Hi Jeff, You can use Python commands to reformat the output. The Python commands can be included in your Python script or with the pml code that you pass with the -d keyword in the terminal if the Python code is separated by semicolons from the pml code.
My email security system mangled the link to your Python script. You can paste the Python code into the body of the email to avoid such issues. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: Jeff Saxon [jmsstarli...@gmail.com] Sent: Saturday, November 07, 2020 7:34 AM To: pymol-users Subject: [EXTERNAL] Re: [PyMOL] Centre of mass pymol script P.S. sorry I ought to further precise my question: From what I have not I can execute pymol in batch mode together with the py script and pdb pymol my.pdb https://urldefense.proofpoint.com/v2/url?u=http-3A__center-5Fof-5Fmass.py&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=NjIje-z1Dq70jac-RIey36yonAOn8GSzwN-J8OEd9pQ&s=FZzhGIvdiSGI8pO9ZgK0Q0zMauIkq-qCa3HZwNxp_z8&e= -d 'select all;com all' -c >> log.txt which gives me log.txt contained COM for each model in the following format: State 1:118.851979 120.668604 84.472229 State 2:126.789728 149.506520 103.196917 State 3:126.379687 149.382354 104.504792 State 4:126.989312 149.372811 103.499396 ..... State 20:125.555854 133.653730 88.441501 Obviously I can pipe this output to another program to convert it into the list format, but is it possible rather to modify the python script, automatically loading all pdbs located from the current directory and save the output automatically in the list format indicated in my first message? сб, 7 нояб. 2020 г. в 14:16, Jeff Saxon <jmsstarli...@gmail.com>: > > Dear Pymol Users, > I am using the Centre of mass python script found in PymolWIKI with > the aim to calculate the centre of mass of the loaded ligand > structure. Could you tell me if it would be possible to apply this > script on the multi_model pdb loaded in pymol in the similar way and > to obtain XYZ coordinates of COM for each conformation? Is it possible > to do it in some scripting manner using no-gui pymol and save output > in the list format like {[name the conformation_1],[x,y,z].... name of > the conformation_N,[x,y,z]}? > Thank you in advance > Cheers, > J. _______________________________________________ PyMOL-users mailing list Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=NjIje-z1Dq70jac-RIey36yonAOn8GSzwN-J8OEd9pQ&s=rHFOXfWCHk9XymS9CsAsCKjrHxeVNqjVZBQGphA-r0Y&e= Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=NjIje-z1Dq70jac-RIey36yonAOn8GSzwN-J8OEd9pQ&s=pdU1DssN4zD2FhI_7dcRfdaksVEZvqe6WNN0-5_ygy0&e= _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
