Re: [PyMOL] Surface and cartoon transparency together?
Hi Petro, Try "Setting > Transparency > Multi-Layer" or "Multi-Layer (Real-time OIT)" See also: https://pymolwiki.org/index.php/transparency_mode Cheers, Thomas On Wed, May 17, 2023 at 4:51 PM Petro wrote: > > HI., I have tried to use surface and cartoon transparency together but then I > can see only the surface. Cartoon disappears completely. Any trick to get it > working? Thanks, > Petro > ___ > 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
Re: [PyMOL] Surface and cartoon transparency together?
Thanks. I will try it. Best regards. Petro. On Wed, 17 May 2023 at 19:49, Jarrett Johnson < jarrett.john...@schrodinger.com> wrote: > Hi Petro, > > You might have luck using Order Independent Transparency: > > `set transparency_mode, 3` > > Hope that helps, > Jarrett J > > On Wed, May 17, 2023 at 10:50 AM Petro wrote: > >> HI., I have tried to use surface and cartoon transparency together but >> then I can see only the surface. Cartoon disappears completely. Any trick >> to get it working? Thanks, >> Petro >> ___ >> 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 > > > > -- > > *Jarrett Johnson* | Senior Developer, PyMOL > > ___ 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] Surface and cartoon transparency together?
Hi Petro, You might have luck using Order Independent Transparency: `set transparency_mode, 3` Hope that helps, Jarrett J On Wed, May 17, 2023 at 10:50 AM Petro wrote: > HI., I have tried to use surface and cartoon transparency together but > then I can see only the surface. Cartoon disappears completely. Any trick > to get it working? Thanks, > Petro > ___ > 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 -- *Jarrett Johnson* | Senior Developer, PyMOL ___ 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] surface representation of the protein-ligand interactions
Right, thank you, Blaine!
It works very well now! Actually there was a problem in the selection
from my part so..
I will play with the surfaces a little bit and then will update this
topic with my questions :-)
Cheers,
Enrico
пн, 10 янв. 2022 г. в 16:25, Mooers, Blaine H.M. (HSC)
:
>
> Hi Enrico,
>
> You do not need the first line of your script.
>
> This one-liner worked for me in the terminal.
>
> pymol -c -d
> "cmd.fetch('3nd3');cmd.show('surface');cmd.set('transparency','0.5');cmd.save('surf.pse');cmd.png('surf.png')"
>
> You might test reversing the order of the cmd.png() and cmd.save() commands.
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology, College of Medicine
> Director of the Laboratory of Biomolecular Structure and Function
> Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
> Full Member, Cancer Biology Program, Stephenson Cancer Center
> University of Oklahoma Health Sciences Center
>
> Mailing Address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> Office: 405-271-8300 Lab: 405-271-8312
>
> Websites:
> Faculty page:
> https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
> BSC-OKC (LBSF):
> https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
> COBRE in Structural Biology: https://www.ou.edu/structuralbiology
>
> From: Ali Saad Kusay via PyMOL-users [pymol-users@lists.sourceforge.net]
> Sent: Monday, January 10, 2022 8:48 AM
> To: Enrico Martinez
> Cc: pymol-users
> Subject: [EXTERNAL] Re: [PyMOL] surface representation of the protein-ligand
> interactions
>
> Hi Enrico,
>
> This is beyond my understanding, try and run this bash script without making
> the surface transparent (to figure out if the issue comes from the
> transparency)
>
> Also try the rebuild command before saving the image:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Rebuild=DwIGaQ=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh=QM8ZtM6vxjrnYB0Cs6BSV-M8WweuPuuTS1xLMGYQdKU=
>
> 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 10/1/22, 11:10 pm, "Enrico Martinez" wrote:
>
> Thank you very much,Ali!
> just one question: when I do the surface calculations using bash
> script operating with the command lines of the pymol it produces
> correctly pse session with the surfaces. BUT if I save an image using
> png, the surface is totally absent. Here are my commands directly from
> the shell script:
>
> $pymol -c -d "
> from pymol import cmd
> cmd.load('${results}/${output}_${lig_name}_${receptor}_rep${i}.pdb')
> cmd.show( 'surface', '${output}* and polymer within 15 of ${output}*
> and not polymer' )
> cmd.set( 'transparency', '0.5' )
> cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
>
> cmd.png('${vizu}/${output}_${lig_name}_rep${i}.png',width=${image},height=${image},dpi=50,ray=0)
> "
> As the result of this workflow, the surface is present in the PSE
> file but not in the png image. Otherwise when I save png directly from
> the pymol's GUI the surface is well captured on the png as well. What
> should I include in my script ?
>
> пн, 10 янв. 2022 г. в 12:18, Ali Saad Kusay :
> >
> > Hi Enrico,
> >
> > You can carve the protein surface around the ligand, i.e. show only the
> surface behind the ligand, see this guide:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_1Of6CNLJyQU0W9yVofmRSV0-3Fdomain-3Dpymol.org=DwIGaQ=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh=eU60ct3XrRn6e7JdG6JrHLyikGkuUbzJY35JQFXvTv8=
> >
> > You can also try and made the surface more transparent, but this
> doesn't always give the best results, see:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_vdsUCOMKzVTp8wQ53fvOudq-3Fdomain-3Dpymolwiki.org=DwIGaQ=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh=pOFWGOP750OszaW7BCL8qGLr_VvBCCumHmvodMSYBeo=
> , i.e.:
> >
> > set
Re: [PyMOL] surface representation of the protein-ligand interactions
Hi Enrico,
You do not need the first line of your script.
This one-liner worked for me in the terminal.
pymol -c -d
"cmd.fetch('3nd3');cmd.show('surface');cmd.set('transparency','0.5');cmd.save('surf.pse');cmd.png('surf.png')"
You might test reversing the order of the cmd.png() and cmd.save() commands.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center
Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312
Websites:
Faculty page:
https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF):
https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
From: Ali Saad Kusay via PyMOL-users [pymol-users@lists.sourceforge.net]
Sent: Monday, January 10, 2022 8:48 AM
To: Enrico Martinez
Cc: pymol-users
Subject: [EXTERNAL] Re: [PyMOL] surface representation of the protein-ligand
interactions
Hi Enrico,
This is beyond my understanding, try and run this bash script without making
the surface transparent (to figure out if the issue comes from the transparency)
Also try the rebuild command before saving the image:
https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Rebuild=DwIGaQ=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh=QM8ZtM6vxjrnYB0Cs6BSV-M8WweuPuuTS1xLMGYQdKU=
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 10/1/22, 11:10 pm, "Enrico Martinez" wrote:
Thank you very much,Ali!
just one question: when I do the surface calculations using bash
script operating with the command lines of the pymol it produces
correctly pse session with the surfaces. BUT if I save an image using
png, the surface is totally absent. Here are my commands directly from
the shell script:
$pymol -c -d "
from pymol import cmd
cmd.load('${results}/${output}_${lig_name}_${receptor}_rep${i}.pdb')
cmd.show( 'surface', '${output}* and polymer within 15 of ${output}*
and not polymer' )
cmd.set( 'transparency', '0.5' )
cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
cmd.png('${vizu}/${output}_${lig_name}_rep${i}.png',width=${image},height=${image},dpi=50,ray=0)
"
As the result of this workflow, the surface is present in the PSE
file but not in the png image. Otherwise when I save png directly from
the pymol's GUI the surface is well captured on the png as well. What
should I include in my script ?
