Re: [PyMOL] Question about visualisation of the spheres objects on PNG image
Thank you very much, Ali!
Yes, actually, I suppose I have set up vdw radii using those commands,
considering specific selections,e.g this is part of my pymol script
that I am using in bash.
$pymol -c -d "
from pymol import cmd
cmd.load('${storage}/${syst_name}/all_clusters.pdb')
cmd.split_states('all_clusters*')
cmd.select('all_clusters*')
cmd.show('spheres', 'sele')
cmd.set('sphere_transparency', '0.2', 'sele')
cmd.color('marine', 'sele' )
cmd.alter('all_clusters*', 'vdw=0.75')
cmd.select('all_clusters*')
cmd.show( 'spheres', 'sele' )
cmd.rebuild()
cmd.bg_color('white')
cmd.save('${syst}/${syst_name}.pse')
cmd.png('${vizu}/${syst_name}.png',width=${image},height=${image},dpi=50,ray=0)
"
Eventually in my saved pml session everything looks fine BUT on the
png image some of the spheres (notably located on the back plane in
the space) are appeared to be smaller compared to the others (although
in pymol all of them were identified using the same selection). So
probably this is an issue of PNG command, which I used to make a
screenshot.
Also one question: as it can be seed from my script I used command
split states for all_clusters object (which contain 100 conformations
of the centre of mass) and then operate with the visualization of
splited states. I noticed that the multi-model object is still exist
along with its separate models, which command could be used to disable
its visualization in GUI (like if I click on it in the context menu,
while operating in gui)?
Cheers,
J.
пт, 26 февр. 2021 г. в 12:29, Ali Saad Kusay :
>
> Hi Jeff,
>
> The sphere size is controlled by the vdw property, to change it:
> alter *, vdw=1.0 # this will set the sphere size to be equal for all atom
> i.e. hydrogens atom would be same size as carbon
>
> you also need to use the "rebuild" command to implement the changes
>
> At this point, you can control the sphere sizes consistently using:
> set sphere_scale, 1.5 # or what ever size you need
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
>
> On 26/2/21, 2:15 am, "Jeff Saxon" wrote:
>
> Dear Pymol Users,
>
> Working on the visualisation of protein-ligand interactions, notably
> focusing on the visualisation of sphres atoms covered protein surface,
> I noticed on the resulted PNG that some sphere objects (located on the
> backing plane) looks VERY small compared to the rest. For example as
> it could be seen while major spheres represent like spheres, some of
> them look like dots, while in the pml session everything looks
> correctly. How could I fix using some pymol settings ?
> Thank you in advance!
> J
>
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Re: [PyMOL] FW: Names of objects in GUI in pymol
It works, thank you Ali!!
Cheers,
J.
вт, 23 февр. 2021 г. в 07:26, Ali Saad Kusay :
>
> Resending since I forgot to copy the PyMOL mailing list
>
> On 23/2/21, 7:17 am, "Ali Saad Kusay" wrote:
>
> Hi Jeff,
>
> There is several ways you can do this with string function in python
> https://www.w3schools.com/python/python_ref_string.asp.
> This is an easy one liner which replace "COG_" of "AA" with nothing if
> found
> label sele, model.replace('COG_','').replace('AA_','')
>
> Another way to do this is lets say you select an object beginning with
> COG_, you can slice away the first 4 characters to get rid of COG_
> label sele, model[4:]
>
> Cheers,
>
> Ali
>
> On 23/2/21, 1:32 am, "Jeff Saxon" wrote:
>
> pardon, just one additional question, which might be alitle bit custom
> issue, however..
>
> Imagine, that I have 2 groups of the pdbs objects loaded into same
> pymol session: 2 pdbs with the prefix COG_*.pdb, and 2 pdbs with the
> prefix AA_*.pdb. Would it be possible to subtract the both prefixes
> from the labels produced using cmd.label('sele', 'model') ? Or
> alternatively I ought to rename the both objects before their
> labelling? What are the other possible solutions ?
>
> пн, 22 февр. 2021 г. в 15:07, Jeff Saxon :
> >
> > Right, this is what I was looking for!
> > Thank you so much, Ali!
> > Cheers,
> > J.
> >
> > пн, 22 февр. 2021 г. в 14:59, Ali Saad Kusay
> :
> > >
> > > No worries Jeff,
> > >
> > > Use editing mode and you can move it with mouse. See around 3:30
> in this video,
> https://protect-au.mimecast.com/s/_r_iCANpgjCwqAQMtGDPTv?domain=m.youtube.com.
