Re: [ccp4bb] generate large symmetry model
Thank you to all for the help. There’s obviously more than one way to skin a cat! In the end pdbcur did the job for me. Great! 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 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of martyn.w...@stfc.ac.uk Sent: 30 June 2011 15:08 To: CCP4BB@JISCMAIL.AC.UK Subject: 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.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. -- 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.
[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