пн, 10 янв. 2022 г. в 12:18, Ali Saad Kusay :
>
> Hi Enrico,
>
> You can carve the protein surface around the ligand, i.e. show only the
surface behind the ligand, see this guide:
https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_1Of6CNLJyQU0W9yVofmRSV0-3Fdomain-3Dpymol.org=DwIGaQ=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh=eU60ct3XrRn6e7JdG6JrHLyikGkuUbzJY35JQFXvTv8=
>
> You can also try and made the surface more transparent, but this doesn't
always give the best results, see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_vdsUCOMKzVTp8wQ53fvOudq-3Fdomain-3Dpymolwiki.org=DwIGaQ=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh=pOFWGOP750OszaW7BCL8qGLr_VvBCCumHmvodMSYBeo=
, i.e.:
>
> set transparency, 0.5
>
> It would help to see an image of what you are working with atm
>
> 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 10/1/22, 10:10 pm, "Enrico Martinez" wrote:
>
> Dear Pymol users!
> Working on the vizualisation of the protein-ligand interactions I
> would like to switch from cartoon to the surface representation of the
> protein, while still being capable to see the ligand-binding cavity
>
Re: [PyMOL] surface representation of the protein-ligand interactions
Hi Enrico,
This is beyond my understanding, try and run this bash script without making
the surface transparent (to figure out if the issue comes from the transparency)
Also try the rebuild command before saving the image:
https://pymolwiki.org/index.php/Rebuild
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 10/1/22, 11:10 pm, "Enrico Martinez" wrote:
Thank you very much,Ali!
just one question: when I do the surface calculations using bash
script operating with the command lines of the pymol it produces
correctly pse session with the surfaces. BUT if I save an image using
png, the surface is totally absent. Here are my commands directly from
the shell script:
$pymol -c -d "
from pymol import cmd
cmd.load('${results}/${output}_${lig_name}_${receptor}_rep${i}.pdb')
cmd.show( 'surface', '${output}* and polymer within 15 of ${output}*
and not polymer' )
cmd.set( 'transparency', '0.5' )
cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
cmd.png('${vizu}/${output}_${lig_name}_rep${i}.png',width=${image},height=${image},dpi=50,ray=0)
"
As the result of this workflow, the surface is present in the PSE
file but not in the png image. Otherwise when I save png directly from
the pymol's GUI the surface is well captured on the png as well. What
should I include in my script ?
пн, 10 янв. 2022 г. в 12:18, Ali Saad Kusay :
>
> Hi Enrico,
>
> You can carve the protein surface around the ligand, i.e. show only the
surface behind the ligand, see this guide:
https://protect-au.mimecast.com/s/1Of6CNLJyQU0W9yVofmRSV0?domain=pymol.org
>
> You can also try and made the surface more transparent, but this doesn't
always give the best results, see:
https://protect-au.mimecast.com/s/vdsUCOMKzVTp8wQ53fvOudq?domain=pymolwiki.org,
i.e.:
>
> set transparency, 0.5
>
> It would help to see an image of what you are working with atm
>
> 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 10/1/22, 10:10 pm, "Enrico Martinez" wrote:
>
> Dear Pymol users!
> Working on the vizualisation of the protein-ligand interactions I
> would like to switch from cartoon to the surface representation of the
> protein, while still being capable to see the ligand-binding cavity
> (as well as non-covalent interactions)
>
> Could you suggest me some combination of the options which could helps
> me with such vizualisaiton?
> I have alread tried
> show surface, all within 5 of my_pdb and not polymer
> set surface_smooth_edges, onset surface_smooth_edges, on
> where my_pdb and not polymer corresponds to the selection of the
ligand
>
> Eventualy this create cool surface representation of the protein and
> but completely hides the ligand-binding cavity
> Many thanks in advance!
> Enrico
>
>
> ___
> PyMOL-users mailing list
> Archives:
https://protect-au.mimecast.com/s/5uDYCP7LAXfKwZVvQF1Df45?domain=mail-archive.com
> Unsubscribe:
https://protect-au.mimecast.com/s/Q3GJCQnMBZfkQ9ZB7FkIfVr?domain=sourceforge.net
>
>
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Unsubscribe:
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Re: [PyMOL] surface representation of the protein-ligand interactions
Thank you very much,Ali!
just one question: when I do the surface calculations using bash
script operating with the command lines of the pymol it produces
correctly pse session with the surfaces. BUT if I save an image using
png, the surface is totally absent. Here are my commands directly from
the shell script:
$pymol -c -d "
from pymol import cmd
cmd.load('${results}/${output}_${lig_name}_${receptor}_rep${i}.pdb')
cmd.show( 'surface', '${output}* and polymer within 15 of ${output}*
and not polymer' )
cmd.set( 'transparency', '0.5' )
cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
cmd.png('${vizu}/${output}_${lig_name}_rep${i}.png',width=${image},height=${image},dpi=50,ray=0)
"
As the result of this workflow, the surface is present in the PSE
file but not in the png image. Otherwise when I save png directly from
the pymol's GUI the surface is well captured on the png as well. What
should I include in my script ?
пн, 10 янв. 2022 г. в 12:18, Ali Saad Kusay :
>
> Hi Enrico,
>
> You can carve the protein surface around the ligand, i.e. show only the
> surface behind the ligand, see this guide:
> https://pymol.org/dokuwiki/doku.php?id=figure:carving_surfaces
>
> You can also try and made the surface more transparent, but this doesn't
> always give the best results, see:
> https://pymolwiki.org/index.php/Transparency, i.e.:
>
> set transparency, 0.5
>
> It would help to see an image of what you are working with atm
>
> 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 10/1/22, 10:10 pm, "Enrico Martinez" wrote:
>
> Dear Pymol users!
> Working on the vizualisation of the protein-ligand interactions I
> would like to switch from cartoon to the surface representation of the
> protein, while still being capable to see the ligand-binding cavity
> (as well as non-covalent interactions)
>
> Could you suggest me some combination of the options which could helps
> me with such vizualisaiton?
