From dieter.blaas at meduniwien.ac.at Tue Aug 1 12:46:10 2017 From: dieter.blaas at meduniwien.ac.at (Dieter Blaas) Date: Tue, 1 Aug 2017 21:46:10 +0200 Subject: [Chimera-users] put outline box at the center of a marker Message-ID: Hi, I'd like to put an outline box with, say 100 x 100 x 100 px around the position of a marker so as to have the marker exactly in the center of the box. Is this possible? Thanks a lot for help, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas at meduniwien.ac.at ------------------------------------------------------------------------ From meng at cgl.ucsf.edu Tue Aug 1 13:22:11 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 1 Aug 2017 13:22:11 -0700 Subject: [Chimera-users] put outline box at the center of a marker In-Reply-To: References: Message-ID: <7E5385D6-1D32-42D0-92B3-4670D408BEAA@cgl.ucsf.edu> Hi Dieter, If you already had a larger map (or create one from scratch with ?vop new? or from atoms/markers with ?molmap"), you could use the Volume Viewer menu Features? Atom Box to crop out a box centered on a selected atom or marker. Then use Volume Viewer menu Features? Data display options, "show outline box..." on the cropped data set. You can move the slider so that no isosurface is shown for the map. However, the box size is specified in units of distance (generally Angstroms) not pixels, and the original map must already enclose that whole volume. I?m also not certain about whether the box would be EXACTLY centered on the marker? it might be slightly off due to rounding and grid-spacing of the original map. If the original map is not in the right place, you can use the ?A?ctive checkboxes in the Model Panel to activate/deactivate for motion and move models separately. Maybe this is too many steps to be convenient, however. vop new Volume Viewer, Features menu I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 1, 2017, at 12:46 PM, Dieter Blaas wrote: > > Hi, > > I'd like to put an outline box with, say 100 x 100 x 100 px around the position of a marker so as to have the marker exactly in the center of the box. Is this possible? > > Thanks a lot for help, best, Dieter From dieter.blaas at meduniwien.ac.at Tue Aug 1 13:36:08 2017 From: dieter.blaas at meduniwien.ac.at (Dieter Blaas) Date: Tue, 1 Aug 2017 22:36:08 +0200 Subject: [Chimera-users] put outline box at the center of a marker In-Reply-To: <7E5385D6-1D32-42D0-92B3-4670D408BEAA@cgl.ucsf.edu> References: <7E5385D6-1D32-42D0-92B3-4670D408BEAA@cgl.ucsf.edu> Message-ID: <3a4c1a79-c2f2-08c5-f86e-f260e4632cc3@meduniwien.ac.at> Hi Elaine, thank you very much! I should have mentioned that I have just a volume no coordinates. I checked Atom Box but it just allows one to draw the box around selected atoms but not around a marker. At least I could not find any option for that. I have set a marker on the volume and want to cut out a box with its center on the marker. Best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas at meduniwien.ac.at ------------------------------------------------------------------------ Am 01.08.2017 um 22:22 schrieb Elaine Meng: > Hi Dieter, > If you already had a larger map (or create one from scratch with ?vop new? or from atoms/markers with ?molmap"), you could use the Volume Viewer menu Features? Atom Box to crop out a box centered on a selected atom or marker. Then use Volume Viewer menu Features? Data display options, "show outline box..." on the cropped data set. You can move the slider so that no isosurface is shown for the map. However, the box size is specified in units of distance (generally Angstroms) not pixels, and the original map must already enclose that whole volume. I?m also not certain about whether the box would be EXACTLY centered on the marker? it might be slightly off due to rounding and grid-spacing of the original map. > > If the original map is not in the right place, you can use the ?A?ctive checkboxes in the Model Panel to activate/deactivate for motion and move models separately. > > Maybe this is too many steps to be convenient, however. > > vop new > > Volume Viewer, Features menu > > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > >> On Aug 1, 2017, at 12:46 PM, Dieter Blaas wrote: >> >> Hi, >> >> I'd like to put an outline box with, say 100 x 100 x 100 px around the position of a marker so as to have the marker exactly in the center of the box. Is this possible? >> >> Thanks a lot for help, best, Dieter From meng at cgl.ucsf.edu Tue Aug 1 13:40:39 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 1 Aug 2017 13:40:39 -0700 Subject: [Chimera-users] put outline box at the center of a marker In-Reply-To: <3a4c1a79-c2f2-08c5-f86e-f260e4632cc3@meduniwien.ac.at> References: <7E5385D6-1D32-42D0-92B3-4670D408BEAA@cgl.ucsf.edu> <3a4c1a79-c2f2-08c5-f86e-f260e4632cc3@meduniwien.ac.at> Message-ID: