[ccp4bb] How to use SHELXE to perform phasing and density modification
Dear all, I have an original sca file with anomalous signal and a heavy atoms sites file in PDB format. PDB FILE : CRYST1 77.780 77.780 187.640 90.00 90.00 120.00 P 61 2 2 SCALE1 0.012857 0.007423 -0.00 -0.0 SCALE2 -0.00 0.014846 -0.000.0 SCALE3 0.00 -0.00 0.005329 -0.0 ATOM 1 S HAT 1 -62.495 123.694 12.804 0.36 20.00 S ATOM 9 S HAT 9 -49.984 90.531 2.130 0.32 20.00 S ATOM 10 S HAT10 -59.282 106.437 9.760 0.74 20.00 S ATOM 84 S HAT84 -60.153 114.024 15.399 0.52 20.00 S ... ... Can I use SHELXE to perform phasing and density modification? How to do it? Thank you for your help! Wei
Re: [ccp4bb] How to use SHELXE to perform phasing and density modification
Dear Wei, There is a new SHELX homepage with extensive documentation and downloading instructions at: http://shelx.uni-ac.gwdg.de/SHELX/ SHELXE requires reflection files name.hkl (native) and name_fa.hkl (data for phasing) and and the heavy atoms in SHELX format in name_fa.res. I recommend running SHELXC to prepare the files and SHELXD to find the heavy atoms, then everything will be in the right format. You can either run the programs from the command line or use a GUI such as hkl2map. If (as it seems) your heavy atoms come from an isomorphous structure, then you can run SHELXC to read XDS_ASCII.HKL or .sca files to make the .hkl, files followed by AnoDe (also part of SHELX) to read name_fa.hkl and name.ent (your original full PDB file, no just the heavy atoms) to make name_fa.res containing the heavy atom sites from the anomalous map. Then you have the files you need to run SHELXE, e.g. shelxe name name_fa -a5 -s0.5 -q but see the documentation for more information about the command line switches, e.g. -n for NCS. The advantage of this is that your final structure will be relative to the same origin as your original PDB file. Best wishes, George On 03/15/2013 10:13 AM, Wei Feng wrote: Dear all, I have an original sca file with anomalous signal and a heavy atoms sites file in PDB format. PDB FILE : CRYST1 77.780 77.780 187.640 90.00 90.00 120.00 P 61 2 2 SCALE1 0.012857 0.007423 -0.00 -0.0 SCALE2 -0.00 0.014846 -0.00 0.0 SCALE3 0.00 -0.00 0.005329 -0.0 ATOM 1 S HAT 1 -62.495 123.694 12.804 0.36 20.00 S ATOM 9 S HAT 9 -49.984 90.531 2.130 0.32 20.00 S ATOM 10 S HAT 10 -59.282 106.437 9.760 0.74 20.00 S ATOM 84 S HAT 84 -60.153 114.024 15.399 0.52 20.00 S ... ... Can I use SHELXE to perform phasing and density modification? How to do it? Thank you for your help! Wei -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] How to use SHELXE to perform phasing and density modification
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Wei, if you are not too familiar with shelx c/d/e, I suggest the following procedure, provided shelx c/d/e are installed: - - get hkl2map from http://webapps.embl-hamburg.de/hkl2map/ - - run hkl2map from a terminal and from the directory where your .sca file is - - provide a project name (I call it 'foo' for now) and run the first two steps, i.e. shelxc and shelxd - - close hkl2map now inside the directory there will be several files, the important ones being foo.hkl, foo_fa.hkl, and foo_fa.res - - use the program coordconv from CCP4 in order to get the fractional coordinates of your substructure and copy the coordinates into the foo_fa.res - - type 'shelxe foo foo_fa -a -h -q' and 'shelxe foo foo_fa -a -h -q - -i' and check if one of the resulting PDB files foo.pdb and foo_i.pdb (together with the corresponding map files foo.phs and foo_i.phs) make sense. Cheers, Tim On 03/15/2013 10:13 AM, Wei Feng wrote: Dear all, I have an original sca file with anomalous signal and a heavy atoms sites file in PDB format. PDB FILE : CRYST1 77.780 77.780 187.640 90.00 90.00 120.00 P 61 2 2 SCALE1 0.012857 0.007423 -0.00 -0.0 SCALE2 -0.00 0.014846 -0.000.0 SCALE3 0.00 -0.00 0.005329 -0.0 ATOM 1 S HAT 1 -62.495 123.694 12.804 0.36 20.00 S ATOM 9 S HAT 9 -49.984 90.531 2.130 0.32 20.00 S ATOM 10 S HAT10 -59.282 106.437 9.760 0.74 20.00 S ATOM 84 S HAT84 -60.153 114.024 15.399 0.52 20.00 S ... ... Can I use SHELXE to perform phasing and density modification? How to do it? Thank you for your help! Wei - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRQvEhUxlJ7aRr7hoRApLYAJ99A/i6FFsWJqlAOOx4zdwhKOTzHACgopdu OBNV+xUMee8l8fo2jwnac+U= =vAB5 -END PGP SIGNATURE-
Re: [ccp4bb] How to use SHELXE to perform phasing and density modification (correction)