> > >
> > > You can move all labels with this command:
> > >
> > > set label_position (x,y,z)
> > >
> > > This will move the labels as needed in the x, y and z directions
> > >
> > > Cheers,
> > >
> > > Ali
> > >
> > >
> > > On 23 Feb 2021, at 12:51 am, Jeff Saxon
> wrote:
> > >
> > > Thank you, Ali!
> > > One question - is there any command which would allow to change
> > > position of the text of the label produced by the label sele,
> model ?
> > > In fact as I noticed, it produces correctly label text just above
> the
> > > object, while I need to move it a litle bit in one of the
> directions
> > > ...
> > > Cheers,
> > >
> > > пн, 22 февр. 2021 г. в 14:14, Ali Saad Kusay
> :
> > >
> > >
> > > Hi Jeff,
> > >
> > >
> > > The name of an object is stored in the model attribute.
> > >
> > > Select an atom in the object and use this command:
> > >
> > > label sele, model
> > >
> > >
> > > If you want to automate this over all your PyMOL objects, you can
> use this script, this will put a label at the centre of each object but it
> has to create a pseudoatom for each one. You can change coords.mean to
> coords.min or cords.max if you want the label to go at the corner of each
> object
> > >
> > > for i in cmd.get_object_list():
> > >
> > >coords = cmd.get_coords(i)
> > >
> > >mean_coords = coords.mean(axis=0).tolist()
> > >
> > >cmd.pseudoatom(i+"_psu", pos=mean_coords)
> > >
> > >
> > >cmd.label(i+"_psu", "'{}'".format(i))
> > >
> > >
> > > Cheers,
> > >
> > >
> > > Ali
> > >
> > >
> > > Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> > >
> > > The University of Sydney School of Pharmacy | Faculty of Medicine
> and Health
> > >
> &g
Re: [PyMOL] Names of objects in GUI in pymol
pardon, just one additional question, which might be alitle bit custom
issue, however..
Imagine, that I have 2 groups of the pdbs objects loaded into same
pymol session: 2 pdbs with the prefix COG_*.pdb, and 2 pdbs with the
prefix AA_*.pdb. Would it be possible to subtract the both prefixes
from the labels produced using cmd.label('sele', 'model') ? Or
alternatively I ought to rename the both objects before their
labelling? What are the other possible solutions ?
пн, 22 февр. 2021 г. в 15:07, Jeff Saxon :
>
> Right, this is what I was looking for!
> Thank you so much, Ali!
> Cheers,
> J.
>
> пн, 22 февр. 2021 г. в 14:59, Ali Saad Kusay :
> >
> > No worries Jeff,
> >
> > Use editing mode and you can move it with mouse. See around 3:30 in this
> > video, https://m.youtube.com/watch?v=yBFzJ3ql4qU&ab_channel=MolecularMemory.
> >
> > You can move all labels with this command:
> >
> > set label_position (x,y,z)
> >
> > This will move the labels as needed in the x, y and z directions
> >
> > Cheers,
> >
> > Ali
> >
> >
> > On 23 Feb 2021, at 12:51 am, Jeff Saxon wrote:
> >
> > Thank you, Ali!
> > One question - is there any command which would allow to change
> > position of the text of the label produced by the label sele, model ?
> > In fact as I noticed, it produces correctly label text just above the
> > object, while I need to move it a litle bit in one of the directions
> > ...
> > Cheers,
> >
> > пн, 22 февр. 2021 г. в 14:14, Ali Saad Kusay :
> >
> >
> > Hi Jeff,
> >
> >
> > The name of an object is stored in the model attribute.
> >
> > Select an atom in the object and use this command:
> >
> > label sele, model
> >
> >
> > If you want to automate this over all your PyMOL objects, you can use this
> > script, this will put a label at the centre of each object but it has to
> > create a pseudoatom for each one. You can change coords.mean to coords.min
> > or cords.max if you want the label to go at the corner of each object
> >
> > for i in cmd.get_object_list():
> >
> >coords = cmd.get_coords(i)
> >
> >mean_coords = coords.mean(axis=0).tolist()
> >
> >cmd.pseudoatom(i+"_psu", pos=mean_coords)
> >
> >
> >cmd.label(i+"_psu", "'{}'".format(i))
> >
> >
> > Cheers,
> >
> >
> > Ali
> >
> >
> > Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> >
> > The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> >
> > 424, Brain and Mind Centre | The University of Sydney | NSW 2050
> >
> >
> > On 22/2/21, 10:47 pm, "Jeff Saxon" wrote:
> >
> >
> >Dear Pymol Users,
> >
> >
> >I am looking for a possibility to display names of the objects in the
> >
> >pymol session. For example I loaded 4 objects corresponded to 2
> >
> >different positions of the same ligand as well as 2 positions of its
> >
> >centres of masses. How would it be possible to display the names of
> >
> >each of these loaded objects just near their visualisations in GUI in
> >
> >order that I could understand who is who without operating with the
> >
> >objects on the context menu?
