Re: [ccp4bb] The Good and the Bad crystal contact?
On 06/29/2011 10:22 PM, Paul Lindblom wrote: Hi everybody, can anybody tell me how crystal contacts are defined? Are there good and bad crystal contacts? They are the most important interactions with impact on the crystal quality, but they are not of covalent nature, aren´t they? With best regards, Paul Look at the PISA documentation - that isextensive.. Eleanor A bad crystal contact is another term for a clash - an impossible fitting which means different atoms are said to be occupying the symmetry equivalent space in the crystal lattice. A good crystal contact is a sensible vdw interaction, a h bond etc which holds the lattices together.. eleanor
Re: [ccp4bb] International Symbol for sin(theta)/lambda
Hi James, Well, I think there's q (or s) which depending on where you're coming from can be 4*pi* sin(theta)/lambda, or 2*sin(theta)/lambda, or . * sin(theta)/lambda) or or * sin(theta)/lambda. Small-angle X-ray scattering (and other fields) uses those as symbols for the momentum transfer vector. I think for SAX I mainly saw s being used, and for imaging mainly q, but I could be mistaken. I myself am always confused by those measures as the prefactor varies from author to author, as does the unit for the wavelength (Angstrom or nm). Bye, Thomas Is there precedent or a conventional shorthand (e.g. greek letter) for sin(theta)/lambda?
Re: [ccp4bb] The Good and the Bad crystal contact?
On 30 Jun 2011, at 01:42, Michael Thompson wrote: the introduction of a disulfide can create artificial crystal contacts, which also aid in crystallization Another example of this is described here: The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction. Meenan NA, Sharma A, Fleishman SJ, Macdonald CJ, Morel B, Boetzel R, Moore GR, Baker D, Kleanthous C. Proc Natl Acad Sci U S A. 2010 Jun 1;107(22):10080-5. Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
[ccp4bb] generate large symmetry model
Does anyone have a rigorous method (or script) for generating an extended lattice e.g 3x3x3 unit cells from any pdb file? Any help gratefully received, Dave David Hargreaves Associate Principal Scientist _ AstraZeneca DECS, CPSS Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693 David.Hargreaves @astrazeneca.com mailto:name.surn...@astrazeneca.com Please consider the environment before printing this e-mail -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
Re: [ccp4bb] generate large symmetry model
Hi Dave, as first step you apply all symmetry operators of the space group to the pdb-file in order to fill the unit cell, and store all copies in the same PDB-file. You can do this with pdbset and the symgen keyword, see http://www.ccp4.ac.uk/dist/html/pdbset.html#symgen Check with coot that all copies are indeed in the asymmetric unit. Once you have filled the unit cell, read in the PDB-file with moleman2 and run xyz frac write mypdb.frac in order to get the fractional coordinates. Now you run a loop over x,y,z to add -1, 0, 1 in order to get the cube of unit cells and re-convert to orthogonal coordinates with moleman2. It's actually quicker than it sounds. Cheers, Tim On Thu, Jun 30, 2011 at 01:52:17PM +0100, Hargreaves, David wrote: Does anyone have a rigorous method (or script) for generating an extended lattice e.g 3x3x3 unit cells from any pdb file? Any help gratefully received, Dave David Hargreaves Associate Principal Scientist _ AstraZeneca DECS, CPSS Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693 David.Hargreaves @astrazeneca.com mailto:name.surn...@astrazeneca.com Please consider the environment before printing this e-mail -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A pgpWMgT9ZBW3Y.pgp Description: PGP signature
Re: [ccp4bb] generate large symmetry model
Well - you have a problem of chain IDS, but pdbset xyzin asymm.pdb xyzout whole-cell.pdb symgen P212121 (say) end will generate a whole unit cell, then pdbset xyzin whole-cell.pdb xyzout whole-cell-+100 symgen x+1,y,z end etc will move that unitcell.pdb You would have to put them all together. or coot can generate symmetry within a large sphere and I suppose write it all out.. Eleanor n 06/30/2011 01:52 PM, Hargreaves, David wrote: Does anyone have a rigorous method (or script) for generating an extended lattice e.g 3x3x3 unit cells from any pdb file? Any help gratefully received, Dave David Hargreaves Associate Principal Scientist _ AstraZeneca DECS, CPSS Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693 David.Hargreaves @astrazeneca.commailto:name.surn...@astrazeneca.com Please consider the environment before printing this e-mail -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
Re: [ccp4bb] generate large symmetry model
As well as pdbset, you can use pdbcur. A combination of keywords genunit, symop and symcommit. I’d probably use genunit (applicable to whatever spacegroup you have), followed by a second call using symop/symcommit to apply unit cell translations. Cheers Martyn From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hargreaves, David Sent: 30 June 2011 13:52 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] generate large symmetry model Does anyone have a rigorous method (or script) for generating an extended lattice e.g 3x3x3 unit cells from any pdb file? Any help gratefully received, Dave David Hargreaves Associate Principal Scientist _ AstraZeneca DECS, CPSS Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693 David.Hargreaves @astrazeneca.commailto:name.surn...@astrazeneca.com Please consider the environment before printing this e-mail AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking compliance with our Code of Conduct and policies.