> I have alread tried
> show surface, all within 5 of my_pdb and not polymer
> set surface_smooth_edges, onset surface_smooth_edges, on
> where my_pdb and not polymer corresponds to the selection of the ligand
>
> Eventualy this create cool surface representation of the protein and
> but completely hides the ligand-binding cavity
> Many thanks in advance!
> Enrico
>
>
> ___
> PyMOL-users mailing list
> Archives:
> https://protect-au.mimecast.com/s/cnxDCMwGxOtqr9lJjhwM0N6?domain=mail-archive.com
> Unsubscribe:
> https://protect-au.mimecast.com/s/ZXpPCNLJyQU0W9R6oh42rcB?domain=sourceforge.net
>
>
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Unsubscribe:
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Re: [PyMOL] surface representation of the protein-ligand interactions
Hi Enrico, You can carve the protein surface around the ligand, i.e. show only the surface behind the ligand, see this guide: https://pymol.org/dokuwiki/doku.php?id=figure:carving_surfaces You can also try and made the surface more transparent, but this doesn't always give the best results, see: https://pymolwiki.org/index.php/Transparency, i.e.: set transparency, 0.5 It would help to see an image of what you are working with atm 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 10/1/22, 10:10 pm, "Enrico Martinez" wrote: Dear Pymol users! Working on the vizualisation of the protein-ligand interactions I would like to switch from cartoon to the surface representation of the protein, while still being capable to see the ligand-binding cavity (as well as non-covalent interactions) Could you suggest me some combination of the options which could helps me with such vizualisaiton? I have alread tried show surface, all within 5 of my_pdb and not polymer set surface_smooth_edges, onset surface_smooth_edges, on where my_pdb and not polymer corresponds to the selection of the ligand Eventualy this create cool surface representation of the protein and but completely hides the ligand-binding cavity Many thanks in advance! Enrico ___ PyMOL-users mailing list Archives: https://protect-au.mimecast.com/s/cnxDCMwGxOtqr9lJjhwM0N6?domain=mail-archive.com Unsubscribe: https://protect-au.mimecast.com/s/ZXpPCNLJyQU0W9R6oh42rcB?domain=sourceforge.net ___ 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] surface stuck on one color
Hi Pymolers I have solved my problem. I am using surface cavity_mode, 3. I need to change the ray_interior_color instead of the surface color. I guess this is because pymol is visualizing the interior of the surface not the exterior. -Yarrow On Thu, Jul 24, 2014 at 11:08 AM, Yarrow Madrona amadr...@uci.edu wrote: I think the problem may have to do with the surface_cavity_mode being set to 3. I try to change the surface_cavity_mode but I still detect cavities instead of the surface. It seems like any option related to the surface is locked. -Yarrow -- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] SURFACE MODEL
Dear Spyros, Do you know about the PyMOL wiki (http://pymolwiki.org/)? Take a look here: http://pymolwiki.org/index.php/Color for an explanation about colors. In the default representation Green: Carbon Blue: Nitrogen Red: Oxygen Yellow: sulfur For coloring eg. color gray will color everything gray. This is done on the command-line. You can also use the gui (top right there is a multicolored square with the letter C, for color) and select many different colors. This can be done for all or individually for each object/pdb you load. Hope this helps! Best regards, Folmer Fredslund 2011/7/17 Spyros Charonis s.charo...@gmail.com: Hello PyMOLers, A quick question on the surface model, is there anywhere where I can learn how molecules are color-coded. The default scheme has green, red, and bits of yellow (I know the accessible to solvents surface is what is shown, but I'm not sure what red, green, and yellow bits mean)? Also, is there a way I can turn the whole thing gray (monochrome) so that I can color in parts I want to examine with my own coloring method? Spyros -- AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on Lean Startup Secrets Revealed. This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on Lean Startup Secrets Revealed. This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] surface display in new pymol
Hi Venki, You need to first issue the following command: set surface_mode, 1 Best, Luca On Jun 8, 2011, at 17:05 , V. Ramakrishnan wrote: On versions 1.3, 1.4, I cannot display a surface of anything that is not in the standard dictionary. For example trying to draw a surface of tRNA shows gaps in the modified bases. Drawing a surface of a ligand such as an antibiotic similarly is just a blank. This was not true in the older versions, e.g. 0.98 or 0.99. I'm using Mac OS X 10.6.7 Does anyone else have this problem and is there a way around it? Thanks, Venki -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] surface for oligosaccharide chains
On Fri, 03 Jul 2009 16:18:10 +0200, Raluca Mihaela ANDREI r.and...@sns.it wrote: Hi! Can somebody tell me why I can't create surfaces for the oligosaccharide chains? By default, the surface and mesh commands ignore all atoms in HETATM records in a PDB file. You can change that with: set surface_mode, 1 set mesh_mode, 1 That means, though, that *all* hetatm atoms will have a surface drawn. If you want to draw a surface for your oligosaccharide chains alone, then you can copy them to a separate object and set the surface_mode flag just for that object: set surface_mode, 0 create saccharide, object selection (fill in your residue selection for selection) set surface_mode, 1, saccharide Hope that helps, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] surface of ligand
set surface_mode, 1 Cheers, Warren -Original Message- From: chaix denis [mailto:ch...@cbs.cnrs.fr] Sent: Tuesday, May 26, 2009 3:55 PM To: pymol-users@lists.sourceforge.net Cc: Chaix Denis; support; pymol-users@lists.sourceforge.net Subject: [PyMOL] surface of ligand Dear users How can I obtain the surface of a ligand in protein pdb file. I just need the simple surface, i doesn't need in this case, the electrostatic surface. Thanks -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://p.sf.net/sfu/creativitycat-com ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] surface area calculation
Dear Luisa, 2009/4/21 Maria Luisa Rodrigues mlrodrig...@igc.gulbenkian.pt: Dear all, Is there any PyMOL command to calculate surface areas? Many thanks, Did you try to search for information yourself first? Anyways, the pymolwiki.org is always a good place to go and then you would have found something like this: http://pymolwiki.org/index.php/Get_Area I hope this is what you are looking for? Best regards, Folmer Fredslund
Re: [PyMOL] Surface Residues
I would like to select surface residues via the surface calculation algorithm of Pymol. Is this possible? Not at present. What is the surface calculation algorithm that Pymol use and is it scattered among many source-code files or is it contained in just one source-code file? It uses a brute-force approach based on VDW spheres of surface atoms and hypothetical waters-in-contact. It is spread over multiple source files, but RepSurface.c has the top-level code. Cheers, Warren From: QT [mailto:rdirect...@gmail.com] Sent: Thursday, January 29, 2009 8:57 PM To: PyMOL-users@lists.sourceforge.net Subject: [PyMOL] Surface Residues Dear all, Once again, I need some help from pymol experts. I would like to select surface residues via the surface calculation algorithm of Pymol. Is this possible? What is the surface calculation algorithm that Pymol use and is it scattered among many source-code files or is it contained in just one source-code file? Thanks in advance. Best, Quyen
