Re: [PyMOL] [EXTERNAL] Re: Centre of mass pymol script
Sorry Blaine, I misspelled your name!
Cheers,
J.
сб, 7 нояб. 2020 г. в 16:18, Jeff Saxon :
>
> 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)
> :
> >
> > 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=DwIGaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=NjIje-z1Dq70jac-RIey36yonAOn8GSzwN-J8OEd9pQ=FZzhGIvdiSGI8pO9ZgK0Q0zMauIkq-qCa3HZwNxp_z8=
> > -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 :
> > >
> > > 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=DwIGaQ=VjzId-SM5S6aVB_cCG
Re: [PyMOL] [EXTERNAL] Re: Centre of mass pymol script
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)
:
>
> 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=DwIGaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=NjIje-z1Dq70jac-RIey36yonAOn8GSzwN-J8OEd9pQ=FZzhGIvdiSGI8pO9ZgK0Q0zMauIkq-qCa3HZwNxp_z8=
> -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 :
> >
> > 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=DwIGaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=NjIje-z1Dq70jac-RIey36yonAOn8GSzwN-J8OEd9pQ=rHFOXfWCHk9XymS9CsAsCKjrHxeVNqjVZBQGphA-r0Y=
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Re: [PyMOL] [EXTERNAL] Re: Centre of mass pymol script
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=DwIGaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=NjIje-z1Dq70jac-RIey36yonAOn8GSzwN-J8OEd9pQ=FZzhGIvdiSGI8pO9ZgK0Q0zMauIkq-qCa3HZwNxp_z8=
-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 :
>
> 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.
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