Re: [ccp4bb] generate large symmetry model
Apologies for suggesting a non-CCP4 solution, but UCSF Chimera can do that and more (interactively!): Tools - Higher Order Structure - Unit cell Petr On Jun 30, 2011, at 2:52 PM, Hargreaves, David wrote: Does anyone have a rigorous method (or script) for generating an extended lattice e.g 3x3x3 unit cells from any pdb file? Any help gratefully received, Dave David Hargreaves Associate Principal Scientist _ AstraZeneca DECS, CPSS Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693 David.Hargreaves @astrazeneca.com Please consider the environment before printing this e-mail AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking compliance with our Code of Conduct and policies.
Re: [ccp4bb] generate large symmetry model
Its obviously not going to be possible to give a unique chain letter for every chain in 27 cells, but forget renaminmg the chains and its very easy to generate the models to look at- might even do it in a triple-nested foreach loop in csh. After generating the whole cell as suggested by David or Eleanor, #untested script! foreach A (-1 +0 +1) foreach B (-1 +0 +1) foreach C (-1 +0 +1) pdbset xyzin wholecell.pdb xyzout sym$A$B$C.pdb eof symgen X$A,Y$B,Z$C eof end end end awk '$1~/CRYST1|SCALE/ wholecell.pdb new.pdb foreach sym??.pdb awk '$1~/ATOM|HETATM/' $file new.pdb end echo END new.pdb and open new.pdb in some viewer that doesn't object to duplicate chain names Tim Gruene wrote: Hi Dave, as first step you apply all symmetry operators of the space group to the pdb-file in order to fill the unit cell, and store all copies in the same PDB-file. You can do this with pdbset and the symgen keyword, see http://www.ccp4.ac.uk/dist/html/pdbset.html#symgen Check with coot that all copies are indeed in the asymmetric unit. Once you have filled the unit cell, read in the PDB-file with moleman2 and run xyz frac write mypdb.frac in order to get the fractional coordinates. Now you run a loop over x,y,z to add -1, 0, 1 in order to get the cube of unit cells and re-convert to orthogonal coordinates with moleman2. It's actually quicker than it sounds. Cheers, Tim On Thu, Jun 30, 2011 at 01:52:17PM +0100, Hargreaves, David wrote: Does anyone have a rigorous method (or script) for generating an extended lattice e.g 3x3x3 unit cells from any pdb file? Any help gratefully received, Dave David Hargreaves Associate Principal Scientist _ AstraZeneca DECS, CPSS Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693 David.Hargreaves @astrazeneca.commailto:name.surn...@astrazeneca.com Please consider the environment before printing this e-mail -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
Re: [ccp4bb] generate large symmetry model
PDBCur (CCP4) should be able to generate the unit cell at once, which then should be translated to 3x3x3 cube. All may be done within a single run of PDBCur, a simple keyword input is required. Same job is doable with PDBSet. Eugene On 30 Jun 2011, at 15:36, Petr Leiman wrote: Apologies for suggesting a non-CCP4 solution, but UCSF Chimera can do that and more (interactively!): Tools - Higher Order Structure - Unit cell Petr On Jun 30, 2011, at 2:52 PM, Hargreaves, David wrote: Does anyone have a rigorous method (or script) for generating an extended lattice e.g 3x3x3 unit cells from any pdb file? Any help gratefully received, Dave David Hargreaves Associate Principal Scientist _ AstraZeneca DECS, CPSS Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693 David.Hargreaves @astrazeneca.com Please consider the environment before printing this e-mail AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking compliance with our Code of Conduct and policies.