Re: [PyMOL] surface properties
Use my hydrophobicity script... Please build this in as preset as I use it all the time. # Written by H. Adam Steinberg # 08/22/2007 ###set custom colors for each amino acid based on hydrophobicity scale (scale derived by S. D. Black and D. R. Mould): set_color ala, [0.525490196, 0.792156863, 0.596078431] set_color arg, [0, 0.678431373, 0.9] set_color asn, [0, 0.717647059, 0.8] set_color asp, [0, 0.678431373, 0.9] set_color cys, [0.584313725, 0.803921569, 0.560784314] set_color gln, [0, 0.729411765, 0.760784314] set_color glu, [0, 0.68627451, 0.894117647] set_color gly, [0.470588235, 0.776470588, 0.631372549] set_color his, [0, 0.694117647, 0.862745098] set_color ile, [0.901960784, 0.898039216, 0.258823529] set_color leu, [0.941176471, 0.91372549, 0.192156863] set_color lys, [0.211764706, 0.741176471, 0.729411765] set_color met, [0.698039216, 0.835294118, 0.48627451] set_color phe, [1, 0.941176471, 0] set_color pro, [0.643137255, 0.819607843, 0.525490196] set_color ser, [0.321568627, 0.752941176, 0.698039216] set_color thr, [0.4, 0.764705882, 0.7] set_color trp, [0.803921569, 0.86667, 0.388235294] set_color tyr, [0.854901961, 0.882352941, 0.325490196] set_color val, [0.752941176, 0.854901961, 0.435294118] ###Select and select separate object for each amino acid: select ala, resn ala select arg, resn arg select asn, resn asn select asp, resn asp select cys, resn cys select gln, resn gln select glu, resn glu select gly, resn gly select his, resn his select ile, resn ile select leu, resn leu select lys, resn lys select met, resn met select phe, resn phe select pro, resn pro select ser, resn ser select thr, resn thr select trp, resn trp select tyr, resn tyr select val, resn val ###Color each amino acid with hydrophobicity color color ala, ala color arg, arg color asn, asn color asp, asp color cys, cys color gln, gln color glu, glu color gly, gly color his, his color ile, ile color leu, leu color lys, lys color met, met color phe, phe color pro, pro color ser, ser color thr, thr color trp, trp color tyr, tyr color val, val ###Show surface show surface, all DeLano Scientific wrote: Mark, PyMOL does not have such abilities at present. Can such concepts even be defined in a precise, objective, and unambiguous fashion? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Mark Collins [mailto:mnc2...@columbia.edu] Sent: Thursday, December 18, 2008 7:38 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] surface properties Hi All I have searched thru the archive and couldn't find an answer, to this. I would like to make pymol surface(s) colored by (1) hydrophobicity and (2) concavity/convexity. These are easily produced in grasp, so one possibility maybe to import some type of grasp file. Thanks in advance for suggestions, websites, or tutorials, etc. Mark -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009 .visitmix.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- ___ H. Adam Steinberg Artist, Scientist http://adam.steinbergs.us Information Technology and Media Center Department of Biochemistry University of Wisconsin-Madison 433 Babcock Drive Madison, WI 53706 608/265-4982 ___
Re: [PyMOL] surface properties
Mark, PyMOL does not have such abilities at present. Can such concepts even be defined in a precise, objective, and unambiguous fashion? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Mark Collins [mailto:mnc2...@columbia.edu] Sent: Thursday, December 18, 2008 7:38 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] surface properties Hi All I have searched thru the archive and couldn't find an answer, to this. I would like to make pymol surface(s) colored by (1) hydrophobicity and (2) concavity/convexity. These are easily produced in grasp, so one possibility maybe to import some type of grasp file. Thanks in advance for suggestions, websites, or tutorials, etc. Mark -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009 .visitmix.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] surface properties
Hi Mark, I remember that Kristian Rother's rTools could do hydrophobicity coloring: http://www.rubor.de/pymol_extensions.html it is some years ago, so maybe it needs some updateing.. Best, Andreas DeLano Scientific wrote: Mark, PyMOL does not have such abilities at present. Can such concepts even be defined in a precise, objective, and unambiguous fashion? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Mark Collins [mailto:mnc2...@columbia.edu] Sent: Thursday, December 18, 2008 7:38 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] surface properties Hi All I have searched thru the archive and couldn't find an answer, to this. I would like to make pymol surface(s) colored by (1) hydrophobicity and (2) concavity/convexity. These are easily produced in grasp, so one possibility maybe to import some type of grasp file. Thanks in advance for suggestions, websites, or tutorials, etc. Mark -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009 .visitmix.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de
Re: [PyMOL] Surface question
Jeff, Extract the ligand into a new object, and then show the surface on that object only: extract lig, ligand-selection show surface, lig Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Jeff Taylor Sent: Wednesday, June 06, 2007 12:52 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Surface question Hello- I have a enzyme-ligand co-structure that I would like to display with a surface representation of the ligand and something different, sticks or cartoon, for the protein. The problem comes when I try to surface the ligand, only the actual solvent exposed portion is shown, when I'd like to show the surface for the entire ligand. Is there a way to do this via atom selection? If not, what are the alternatives? Split up the PDB file? Thank you. -Jeff Taylor -- --- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Surface vertex list
Hi Jim, Hmmm. I think your best option is to color the surface according to the atoms and write the surface in povray format. This will give you all the vertices. Just another thought springing to mind, you could cycle over the atoms using a script, writing away only the part of the surface belonging to the active atom. I don't think the vertices are available otherwise, and you would need to dive into the source code to get them out otherwise. Best, Tsjerk On 4/17/07, jjv5 j...@jjv5.net wrote: Hello, Is there a way to access the individual vertices of a surface abd there association with atoms? I know it's done under the hood, but can I write some code that say returns a list of surface vertices associated with a particular atom? In the end, I'd like to know if two atoms share a surface vertex to determine if they are surface neighbors. Thanks, Jim - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
Re: [PyMOL] surface coloring fails with gradient loaded