> >
> >
> >
> >___
> >
> >PyMOL-users mailing list
> >
> >Archives:
> > https://protect-au.mimecast.com/s/I4YSC2xMQziByPypTnzh0G?domain=mail-archive.com
> >
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> > https://protect-au.mimecast.com/s/hFDYC3QNPBiyN6NpCqFgvq?domain=sourceforge.net
> >
> >
> >
> >
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Re: [PyMOL] Names of objects in GUI in pymol
Thank you, Ali!
One question - is there any command which would allow to change
position of the text of the label produced by the label sele, model ?
In fact as I noticed, it produces correctly label text just above the
object, while I need to move it a litle bit in one of the directions
...
Cheers,
пн, 22 февр. 2021 г. в 14:14, Ali Saad Kusay :
>
> Hi Jeff,
>
> The name of an object is stored in the model attribute.
> Select an atom in the object and use this command:
> label sele, model
>
> If you want to automate this over all your PyMOL objects, you can use this
> script, this will put a label at the centre of each object but it has to
> create a pseudoatom for each one. You can change coords.mean to coords.min or
> cords.max if you want the label to go at the corner of each object
> for i in cmd.get_object_list():
> coords = cmd.get_coords(i)
> mean_coords = coords.mean(axis=0).tolist()
> cmd.pseudoatom(i+"_psu", pos=mean_coords)
>
> cmd.label(i+"_psu", "'{}'".format(i))
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
> On 22/2/21, 10:47 pm, "Jeff Saxon" wrote:
>
> Dear Pymol Users,
>
> I am looking for a possibility to display names of the objects in the
> pymol session. For example I loaded 4 objects corresponded to 2
> different positions of the same ligand as well as 2 positions of its
> centres of masses. How would it be possible to display the names of
> each of these loaded objects just near their visualisations in GUI in
> order that I could understand who is who without operating with the
> objects on the context menu?
>
>
> ___
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> https://protect-au.mimecast.com/s/YdVUCVARKgCWQ4kOsG8z8B?domain=mail-archive.com
> Unsubscribe:
> https://protect-au.mimecast.com/s/u68CCWLVXkUMopXluxT1mn?domain=sourceforge.net
>
>
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[PyMOL] Names of objects in GUI in pymol
Dear Pymol Users, I am looking for a possibility to display names of the objects in the pymol session. For example I loaded 4 objects corresponded to 2 different positions of the same ligand as well as 2 positions of its centres of masses. How would it be possible to display the names of each of these loaded objects just near their visualisations in GUI in order that I could understand who is who without operating with the objects on the context menu? ___ 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
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&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 :
> > >
> > > 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.proofpo
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&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 :
> >
> > 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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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 center_of_mass.py -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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[PyMOL] Centre of mass pymol script
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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[PyMOL] Autodock analisis in Pymol
Dear all, probably it is not a very pymol-oriented question, but otherwise I am looking for people who worked with autodock tools, or maybe who dealt with some pymol plugins suitable to handle DLG filles of AT runs? Particularly, I am looking for some methods for combining/reclusterization of autodock conformations (in DLG or PDB... ), with the possibility to sort the clusters according to the energies computed by AT as well as using custom selections (for example centre of mass of the ligand). I will be thankful for any suggestions! Cheers, J. ___ 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
Re: [PyMOL] [EXTERNAL] Generation of images using png
just left my Mac during the night to generate images:
new benchmark record:
PyMOL>
cmd.draw(800,800);cmd.png('/img/cne_998.png',width=800,height=800,dpi=50,ray=1)
Ray: render time: 18259.74 sec. = 0.2 frames/hour (18259.74 sec. accum.).
:-)
ср, 21 окт. 2020 г. в 15:31, Jeff Saxon :
>
> Here are some benchmarks
> 1)This is an example for rendering of the image based on a multi-model
> pdb of 240 frames (all states splitted into the same model)
> Ray: render time: 698.52 sec. = 5.2 frames/hour (698.52 sec. accum.).