Hi Dieter, A marker is just a fake atom, so you can select the marker (Ctrl-click it) and use that atom box feature? at least, it worked when I tried it just now! Best, Elaine > On Aug 1, 2017, at 1:36 PM, Dieter Blaas wrote: > > Hi Elaine, > > thank you very much! I should have mentioned that I have just a volume no coordinates. I checked Atom Box but it just allows one to draw the box around selected atoms but not around a marker. At least I could not find any option for that. I have set a marker on the volume and want to cut out a box with its center on the marker. > > Best, Dieter > > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Fax: 0043 1 4277 9616, > e-mail: dieter.blaas at meduniwien.ac.at > ------------------------------------------------------------------------ > > Am 01.08.2017 um 22:22 schrieb Elaine Meng: >> Hi Dieter, >> If you already had a larger map (or create one from scratch with ?vop new? or from atoms/markers with ?molmap"), you could use the Volume Viewer menu Features? Atom Box to crop out a box centered on a selected atom or marker. Then use Volume Viewer menu Features? Data display options, "show outline box..." on the cropped data set. You can move the slider so that no isosurface is shown for the map. However, the box size is specified in units of distance (generally Angstroms) not pixels, and the original map must already enclose that whole volume. I?m also not certain about whether the box would be EXACTLY centered on the marker? it might be slightly off due to rounding and grid-spacing of the original map. >> >> If the original map is not in the right place, you can use the ?A?ctive checkboxes in the Model Panel to activate/deactivate for motion and move models separately. >> >> Maybe this is too many steps to be convenient, however. >> >> vop new >> >> Volume Viewer, Features menu >> >> >> I hope this helps, >> Elaine >> ---------- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >>> On Aug 1, 2017, at 12:46 PM, Dieter Blaas wrote: >>> >>> Hi, >>> I'd like to put an outline box with, say 100 x 100 x 100 px around the position of a marker so as to have the marker exactly in the center of the box. Is this possible? >>> Thanks a lot for help, best, Dieter > From dieter.blaas at meduniwien.ac.at Tue Aug 1 13:47:41 2017 From: dieter.blaas at meduniwien.ac.at (Dieter Blaas) Date: Tue, 1 Aug 2017 22:47:41 +0200 Subject: [Chimera-users] put outline box at the center of a marker In-Reply-To: References: <7E5385D6-1D32-42D0-92B3-4670D408BEAA@cgl.ucsf.edu> <3a4c1a79-c2f2-08c5-f86e-f260e4632cc3@meduniwien.ac.at> Message-ID: Hi Elaine, yes, it works! Just two more questions: If I use 'padding 100' does it mean that it draws a box with 100 x 100 x 100 A? And how can I save the volume enclosed in the box in the correct orientation with respect to the original volume? best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas at meduniwien.ac.at ------------------------------------------------------------------------ Am 01.08.2017 um 22:40 schrieb Elaine Meng: > Hi Dieter, > A marker is just a fake atom, so you can select the marker (Ctrl-click it) and use that atom box feature? at least, it worked when I tried it just now! > Best, > Elaine > >> On Aug 1, 2017, at 1:36 PM, Dieter Blaas wrote: >> >> Hi Elaine, >> >> thank you very much! I should have mentioned that I have just a volume no coordinates. I checked Atom Box but it just allows one to draw the box around selected atoms but not around a marker. At least I could not find any option for that. I have set a marker on the volume and want to cut out a box with its center on the marker. >> >> Best, Dieter >> >> ------------------------------------------------------------------------ >> Dieter Blaas, >> Max F. Perutz Laboratories >> Medical University of Vienna, >> Inst. Med. Biochem., Vienna Biocenter (VBC), >> Dr. Bohr Gasse 9/3, >> A-1030 Vienna, Austria, >> Tel: 0043 1 4277 61630, >> Fax: 0043 1 4277 9616, >> e-mail: dieter.blaas at meduniwien.ac.at >> ------------------------------------------------------------------------ >> >> Am 01.08.2017 um 22:22 schrieb Elaine Meng: >>> Hi Dieter, >>> If you already had a larger map (or create one from scratch with ?vop new? or from atoms/markers with ?molmap"), you could use the Volume Viewer menu Features? Atom Box to crop out a box centered on a selected atom or marker. Then use Volume Viewer menu Features? Data display options, "show outline box..." on the cropped data set. You can move the slider so that no isosurface is shown for the map. However, the box size is specified in units of distance (generally Angstroms) not pixels, and the original map must already enclose that whole volume. I?m also not certain about whether the box would be EXACTLY