Martin, Just FYI, the gradient display in PyMOL you and I have been working on is still too immature to be considered supportable or supported. Indeed, prior to your post, you were one of the few PyMOL users even aware of it. For everyone else, I suppose I should announce that one of the many new features pending for PyMOL 1.0 is the ability to display fieldlines in maps such as illustrated here: http://pymol.sf.net/pmimag/fieldlines.jpg The bugs are still being worked out, but usage parallels that of isomesh with ramp-based coloring by map potential. If you have SVN source, then gradient ? for usage. Note that this feature will not be supported by DeLano Scientific until after the 1.0 release. As for your question, mdo movie commands should be limited to localized state changes within PyMOL. Performing I/O or running external system calls (e.g. APBS) within a movie command is likely to not work, and may cause trouble, such crashes or hangs. The way to approach your need is to either precompute and preload all of your maps into PyMOL states (impractical for 600 maps), or to write a Python script which takes over from PyMOL in terms of sequencing, performing electrostatics, calculations, and rendering the movie. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Martin Höfling Sent: Friday, December 15, 2006 8:01 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] surface coloring fails with gradient loaded Hi there, i am trying to render fieldlines and sf potential together in a movie. The movie setup is like this: import os set gradient_spacing=5 load ProtOut.pdb,prot load trajshort.xtc,prot mset 1 -7 show surface set surface_solvent=1 for a in range(1,7): cmd.mdo(a,delete flines;delete dxmap;delete dxmap2;delete rmp;delete rmp2;save prot.pdb,prot;os.system(\pdb2pqr --ff=amber prot.pdb prot.pqrlog.txt\);os.system(\apbs apbs.inlog.txt\);load apbsout.dx,dxmap;load apbsout.dx,dxmap2;ramp_new rmp,dxmap, [-1.5,-0.75,0];ramp_new rmp2,dxmap,[-10,0,10];gradient flines,dxmap,-10,10,prot,carve=15;color rmp,flines;set surface_color=rmp,prot) set ray_trace_frames=1 set cache_frames=1 mclear Is there anything wrong on this setup? the surface is always white. If i do a show surface in every frame, then it seems to me as if the surface is calculated for all frames (600 in total). This is too slow to do it on every step. Any ideas? Cheers Martin - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Surface Edge
Paul, I think the reason the surface coloring spills over is because there are some surface triangles that are shared by the selection you want (red) and the neighboring residues (grey)... So it should work if you only use one selection, by saying something like: load my_protein.pdb, show surface, color grey, color red, (something at the center of the pocket) expand 8 Hope this helps, -bob On 9/20/06, Paul Wilhelm Elsinghorst p...@uni-bonn.de wrote: Hi, please have a look at this image: http://pwe.no-ip.org/other/1.png I'm having trouble with the edge of a surface selection. It seems that there is always some more surface shown than the selected part. What I did is, that I selected the red part to show the surface in obj1 and to hide the surface in obj2 which is grey. obj1 and obj2 are copies of each other. I hoped that this would show a sharp border red/grey as I want to change the transparency in obj2 (grey) to fade out. How do I get pymol to show sharp borders and have no overlapping (dotted) parts as in the image? Paul - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Surface Edge
pymol-users-boun...@lists.sourceforge.net wrote on 09/20/2006 07:28:00 AM: Paul, I think the reason the surface coloring spills over is because there are some surface triangles that are shared by the selection you want (red) and the neighboring residues (grey)... So it should work if you only use one selection, by saying something like: load my_protein.pdb, show surface, color grey, color red, (something at the center of the pocket) expand 8 Hope this helps, -bob I think this is the right approach. If you invert the selection for the other surface, you should be able to avoid having triangles in both surfaces. Like this: load my_protein.pdb create pocket, chain a create rest_of_protein, chain a color red, pocket color gray, rest_of_protein show surface, pocket and resi 10-15 show surface, rest_of_protein and not(resi 10-15) set transparency=0.5, rest_of_protein This gave a sharp edge when I just tried it. If you don't like the jagged look of the edge, try changing the color statements above, to color gray, pocket color red, pocket and resi 10-15 color gray, rest_of_protein Now your red triangles will fade into the semi-transparent gray surface. Hope that helps, Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th floor New York, NY 10014 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
Re: [PyMOL] Surface Edge
I believe that you need to make these new objects to correct the problem, at least this is a quick fix that I have done in the past. There may be a more elegant solution: load my.pdb, obj1 load my.pdb, obj2 [whatever to each obj] When loaded separately you don't have this problem. Cheers, JTM We can be sure that if a detailed understanding of the molecular basis of chemo-therapeutic activity were to be obtained, the advance of medicine would be greatly accelerated. Linus Pauling, Nobel Laureate 1954 ...everything that living things do can be understood in terms of the jigglings and wigglings of atoms. Richard Feynman, Nobel Laureate 1965 Jason Thomas Maynes, MD/PhD Department of Biochemistry and Molecular Biophysics Resident in Anaesthesia and Paediatrics Faculty of Medicine Washington University in St. Louis jmay...@biochem.wustl.edu Paul, I think the reason the surface coloring spills over is because there are some surface triangles that are shared by the selection you want (red) and the neighboring residues (grey)... So it should work if you only use one selection, by saying something like: load my_protein.pdb, show surface, color grey, color red, (something at the center of the pocket) expand 8 Hope this helps, -bob On 9/20/06, Paul Wilhelm Elsinghorst p...@uni-bonn.de wrote: Hi, please have a look at this image: http://pwe.no-ip.org/other/1.png I'm having trouble with the edge of a surface selection. It seems that there is always some more surface shown than the selected part. What I did is, that I selected the red part to show the surface in obj1 and to hide the surface in obj2 which is grey. obj1 and obj2 are copies of each other. I hoped that this would show a sharp border red/grey as I want to change the transparency in obj2 (grey) to fade out. How do I get pymol to show sharp borders and have no overlapping (dotted) parts as in the image? Paul - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: : [PyMOL] Surface Vertex Coordinates
