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=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM=6yGrvyC36T9_kcNYvKJuml1-crRw2Sxuz4rvhpoS8ac=
> > > Unsubscribe:
> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM=1dpWe_laCFcfkMNzKcE1bNSXz6dvC6fkVX1QqUEUdjc=
___
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
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=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM=6yGrvyC36T9_kcNYvKJuml1-crRw2Sxuz4rvhpoS8ac=
> > Unsubscribe:
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM=1dpWe_laCFcfkMNzKcE1bNSXz6dvC6fkVX1QqUEUdjc=
___
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
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=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM=6yGrvyC36T9_kcNYvKJuml1-crRw2Sxuz4rvhpoS8ac=
> Unsubscribe:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM=1dpWe_laCFcfkMNzKcE1bNSXz6dvC6fkVX1QqUEUdjc=
___
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