> 2) This is the same for 20 model pdb
>
> Ray: render time: 19.26 sec. = 186.9 frames/hour (19.26 sec. accum.).
>
> My hardware is iMAC 3.4 ghz Core i7, 16Go 13000 DDR3
> I am using pymol 2.4.1 (full version)
>
> ср, 21 окт. 2020 г. в 14:59, Jeff Saxon :
> >
> > thank you, Blaine!
> > actually this problem only exists for the saving image of the system
> > consisted of many models loaded into save pymol session after its
> > splitting
> > I've already tried with dpi=50 (keeping the same resolution) but It
> > did not produce any differences :-)
> > Cheers,
> > J.
> >
> > ср, 21 окт. 2020 г. в 13:18, Mooers, Blaine H.M. (HSC)
> > :
> > >
> > > Hi Jeff,
> > >
> > > 10 minutes is a long time for a 800 by 800 pixel image.
> > > Maybe you need to use a computer with more memory.
> > >
> > > You can set the dpi in the argument to the png command to a lower value
> > > like 300 or 200 to speed up writing the png file.
> > > You can also turn off the casting of shadows: cmd.do("set
> > > ray_shadows,off"), which might save a few seconds.
> > >
> > > 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: Wednesday, October 21, 2020 4:03 AM
> > > To: pymol-users
> > > Subject: [EXTERNAL] [PyMOL] Generation of images using png
> > >
> > > Dear PyMol users,
> > > I am generating png images of protein-ligand complex using png command
> > > of pymol. This is the syntax that I am using from my bash script:
> > >
> > > image=800
> > > pdb='my.pdb'
> > > # load pdb, split states, make image
> > > MacPyMOL -c -d "
> > > from pymol import cmd
> > > cmd.load('${pdb}')
> > > cmd.split_states('complex*')
> > > cmd.bg_color('white')
> > >
> > > cmd.draw(${image},${image});cmd.png('test.png',width=${image},height=${image},ray=1)
> > > "
> > >
> > > Briefly, it works well but the time of the production of each image is
> > > up to 10 minutes (in the case if I have many models in my.pdb). Is it
> > > possible to speed PNG, while keeping the same resolution of image
> > > (800x800)?
> > >
> > > 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=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM&s=6yGrvyC36T9_kcNYvKJuml1-crRw2Sxuz4rvhpoS8ac&e=
> > > Unsubscribe:
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Re: [PyMOL] [EXTERNAL] Generation of images using png
Here are some benchmarks
1)This is an example for rendering of the image based on a multi-model
pdb of 240 frames (all states splitted into the same model)
Ray: render time: 698.52 sec. = 5.2 frames/hour (698.52 sec. accum.).
2) This is the same for 20 model pdb
Ray: render time: 19.26 sec. = 186.9 frames/hour (19.26 sec. accum.).
My hardware is iMAC 3.4 ghz Core i7, 16Go 13000 DDR3
I am using pymol 2.4.1 (full version)
ср, 21 окт. 2020 г. в 14:59, Jeff Saxon :
>
> thank you, Blaine!
> actually this problem only exists for the saving image of the system
> consisted of many models loaded into save pymol session after its
> splitting
> I've already tried with dpi=50 (keeping the same resolution) but It
> did not produce any differences :-)
> Cheers,
> J.
>
> ср, 21 окт. 2020 г. в 13:18, Mooers, Blaine H.M. (HSC)
> :
> >
> > Hi Jeff,
> >
> > 10 minutes is a long time for a 800 by 800 pixel image.
> > Maybe you need to use a computer with more memory.
> >
> > You can set the dpi in the argument to the png command to a lower value
> > like 300 or 200 to speed up writing the png file.
> > You can also turn off the casting of shadows: cmd.do("set
> > ray_shadows,off"), which might save a few seconds.
> >
> > 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: Wednesday, October 21, 2020 4:03 AM
> > To: pymol-users
> > Subject: [EXTERNAL] [PyMOL] Generation of images using png
> >
> > Dear PyMol users,
> > I am generating png images of protein-ligand complex using png command
> > of pymol. This is the syntax that I am using from my bash script:
> >
> > image=800
> > pdb='my.pdb'
> > # load pdb, split states, make image
> > MacPyMOL -c -d "
> > from pymol import cmd
> > cmd.load('${pdb}')
> > cmd.split_states('complex*')
> > cmd.bg_color('white')
> >
> > cmd.draw(${image},${image});cmd.png('test.png',width=${image},height=${image},ray=1)
> > "
> >
> > Briefly, it works well but the time of the production of each image is
> > up to 10 minutes (in the case if I have many models in my.pdb). Is it
> > possible to speed PNG, while keeping the same resolution of image
> > (800x800)?