Laurence, Does it do all drawing objects or just surfaces ? All objects except labels. However, triangle normals aren't current exported, which means that surfaces and cartoons don't look nearly as good...I'm not sure if this is something that can be added in VRML2 or not. and will it be in MacPyMol ? Yes, with the next release. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: Laurence Pearl [mailto:laurence.pe...@icr.ac.uk] Sent: Friday, March 17, 2006 5:03 AM To: Warren DeLano; h...@genome.stanford.edu Cc: pymol-users@lists.sourceforge.net Subject: RE: : [PyMOL] Surface Vertex Coordinates Does it do all drawing objects or just surfaces ? and will it be in MacPyMol ? Laurence -- -- Laurence H. Pearl Section of Structural Biology, Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK Phone +44-(0)20 7153 5422 : Secretary +44-(0)20 7153 5443 : FAX +44-(0)20 7153 5457 -- -- Live Simply and do Serious Things .. - Dorothy Crowfoot Hodgkin -- -- Warren DeLano war...@delsci.com 03/17/06 6:56 AM Of course it would be a whole lot easier if PyMol output VRML directly . Warren ? Chris Want's latest VRML2 code is now in CVS (with a few minor tweaks of my own...) save my_vrml.wrl Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Laurence Pearl Sent: Wednesday, March 15, 2006 9:35 AM To: Benjamin Hitz Cc: pymol-users@lists.sourceforge.net Subject: Re: : [PyMOL] Surface Vertex Coordinates The Povray intermediate file generated when you do 'ray renderer = 1' contains all vertices, normals and colouring information for cartoon and surface object types. However you do need to produce a parsing script to extract these in to a useful form for importing into other programs. Have a look at the front cover of Mol Cell vol 20(4) - I generated a cartoon of the protein in PyMol, output it as a povray file, and then converted it to VRML using a jiffy produced by Chris Richardson, and then used it as an object in the Blender 3D modelling package to generate the picture. Of course it would be a whole lot easier if PyMol output VRML directly . Warren ? Laurence Pearl On 15 Mar 2006, at 17:01, Benjamin Hitz wrote: I am interested in the coordinates of the vertices of the mesh representation of the molecular surface. Is there any method to read them out? Thanks Me too. With coloring and/or other property information as well. -- Ben Hitz Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium Stanford University ** h...@genome.stanford.edu --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel? cmd=lnkkid=110944bid=241720dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- -- -- Laurence H. Pearl Section of Structural Biology, Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK Phone +44-(0)20 7153 5422 : Secretary +44-(0)20 7153 5443 FAX +44-(0)20 7153 5457 : E-Mail laurence.pe...@icr.ac.uk -- -- -- Live Simply and do Serious Things .. - Dorothy Crowfoot Hodgkin -- -- -- --- This SF.Net email is sponsored
RE: : [PyMOL] Surface Vertex Coordinates
Of course it would be a whole lot easier if PyMol output VRML directly . Warren ? Chris Want's latest VRML2 code is now in CVS (with a few minor tweaks of my own...) save my_vrml.wrl Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Laurence Pearl Sent: Wednesday, March 15, 2006 9:35 AM To: Benjamin Hitz Cc: pymol-users@lists.sourceforge.net Subject: Re: : [PyMOL] Surface Vertex Coordinates The Povray intermediate file generated when you do 'ray renderer = 1' contains all vertices, normals and colouring information for cartoon and surface object types. However you do need to produce a parsing script to extract these in to a useful form for importing into other programs. Have a look at the front cover of Mol Cell vol 20(4) - I generated a cartoon of the protein in PyMol, output it as a povray file, and then converted it to VRML using a jiffy produced by Chris Richardson, and then used it as an object in the Blender 3D modelling package to generate the picture. Of course it would be a whole lot easier if PyMol output VRML directly . Warren ? Laurence Pearl On 15 Mar 2006, at 17:01, Benjamin Hitz wrote: I am interested in the coordinates of the vertices of the mesh representation of the molecular surface. Is there any method to read them out? Thanks Me too. With coloring and/or other property information as well. -- Ben Hitz Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium Stanford University ** h...@genome.stanford.edu --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel? cmd=lnkkid=110944bid=241720dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- -- -- Laurence H. Pearl Section of Structural Biology, Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK Phone +44-(0)20 7153 5422 : Secretary +44-(0)20 7153 5443 FAX +44-(0)20 7153 5457 : E-Mail laurence.pe...@icr.ac.uk -- -- -- Live Simply and do Serious Things .. - Dorothy Crowfoot Hodgkin -- -- -- --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720; dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: : [PyMOL] Surface Vertex Coordinates
The Povray intermediate file generated when you do 'ray renderer = 1' contains all vertices, normals and colouring information for cartoon and surface object types. However you do need to produce a parsing script to extract these in to a useful form for importing into other programs. Have a look at the front cover of Mol Cell vol 20(4) - I generated a cartoon of the protein in PyMol, output it as a povray file, and then converted it to VRML using a jiffy produced by Chris Richardson, and then used it as an object in the Blender 3D modelling package to generate the picture. Of course it would be a whole lot easier if PyMol output VRML directly . Warren ? Laurence Pearl On 15 Mar 2006, at 17:01, Benjamin Hitz wrote: I am interested in the coordinates of the vertices of the mesh representation of the molecular surface. Is there any method to read them out? Thanks Me too. With coloring and/or other property information as well. -- Ben Hitz Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium Stanford University ** h...@genome.stanford.edu --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel? cmd=lnkkid=110944bid=241720dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Laurence H. Pearl Section of Structural Biology, Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK Phone +44-(0)20 7153 5422 : Secretary +44-(0)20 7153 5443 FAX +44-(0)20 7153 5457 : E-Mail laurence.pe...@icr.ac.uk -- Live Simply and do Serious Things .. - Dorothy Crowfoot Hodgkin --
Re: : [PyMOL] Surface Vertex Coordinates
On Wed, Mar 15, 2006 at 09:01:19AM -0800, Benjamin Hitz wrote: I am interested in the coordinates of the vertices of the mesh representation of the molecular surface. Is there any method to read them out? Thanks Me too. With coloring and/or other property information as well. povscript+ will do all of this, in a somewhat-standardized GTS (gts.sf.net) format that is easy to port to a number of other programs. It will also dump surfaces as vertex2 objects in povray. HTH, Tim -- - Tim Fenn f...@stanford.edu Stanford University, School of Medicine James H. Clark Center 318 Campus Drive, Room E300 Stanford, CA 94305-5432 Phone: (650) 736-1714 FAX: (650) 736-1961 -
Re: [PyMOL] Surface of cavity
Hi, you may try to use caver: http://viper.chemi.muni.cz/caver/concept.php or castp http://cast.engr.uic.edu/cast/oldindex.php regards andrea 2006/1/21, Paul Wilhelm Elsinghorst p...@uni-bonn.de: Hi, a little question regarding cavity surfaces :-) I have a set of active atoms (GOLD output) that surround a cavity. Now I want to dipslay the surface only for the cavity wall, not on the outside. Any ideas? Paul -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.0 (GNU/Linux) iD8DBQBD0eKigFneuXxhreARAnFLAJ9Z3o6zMiphEzzKpVzMXtdXxh6dBwCeMp9u ZIoavXwL2DE+hMObJhTiD8o= =uZkv -END PGP SIGNATURE- -- La conoscenza libera il genere umano dalla superstizione J. Watson
Re: [PyMOL] Surface of cavity
