sparx-em.org

SparxWiki - SPARX Wiki

Show local site map. Valid HTML 4.01. Sparx documentation is available in a number of narratives and as collection of manual pages. List of commands and applications grouped by categories. Download and install SPARX/EMAN2. Read and write images in SPARX/EMAN2 and how to handle image file attributes (necessary to run programs in SPARX). Use CTF in SPARX. Determine single particle structure using stain data. Determine single particle structure using cryo data. Write/edit a manual page.

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Pawel Penczek

MSB●●●220

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US

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pa●●●●●●●●●●●●●@uth.tmc.edu

View this contact

The University of Texas - Houston Medical School

Pawel Penczek

MSB●●●220

Ho●●on , TX, 77030

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pa●●●●●●●●●●●●●@uth.tmc.edu

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Show local site map. Valid HTML 4.01. Sparx documentation is available in a number of narratives and as collection of manual pages. List of commands and applications grouped by categories. Download and install SPARX/EMAN2. Read and write images in SPARX/EMAN2 and how to handle image file attributes (necessary to run programs in SPARX). Use CTF in SPARX. Determine single particle structure using stain data. Determine single particle structure using cryo data. Write/edit a manual page.

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SparxWiki - SPARX Wiki | sparx-em.org Reviews

https://sparx-em.org

Show local site map. Valid HTML 4.01. Sparx documentation is available in a number of narratives and as collection of manual pages. List of commands and applications grouped by categories. Download and install SPARX/EMAN2. Read and write images in SPARX/EMAN2 and how to handle image file attributes (necessary to run programs in SPARX). Use CTF in SPARX. Determine single particle structure using stain data. Determine single particle structure using cryo data. Write/edit a manual page.

INTERNAL PAGES

sparx-em.org

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Installer - SPARX Wiki

http://www.sparx-em.org/sparxwiki/Installer

Show local site map. Valid HTML 4.01. How to obtain EMAN2/SPARX. Stable releases of SPARX are here. To download the daily release (snapshots taken at noon CT US time) of EMAN2/SPARX please visit the EMAN2 website:. Http:/ ncmi.bcm.tmc.edu/ncmi/software/counter 222/software 86/. Where you can find links to the source code and the binary distributions for Linux, Mac OS X and Windows. How to install EMAN2/SPARX on a Mac OS. Install run this command from a terminal window: e2version.py. The easiest way of in...

2

Stain - SPARX Wiki

http://www.sparx-em.org/sparxwiki/Stain

Show local site map. Valid HTML 4.01. Sequence of steps necessary to detemine single particle structure using negative stain data. Convert scanned tiff micrographs into spider. Files The files can be examined using e2display.py. I Run sxcopyfromtif.py. Type and to send the program to background so as to free the current window:. Ii Set foc=f because all the stain micrographs are scanned from films. Iv At this stage, one has to be aware about the pixel size. Of scanned micrograph, or CCD frames. Iii One d...

3

FindPage - SPARX Wiki

http://www.sparx-em.org/sparxwiki/FindPage

Show local site map. Valid HTML 4.01. Containing all the following terms. Containing one or more of the following terms. Not containing the following terms. Last modified since (e.g. 2 weeks before). 123 - application/vnd.lotus-1-2-3. 3dm - text/vnd.in3d.3dml. 3dml - text/vnd.in3d.3dml. Abc - text/vnd.abc. Ac - application/vnd.nokia.n-gage.ac xml. Acc - application/vnd.americandynamics.acc. Acu - application/vnd.acucobol. Acutc - application/vnd.acucorp. Aep - application/vnd.audiograph. C - text/x-c hdr.

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RecentChanges - SPARX Wiki

http://www.sparx-em.org/sparxwiki/RecentChanges

Show local site map. Valid HTML 4.01. The use of categories. Helps organize your information. Marks older pages that have at least one backup version stored (click for an author diff). Marks pages edited since you set your bookmark (click for a bookmark diff). Marks pages created since you set your bookmark, and were not edited after creation. An editing conflict happened, please resolve it by merging both versions of the problematic paragraphs together.

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HowToUseSparx - SPARX Wiki

http://www.sparx-em.org/sparxwiki/HowToUseSparx

Show local site map. Valid HTML 4.01. The SPARX system is activated by typing. Should that fail, please change. Script to executable by typing. Example of an interactive session:. A = test image 3d(1). Calculate 2-D projection [phi, theta, psi, sx, sy]. P = prg(a, [12,23,-55,-2.3,4.1]). Write image to the disk in hdf format, it can be viewed using e2display.py. Rotate and shift the image (angle, sx, sy). Q = rot shift2D(p, 33., 3.8, 2.3). Writing a simple loop. Nx = p.get xsize(). Ny = p.get ysize().

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Software Tools For Molecular Microscopy - Wikibooks, open books for an open world

https://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy

Software Tools For Molecular Microscopy. From Wikibooks, open books for an open world. The latest reviewed version. On 9 May 2016. There are 2 pending changes. There are a large number of software tools. Or software applications that have been specifically developed for the field sometimes referred to as molecular microscopy. Or cryoEM. Several special issues of the Journal of Structural Biology. MRC IMAGE PROCESSING PACKAGE. BBHP - Burnham-Brandeis Helical Package. FEI Xplore3D Tomography Suite. Appion"...

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SparxWiki - SPARX Wiki

Show local site map. Valid HTML 4.01. Sparx documentation is available in a number of narratives and as collection of manual pages. List of commands and applications grouped by categories. Download and install SPARX/EMAN2. Read and write images in SPARX/EMAN2 and how to handle image file attributes (necessary to run programs in SPARX). Use CTF in SPARX. Determine single particle structure using stain data. Determine single particle structure using cryo data. Write/edit a manual page.

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