> >
> > 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=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM&s=6yGrvyC36T9_kcNYvKJuml1-crRw2Sxuz4rvhpoS8ac&e=
> > Unsubscribe:
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM&s=1dpWe_laCFcfkMNzKcE1bNSXz6dvC6fkVX1QqUEUdjc&e=
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Re: [PyMOL] [EXTERNAL] Generation of images using png
thank you, Blaine!
actually this problem only exists for the saving image of the system
consisted of many models loaded into save pymol session after its
splitting
I've already tried with dpi=50 (keeping the same resolution) but It
did not produce any differences :-)
Cheers,
J.
ср, 21 окт. 2020 г. в 13:18, Mooers, Blaine H.M. (HSC)
:
>
> Hi Jeff,
>
> 10 minutes is a long time for a 800 by 800 pixel image.
> Maybe you need to use a computer with more memory.
>
> You can set the dpi in the argument to the png command to a lower value like
> 300 or 200 to speed up writing the png file.
> You can also turn off the casting of shadows: cmd.do("set ray_shadows,off"),
> which might save a few seconds.
>
> 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: Wednesday, October 21, 2020 4:03 AM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] Generation of images using png
>
> Dear PyMol users,
> I am generating png images of protein-ligand complex using png command
> of pymol. This is the syntax that I am using from my bash script:
>
> image=800
> pdb='my.pdb'
> # load pdb, split states, make image
> MacPyMOL -c -d "
> from pymol import cmd
> cmd.load('${pdb}')
> cmd.split_states('complex*')
> cmd.bg_color('white')
>
> cmd.draw(${image},${image});cmd.png('test.png',width=${image},height=${image},ray=1)
> "
>
> Briefly, it works well but the time of the production of each image is
> up to 10 minutes (in the case if I have many models in my.pdb). Is it
> possible to speed PNG, while keeping the same resolution of image
> (800x800)?
>
> 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=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM&s=6yGrvyC36T9_kcNYvKJuml1-crRw2Sxuz4rvhpoS8ac&e=
> Unsubscribe:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM&s=1dpWe_laCFcfkMNzKcE1bNSXz6dvC6fkVX1QqUEUdjc&e=
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[PyMOL] Generation of images using png
Dear PyMol users,
I am generating png images of protein-ligand complex using png command
of pymol. This is the syntax that I am using from my bash script:
image=800
pdb='my.pdb'
# load pdb, split states, make image
MacPyMOL -c -d "
from pymol import cmd
cmd.load('${pdb}')
cmd.split_states('complex*')
cmd.bg_color('white')
cmd.draw(${image},${image});cmd.png('test.png',width=${image},height=${image},ray=1)
"
Briefly, it works well but the time of the production of each image is
up to 10 minutes (in the case if I have many models in my.pdb). Is it
possible to speed PNG, while keeping the same resolution of image
(800x800)?
Cheers,
J.
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Re: [PyMOL] [EXTERNAL] png command in Educational Pymol
Right, thank you! just tested it with the recent Pymol version.
one question - is there any way to plot the name of the loaded pdb on
the image (produced by PNG command) in some automatic fashion (it
could be useful when I use it directly from terminal, without GUI)?
вт, 20 окт. 2020 г. в 14:46, Thomas Holder :
>
> See last question here ("Ray tracing does not work"):
> https://pymol.org/edu/faq.php
>
> Cheers,
> Thomas
>
> On Tue, Oct 20, 2020 at 1:18 PM Mooers, Blaine H.M. (HSC)
> wrote:
> >
> > Hi Jeff,
> >
> > I have the incentive version of PyMOL.
> > It too is saving draw images with ray tracing when using the batch mode and
> > also when using the pymol api in Jupyter.
> > As you report, saving a draw image from inside PyMOL works.
> >
> > This is a very annoying bug.
> > You should report it as an issue on the PyMOL github site.
> >
> > Perhaps this is not an issue with an order version of PyMOL.
> > Try one from before the switch from lines to cartoon as the default
> > molecular representation (say version 2.1).
> >
> > 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: Tuesday, October 20, 2020 5:48 AM
> > To: Mooers, Blaine H.M. (HSC); pymol-users
> > Subject: Re: [EXTERNAL] [PyMOL] png command in Educational Pymol
> >
> > Hi Blaine,
> > I've just checked on trial 26 day version of Pymol it use always RAY=1
> > while I run pymol from script regardless of ray flag (tested with
> > ray=1, ray=0, without ray as in you case etc :-)
> > I am going to try open source pymol!
