CCP4 wiki - User contributions [en]

Programs to convert X-ray diffraction image file formats to graphics file formats

2009-11-11T04:26:01Z

Torelli:

=== Considerations and programs to convert X-ray diffraction images into a graphics file format ===
<nowiki> The following information was compiled from a series of responses to a post on the CCP4bb on October 21, 2009 by Andrew Torelli who asked about free utilities/programs that could convert X-ray diffraction image file formats to a graphics file format that could be edited by programs such as Photoshop. The specific responses are worthwhile to read and can be searched in the CCP4bb archives using the subject query "X-ray diffraction image --> .jpg". The summary is below:
</nowiki>

<nowiki> A notable consideration (provided by Jim Pflugrath) is that "A JPEG has fixed colors for the pixel values. A diffraction image has to use a viewer to convert the pixel values (counts) to a color. One problem with just using a converter to jpeg is how to convert intensities to color (i.e. computer display values)."
</nowiki>

<nowiki> Additionally, Morten Kjeldgaard noted that opening saved images (particularly TIFF images) in Photoshop will require "Image -> Adjustments -> Equalize" to see anything other than black.
</nowiki>
Specific program suggestions:

* [http://www.ccp4.ac.uk/html/DiffractionImage.html|''diff2jpeg''] - a CCP4 utility within the "DiffractionImage" library for handling different diffraction file formats.

* [http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4i_diffraction_image_display_%28idiffdisp%29|''idiffdisp''] - a CCP4 utility.

* [http://www.ccp4.ac.uk/dist/html/ipdisp.html|''ipdisp''] - a CCP4 utility.

* [http://www.mrc-lmb.cam.ac.uk/harry/mosflm/|''Mosflm''] has capability including control over grayscale. See FAQ section for details.

* [http://www.scripps.edu/~arvai/adxv.html|''ADXV''] - reportedly easy to install and can save in TIFF format. Also will save image to match coloring in view window.

* [http://www.marresearch.com/download.html#Utilities|''Marview''] - can be installed using Linux_glibc-2.3.3 (RedHat9, WS3, etc). Just download it, unpack (gunzip marView.gz).
first: chmod a+x marView
a) to run the program from terminal:
./marView
or make an alias (.bashrc): alias marview=/home/user/Desktop/marview/./marView
b) alternatively, place the program in the Desktop and just double-click to start it up.

* demo version of [http://www.rigaku.com/downloads/software/index.html#free|''d*TREK''] is freely available from Rigaku and has dtdisplay for this purpose.

* [http://cci.lbl.gov/labelit|''Labelit'']
- labelit.png <filename> <output.png> [-large]

* [http://www.imagemagick.org/script/index.php|''ImageMagick''] - part of most linux distros. See also [https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0910&L=CCP4BB&D=0&X=2FA4086DA38435B93C&Y=att29%40cornell.edu&P=196309|''James Holton's helpful and detailed reply''] made to the CCP4bb on October 21, 2009 to the original post.
- convert -depth 16 -type Grayscale -colorspace GRAY -endian LSB -size 3072x3072+512 GRAY:test_0_001.img test_0_001.jpg

Programs to convert X-ray diffraction image file formats to graphics file formats

2009-11-09T22:48:26Z

Torelli:

<nowiki> The following information was compiled from a series of responses to a post on the CCP4bb on October 21, 2009 by Andrew Torelli who asked about free utilities/programs that could convert X-ray diffraction image file formats to a graphics file format that could be edited by programs such as Photoshop. The specific responses are worthwhile to read and can be searched in the CCP4bb archives using the subject query "X-ray diffraction image --> .jpg". The summary is below:
</nowiki>

<nowiki> A notable consideration (provided by Jim Pflugrath) is that "A JPEG has fixed colors for the pixel values. A diffraction image has to use a viewer to convert the pixel values (counts) to a color. One problem with just using a converter to jpeg is how to convert intensities to color (i.e. computer display values)."
</nowiki>

<nowiki> Additionally, Morten Kjeldgaard noted that opening saved images (particularly TIFF images) in Photoshop will require "Image -> Adjustments -> Equalize" to see anything other than black.
</nowiki>
Specific program suggestions:

- diff2jpeg - a CCP4 utility within the "DiffractionImage" library for handling different diffraction file formats. See: http://www.ccp4.ac.uk/html/DiffractionImage.html

- idiffdisp - a CCP4 utility. See also CCP4wiki page: http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4i_diffraction_image_display_%28idiffdisp%29

- ipdisp - a CCP4 utility. See also:
http://www.ccp4.ac.uk/dist/html/ipdisp.html

- Mosflm has capability including control over gr[e|a]yscale. See FAQ section for details.

