![Page 1: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/1.jpg)
Structural Biology: A Collaborative NecessityOr:
Collaborative Computing – does it have a future?Or:
What should MX Software deliver now?
• West Coast Crystallographic Meeting
• Monterey: March 11th 2007
![Page 2: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/2.jpg)
How has MX changed in 2007?
• The Internet – questions can be asked and answered; information found
• Much more work done much faster, so desperate need for organisation of information
• Better languages, Faster Computers, Better graphics
• But still need good appropriate algorithms..
![Page 3: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/3.jpg)
Has CCP4 helped develop New Algorithms?
• Yes… maybe, but developers are free spirits – very little “contracted” software
• CCP4MG• Coot• Acorn• New density modification from KDC
• CCP4 provides distribution and support; author keeps copyright, References flagged
![Page 4: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/4.jpg)
What helps algorithm development?
• Common Data structures ( formats?)
•Library routines for data handling, crystallographic operations ( Symmetry, FFTs, etc) :
Libraries must be accessible to developers and there needs to be a way to update them to add routines, and to debug. They must be well documented and curated.
![Page 5: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/5.jpg)
Cooperation – is it possible? desirable?
• Advantages•Can speed up developments if library routines are well documented and accessible :
•Shared efforts for maintenance and distribution extends the code lifetime
• Common style helps users
•Organising crystallographic data is not easy and requirements change– maybe we can agree on and provide a better standard?
•Mtz model carries vital information with it.
![Page 6: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/6.jpg)
Cooperation – is it possible? desirable?
• Disadvantages•Time consuming – consultation essential :
•Needs commitment by developers of algorithms and libraries– often faster to make a quick cludgey fix than read library; new routines may need to be added to libraries
•Harder to get credit, raise funds
•Licensing issues!
![Page 7: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/7.jpg)
Friendly Discussion Amongst Developers??
![Page 8: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/8.jpg)
The Future - Automation ?
• Chemists now use crystallography as a tool and the software is robust.
• MX will often be used in the same way in future– a handy technique the user cannot be expected to understand or criticise.
•Obviously, automation modules must be designed by good crystallographers
( How will the good crystallographers be trained?)
![Page 9: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/9.jpg)
What level of knowledge to assume- Discuss?
• Assessing the experiment• Some understanding of crystal lattices, symmetry, point
groups & spacegroups• Something about intensity statistics (at least that they exist!) • I think it is important to know the structure factor equation
• Much basic information in
http://www.ccp4.ac.uk/docs.php
• (But there are still pathological cases.. See CCP4BB!)
![Page 10: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/10.jpg)
• Acquiring some crystallographic know-how. How much time will people devote to this?
Extracts from York tutorials given by Johan Turkenburg (most slides taken from the web)
16 slides I thought essential follow!
![Page 11: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/11.jpg)
Crystal: unit cell + lattice + symmetry
![Page 12: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/12.jpg)
The unit cell in three dimensions.The unit cell is defined by three vectors a, b, and c, and three angles , , .
a
b
c
is angle between b and c; between a and c; between a and b
Unit cells are usually defined in terms of the lengths of the three vectors and the three angles. For example, a=94.2Å, b=72.6Å, c=30.1Å, =90°, =102.1°, =90°.
![Page 13: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/13.jpg)
Crystal System
Minimum Symmetry
Bravais Lattices
Unit Cell Geometry
1. Triclinic None 1. Primitive (P) a b c;
2. Monoclinic One 2fold axis
2. Primitive (P)3. Base-Centered (C)
a b c; = = 90
3. Orthorhombic Three orthogonal 2fold axes
4. Primitive (P)5. Base-Centered (C)6. Body-Centered (I)7. Face-Centered (F)
a b c; = = = 90
4. Tetragonal One 4fold axis
8. Primitive (P)9. Body-Centered (I)
a = b c; = = = 90
5. Trigonal One 3fold axis
10. Primitive (P) a = b c; = = 90, = 120
11. Rhombohedral (R) a = b = c; = = 90
6. Hexagonal One 6fold axis
10. Primitive (P) a = b c; = = 90, = 120
7. Cubic Four 3fold axes
12. Primitive (P)13. Body-Centered (I)14. Face-Centered (F)
a = b = c; = = = 90
The Seven Crystal SystemsThe 230 space groups can be grouped into seven crystal systems
![Page 14: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/14.jpg)
![Page 15: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/15.jpg)
Owing to symmetry requirementssome unit cells may not be primitive:
Therefore we can have:
• P - primitive• I – body centred • A, B, C – face centred• F – all-face centred unit cells
ab
cP I
F
C B A
In total only 14 different combinations of a, b, c and can exist = 14 Bravais’ lattices
![Page 16: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/16.jpg)
Symmetry Operators and ElementsApart from the identity and translational symmetry, protein crystals can only contain the following symmetry elements:
Proper rotation: Rotate by 360°/n. n = 2 3 4 or 6
Screw rotation: Rotate by 360°/n & translate by d(m/n); d= unit cell edge.