> > Cheers,
> > J
> >
> > вт, 20 окт. 2020 г. в 12:39, Mooers, Blaine H.M. (HSC)
> > :
> > >
> > > Hi Jeff,
> > >
> > > I do not know the answer to your question. This is a work around.
> > > Try dropping ray=0 and adding the draw command with the dimensions in
> > > pixels (width, height).
> > >
> > > cmd.draw(1600,1600);cmd.png('test1600.png')
> > >
> > > I would not use the Educational PyMOL for the kind of serious work that
> > > you are trying to do.
> > > The PyMOL Wiki has several pages about open source versions of PyMOL.
> > > Use one of those instead.
> > >
> > > 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: Tuesday, October 20, 2020 5:24 AM
> > > To: pymol-users
> > > Subject: [EXTERNAL] [PyMOL] png command in Educational Pymol
> > >
> > > hello,
> > > I am using educational version of Pymol to generate png image of
> > > protein-ligand complex
> > >
> > > First, there are no problems in the case of PNG command from pymol's
> > > GUI. However if I run the same from script from terminal:
> > >
> > > MacPyMOL -c -d "
> > > from pymol import cmd
> > > cmd.load('${pdb}')
> > > cmd.png('${storage}/${experiment}/${pdb_name}.png',ray=0)
> > > "
> > > it does not produce an image with the following message:
> > >
> > > ! Ray tracing is not supported in Educational-Use-Only PyMOL. This
> > > version
> > >
> > > ! has a reduced set of features compared to the full Incentive PyMOL
> > > version.
> > >
> > > ! Please visit
> > > https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_edu&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=wc9BhPQsimg9JTvkDK5bNL1mUeSQplkvyIKIvNtXP5A&e=
> > > for details. If you want to generate
> > >
> >
[PyMOL] Visualisation of ligand clusters
Dear Pymol Users, I am dealing with the analysis of protein-ligand binding predicted by Auto-Dock, mainly focusing on the visualization of ligand clusters on the surface of the receptor. Assuming that I have in current pymol session several distinct clusters of ligand, would it be possible to color each of the cluster automatically using some dynamical selection to discriminate between structures within each of the cluster (e.g. based on the distances) ? For example having 3 distinct clusters (on the distance of 5A between each other) composed on 10, 5 and 5 structures I would like to colour them in blue, red in yellow. Looking forward to hearing your ideas! Cheers, J ___ 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
Re: [PyMOL] Open source Pymol for MAC
hey Michel, I always use homebrew without sudo, since Error: Running Homebrew as root is extremely dangerous and no longer supported. As Homebrew does not drop privileges on installation you would be giving all build scripts full access to your system. вт, 20 окт. 2020 г. в 12:55, Michel Rickhaus : > > Have you tried running it with sudo? > > Cheers > Michel > > On Tue, 20 Oct 2020 at 12:53, Jeff Saxon wrote: >> >> Hello, >> >> I am trying to install Open source version of Pymol on my mac using >> recommended method. Although I've never had problems with brew, here I >> got the following error message: >> >> brew install brewsci/bio/pymol >> >> touch: /usr/local/Homebrew/.git/FETCH_HEAD: Permission denied >> >> touch: >> /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/.git/FETCH_HEAD: >> Permission denied >> >> fatal: Unable to create '/usr/local/Homebrew/.git/index.lock': Permission >> denied >> >> fatal: Unable to create '/usr/local/Homebrew/.git/index.lock': Permission >> denied >> >> error: could not lock config file .git/config: Permission denied >> >> ==> Tapping brewsci/bio >> >> fatal: could not create leading directories of >> '/usr/local/Homebrew/Library/Taps/brewsci/homebrew-bio': Permission >> denied >> >> Error: Failure while executing; `git clone >> https://github.com/brewsci/homebrew-bio >> /usr/local/Homebrew/Library/Taps/brewsci/homebrew-bio` exited with >> 128. >> >> Could you suggest me another solution? >> Cheers, >> J >> >> >> ___ >> 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 ___ 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
[PyMOL] Open source Pymol for MAC
Hello, I am trying to install Open source version of Pymol on my mac using recommended method. Although I've never had problems with brew, here I got the following error message: brew install brewsci/bio/pymol touch: /usr/local/Homebrew/.git/FETCH_HEAD: Permission denied touch: /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/.git/FETCH_HEAD: Permission denied fatal: Unable to create '/usr/local/Homebrew/.git/index.lock': Permission denied fatal: Unable to create '/usr/local/Homebrew/.git/index.lock': Permission denied error: could not lock config file .git/config: Permission denied ==> Tapping brewsci/bio fatal: could not create leading directories of '/usr/local/Homebrew/Library/Taps/brewsci/homebrew-bio': Permission denied Error: Failure while executing; `git clone https://github.com/brewsci/homebrew-bio /usr/local/Homebrew/Library/Taps/brewsci/homebrew-bio` exited with 128. Could you suggest me another solution? Cheers, J ___ 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
Re: [PyMOL] [EXTERNAL] png command in Educational Pymol
Hi Blaine,
I've just checked on trial 26 day version of Pymol it use always RAY=1
while I run pymol from script regardless of ray flag (tested with
ray=1, ray=0, without ray as in you case etc :-)
I am going to try open source pymol!
