Re: [ccp4bb] carving up maps (was re: pymol help)
Having put the make my density look publishable (mapcover) command in BobScript, my conscience wouldn't ever let me use it as it gives a false impression of experimental maps! It is useful, though, in a couple of cases: where the map is not representing electron density but calculated from the structure (e.g. binding pockets...) and - artistic tip for the day - to draw a map in two colours which I have used in presentations to help show ligand density. You draw the map in one colour, then increase the map line width ever so slightly and draw it again with map cover and in a different colour. The ligand density is then highlighted but the rest of the structure and noise are still visible. However, the original question seemed to be targeted at obscuring information (the ligand structure) rather than showing it. I assume this is not for academic purposes! My suggestion there would be to use a low resolution map (say calculated to 3.5A) covering where the ligand is and the full resolution map for the rest of the molecule. (Effectively rendering the ligand density as a blob). Otherwise Tassos is spot on... use Illustrator... Cheers, Robert
Re: [ccp4bb] carving up maps (was re: pymol help)
Along those lines, one of the things you can do with PyMOL is color map density based on the color of the nearest atom (if any): Example image at: http://delsci.com/img/map_color.jpg Example script: load ref.pdb load map.xplor isomesh mesh, ref, 1.0 ramp_new ramp, ref, [0,1.5,2], [-1, -1, grey70] color ramp, mesh Cheers, Warren -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Robert Esnouf Sent: Thursday, November 01, 2007 5:06 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] carving up maps (was re: pymol help) Having put the make my density look publishable (mapcover) command in BobScript, my conscience wouldn't ever let me use it as it gives a false impression of experimental maps! It is useful, though, in a couple of cases: where the map is not representing electron density but calculated from the structure (e.g. binding pockets...) and - artistic tip for the day - to draw a map in two colours which I have used in presentations to help show ligand density. You draw the map in one colour, then increase the map line width ever so slightly and draw it again with map cover and in a different colour. The ligand density is then highlighted but the rest of the structure and noise are still visible. However, the original question seemed to be targeted at obscuring information (the ligand structure) rather than showing it. I assume this is not for academic purposes! My suggestion there would be to use a low resolution map (say calculated to 3.5A) covering where the ligand is and the full resolution map for the rest of the molecule. (Effectively rendering the ligand density as a blob). Otherwise Tassos is spot on... use Illustrator... Cheers, Robert
[ccp4bb] carving up maps (was re: pymol help)
I'd be curious to know if there is any consensus in the community with using the carve command for showing maps. I have never felt comfortable showing density within a cutoff radius of a particular residue or--even worse--a ligand, and felt the figures should display the extraneous bits as well. The burden was on the crystallographer to find an appropriate view (slab, sigma, etc...) to display the map. The Bobscript manual appears to agree with me on this one as it states: http://www.strubi.ox.ac.uk/bobscript/doc24.html If your density is good then you will just have density over residue 999, but if things are not so hot then you may want to cheat and just draw the bits of density near to the selected atoms. Just curious, Andy -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Senior Research Scientist Hauptman-Woodward Institute Assistant Professor Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick On 10/29/07 4:40 AM, Stefan Schmelz [EMAIL PROTECTED] wrote: Dear Yanming, To show pretty density of a model you have to import a ccp4 density map and display it around your ligand. The simplest solution is using ccp4 and tick the box Generate weighted difference maps files in CCP4 format when running Refmac5 (one or two cycles are enough). Specify names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4. This renamed map (e.g. fwt.ccp4) can be opened in pymol. To show density around our ligand you can use the following command: isomesh map, name_of_fwtmap, 1.0, ligand, carve=1.8 (map = greats an object name map, name_of_fwtmap = name of your map, 1.0 = Sigma level, carve=1.8 = width map is displayed around your ligand This will allow you to show a pretty electron density map around your ligand without any chemical info of the ligand. Stefan Schmelz Yanming Zhang wrote: Hi, all, I want to make a pymol figure wich can show the pretty density of a ligand. But we don't want to show the detailed chemical info of the ligand. If I use a large enough sphere_scale for the ligand, the chemical info will be hidden but the density map will be disrupted. If I use a smaller sphere_scale, the density looks great but the chemical info of the ligand will be visible. How should I overcome this dilemma? Thank you very much for your help. Yanming