Proper Rotations
Two-fold
Three-fold
Four-fold
Six-fold
Symbol (n)
2
3
4
6
Screw Rotations
Symbol (nm)
21
31, 32
41, 42, 43
61, 62, 63, 64, 65
![Page 17: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/17.jpg)
Space group diagram P212121
Know where Int Tab A is!!
![Page 18: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/18.jpg)
Indexing Conventions: http://www.ccp4.ac.uk/dist/html/reindexing.html
Example: • Reindexing (CCP4: General) - information about changing indexing regime • etc• All P3i and H3:
(h,k,l) not equivalent to (-h,-k,l) or (k,h,-l) or (-k,-h,-l) so we need to check all 4 possibilities:
• real axes:(a,b,c) and (-a,-b,c) and (b,a,-c) and (-b,-a,c)• reciprocal axes: (a*,b*,c*) and (-a*,-b*,c*) and (b*,a*,-c*) and (-b*,-a*,c*)• i.e. reindex (h,k,l) to (-h,-k,l) or (h,k,l) to (k,h,-l) or (h,k,l) to (-k,-h,-l).
• N.B. For trigonal space groups, symmetry equivalent reflections can be conveniently described as (h,k,l), (k,i,l) and (i,h,l) where i=-(h+k).
• Replacing the 4 basic sets with a symmetry equivalent gives a bewildering range of possibilities!.
![Page 19: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/19.jpg)
Many choices of Asymmetric unit and unit cell See http://www.ccp4.ac.uk/dist/html/alternate_origins.html
Unit cell = The smallest volume from which the entire crystal can be constructed by translation only.
![Page 20: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/20.jpg)
Diffraction Geometry
![Page 21: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/21.jpg)
Diffraction lattice and symmetry does not mirror crystal symmetry exactly:
Use Reciprocal Space definitions to describe it..
• First we need to define the relation between real space and reciprocal space. (Ie crystal lattice and diffraction space)
• This requires us to look at Bragg planes and Miller indices.
![Page 22: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/22.jpg)
Definitions used for reciprocal space• To go from real to reciprocal space we define a set of
axes a*, b* and c* such that:• a* is perpendicular to b and c (b.a* = c.a* = 0)• b* is perpendicular to a and c (a.b* = c.b* = 0)• c* is perpendicular to a and b (a.c* = b.c* = 0)• a.a* = b.b* = c.c* = 1
• For orthogonal system, the length of a* is 1/(length a)• The length of a reciprocal vector d* is related to the
interplanar spacing in real space as 1/d
![Page 23: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/23.jpg)
Structure Factor EquationVery useful IF you know atom positions
Very useful for understanding crystallography
![Page 24: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/24.jpg)
Adding one (or more) atoms in known positions changes the structure factor in a known way
FP
Native
Derivative
FPH
Alternate representation: Structure factor can be represented by 2-d vectors.
![Page 25: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/25.jpg)
Symmetry in reciprocal space
•No translations
•So point groups!
•But: Centrosymmetry: Friedel’s law Ihkl = I-h-k-l
•=> 11 Laue groups
![Page 26: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/26.jpg)
Systematic absences• Translational symmetry such as screw axes and lattice
centring, leads to some reflections being ‘absent’. This can be shown using Structure Factor Formula
• If a space group has a 21 screw axis along b, then this will affect the reflections 0k0: only k=2n observed
• If a space group has a 62 or 64 screw axis along c, then this will affect the reflections 00l: only l=(6/2)n observed
• Beware – a non-crystallographic translation of(0.2,0.3,1/3) will ALSO give these absences
![Page 27: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/27.jpg)
Centric and Acentric reflections Centrosymmetric zones
• If Ihkl = I-h-k-l for a subset of reflections under the space group symmetry without invoking Friedel’s law, then these reflections are centric.
