regularly. Which version do you use, OSX or Linux? If you call the "About" (Linux) or "About focus" (OSX) panel, which revision number do you see? Is that 37778f87?

Does it look like this?

screen shot 2018-04-17 at 14 00 48
acdrennan commented 6 years ago

I use OS X.

Actually, now I cannot get past the project initialization page, so am unable to check the "About Focus". I get this error in the terminal: /programs/i386-mac/focus/1.1.0_nightly/bin/focus: line 6: 20400 Segmentation fault: 11 ${binDir}/../focus/focus.app/Contents/MacOS/focus $*

sthennin commented 6 years ago

Dear Amanda, I understand that you work on a Mac with OSX, but have SBGRID install the software onto your Mac? SBGRID is probably downloading our pre-compiled binaries from https://focus.c-cina.unibas.ch/download.php and pushing them onto your Mac in the background. We have three different OSX versions, for OS 10.10, 10.11, and 10.12. Are you sure that SBGRID is pushing the correct version to your computer? On my Mac, the correct version works.

sthennin commented 6 years ago

Hi, For 2D crystal analsysis,you don’t need a GPU. Only MotionCor2, gCTF, and gAutomatch need the NVIDIA GPU. FOCUS itself uses any GPU that is in the computer, including OS X.

Henning.

Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62

On Apr 19, 2018, at 9:23 PM, acdrennan notifications@github.com<mailto:notifications@github.com> wrote:

I think my mac (OS 10.12.6) has an internal GPU, but it isn't made by NVIDIA, and CUDA only runs on NVIDIA cards...

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/C-CINA/focus/issues/219#issuecomment-382852384, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AGTM4H0FqiO39dW-0IQc-7MXtW70T5uuks5tqOQ9gaJpZM4TRyFn.

acdrennan commented 6 years ago

Hi Henning, When I try to run the "Import 2D Image" script I get this output (see below). I am trying to get IT to install gawk for me today, hopefully that will fix the problem.

#################################import_image#################################

==== RELION installation directory not found. Is it installed ??? ===================================================================================================================================== ==== /usr/local/relion ================================================================================================================================================================================ ==== The location of RELION installation is defined in Preferences. ===================================================================================================================================

==== cuda library path /usr/local/cuda/lib64 is not a valid directory. ================================================================================================================================ ############################import_image finished.############################ /usr/local/Cellar/gawk: Command not found.

acdrennan commented 6 years ago

Ok, I've got gawk installed, but now I am getting this error: #################################import_image################################# ==== cuda library path /usr/local/cuda/lib64 is not a valid directory. ================================================================================================================================ ==== Running: clip unpack image_2dx.tif image_2dx.mrc ================================================================================================================================================= ############################import_image finished.############################ /Applications/IMOD/bin/clip: line 3: /bin/realbin/clip: No such file or directory

rdrighetto commented 6 years ago

Hi,

It is trying to run the program 'clip' from IMOD, but is not finding it. Please install IMOD and tell FOCUS where it is located, by clicking on "Preferences" >> "Software" tab. The full list of external program dependencies is available on the Focus Wiki: https://focus.c-cina.unibas.ch/wiki/doku.php?id=1_0:external-tools

Best wishes,

-- Ricardo Diogo Righetto

2018-04-20 22:58 GMT+02:00 acdrennan notifications@github.com:

Ok, I've got gawk installed, but now I am getting this error: #################################import_image############### ################## ==== cuda library path /usr/local/cuda/lib64 is not a valid directory.

==================================================================== ==== Running: clip unpack image_2dx.tif image_2dx.mrc

============================================================

############################import_image finished.##################### ####### /Applications/IMOD/bin/clip: line 3: /bin/realbin/clip: No such file or directory

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sthennin commented 6 years ago

Hi, We also added some changes to scripts in FOCUS, and updated the third-party software installation manual pages on https://focus.c-cina.unibas.ch/wiki/doku.php?id=1_0:external-tools specifically for OSX. Please give it a try now, after updating to the newest version. Thanks.

acdrennan commented 6 years ago

Yes, I have it working this morning. I am trying to work out some strange FFTs but I am happy that it is up and running. Thank you!