Hi Paul, I have a set of active atoms (GOLD output) that surround a cavity. Now I want to dipslay the surface only for the cavity wall, not on the outside. try this: show surface for the whole protein and then hide surface for not the active residues - something like this: from pymol import cmd from pymol import stored # load your protein and the active atoms as GOLD output cmd.load(protein.pdb, prot) cmd.load(active_atoms.pdb, act_res) # create a list of the activ residue-id's stored.act_res=[] cmd.iterate(act_res, stored.act_res.append(resi)) # create selection of the actives cmd.select(act_res,resi %s %stored.act_res[0]) for i in stored.act_res: cmd.select(act_res,act_res or resi %s %i) # create selection of the non-actives cmd.select(not_act_res, prot and not act_res) # show surface cmd.show(surface, prot) cmd.hide(surface, not_act_res ) cmd.delete(not_act_res) Cheers, Betty
RE: [PyMOL] Surface of cavity
Paul, PyMOL generally shows all sides of an exposed atom, but perhaps you could load both the GOLD output and the original structure. You could then only show the surface on the atoms in the original structure with corresponding atoms in the gold output as follows: load orig.pdb load gold.pdb then show surface, orig in gold or show surface, orig like gold That might produce something close to what you want. Note that: in matches chains, segments, residue names, residue ids, and atom names. like just matches residue ids and atom names. You can use alter all, segi='' alter all, chain='' to clear out the segment and/or chain IDs before using in to selectively reduce its stringency. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Paul Wilhelm Elsinghorst Sent: Friday, January 20, 2006 11:33 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Surface of cavity Hi, a little question regarding cavity surfaces :-) I have a set of active atoms (GOLD output) that surround a cavity. Now I want to dipslay the surface only for the cavity wall, not on the outside. Any ideas? Paul
Re: [PyMOL] surface representation showing mutations
Hi Sarma, I can change the color of the surface to gray or a rainbow gradient using the options but can't find a way to specify the residues that need to be colored differently in a surface representation. You most likely need to select the residues first. That will give you an extra entry in the right panel which you can then modify (e.g. change color). You can select specific residues via the PyMOL sequence view (Display - View Sequence). Notice that when you select residues they are highlighted in the structure (purple dots) and you get an extra entry in the right panel. You can then change the color for those specific residues. Another way to select residues is the command (you can enter them in any of the two PyMOL windows): select name, selection For example: select protein_x_interaction, residue 456+874 You will then get a protein_x_interaction in the right panel. Ranges of residues can be selected with (notice the : between the first and last residue): select protein_y_interaction, residue 53:87 Hope this is of help to you! Kind Regards, ./ Kristoffer Denmark
RE: [PyMOL] surface representation showing mutations
Have you tried the select resi function? This allows you to specify the identification numbers of the amino-acids you want to select (and color). Have a look here for the complete description: http://pymol.sourceforge.net/newman/user/S0220commands.html Regards, Grégori Gerebtzoff Division of Biophysical Chemistry Biozentrum, University of Basel Klingelbergstrasse 70 CH-4056 Basel / Switzerland
Re: [PyMOL] surface representation showing mutations
Sarma, I am trying to create a surface representation of a protein with mutations that abolish activity in one color (say yellow) and the ones that don't change activity in another (say green). The rest of the residues colored gray. I can change the color of the surface to gray or a rainbow gradient using the options but can't find a way to specify the residues that need to be colored differently in a surface representation. One easy way to go about coloring residues differently based on some property like a residue number is to create atom selections for the various sets of residues in which you're interested and then color those selections using the PyMOL menu commands... Look in the Command Syntax and Atom Selections section of the PyMOL User's Manual (http://pymol.sourceforge.net/newman/user/toc.html) in order to learn about atom selections. You can enter a command like select mymuts, all and resi 23,32,45 to create a selection consisting of all atoms in residues 23, 32, and 45, and then something like color green, mymuts to color these residues green. So something like this might be what you want: select mymut, (resi 23,32,45) select mywt, (resi 1,2,3,4,5) color grey, all color yellow, mymut color green, mywt If you don't foresee needing the atom selections for anything else, you could just combine the atom selection with the color command (color yellow, (resi 23,32,45)), but it's most often useful to create an independent atom selection. If you want to color even more precisely by a parameter such as the strength of the mutant's inactivity -- so multiple values instead of just 0/1 -- then you could try looking at the Sequence Conservation example on my PyMOL page (this is documented at http://mccammon.ucsd.edu/~cmura/PyMOL for now; I'll eventually migrate this stuff into PyMolWiki and post updates of new stuff at http://www.pymolwiki.org/index.php/Cmura). Good luck, Cameron === pymol-users-requ...@lists.sourceforge.net wrote (on 04/03/2005 08:19 PM): === Today's Topics: 1. surface representation showing mutations (Ganapathy Sarma) Subject: [PyMOL] surface representation showing mutations From: Ganapathy Sarma gnsa...@gmail.com Date: Sun, 03 Apr 2005 18:13:49 -0700 To: pymol-users@lists.sourceforge.net Hello PYMOLers, I am a very new entry to the world of Pymol after seeing the program in action at a recent conference. I am trying to create a surface representation of a protein with mutations that abolish activity in one color (say yellow) and the ones that don't change activity in another (say green). The rest of the residues colored gray. I can change the color of the surface to gray or a rainbow gradient using the options but can't find a way to specify the residues that need to be colored differently in a surface representation. Any help is appreciated. Thanks, Sarma
Re: [PyMOL] surface/grid questions
Dear Marcelo, * castilho casti...@if.sc.usp.br [2004-08-23 17:02] wrote: My name is Marcelo and I am a basic-level pymol user. I work with docking programs and I am trying to make pymol our default program for analysing docking results...this brings me to some questions: Is it possible to colour protein surface according to Hydrogen donor/acceptor properties in pymol ? I guess that depends on whether you can define what constitutes a donor or acceptor easily enough. I think with sufficient logical operations you could. For example: select donor, name N or (resn ASN and elem N) or (resn GLN and elem N) etc. Then you could colour the donor selection as you like. Does Pymol computes a ligand-protein interface (for example just the contact area between the ligand and the protein)? is it possible to see just this surface area according to the previous question schema ? If you have the ligand and protein in separate objects, let's call them ligand and protein, you can do this: show surf, ligand within 3. of protein show surf, protein within 3. of ligand where it will show the surface only for atoms within 3 Angstroms of the other molecule. You could also include the byres keyword which might remove some holes in the surface if desired: show surf, byres ligand within 3. of protein If the structure file you read in contains both, then you can create separate objects from the single initial object: create protein, initial and chain A create ligand, initial and chain B where I'm assuming that the protein has the A chain identifier and the ligand has the B chain identifier and the initial object was called initial. Does pymol read grid (Goodford's grids) ? in case not, how can I convert GRID maps into something pymol can read ? It appears that you can convert Goodfords grid format to other map formats (e.g. Brix and CCP4) using the Bsoft program package: http://www.niams.nih.gov/rcn/labbranch/lsbr/software/bsoft/bsoft.html The software contains the code for reading and writing GRID files, so perhaps that could be incorporated into PyMOL. (I couldn't find any license file, though I suppose the author could be contacted directly.) Hope this helps. Cheers, Rob -- Robert L. Campbell, Ph.D. r...