• In P21: Ihkl = I-hk-l so for all k=0 reflections, Ih0l = I-h0-l • • Most reflections are acentric• This is relevant because:
1. Centric and Acentric intensities have different statistical properties
2. Centric phases must be or +180.
![Page 28: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/28.jpg)
Does CCP4 help guide Users through this?
• We hope so, but the best critics are the users themselves
• In general some knowledge is assumed
• As far as possible programmers try to illustrate important information by presenting it graphically.
• Links to documentation where possible
![Page 29: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/29.jpg)
CCP4 Main Page
• CCP4 Documentation• Individual Program Documentation • Tutorials • Maths for Protein Crystallographers • Crystallographic guidance • Roadmaps through the Suite • Talks
![Page 30: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/30.jpg)
Example from CCP4 Main Page
• CCP4 Documentation• Individual program documentation
• CCP4 Tutorial
• Maths for Protein Crystallographers• Eleanor Dodson prepared a document containing all the
maths a protein crystallographer might need. It helps to have this all together, and available on the web, so Maria Turkenburg developed it further. It is distributed with the suite as a set of documents in which certain symbols are represented by small .gif-pictures. They are available here:
• Basic Maths for Protein Crystallographers
![Page 31: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/31.jpg)
An aside- Project Book-keeping
• There is an urgent need for data management.
Each specific application program needs to define its requirements and its product along with a book-keeping header
e.g. Protein production needs sequence, so does automatic model building – how to pass this info on via intervening steps
– from laboratory to beamline to structure solution ?
![Page 32: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/32.jpg)
Brief Introduction to the Graphical User Interface• Designed - to keep a record of what has been done within a project
directory/folder It is far from perfect but at least it exists!
- to provide easy access to the tasks required for each crystallographic module
- to provide diagnostic information, mostly via graphs, summaries, and as a last resort, log files
-CANNOT “manage” your work pattern! You must do
that..
![Page 33: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/33.jpg)
GUI Structure Solution Modules• Data Processing• Experimental phasing• Molecular Replacement• Density Improvement• Model building• Refinement• Structure Analysis• Validation and Deposition• Reflection, Coordinate, Map and Graphical utilities• Clipper applications• Program list• Needs logical up-dating! Currently underway –
CCP4BB request for feedback soon..
![Page 34: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/34.jpg)
Lots of Graphical analysis from CCP4 software
![Page 35: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/35.jpg)
Scala Analysis(Scaling and Merging)
![Page 36: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/36.jpg)
Use hklview to see diffraction zones
![Page 37: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/37.jpg)
Intensity DistributionsThe structure factor equation means we can predict
some properties of all INTENSITY distributions
• These should be inspected as soon as data are processed
• Intensity distribution v resolution • Wilson Plot• Moments
• SFCHECK good too
![Page 38: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/38.jpg)
![Page 39: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/39.jpg)
Intensity Analysis
![Page 40: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/40.jpg)
Intensity Analysis
![Page 41: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/41.jpg)
Lead to: Refinement problems
![Page 42: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/42.jpg)
What level of knowledge to assume- Validation
• Assessing how well the model describes the experiment and fits with expectation - COOT lists many tools
• Protein geometry – Ramachandran plots Need a tool not part of refinement
• Sensible contacts (Molprobity, PISA etc) • Density Fit• Unmodelled map features• Critical facilities
![Page 43: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/43.jpg)
Solving the structure – Automation as it is now
• From data through experimental phases to model
• ShelxD/ShelxE: Decisions made within program, based on good methodology.
• Solve & Resolve. Decisions made by programmer, based on expert knowledge.
• AutoSharp: links several programs using scripting. Decisions made at scripting level?, based on expert knowledge.
![Page 44: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/44.jpg)
More Automation Procedures• From homologous model to final model.• Molrep: Input experimental data and model –
output model of asymmetric unit. (Mr Bump – Balbes)
• Arp-Warp/Refmac5. Model building using refinement & map interpretation. This uses a GUI to set a protocol, interpreted into a C-shell script.
• Some CCP4 GUI tasks
![Page 45: Structural Biology: A Collaborative Necessity Or: Collaborative Computing – does it have a future? Or: What should MX Software deliver now? West Coast](https://reader035.vdocument.in/reader035/viewer/2022070410/56649ec05503460f94bcb5d3/html5/thumbnails/45.jpg)
Automation Thoughts• Should procedures aim to be “black boxes”?• Yees – but I think there are too many difficult
cases for this..
• Can MX be automated? Will Automation lead to rigidity?
• There is a danger of this – not so serious if the approach is modular, linked by scripting..
• Will automation destroy our critical facilities