User contributions
From CCP4 wiki
Jump to navigationJump to search- 14:38, 14 December 2010 diff hist +323 N Split NMR-style multiple model pdb files into individual models Created page with 'This assumes that you have a correctly formatted pdb file that contains both MODEL and ENDMDL records. It gets split into individual pdb files names model_###.pdb. grep -n 'MOD…'
- 14:31, 14 December 2010 diff hist +69 Useful scripts (aka smart piece of code)
- 15:32, 10 December 2010 diff hist +29 Useful scripts (aka smart piece of code)
- 15:31, 10 December 2010 diff hist -3 Renumber files
- 15:30, 10 December 2010 diff hist +55 Calculate average I/sigma from .sca file
- 15:30, 10 December 2010 diff hist +55 Print the shifts in individual atom positions
- 15:29, 10 December 2010 diff hist +54 Get systematic absences from .sca file
- 15:28, 10 December 2010 diff hist +58 Renumber files
- 15:27, 10 December 2010 diff hist +525 N Renumber files Created page with 'Let's say you have a list of images named something_###.img with ### spanning 381-560, and you want to renumber them to be from 1 to 180. '''echo | awk '{for(i=1;i<181;i++) prin…'
- 15:06, 10 December 2010 diff hist +21 Useful scripts (aka smart piece of code)
- 14:48, 4 November 2010 diff hist +145 Calculate average I/sigma from .sca file
- 03:52, 2 November 2010 diff hist +469 N Calculate average I/sigma from .sca file Created page with 'This python script will analyze a .sca-file and print out the key statistics missing from the standard SCALEPACK log-file, namely <math><I/sigma></math> per resolution shell. Sy…'
- 03:42, 2 November 2010 diff hist -7 Useful scripts (aka smart piece of code)
- 03:41, 2 November 2010 diff hist +54 Useful scripts (aka smart piece of code)
- 16:40, 14 July 2010 diff hist +14 Morph with Chimera
- 16:39, 14 July 2010 diff hist +383 Morph with Chimera
- 16:28, 14 July 2010 diff hist +286 Morph with Chimera
- 16:53, 3 July 2010 diff hist +1,187 N Morph with Chimera Created page with 'Making a morph movie with UCSF Chimera is extremely easy. There are tutorials on the website [http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html], but here is an outline: …'
- 16:37, 3 July 2010 diff hist +60 Morphing current
- 16:33, 3 July 2010 diff hist +544 N Print the shifts in individual atom positions Created page with 'This can be done with one command line (albeit a rather long one). Below is the code with (remove backslashes if pasting as a single line) grep 'ATOM\|HETATM' file1.pdb file2.p…'
- 16:30, 3 July 2010 diff hist +52 Useful scripts (aka smart piece of code)
- 23:21, 11 December 2008 diff hist +1 Get systematic absences from .sca file
- 23:20, 11 December 2008 diff hist +901 N Get systematic absences from .sca file New page: Scalepack outputs only systematic absences, and not the rest of reflections. The best way to identify screw axis is probably to look at the whole set of reflections, so that you can compa...
- 23:01, 11 December 2008 diff hist +1 Useful scripts (aka smart piece of code)
- 22:58, 11 December 2008 diff hist +45 Useful scripts (aka smart piece of code)
- 22:53, 11 December 2008 diff hist +183 N Useful scripts (aka smart piece of code) New page: This page is a collection of scripts used to resolve variety of minor problems. Posts include brief description and the code. The list is still very short, so there is no hierarchy.
- 22:50, 11 December 2008 diff hist +48 Xtal computing
- 13:33, 26 June 2008 diff hist +517 Operating systems and Linux distributions →Irix (SGI)
- 16:11, 23 May 2008 diff hist 0 Crystals →Crystal Growth
- 16:11, 23 May 2008 diff hist -47 Crystals →Crystal Growth
- 16:10, 23 May 2008 diff hist +47 Crystals →Crystal Growth
- 14:25, 23 May 2008 diff hist +77 Conditions prone to salt crystallization
- 14:24, 23 May 2008 diff hist +63 Conditions prone to salt crystallization
- 14:23, 23 May 2008 diff hist +6 Conditions prone to salt crystallization
- 14:22, 23 May 2008 diff hist +85 Conditions prone to salt crystallization
- 14:18, 23 May 2008 diff hist +418 N Conditions prone to salt crystallization New page: <table border = "1"> <tr> <td>Screen and #</td> <td>Condition</td> <td>Protein buffer</td> <td>Confirmed by diffraction</td> <td>Signature and comment</td> </tr> <tr> <td>Hampton PEG/ion #...
- 14:08, 23 May 2008 diff hist +47 Crystals →Crystal Growth
- 16:25, 14 February 2008 diff hist +1,090 Crystallization screens and methods →The PACT screen
- 16:05, 14 February 2008 diff hist +1,680 N Crystal growth: Tips and Tricks New page: == I tried Hampton Screen I & II with my protein and have no crystals. What can I do? == 1. There are other screens. While it is proably true that when proteins do crystalize, they in ...
- 14:41, 11 February 2008 diff hist +14 m Data quality
- 06:08, 9 February 2008 diff hist 0 Expression and Purification: Tips and Tricks
- 06:06, 9 February 2008 diff hist +1,241 N Servers for ligand topologies/parameters New page: == How to generate topology/parameter files for unknown ligand == What is meant here by unknown ligand is that it is not found in the standard monomer library in CCP4 or on the [http://x...
- 05:44, 9 February 2008 diff hist +1,882 N Data quality New page: == What is the resolution of my dataset? == First of all, it is limited by completeness. In practical terms this means that the highest resolution you can get is the resolution at the ed...
- 05:13, 9 February 2008 diff hist +1,134 N Refinement New page: == Wrong space group == Sometimes crystal symmetry combines with non-crystallographic symmetry (NCS) and produces a diffraction pattern resembling higher symmetry space group than what y...
- 16:34, 8 February 2008 diff hist +1,248 N Expression and Purification: Tips and Tricks New page: == How pure should be the protein for crystallization? == Everyone knows that protein must be "very pure" for crystallization. It is expected that no extra bands will be seen on an overl...