@post.queensu.ca Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
RE: [PyMOL] Surface triangulation of isopotential surfaces
Nuno, For a couple of reasons, I curently believe that electrostatic calculations based on point charge models are not valid near or within the protein surface -- you need to be at least one atom radius beyond the molecular envelope in order to draw physically meaningful interpretations. Why? 1) Real atoms aren't point charges. 2) Atomic point charges are parameterized by fitting electrostatic potentials over a series of shells outside the molecular envelope. In other words, despite the fact that this is commonly done, I question whether or not it is valid to display or interpret electrostatic potentials directly at the protein vdw surface. That is why I now encourage the use of space-filling representations and solvent accessible surfaces, such as dots with dot_solvent = 1, when viewing electrostatic potentials. PyMOL could probably do more to make this easy, such as projecting the ESP on the solvent accessible surface back onto a molecular surfaces... Do others agree with this analysis, or am I just a lone heretic? Cheers, Wraren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Nuno Micaelo Sent: Wednesday, February 04, 2004 1:49 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Surface triangulation of isopotential surfaces How do i improve the surface triangulation of isopotential surfaces? The isosurface triangulation near the protein is very poor and is independent of the grid size chosen in MEAD. Thanks for your attention. -- º¤ø,¸,ø¤º*`*º¤ø,¸¸,ø¤º*`*º¤ø,¸¸,ø¤º*` ,ø¤º*`*º¤ø,¸¸,ø¤º*`*º¤ø,¸¸,ø¤º*`*º¤ø, Nuno Miguel da Silva Micaelo Instituto de Tecnologia Química e Biológica ITQB - Protein Modeling Group º¤ø,¸,ø¤º*`*º¤ø,¸¸,ø¤º*`*º¤ø,¸¸,ø¤º*` ,ø¤º*`*º¤ø,¸¸,ø¤º*`*º¤ø,¸¸,ø¤º*`*º¤ø, N’×zf¢–+,¦‰ì¢·o! –*lx*'ÛM8·¦‰êÞ ‰ßz·§qê':—§NŠ%°7¯zZ)™éíjwHž× «b¢tžzØ^n·švØh|G%Š› iËb¾+ræ빪òߘ§v¡z)‚m§ÿðà œ–*lyÊ'¢¸?¢Çg?#.ë ®ÉšŠX§‚X¬´üŒ8»¬z»%ŠËl²‹«qçè® §zØm¶›?þX¬¶Ë(º· ~ŠàzwþX¬¶ÏåŠËbú?§)¨–ë
RE: [PyMOL] surface area calculation
Joel, Yes, PyMOL does have this capability, but it is immature and not routinely validated. The basic concepts are: 1) get_area selection command will return the effective surface area of the dots that you would see from show dots, selection. This is a discrete approximation -- not an exact calculation. 2) you can use the dot_solvent setting to control whether you get solvent surface area or a molecular surface area. 1=solvent, 0=molecular 3) the accuracy of the measurement depends on the density of dots, which is controlled by the dot_density setting (1-4). 4) the solvent radius is controlled by the solvent_radius setting (default 1.4). For example: PyMOL load $TUT/1hpv.pdb PyMOL show dots, resn arg PyMOL get_area resn arg cmd.get_area: 1147.956 Angstroms^2. PyMOLset dot_solvent, on PyMOLget_area resn arg cmd.get_area: 673.084 Angstroms^2. PyMOLset dot_density, 3 PyMOLget_area resn arg cmd.get_area: 674.157 Angstroms^2. PyMOLset dot_density, 4 PyMOLget_area resn arg cmd.get_area: 672.056 Angstroms^2. PyMOLget_area all cmd.get_area: 13837.804 Angstroms^2. This code has not been recently validated (though I did check it a couple years back), so I would suggest that people perform some kind of independent check on their system before trusting the results. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Harp, Joel M Sent: Wednesday, November 12, 2003 2:10 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] surface area calculation Is it possible to get pymol to calculate surface area for a defined object? For instance, can it calculate surface area occupied by arginines. Thanks, Joel Joel M. Harp Vanderbilt University
RE: [PyMOL] surface area calculation
Close, but it depends on whether you want the surface area of the residues alone, or in the context of the molecule. load protein.pdb get_area resn arg will be less than create arg_object, resn arg get_area arg_object This is because the first example will give you only the exposed area of the arginines in the presence of the other atoms, whereas the second gives the area of the arginines in isolation. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Kaushik Raha Sent: Wednesday, November 12, 2003 2:50 PM To: Harp, Joel M Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] surface area calculation To calculate surface area for a defined object from the PyMOL command line type: print cmd.get_area(obj) where obj is the name of your object. for arginines: create ARG, resn ARG print cmd.get_area(ARG) Kaushik. On Wednesday, November 12, 2003, at 05:10 PM, Harp, Joel M wrote: Is it possible to get pymol to calculate surface area for a defined object? For instance, can it calculate surface area occupied by arginines. Thanks, Joel Joel M. Harp Vanderbilt University
RE: [PyMOL] surface
Molecular (a discrete approximation to the Connolly surface). -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Dennis Wolan Sent: Tuesday, April 29, 2003 2:42 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] surface Dear all, This has probably been asked a thousand times, but is the default surface representation a molecular surface or a solvent accessible surface? Thanks in advance, Dennis
RE: [PyMOL] surface charge?
Camille, This capability exists in the development version, but isn't ready for prime-time yet. Look for it in the next release. In the meantime, you might try using raster3d to render your grasp surface, via its ungrasp tool. http://www.bmsc.washington.edu/raster3d/html/r3d_filters.html#grasp Or you can load the converted grasp surface into PyMOL as a .r3d file and render it there. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of cami...@mrc-lmb.cam.ac.uk Sent: Wednesday, April 23, 2003 3:01 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] surface charge? Hi Warren, I'm using PyMol to make the figures in a paper I am currently writing. I know that pymol can generate surfaces at the moment but not charge. Is there any way to colour a surface by charge in pymol using charges calculated in grasp? ...or can I import a grasp surface? I heard that this sort of thing was in the pipe-line, do you have a rough estimate of when it will be available? Camille p.s. I'm working on os x with npymol. --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