Cheers,
J
вт, 20 окт. 2020 г. в 12:39, Mooers, Blaine H.M. (HSC)
:
>
> Hi Jeff,
>
> I do not know the answer to your question. This is a work around.
> Try dropping ray=0 and adding the draw command with the dimensions in pixels
> (width, height).
>
> cmd.draw(1600,1600);cmd.png('test1600.png')
>
> I would not use the Educational PyMOL for the kind of serious work that you
> are trying to do.
> The PyMOL Wiki has several pages about open source versions of PyMOL.
> Use one of those instead.
>
> 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: Tuesday, October 20, 2020 5:24 AM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] png command in Educational Pymol
>
> hello,
> I am using educational version of Pymol to generate png image of
> protein-ligand complex
>
> First, there are no problems in the case of PNG command from pymol's
> GUI. However if I run the same from script from terminal:
>
> MacPyMOL -c -d "
> from pymol import cmd
> cmd.load('${pdb}')
> cmd.png('${storage}/${experiment}/${pdb_name}.png',ray=0)
> "
> it does not produce an image with the following message:
>
> ! Ray tracing is not supported in Educational-Use-Only PyMOL. This version
>
> ! has a reduced set of features compared to the full Incentive PyMOL version.
>
> ! Please visit
> https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_edu&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=wc9BhPQsimg9JTvkDK5bNL1mUeSQplkvyIKIvNtXP5A&e=
> for details. If you want to generate
>
> ! figures for publication, then please obtain an academic license,
>
> ! see
> https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_academic&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=AyyjBPHDzcks30uu67ZXdfPu0lx4oJroZwNpS2_J1Yc&e=
>
> note that ray is disabled in my command (since I do not need a HQ
> image) and as I've mentioned there were no problems to create an image
> from gui session using the same command. Could it be fixed for my case
> or I need another version of Pymol ?
>
> Thank you !
>
>
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[PyMOL] png command in Educational Pymol
hello,
I am using educational version of Pymol to generate png image of
protein-ligand complex
First, there are no problems in the case of PNG command from pymol's
GUI. However if I run the same from script from terminal:
MacPyMOL -c -d "
from pymol import cmd
cmd.load('${pdb}')
cmd.png('${storage}/${experiment}/${pdb_name}.png',ray=0)
"
it does not produce an image with the following message:
! Ray tracing is not supported in Educational-Use-Only PyMOL. This version
! has a reduced set of features compared to the full Incentive PyMOL version.
! Please visit http://pymol.org/edu for details. If you want to generate
! figures for publication, then please obtain an academic license,
! see http://pymol.org/academic
note that ray is disabled in my command (since I do not need a HQ
image) and as I've mentioned there were no problems to create an image
from gui session using the same command. Could it be fixed for my case
or I need another version of Pymol ?
Thank you !
___
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[PyMOL] pymol from no-gui mode
Dear PyMol users,
I would like to integrate pymol in my scripting workflow in order to
save images/pymol sessions of different protein-ligand complexes.
Notably I have a typical autodock output in multi-model format of 20
ligand poses and 1 snapshot of the protein. I need to execute from the
terminal the sequence of pymol commands integrated in a simple bash
workflow:
for pdb in "${storage}"/"${experiment}"/*.pdb ; do
pdb_name=$(basename "$pdb" .pdb)
pymol $pdb
done
The final aim is to make visualization between protein and each of the
ligand model on the same plane (to see ligand clusters obtained from
autodock)
Here what I do in pymol GUI:
load $pdb
set white background # set white background
dss # show ss of the protein in cartoon
split states complex* # the beginning of pdb name is "complex"
select polymer
color gray # color polymer in gray
select not polymer
show as stics # show ligand as stics
save current session in pse
# optionally: colour each of the ligand cluster by individual colour#
png ${pdb_name} # make a nice png of the protein bound to 20 different
conformations :-)
Is it possible to run all of these commands in terminal or
alternatively providing some sort of batch file recognized by pymol (i
am working in mac with an educational version of pymol) ?