centered on the marker? it might be slightly off due to rounding and grid-spacing of the original map. >>> >>> If the original map is not in the right place, you can use the ?A?ctive checkboxes in the Model Panel to activate/deactivate for motion and move models separately. >>> >>> Maybe this is too many steps to be convenient, however. >>> >>> vop new >>> >>> Volume Viewer, Features menu >>> >>> >>> I hope this helps, >>> Elaine >>> ---------- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> >>>> On Aug 1, 2017, at 12:46 PM, Dieter Blaas wrote: >>>> >>>> Hi, >>>> I'd like to put an outline box with, say 100 x 100 x 100 px around the position of a marker so as to have the marker exactly in the center of the box. Is this possible? >>>> Thanks a lot for help, best, Dieter From meng at cgl.ucsf.edu Tue Aug 1 14:10:36 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 1 Aug 2017 14:10:36 -0700 Subject: [Chimera-users] put outline box at the center of a marker In-Reply-To: References: <7E5385D6-1D32-42D0-92B3-4670D408BEAA@cgl.ucsf.edu> <3a4c1a79-c2f2-08c5-f86e-f260e4632cc3@meduniwien.ac.at> Message-ID: <73436BA2-AF9F-4F07-A74B-DA5F5E246BEB@cgl.ucsf.edu> Hi Dieter, I believe that the box is already drawn along the same axes as the original map, so it's automatically in the same orientation. You can save the region with the ?volume? command, specifying the region bounds and any other file-saving options you might want: The region bounds are shown in the VV dialog as described below. Yes, if you just have one atom or marker selected, it would make the padding value the side-length of the cube centered on that point. If your data is in Angstroms (e.g. not nanometers) the size will be in those units. However, there is still the caveat of it not being exactly centered, depending on the grid size of the original map and the position of the marker. If I choose padding 2 or some other small size relative to the spacing, I can see that the marker isn?t exactly in the center or the box isn?t exactly a cube. You can check region bounds (VV menu Features? Region bounds) to see if it?s really a cube and even change the values to make it so, but that might put the point farther from the center. You can go back to the full-sized original map with VV menu Features? Subregion selection, clicking the ?Full? button. Best, Elaine > On Aug 1, 2017, at 1:47 PM, Dieter Blaas wrote: > > Hi Elaine, > yes, it works! Just two more questions: If I use 'padding 100' does it mean that it draws a box with 100 x 100 x 100 A? And how can I save the volume enclosed in the box in the correct orientation with respect to the original volume? > best, Dieter From dieter.blaas at meduniwien.ac.at Tue Aug 1 14:17:44 2017 From: dieter.blaas at meduniwien.ac.at (Dieter Blaas) Date: Tue, 1 Aug 2017 23:17:44 +0200 Subject: [Chimera-users] put outline box at the center of a marker In-Reply-To: <73436BA2-AF9F-4F07-A74B-DA5F5E246BEB@cgl.ucsf.edu> References: <7E5385D6-1D32-42D0-92B3-4670D408BEAA@cgl.ucsf.edu> <3a4c1a79-c2f2-08c5-f86e-f260e4632cc3@meduniwien.ac.at> <73436BA2-AF9F-4F07-A74B-DA5F5E246BEB@cgl.ucsf.edu> Message-ID: Many thanks, will try! best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas at meduniwien.ac.at ------------------------------------------------------------------------ Am 01.08.2017 um 23:10 schrieb Elaine Meng: > Hi Dieter, > I believe that the box is already drawn along the same axes as the original map, so it's automatically in the same orientation. You can save the region with the ?volume? command, specifying the region bounds and any other file-saving options you might want: > > > The region bounds are shown in the VV dialog as described below. > > Yes, if you just have one atom or marker selected, it would make the padding value the side-length of the cube centered on that point. If your data is in Angstroms (e.g. not nanometers) the size will be in those units. However, there is still the caveat of it not being exactly centered, depending on the grid size of the original map and the position of the marker. If I choose padding 2 or some other small size relative to the spacing, I can see that the marker isn?t exactly in the center or the box isn?t exactly a cube. > > You can check region bounds (VV menu Features? Region bounds) to see if it?s really a cube and even change the values to make it so, but that might put the point farther from the center. > > You can go back to the full-sized original map with VV menu Features? Subregion selection, clicking the ?Full? button. > Best, > Elaine > >> On Aug 1, 2017, at 1:47 PM, Dieter Blaas wrote: >> >> Hi Elaine, >> yes, it works! Just two more questions: If I use 'padding 100' does it mean that it draws a box with 100 x 100 x 100 A? And how can I save the volume enclosed in