- ADXV - reportedly easy to install and can save in TIFF format. Also will save image to match coloring in view window: http://www.scripps.edu/~arvai/adxv.html

- Marview - can be installed using Linux_glibc-2.3.3 (RedHat9, WS3, etc). Just download it, unpack (gunzip marView.gz). See also http://www.marresearch.com/download.html#Utilities
# chmod a+x marView

a) to run the program from terminal
# ./marView or

# kate .bashrc:
alias marview=/home/user/Desktop/marview/./marView

b) alternativelly, place the program in the Desktop and just double-click to start it up.

- demo version of d*TREK is freely available from Rigaku and has dtdisplay for this purpose.

- Labelit - see http://cci.lbl.gov/labelit
- labelit.png <filename> <output.png> [-large]

- ImageMagick - part of most linux distros. See also James Holton's helpful and detailed reply to my original post.
- convert -depth 16 -type Grayscale -colorspace GRAY -endian LSB -size 3072x3072+512 GRAY:test_0_001.img test_0_001.jpg

Programs to convert X-ray diffraction image file formats to graphics file formats

2009-11-09T22:45:46Z

Torelli:

<nowiki> The following information was compiled from a series of responses to a post on the CCP4bb on October 21, 2009 by Andrew Torelli who asked about free utilities/programs that could convert X-ray diffraction image file formats to a graphics file format that could be edited by programs such as Photoshop. The specific responses are worthwhile to read and can be searched in the CCP4bb archives using the subject query "X-ray diffraction image --> .jpg". The summary is below:
</nowiki>
A notable consideration (provided by Jim Pflugrath) is that "A JPEG has fixed colors for the pixel values. A diffraction image has to use a viewer to convert the pixel values (counts) to a color. One problem with just using a converter to jpeg is how to convert intensities to color (i.e. computer display values)."

Additionally, Morten Kjeldgaard noted that opening saved images (particularly TIFF images) in Photoshop will require "Image -> Adjustments -> Equalize" to see anything other than black.

Specific program suggestions:

- diff2jpeg - a CCP4 utility within the "DiffractionImage" library for handling different diffraction file formats. See: http://www.ccp4.ac.uk/html/DiffractionImage.html

- idiffdisp - a CCP4 utility. See also CCP4wiki page: http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4i_diffraction_image_display_%28idiffdisp%29

- ipdisp - a CCP4 utility. See also:
http://www.ccp4.ac.uk/dist/html/ipdisp.html

- Mosflm has capability including control over gr[e|a]yscale. See FAQ section for details.

- ADXV - reportedly easy to install and can save in TIFF format. Also will save image to match coloring in view window: http://www.scripps.edu/~arvai/adxv.html

- Marview - can be installed using Linux_glibc-2.3.3 (RedHat9, WS3, etc). Just download it, unpack (gunzip marView.gz). See also http://www.marresearch.com/download.html#Utilities
# chmod a+x marView

a) to run the program from terminal
# ./marView or

# kate .bashrc:
alias marview=/home/user/Desktop/marview/./marView

b) alternativelly, place the program in the Desktop and just double-click to start it up.

- demo version of d*TREK is freely available from Rigaku and has dtdisplay for this purpose.

- Labelit - see http://cci.lbl.gov/labelit
- labelit.png <filename> <output.png> [-large]

- ImageMagick - part of most linux distros. See also James Holton's helpful and detailed reply to my original post.
- convert -depth 16 -type Grayscale -colorspace GRAY -endian LSB -size 3072x3072+512 GRAY:test_0_001.img test_0_001.jpg

Programs to convert X-ray diffraction image file formats to graphics file formats

2009-11-09T22:42:03Z

Torelli: New page: The following information was compiled from a series of responses to a post on the CCP4bb on October 21, 2009 by Andrew Torelli who asked about free utilities/programs that could conve...