Sorry, a better command line for running SHELXE in this case would have been: shelxe name name_fa -a5 -s0.5 -q -h -z this ensures that the heavy atoms are refined before calculating the initial phases, this often gives much better maps. If you are not sure whether the space group is P6122 or P6522, then you should run shelxe twice, once with and once without -i (which would invert the space group and atom coordinates). It is usually worth trying different solvent contents (-s). George On 03/15/2013 11:09 AM, George Sheldrick wrote: Dear Wei, There is a new SHELX homepage with extensive documentation and downloading instructions at: http://shelx.uni-ac.gwdg.de/SHELX/ SHELXE requires reflection files name.hkl (native) and name_fa.hkl (data for phasing) and and the heavy atoms in SHELX format in name_fa.res. I recommend running SHELXC to prepare the files and SHELXD to find the heavy atoms, then everything will be in the right format. You can either run the programs from the command line or use a GUI such as hkl2map. If (as it seems) your heavy atoms come from an isomorphous structure, then you can run SHELXC to read XDS_ASCII.HKL or .sca files to make the .hkl, files followed by AnoDe (also part of SHELX) to read name_fa.hkl and name.ent (your original full PDB file, no just the heavy atoms) to make name_fa.res containing the heavy atom sites from the anomalous map. Then you have the files you need to run SHELXE, e.g. shelxe name name_fa -a5 -s0.5 -q but see the documentation for more information about the command line switches, e.g. -n for NCS. The advantage of this is that your final structure will be relative to the same origin as your original PDB file. Best wishes, George On 03/15/2013 10:13 AM, Wei Feng wrote: Dear all, I have an original sca file with anomalous signal and a heavy atoms sites file in PDB format. PDB FILE : CRYST1 77.780 77.780 187.640 90.00 90.00 120.00 P 61 2 2 SCALE1 0.012857 0.007423 -0.00 -0.0 SCALE2 -0.00 0.014846 -0.00 0.0 SCALE3 0.00 -0.00 0.005329 -0.0 ATOM 1 S HAT 1 -62.495 123.694 12.804 0.36 20.00 S ATOM 9 S HAT 9 -49.984 90.531 2.130 0.32 20.00 S ATOM 10 S HAT 10 -59.282 106.437 9.760 0.74 20.00 S ATOM 84 S HAT 84 -60.153 114.024 15.399 0.52 20.00 S ... ... Can I use SHELXE to perform phasing and density modification? How to do it? Thank you for your help! Wei -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] How to use SHELXE to perform phasing and density modification
Dear George, Thank you very much for your help! Wei At 2013-03-15 18:09:09,George Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Dear Wei, There is a new SHELX homepage with extensive documentation and downloading instructions at: http://shelx.uni-ac.gwdg.de/SHELX/ SHELXE requires reflection files name.hkl (native) and name_fa.hkl (data for phasing) and and the heavy atoms in SHELX format in name_fa.res. I recommend running SHELXC to prepare the files and SHELXD to find the heavy atoms, then everything will be in the right format. You can either run the programs from the command line or use a GUI such as hkl2map. If (as it seems) your heavy atoms come from an isomorphous structure, then you can run SHELXC to read XDS_ASCII.HKL or .sca files to make the .hkl, files followed by AnoDe (also part of SHELX) to read name_fa.hkl and name.ent (your original full PDB file, no just the heavy atoms) to make name_fa.res containing the heavy atom sites from the anomalous map. Then you have the files you need to run SHELXE, e.g. shelxe name name_fa -a5 -s0.5 -q but see the documentation for more information about the command line switches, e.g. -n for NCS. The advantage of this is that your final structure will be relative to the same origin as your original PDB file. Best wishes, George On 03/15/2013 10:13 AM, Wei Feng wrote: Dear all, I have an original sca file with anomalous signal and a heavy atoms sites file in PDB format. PDB FILE : CRYST1 77.780 77.780 187.640 90.00 90.00 120.00 P 61 2 2 SCALE1 0.012857 0.007423 -0.00 -0.0 SCALE2 -0.00 0.014846 -0.000.0 SCALE3 0.00 -0.00 0.005329 -0.0 ATOM 1 S HAT 1 -62.495 123.694 12.804 0.36 20.00 S ATOM 9 S HAT 9 -49.984 90.531 2.130 0.32 20.00 S ATOM 10 S HAT10 -59.282 106.437 9.760 0.74 20.00 S ATOM 84 S HAT84 -60.153 114.024 15.399 0.52 20.00 S ... ... Can I use SHELXE to perform phasing and density modification? How to do it? Thank you for your help! Wei -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
