Re: [ccp4bb] on openning the PDB file and the mtz file by Coot
On 03/19/2015 07:20 AM, Smith Liu wrote: Suppose I have a PDB file and a mtz file (PDB file from protein A, mtz file from protein B, which is a homology protein of protein A) which are not from the same refinment (thus not fit automatically in Coot), will you please tell me what modification I should make on the files in order to have the Coot to fit the protein bakbone (and the sidechains) and the electron density? Hi Smith ... Open your protein-A-ref1.pdb file (File/Open Coordinates...) and protein-A-ref1.mtz file (File/Auto Open MTZ ...), then open your homologous protein-B.pdb and superpose it with Calculcate/SSM Superpose ... or if you are not happy with the result you can try to improve the superposition with Calculate/LSQ Superpose ... Best regards Carlos I am looking forward to getting your reply. Smith -- Carlos CONTRERAS MARTEL, Ph.D. (CR1 CNRS) carlos.contreras-mar...@ibs.fr Bacterial Pathogenesis Group Institut de Biologie Structurale UMR5075 CEA-CNRS-Université Joseph Fourier Grenoble 1 IBS 71, avenue des Martyrs CS 10090 38044 Grenoble CEDEX 9 FRANCE tel : (+33) (0)4 57 42 86 41 http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en
[ccp4bb] on openning the PDB file and the mtz file by Coot
Dear All, When we by Coot open the PDB fle and the mtz file from the same refinement, the protein backbone (and the sidechains) and the electron density always fit automatically. Will you please tell me the mechanism of the Coot how the PDB file automatically fit the mtz file in its graphical window? Suppose I have a PDB file and a mtz file (PDB file from protein A, mtz file from protein B, which is a homology protein of protein A) which are not from the same refinment (thus not fit automatically in Coot), will you please tell me what modification I should make on the files in order to have the Coot to fit the protein bakbone (and the sidechains) and the electron density? I am looking forward to getting your reply. Smith
Re: [ccp4bb] on openning the PDB file and the mtz file by Coot
Hi Smith, Both PDB and MTZ have records on their headers to specify the cell dimensions and space group. And for an MTZ, once the cell dimension and space group are fixed, its coordinate origins can also be fixed. For a PDB, its CRYST1 record specifies its unit cell dimensions and space group. The position of each atom (X,Y, Z) with respect to the coordinate origins is specified by the ATOM records. To place your pdb in the right position in the map, you need to edit the CRYST1 record (one line) and the ATOM records (many many lines). It's very easy to edit the CRYST1 record with a text editor, but very difficult (almost impossible) to edit the ATOM records manually. You can follow Carlos's advice to edit ATOM with Coot. All the best, Steven On Thu, Mar 19, 2015 at 2:20 AM, Smith Liu smith_liu...@163.com wrote: Dear All, When we by Coot open the PDB fle and the mtz file from the same refinement, the protein backbone (and the sidechains) and the electron density always fit automatically. Will you please tell me the mechanism of the Coot how the PDB file automatically fit the mtz file in its graphical window? Suppose I have a PDB file and a mtz file (PDB file from protein A, mtz file from protein B, which is a homology protein of protein A) which are not from the same refinment (thus not fit automatically in Coot), will you please tell me what modification I should make on the files in order to have the Coot to fit the protein bakbone (and the sidechains) and the electron density? I am looking forward to getting your reply. Smith -- Steven Chou