The following information was compiled from a series of responses to a post on the CCP4bb on October 21, 2009 by Andrew Torelli who asked about free utilities/programs that could convert X-ray diffraction image file formats to a graphics file format that could be edited by programs such as Photoshop. The specific responses are worthwhile to read and can be searched in the CCP4bb archives using the subject query "X-ray diffraction image --> .jpg". The summary is below:

A notable consideration (provided by Jim Pflugrath) is that "A JPEG has fixed colors for the pixel values. A diffraction image has to use a viewer to convert the pixel values (counts) to a color. One problem with just using a converter to jpeg is how to convert intensities to color (i.e. computer display values)."
Additionally, Morten Kjeldgaard noted that opening saved images (particularly TIFF images) in Photoshop will require "Image -> Adjustments -> Equalize" to see anything other than black.

Specific program suggestions:

- diff2jpeg - a CCP4 utility within the "DiffractionImage" library for handling different diffraction file formats. See: http://www.ccp4.ac.uk/html/DiffractionImage.html

- idiffdisp - a CCP4 utility. See also CCP4wiki page: http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4i_diffraction_image_display_%28idiffdisp%29

- ipdisp - a CCP4 utility. See also:
http://www.ccp4.ac.uk/dist/html/ipdisp.html

- Mosflm has capability including control over gr[e|a]yscale. See FAQ section for details.

- ADXV - reportedly easy to install and can save in TIFF format. Also will save image to match coloring in view window: http://www.scripps.edu/~arvai/adxv.html

- Marview - can be installed using Linux_glibc-2.3.3 (RedHat9, WS3, etc). Just download it, unpack (gunzip marView.gz). See also http://www.marresearch.com/download.html#Utilities
# chmod a+x marView

a) to run the program from terminal
# ./marView or

# kate .bashrc:
alias marview=/home/user/Desktop/marview/./marView

b) alternativelly, place the program in the Desktop and just double-click to start it up.

- demo version of d*TREK is freely available from Rigaku and has dtdisplay for this purpose.

- Labelit - see http://cci.lbl.gov/labelit
- labelit.png <filename> <output.png> [-large]

- ImageMagick - part of most linux distros. See also James Holton's helpful and detailed reply to my original post.
- convert -depth 16 -type Grayscale -colorspace GRAY -endian LSB -size 3072x3072+512 GRAY:test_0_001.img test_0_001.jpg

Crystallography

2009-11-09T22:35:00Z

Torelli: /* Tricks and Tips */

== Crystallographic Theory ==
* [[Basics of Crystallography]]
* [[Phase problem]], and [[Phasing]]
* [[Twinning]]
* [[R-factors]]
* [[Bulk solvent correction]]
* [http://www.mpimf-heidelberg.mpg.de/~holmes/ Fiber diffraction]
* [[References and links]]

== Crystallography Software ==

=== For Specific Tasks ===
* [[Data reduction]]
* [[Molecular replacement]] (MR)
* [[Substructure determination]]
* [[Experimental phasing]] (SIR/MIR and SAD/MAD)
* [[Electron density modification]]
* [[Automated Model building]]
* [[Interactive Model building]]
* [[Refinement]]
* [[Model validation]]
* [[Model Evaluation]]
* [[Loop modelling]]

=== Automated Pipelines for Structure Solution ===
*[[Ants]]
*[http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)]
*[[AutoSHARP]]
*[[BALBES]]
*[[BNP]]
*[[CRANK]]
*[[Elves]]
*[[MrBUMP]] - molecular replacement
*[[Phenix]] - comprehensive package
*[[HKL2MAP]] - SAD/MAD/SIRAS/SIR phasing based on [[SHELXC/D/E]]