Re: [ccp4bb] carving up maps (was re: pymol help)
Dear Andrew, Thank you for that posting; I would like to simply agree with the Bobscript manual and your suggested practice. I think the 'carve' commands should not be there; if you wonder why, take a ligand, put it wherever you want in space, set the map sigma to -0.5, display a map with carve=1.2 and think if this picture is informative, especially in the context of your favorite competitor publishing it in Nature. A. PS Yanming, if you really want to do that what you ask for, ADOBE ILLUSTRATOR IS THE BEST WAY TO GO From: [EMAIL PROTECTED] Subject:Re: [ccp4bb] pymol help Date: October 29, 2007 8:44:46 GMT+01:00 To: CCP4BB@JISCMAIL.AC.UK Reply-To: [EMAIL PROTECTED] Dear all, Sorry I did not make it clear in my first email. Now my question can boil down to: IS IT POSSIBLE TO ONLY ZOOM ONE OBJECT AND KEEP ALL THE OTHER OBJECTS UN-ZOOMED IN PYMOL? thanks Yanming On Oct 29, 2007, at 13:43, Andrew Gulick wrote: I'd be curious to know if there is any consensus in the community with using the carve command for showing maps. I have never felt comfortable showing density within a cutoff radius of a particular residue or--even worse--a ligand, and felt the figures should display the extraneous bits as well. The burden was on the crystallographer to find an appropriate view (slab, sigma, etc...) to display the map. The Bobscript manual appears to agree with me on this one as it states: http://www.strubi.ox.ac.uk/bobscript/doc24.html If your density is good then you will just have density over residue 999, but if things are not so hot then you may want to cheat and just draw the bits of density near to the selected atoms. Just curious, Andy -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Senior Research Scientist Hauptman-Woodward Institute Assistant Professor Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick On 10/29/07 4:40 AM, Stefan Schmelz [EMAIL PROTECTED] wrote: Dear Yanming, To show pretty density of a model you have to import a ccp4 density map and display it around your ligand. The simplest solution is using ccp4 and tick the box Generate weighted difference maps files in CCP4 format when running Refmac5 (one or two cycles are enough). Specify names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4. This renamed map (e.g. fwt.ccp4) can be opened in pymol. To show density around our ligand you can use the following command: isomesh map, name_of_fwtmap, 1.0, ligand, carve=1.8 (map = greats an object name map, name_of_fwtmap = name of your map, 1.0 = Sigma level, carve=1.8 = width map is displayed around your ligand This will allow you to show a pretty electron density map around your ligand without any chemical info of the ligand. Stefan Schmelz Yanming Zhang wrote: Hi, all, I want to make a pymol figure wich can show the pretty density of a ligand. But we don't want to show the detailed chemical info of the ligand. If I use a large enough sphere_scale for the ligand, the chemical info will be hidden but the density map will be disrupted. If I use a smaller sphere_scale, the density looks great but the chemical info of the ligand will be visible. How should I overcome this dilemma? Thank you very much for your help. Yanming
Re: [ccp4bb] carving up maps (was re: pymol help)
Anastassis Perrakis wrote: Dear Andrew, Thank you for that posting; I would like to simply agree with the Bobscript manual and your suggested practice. I think the 'carve' commands should not be there; if you wonder why, take a ligand, put it wherever you want in space, set the map sigma to -0.5, display a map with carve=1.2 and think if this picture is informative, especially in the context of your favorite competitor publishing it in Nature. A. The fact that a tool can be misused does not necessarily mean that there is something wrong with the tool, just with some users. I agree that with current ray-traced images there is less need for this tool than in the old blackwhite line diagrams where a lack of 3D perception easily led to cluttered images. However, if showing the density of interest really benefits from this trick then it's fine with me as long as you indicate in the legend what map and carve settings were used. Bart -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 ==
Re: [ccp4bb] carving up maps (was re: pymol help)
This is not such a problem when using the old Map-cover command in O, because the cut-offs are flat planes, you would get cubic density around each atom which would raise the suspicion of even the most gullible reader. But a better solution would be to not contour the carved surface- leave a gaping hole in the net where something else is connected. Another way to describe this- contour the real density, but only display the contours within certain radius of selected atoms. Then in Anastassis's example there would be no density for the atoms because the contour is outside the cutoff. Anastassis Perrakis wrote: Dear Andrew, Thank you for that posting; I would like to simply agree with the Bobscript manual and your suggested practice. I think the 'carve' commands should not be there; if you wonder why, take a ligand, put it wherever you want in space, set the map sigma to -0.5, display a map with carve=1.2 and think if this picture is informative, especially in the context of your favorite competitor publishing it in Nature. A. PS Yanming, if you really want to do that what you ask for, ADOBE ILLUSTRATOR IS THE BEST WAY TO GO *From: * [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] *Subject: * *Re: [ccp4bb] pymol help* *Date: * October 29, 2007 8:44:46 GMT+01:00 *To: * CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK *Reply-To: * [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Dear all, Sorry I did not make it clear in my first email. Now my question can boil down to: IS IT POSSIBLE TO ONLY ZOOM ONE OBJECT AND KEEP ALL THE OTHER OBJECTS UN-ZOOMED IN PYMOL? thanks Yanming On Oct 29, 2007, at 13:43, Andrew Gulick wrote: I'd be curious to know if there is any consensus in the community with using the carve command for showing maps. I have never felt comfortable showing density within a cutoff radius of a particular residue or--even worse--a ligand, and felt the figures should display the extraneous bits as well. The burden was on the crystallographer to find an appropriate view (slab, sigma, etc...) to display the map. The Bobscript manual appears to agree with me on this one as it states: http://www.strubi.ox.ac.uk/bobscript/doc24.html If your density is good then you will just have density over residue 999, but if things are not so hot then you may want to cheat and just draw the bits of density near to the selected atoms. Just curious, Andy -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Senior Research Scientist Hauptman-Woodward Institute Assistant Professor Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick On 10/29/07 4:40 AM, Stefan Schmelz [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Dear Yanming, To show pretty density of a model you have to import a ccp4 density map and display it around your ligand. The simplest solution is using ccp4 and tick the box Generate weighted difference maps files in CCP4 format when running Refmac5 (one or two cycles are enough). Specify names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4. This renamed map (e.g. fwt.ccp4) can be opened in pymol. To show density around our ligand you can use the following command: isomesh map, name_of_fwtmap, 1.0, ligand, carve=1.8 (map = greats an object name map, name_of_fwtmap = name of your map, 1.0 = Sigma level, carve=1.8 = width map is displayed around your ligand This will allow you to show a pretty electron density map around your ligand without any chemical info of the ligand. Stefan Schmelz Yanming Zhang wrote: Hi, all, I want to make a pymol figure wich can show the pretty density of a ligand. But we don't want to show the detailed chemical info of the ligand. If I use a large enough sphere_scale for the ligand, the chemical info will be hidden but the density map will be disrupted. If I use a smaller sphere_scale, the density looks great but the chemical info of the ligand will be visible. How should I overcome this dilemma? Thank you very much for your help. Yanming
Re: [ccp4bb] carving up maps (was re: pymol help)
I don't like using 'carve' options but I can see where it may come useful. On the positive side, in the age where deposition of coordinates and structure factors is almost mandatory, there shouldn't be a question of how your map looks because presumably the skeptical reader can go and calculate one for themselves. If someone wanted to fib in an image - they can do it in a million different ways regardless of whether 'carve' is used or not (you can create entire fake maps to show whatever features you want, if you're completely evil-minded). Artem -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Andrew Gulick Sent: Monday, October 29, 2007 8:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] carving up maps (was re: pymol help) I'd be curious to know if there is any consensus in the community with using the carve command for showing maps. I have never felt comfortable showing density within a cutoff radius of a particular residue or--even worse--a ligand, and felt the figures should display the extraneous bits as well. The burden was on the crystallographer to find an appropriate view (slab, sigma, etc...) to display the map. The Bobscript manual appears to agree with me on this one as it states: http://www.strubi.ox.ac.uk/bobscript/doc24.html If your density is good then you will just have density over residue 999, but if things are not so hot then you may want to cheat and just draw the bits of density near to the selected atoms. Just curious, Andy -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Senior Research Scientist Hauptman-Woodward Institute Assistant Professor Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick On 10/29/07 4:40 AM, Stefan Schmelz [EMAIL PROTECTED] wrote: Dear Yanming, To show pretty density of a model you have to import a ccp4 density map and display it around your ligand. The simplest solution is using ccp4 and tick the box Generate weighted difference maps files in CCP4 format when running Refmac5 (one or two cycles are enough). Specify names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4. This renamed map (e.g. fwt.ccp4) can