Sorry Blaine, I misspelled your name! Cheers, J. сб, 7 нояб. 2020 г. в 16:18, Jeff Saxon <jmsstarli...@gmail.com>: > > Hi Blame, > I was talking about this pymol script (it can be downloaded directly > from the page below) > https://pymolwiki.org/index.php/Center_of_mass > > I used all of the post-processing steps in bash scripts using AWK. Now > I would like to understand how it may work inside this python script. > Here is my shell solution :-) > > #!/bin/bash > pymol='/Applications/PyMOL.app/Contents/MacOS/MacPyMOL' > home=$PWD > # this is multi-model pdb with the ligand > pdb=${home}/lig_1AllBoxes_7000_cne_998.pdb > # remove previous outputs > rm "${home}"/*.txt > # > #it has begun! > #calculate com using pymol, grep the important lines with the results > $pymol $pdb center_of_mass.py -d 'select all;com all' -c > > ${home}/log.txt; grep '^State' ${home}/log.txt > ${home}/out.txt > > # convert output to python like list format > awk -F'[ :]' 'BEGIN{ > printf "[" > } > NR>0{ > printf "[%.3f,%.3f,%.3f],",$3,$4,$5 > } > END{ > printf "]\n" > }' ${home}/out.txt | sed 's/,\]$/]/' > ${home}/COM_array.txt > > echo "Well done!" > > сб, 7 нояб. 2020 г. в 16:08, Mooers, Blaine H.M. (HSC) > <blaine-moo...@ouhsc.edu>: > > > > 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=
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