Hi Andrew, It depends on the version of DOCK you are using - make sure you specify the correct version when opening the file of docked ligands. We have version-specific code that should show the scores for output from versions 3, 3.5, 3.5.x, 4, 5, 6. For example, output from versions 4,5,6 include comments before each ligand residue in a specific format interpreted by the ViewDock tool as ligand descriptors. If PDB format, the comments look something like REMARK Number : 1 REMARK Source num : 1 REMARK Name : MFCD00047559 REMARK Description : CBZ-L-GLU_ANHYDRIDE REMARK Energy score : -16.72 REMARK van der Waals component -16.72 REMARK electrostatic component 0.00 REMARK RMSD from input orientation (A) : 1.26 If Mol2 format, the comments look something like ########## Number : 1 ########## Source num : 22 ########## Name : test_22 ########## Description : ribose-monophosphate ########## Reflect : 0 ########## Energy score : -42.64 ########## intermolecular van der Waals -21.10 ########## intermolecular electrostatic -21.54 ########## RMSD from input orientation (A) : 40.86 In these examples, options under "Column...Show" would be Number, Source num, Name, Description, etc. After making sure you have chosen the correct format when opening the file of docked ligands, (1) look in that file with a text editor to make sure it includes the descriptors/values you are expecting to see in the ViewDock interface (2) if it does contain those descriptors/values, you could send us an example file (e-mail to me would only be shared with a few others on the Chimera team) Another option (especially if you are using some modified version of DOCK) is to reformat the output ligand file so that the descriptors appear in the form above and open it with ViewDock as "dock 4,5,6" output. The basic format is REMARK (if PDB) or ########## (if Mol2) followed by descriptor name, :, descriptor value preceding each docked ligand molecule. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 31, 2007, at 12:01 AM, Воронков андрей wrote:
Dear Chimera users, I have ranked database from DOCK. I need to see energies of these structures and their ranking. I open them by View Dock, but in the field Column menu I can see only name field. Why I don't have energy field there and how can I get it? Respectively yours, Andrew
PS "Descriptors can be shown in or removed from the upper panel using the Column menu." -this is from manual, but I can;t make shown any descriptos but the name of the structure _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users