be opened in pymol. To show density around our ligand you can use the following command: isomesh map, name_of_fwtmap, 1.0, ligand, carve=1.8 (map = greats an object name map, name_of_fwtmap = name of your map, 1.0 = Sigma level, carve=1.8 = width map is displayed around your ligand This will allow you to show a pretty electron density map around your ligand without any chemical info of the ligand. Stefan Schmelz Yanming Zhang wrote: Hi, all, I want to make a pymol figure wich can show the pretty density of a ligand. But we don't want to show the detailed chemical info of the ligand. If I use a large enough sphere_scale for the ligand, the chemical info will be hidden but the density map will be disrupted. If I use a smaller sphere_scale, the density looks great but the chemical info of the ligand will be visible. How should I overcome this dilemma? Thank you very much for your help. Yanming
Re: [ccp4bb] carving up maps (was re: pymol help)
contour the real density, but only display the contours within certain radius of selected atoms. That is exactly what PyMOL does. -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Edward Berry Sent: Monday, October 29, 2007 4:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] carving up maps (was re: pymol help) This is not such a problem when using the old Map-cover command in O, because the cut-offs are flat planes, you would get cubic density around each atom which would raise the suspicion of even the most gullible reader. But a better solution would be to not contour the carved surface- leave a gaping hole in the net where something else is connected. Another way to describe this- contour the real density, but only display the contours within certain radius of selected atoms. Then in Anastassis's example there would be no density for the atoms because the contour is outside the cutoff. Anastassis Perrakis wrote: Dear Andrew, Thank you for that posting; I would like to simply agree with the Bobscript manual and your suggested practice. I think the 'carve' commands should not be there; if you wonder why, take a ligand, put it wherever you want in space, set the map sigma to -0.5, display a map with carve=1.2 and think if this picture is informative, especially in the context of your favorite competitor publishing it in Nature. A. PS Yanming, if you really want to do that what you ask for, ADOBE ILLUSTRATOR IS THE BEST WAY TO GO *From: * [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] *Subject: * *Re: [ccp4bb] pymol help* *Date: * October 29, 2007 8:44:46 GMT+01:00 *To: * CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK *Reply-To: * [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Dear all, Sorry I did not make it clear in my first email. Now my question can boil down to: IS IT POSSIBLE TO ONLY ZOOM ONE OBJECT AND KEEP ALL THE OTHER OBJECTS UN-ZOOMED IN PYMOL? thanks Yanming On Oct 29, 2007, at 13:43, Andrew Gulick wrote: I'd be curious to know if there is any consensus in the community with using the carve command for showing maps. I have never felt comfortable showing density within a cutoff radius of a particular residue or--even worse--a ligand, and felt the figures should display the extraneous bits as well. The burden was on the crystallographer to find an appropriate view (slab, sigma, etc...) to display the map. The Bobscript manual appears to agree with me on this one as it states: http://www.strubi.ox.ac.uk/bobscript/doc24.html If your density is good then you will just have density over residue 999, but if things are not so hot then you may want to cheat and just draw the bits of density near to the selected atoms. Just curious, Andy -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Senior Research Scientist Hauptman-Woodward Institute Assistant Professor Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick On 10/29/07 4:40 AM, Stefan Schmelz [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Dear Yanming, To show pretty density of a model you have to import a ccp4 density map and display it around your ligand. The simplest solution is using ccp4 and tick the box Generate weighted difference maps files in CCP4 format when running Refmac5 (one or two cycles are enough). Specify names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4. This renamed map (e.g. fwt.ccp4) can be opened in pymol. To show density around our ligand you can use the following command: isomesh map, name_of_fwtmap, 1.0, ligand, carve=1.8 (map = greats an object name map, name_of_fwtmap = name of your map, 1.0 = Sigma level, carve=1.8 = width map is displayed around your ligand This will allow you to show a pretty electron density map around your ligand without any chemical info of the ligand. Stefan Schmelz Yanming Zhang wrote: Hi, all, I want to make a pymol figure wich can show the pretty density of a ligand. But we don't want to show the detailed chemical info of the ligand. If I use a large enough sphere_scale for the ligand, the chemical info will be hidden but the density map will be disrupted. If I use a smaller sphere_scale, the density looks great but the chemical info of the ligand will be visible. How should I overcome this dilemma? Thank you very much for your help. Yanming