=== Web services ===
*[http://cluster.embl-hamburg.de/ARPwARP/remote-http.html ARP/wARP web services (model building)]
*[http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)] - see example at [[xds:1RQW]]
*[http://tuna.tamu.edu/ Bias removal server]
*[http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp York suite (Balbes, Modsearch, Zanuda)]
*[http://www.doe-mbi.ucla.edu/~sawaya/anisoscale Diffraction Anisotropy Server]
*[http://iterate.sourceforge.net/ Bravais Lattice Determination by Projections]

=== Software Packages ===
(large packages first)
* [[CCP4]]
* [[CNS]]
* [[PHENIX]]
* [[SHELX C/D/E]] and [[SHELXL]] (homepage at [http://shelx.uni-ac.gwdg.de/SHELX], [http://dx.doi.org/10.1107/S0108767307043930 overview paper])
* moleman, lsqman, ... from [http://xray.bmc.uu.se/usf/ Uppsala Software Factory]
* XDS [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds homepage] and [http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDS XDSwiki]
* HKL [http://www.hkl-xray.com homepage]
* [[COOT]]
* [http://www.pymolwiki.org/index.php/Main_Page PyMol] wiki
* [[CCP4mg]]
* [[O]]
* [[ARP/wARP]]
* [[SHARP]] [http://www.globalphasing.com homepage]
* [http://www.solve.lanl.gov/index.html Solve/Resolve]
* ...

=== Libraries for crystallography and related areas ===
* [[Clipper]]
* [[cctbx|Crystallographic Toolbox]]
* [[CCP4]] library; documentation at [http://www.ccp4.ac.uk/html/INDEX.html]
* [[mmdb]]

=== Tricks and Tips ===
* [[Solve-TAT|Solving a structure]]
* [[Buildn-TAT|Model building and refinement]]
* [[Evaluation-TAT|Model Evaluation and Interpretation]]
* [[Finding symmetry elements in P1]]
* [[Programs to convert X-ray diffraction image file formats to graphics file formats]]

== Teaching crystallography ==
* [[Crystallography courses on the web]]
* [[Test data sets]]

== Understanding and extending the properties and limitations of crystallographic computations ==

=== Ensemble refinement, and molecular dynamics ===
# Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases. Burling FT, Weis WI, Flaherty KM, Brünger AT. Science (1996) 271, 72-77 [http://dx.DOI.org/10.1126/science.271.5245.72]
# Heterogeneity and Inaccuracy in Protein Structures Solved by X-Ray Crystallography. DePristo MA,de Bakker PIW, Blundell TL (2004) Structure 12, 831-838 [http://dx.doi.org/10.1016/j.str.2004.02.031]
# Ensemble Refinement of Protein Crystal Structures: Validation and Application. Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN, Structure 15, 1040 - 1052 [http://dx.doi.org/10.1016/j.str.2007.06.019]
# A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Vitkup D, Petsko GA, Karplus M. Nature Structural Biology 4, 202 - 208 (1997) [http://dx.doi.org/10.1038/nsb0397-202] (Vitkup et al showed that fitting a single model to MD-simulation derived "data" gave ~20% R, which means multiple conformers are sufficient to explain the "R-Factor Gap" between the 20% usually obtained for macromolecules, and the 5% routinely obtained for small molecules)

=== Electron microscopy and X-ray ===
# Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallography. Harms J, Tocilj A, Levin I, Agmon I, Stark H, Kölln I, van Heel M, Cuff M, Schlünzen F, Bashan A, Franceschi F, Yonath A. Structure 7, 931-941 (1999) [http://dx.doi.org/10.1016/S0969-2126(99)80120-8]

=== NMR versus X-ray ===
A couple of papers analysing and comparing NMR and X-ray methods/structures:
# Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. Shaanan B, Gronenborn AM, Cohen GH, Gilliland GL, Veerapandian B, Davies DR, Clore GM. Science (1992), 257, 961 [http://dx.doi.org/10.1126/science.1502561]
# X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Biology 4, 862-865 (1997). Preprint [http://atbweb.stanford.edu/scripts/papers.php?sendfile=162 available] from Axel Brunger's "publications" website.
# Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors. S.B. Nabuurs, C.A.E.M. Spronk, G.W. Vuister, G. Vriend. PLoS Comput Biol 2(2): e9. [http://dx.doi.org/10.1371/journal.pcbi.0020009]