Re: [ccp4bb] generate large symmetry model
You can do this with PyMOL with the supercell script: http://pymolwiki.org/index.php/Supercell Cheers, Thomas On 06/30/2011 02:52 PM, Hargreaves, David wrote: Does anyone have a rigorous method (or script) for generating an extended lattice e.g 3x3x3 unit cells from any pdb file? Any help gratefully received, Dave *David Hargreaves* Associate Principal Scientist -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] International Symbol for sin(theta)/lambda
This has been a point of confusion Here are the conventions used in a few of the classic SAXS text vs. recent reviews: -- I believe Guinier actually used the variable u in his thesis, but must have changed at some point (I don't have it handy to check at the moment). Guinier Fournet (1955) h = 4pi Sin(theta)/lambda where 2*theta = scattering angle Glatter Kratky (1982) (including chapters by Porod and other authors) h = 4pi Sin(theta)/lambda --- so h makes sense if one is familiar with crystallography derivations. Feigin Svergun (1987) s = 4pi Sin(theta)/lambda The notation s seems to come from the notation for scattering vectors. Svergun publications consistently use s this way, though the software can define s with or without the 2pi and in either inverse nanometers or inverse Angstroms. In my experience very few use 2Sin(theta)/lambda, though it is more familiar to crystallographers as the inverse of the d-spacing. But q is widely used in BioSAXS: Putnam, Hammel, Hura Tainer (2007) q = 4 pi Sin(theta)/lambda Jacques and Trewhella (2010)q = 4 pi Sin(theta)/lambda Why q? I haven't traced it back yet. From generalized coordinate of classical mechanics maybe? On Jun 30, 2011, at 3:37 AM, James Stroud wrote: Hello All, Is there precedent or a conventional shorthand (e.g. greek letter) for sin(theta)/lambda? Thanks in advance for any help or suggestions. James
Re: [ccp4bb] International Symbol for sin(theta)/lambda
The most extreme degree of confusion (or at least of requirement for fast mental arithmetic) I have come across in relation to this topic is the habit of small-molecule crystallographers working on accurate density studies to characterise the resolution limit of their datasets by quoting the maximum value of sin(theta)/lambda in Angstrom^-1. Upon being told of a dataset with a resolution of 1.25 in sin(theta)/lambda you have to quickly deduce that the maximum d* value is 2.50 and therefore, in protein crystallographer lingo, the resolution limit dmin is 0.40 Angstrom. Then, you start feeling very envious. With best wishes, Gerard. -- On Thu, Jun 30, 2011 at 02:07:28PM -0400, Richard Edward Gillilan wrote: This has been a point of confusion Here are the conventions used in a few of the classic SAXS text vs. recent reviews: -- I believe Guinier actually used the variable u in his thesis, but must have changed at some point (I don't have it handy to check at the moment). Guinier Fournet (1955) h = 4pi Sin(theta)/lambda where 2*theta = scattering angle Glatter Kratky (1982) (including chapters by Porod and other authors) h = 4pi Sin(theta)/lambda --- so h makes sense if one is familiar with crystallography derivations. Feigin Svergun (1987) s = 4pi Sin(theta)/lambda The notation s seems to come from the notation for scattering vectors. Svergun publications consistently use s this way, though the software can define s with or without the 2pi and in either inverse nanometers or inverse Angstroms. In my experience very few use 2Sin(theta)/lambda, though it is more familiar to crystallographers as the inverse of the d-spacing. But q is widely used in BioSAXS: Putnam, Hammel, Hura Tainer (2007) q = 4 pi Sin(theta)/lambda Jacques and Trewhella (2010)q = 4 pi Sin(theta)/lambda Why q? I haven't traced it back yet. From generalized coordinate of classical mechanics maybe? On Jun 30, 2011, at 3:37 AM, James Stroud wrote: Hello All, Is there precedent or a conventional shorthand (e.g. greek letter) for sin(theta)/lambda? Thanks in advance for any help or suggestions. James -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
[ccp4bb] nmr question
Dear members, I know that it is not possible to solve a structure by nmr of more than approx. 30 kda. But I have to admit that I dont know why. What exactly is overlapping? With best regards, Lena
Re: [ccp4bb] nmr question
There are about 20 structures solved by NMR with chain lengths above 300 residues. Some of them are solved by combination of restraints and modeling (e.g. 2010 Nature paper describing implementation of Rosetta modeling coupled with backbone-only data, by Raman/Montelione/Baker et al.). Principal problems from the perspective of a non-specialist are: a) separation between resonances - complete (multidimensional!) overlaps are ruinous for assignment b) intensity of each resonance - for larger molecules there is less moles of resonating nuclei c) relaxation issues in large proteins (the need for expensive and hard to do deuterium labeling is the result of this) I am sure that true NMR experts would have much more to say on the subject :) Artem On Thu, Jun 30, 2011 at 5:20 PM, Lena Griese lena.gri...@googlemail.comwrote: Dear members, I know that it is not possible to solve a structure by nmr of more than approx. 30 kda. But I have to admit that I dont know why. What exactly is overlapping? With best regards, Lena