Thank you in advance for any suggestions!
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Re: [PyMOL] [EXTERNAL] Protein-ligand multi-model pdb extracted from docking
hello Blaine,
Thank you very much for your response!
sorry I did not explain my problem correctly, in fact after splitting
of the state I could see all states as the separate models. The
problem is only in the multi-model pdb that I obtained from DGL file
of autodock (which normally contains only the coordinates for
ligand!). I converted this file to PDB obtaining the correct
multi-model PDB of the ligand but then just cut it with the
receptor.pdb. So eventually I have the protein only within the first
frame. What I am looking for to fuse protein.pdb with EACH of the
model of the ligand. Probably we can do it via Pymol, starting from 2
pdbs: 1) multi-model pdb of the ligand (e.g. with 20 models) and 2)
receptor.pdb with 1 model of protein. There is no problem with
superimposition of both, I need just to save it correctly in a
multi-model file to see 20 frames containing both protein and ligand.
Cheers,
J.
чт, 15 окт. 2020 г. в 11:05, Mooers, Blaine H.M. (HSC)
:
>
> Hi Jeff,
>
> I would se the pdb file 1nmr as a template to reformat your file accordingly:
> fetch 1nmr, type=pdb.
> Open it with a text editor
> You will see the that END is used only once, at the every bottom of the file
> after the last model.
> This is why you are not seeing multiple models with all_states.
>
> You need to end the protein model with TER and then ENDMDL and start the
> ligand with 'MODEL2'
>
> TER1291 VAL A 85
> ENDMDL
> MODEL2
>
> 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: Thursday, October 15, 2020 2:34 AM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] Protein-ligand multi-model pdb extracted from
> docking
>
> Hello there.
>
> I am dealing with the extraction of ligand coordinates (in PDB) from
> the typical autodock output file (DLG). Using simple shell routine I
> can do it in just few steps:
>
># convert DLG to PDBQT
> grep '^DOCKED' test.dlg | cut -c9- > ${output}/test.pdbqt
> # convert PDBQT to PDB
> cut -c-66 ${output}/test.pdbqt > ${output}/test.pdb
> # take pdb of the receptor protein (used for this docking!) and add
> it to the ligand ensemble
> cat receptor.pdb ${output}/test.pdb | grep -v '^END ' | grep -v
> '^END$' > ${output}/complex_test.pdb
>
> The problem of this routine is in the last step when I add the
> receptor pdb to the ligand ensemble - it actually creates multi-model
> pdb (nmr like format) where the receptor is present only in the first
> model (and the ligands in the rest). So I can not examine in PyMol
> protein-ligand interactions (only even if I use split_states to
> separate all models).
>
> Could someone suggest a modification of my shell routine capable of
> adding a receptor.pdb to each of the ligand models (thus obtaining
> complex in proper multi-model format similar to NMR structure or
> molecular dynamics trajectory)?
>
> Thanks!!
> J.
>
>
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[PyMOL] Protein-ligand multi-model pdb extracted from docking
Hello there.
I am dealing with the extraction of ligand coordinates (in PDB) from
the typical autodock output file (DLG). Using simple shell routine I
can do it in just few steps:
# convert DLG to PDBQT
grep '^DOCKED' test.dlg | cut -c9- > ${output}/test.pdbqt
# convert PDBQT to PDB
cut -c-66 ${output}/test.pdbqt > ${output}/test.pdb
# take pdb of the receptor protein (used for this docking!) and add
it to the ligand ensemble
cat receptor.pdb ${output}/test.pdb | grep -v '^END ' | grep -v
'^END$' > ${output}/complex_test.pdb
The problem of this routine is in the last step when I add the
receptor pdb to the ligand ensemble - it actually creates multi-model
pdb (nmr like format) where the receptor is present only in the first
model (and the ligands in the rest). So I can not examine in PyMol
protein-ligand interactions (only even if I use split_states to
separate all models).
Could someone suggest a modification of my shell routine capable of
adding a receptor.pdb to each of the ligand models (thus obtaining
complex in proper multi-model format similar to NMR structure or
molecular dynamics trajectory)?
Thanks!!
J.
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