User contributions
14 December 2010
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…'
Useful scripts (aka smart piece of code)
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+69
10 December 2010
Useful scripts (aka smart piece of code)
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+29
Renumber files
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-3
Calculate average I/sigma from .sca file
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+55
Print the shifts in individual atom positions
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+55
Get systematic absences from .sca file
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+54
Renumber files
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+58
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…'
Useful scripts (aka smart piece of code)
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+21
4 November 2010
2 November 2010
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…'
Useful scripts (aka smart piece of code)
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-7
Useful scripts (aka smart piece of code)
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+54
14 July 2010
Morph with Chimera
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+14
Morph with Chimera
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+383
Morph with Chimera
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+286
3 July 2010
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: …'
Morphing
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+60
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…'
Useful scripts (aka smart piece of code)
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+52
11 December 2008
Get systematic absences from .sca file
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+1
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...
Useful scripts (aka smart piece of code)
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+1
Useful scripts (aka smart piece of code)
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+45
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.
Xtal computing
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+48
26 June 2008
23 May 2008
Crystals
Crystal Growth
Crystals
Crystal Growth
-47
Crystals
Crystal Growth
+47
Conditions prone to salt crystallization
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+77
Conditions prone to salt crystallization
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+63
Conditions prone to salt crystallization
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+6
Conditions prone to salt crystallization
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+85
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 #...
Crystals
Crystal Growth
+47
14 February 2008
Crystallization screens and methods
The PACT screen
+1,090
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 ...
11 February 2008
9 February 2008
Expression and Purification: Tips and Tricks
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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...
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...
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...