the box in the correct orientation with respect to the original volume? >> best, Dieter From matzov.donna at weizmann.ac.il Wed Aug 2 04:37:19 2017 From: matzov.donna at weizmann.ac.il (Matzov Donna) Date: Wed, 2 Aug 2017 11:37:19 +0000 Subject: [Chimera-users] Volume transparancy Message-ID: <37E4FF96D5A9144BB2D386E895D47AACBFC8B520@ibwmbx03> Hello, I'm trying to make a movie such that a ribbon model would appear while its maps (represented as surface) is already shown and is partially transparent. For that I wanted to set the ribbon transparency to 100 and then use the following command: transparency 0,r frames 100 The problem is that when when the ribbon in 100% transparent, the shape is still apparent in the partially transparent map. the ribbon shapes are not seen only when the map is not transparent at all. Is there a way to fix that? Thanks, Donna -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Aug 2 10:56:07 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 2 Aug 2017 10:56:07 -0700 Subject: [Chimera-users] Volume transparancy In-Reply-To: <37E4FF96D5A9144BB2D386E895D47AACBFC8B520@ibwmbx03> References: <37E4FF96D5A9144BB2D386E895D47AACBFC8B520@ibwmbx03> Message-ID: Hello Donna, Unfortunately multiple transparencies often don?t work well together. I would use ?movie crossfade? instead of ribbon transparency. In that case, you wouldn?t be able to have the scene moving (rotating, zooming, etc.) at the same time, since the crossfade is simply a pixel-for-pixel interpolation. When the scene is not moving, specify a crossfade transition between ribbon hidden and ribbon shown. You can specify the number of frames. It will show up in the recorded movie even though not shown on the screen. In our next-gen software ChimeraX, however, there is a ?crossfade? that is shown on the screen: Another possibility for avoiding multiple transparent models is showing the surface as mesh, but then you would probably need to tinker with mesh fineness, linewidth, and lighting. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 2, 2017, at 4:37 AM, Matzov Donna wrote: > > Hello, > I'm trying to make a movie such that a ribbon model would appear while its maps (represented as surface) is already shown and is partially transparent. For that I wanted to set the ribbon transparency to 100 and then use the following command: > > transparency 0,r frames 100 > > The problem is that when when the ribbon in 100% transparent, the shape is still apparent in the partially transparent map. the ribbon shapes are not seen only when the map is not transparent at all. > > Is there a way to fix that? > Thanks, > Donna > From matthewd at bcm.edu Wed Aug 2 11:05:11 2017 From: matthewd at bcm.edu (Dougherty, Matthew T) Date: Wed, 2 Aug 2017 18:05:11 +0000 Subject: [Chimera-users] Volume transparancy In-Reply-To: References: <37E4FF96D5A9144BB2D386E895D47AACBFC8B520@ibwmbx03>, Message-ID: another approach is to disable the display of the model at frame 101. This will remove the defects and improve your overall graphics computation. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= ________________________________ From: Chimera-users on behalf of Elaine Meng Sent: Wednesday, August 2, 2017 12:56:07 PM To: Matzov Donna Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Volume transparancy Hello Donna, Unfortunately multiple transparencies often don?t work well together. I would use ?movie crossfade? instead of ribbon transparency. In that case, you wouldn?t be able to have the scene moving (rotating, zooming, etc.) at the same time, since the crossfade is simply a pixel-for-pixel interpolation. When the scene is not moving, specify a crossfade transition between ribbon hidden and ribbon shown. You can specify the number of frames. It will show up in the recorded movie even though not shown on the screen. In our next-gen software ChimeraX, however, there is a ?crossfade? that is shown on the screen: Another possibility for avoiding multiple transparent models is showing the surface as mesh, but then you would probably need to tinker with mesh fineness, linewidth, and lighting. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 2, 2017, at 4:37 AM, Matzov Donna wrote: > > Hello, > I'm trying to make a movie such that a ribbon model would appear while its maps (represented as surface) is already shown and is partially transparent. For that I wanted to set the ribbon transparency to 100 and then use the following command: > > transparency 0,r frames 100 > > The problem is that when when the ribbon in 100% transparent, the shape is still apparent in the partially transparent map. the ribbon shapes are not seen only when the map is not transparent at all. > > Is there a way to fix that? > Thanks, > Donna > _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimera-2Dusers&d=DwIGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=ibveGQtX1lCuoaFiArA0sEc8t3VwtUdnLsy94Nbyhyo&s=MnzDPhRns1yhUmwz59YslpQ7MZ6Wmh4S0Hq0jfoN51I&e= -------------- next part -------------- An HTML attachment was scrubbed... URL: From pbgvanerp at gmail.com Thu Aug 3 13:22:21 2017 From: pbgvanerp at gmail.com (Paul van Erp) Date: Thu, 3 Aug 2017 14:22:21 -0600 Subject: [Chimera-users] surface calculation failed on new laptop Message-ID: Dear chimera users and developers, Recently I purchased a new laptop. One of the primary uses of this laptop is rendering structures using chimera and running VR simulations of these structures. I've used the new ChimeraX successfully for this. However I also use the old version of chimera for structure visualization, coloring according to attribute lists and I create morph models between structures. The new laptop is unable to calculate virtually any surface. I've gone through the various troubleshooting pages and tried many things. None seem to be effective. Is it possible that the surface calculation would be more successful on a different computer? Also would this depend on the hardware? or might a similar computer from a different brand suffice? Any help you could offer would be greatly appreciated. Thanks in advance, Regards, Paul van Erp -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Aug 3 13:53:52 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 3 Aug 2017 13:53:52 -0700 Subject: [Chimera-users] surface calculation failed on new laptop In-Reply-To: References: Message-ID: Hi Paul, Sorry about the difficulties. I can?t speak as to the hardware issues, but the following alternatives to MSMS surface calculations in Chimera should not be susceptible to the numerical falilures: (1) ?molmap? to make an isosurface, but shape will not be quite the same as the solvent-excluded molecular surface See under #3 in the surface workarounds page: (2) semi-secret grid method of generating a solvent-excluded molecular surface. See In both cases, be VERY careful to only specify the protein atoms, for example: molmap #0&protein 4 gridSpacing 0.5 - or - surf #0&protein grid .5 ?otherwise all the other atoms (solvent, ligands, etc.) will be assimilated into the blob. Also, these alternative-method surfaces in Chimera aren't automatically associated with atoms, so to get coloring by atom or residue attribute, you have to color the underlying atoms by said attribute, then use the Color Zone tool (or ?scolor? command with zone option) to propagate the atom coloring to nearby surface patches. You can also color them by map values (electrostatic potential, etc.). ChimeraX uses the same grid method as mentioned above, but it is more fully integrated and easier to specify/color by atom. However, as you probably know, ChimeraX does not yet have coloring by attribute. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 3, 2017, at 1:22 PM, Paul van Erp wrote: > > Dear chimera users and developers, > > Recently I purchased a new laptop. One of the primary uses of this laptop is rendering structures using chimera and running VR simulations of these structures. I've used the new ChimeraX successfully for this. However I also use the old version of chimera for structure visualization, coloring according to attribute lists and I create morph models between structures. The new laptop is unable to calculate virtually any surface. > > I've gone through the various troubleshooting pages and tried many things. None seem to be effective. > > Is it possible that the surface calculation would be more successful on a different computer? Also would this depend on the hardware? or might a similar computer from a different brand suffice? > > Any help you could offer would be greatly appreciated. > Thanks in advance, > Regards, > Paul van Erp From pett at cgl.ucsf.edu Thu Aug 3 13:57:43 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 3 Aug 2017 13:57:43 -0700 Subject: [Chimera-users] surface calculation failed on new laptop In-Reply-To: References: Message-ID: <8E9435C4-E63B-422A-A26B-0C48C6074851@cgl.ucsf.edu> The other option is to dual boot into Linux, which for whatever reason is far less susceptible to these surfacing failures than Windows. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Aug 3, 2017, at 1:53 PM, Elaine Meng wrote: > > Hi Paul, > Sorry about the difficulties. I can?t speak as to the hardware issues, but the following alternatives to MSMS surface calculations in Chimera should not be susceptible to the numerical falilures: > > (1) ?molmap? to make an isosurface, but shape will not be quite the same as the solvent-excluded molecular surface > See under #3 in the surface workarounds page: > > > (2) semi-secret grid method of generating a solvent-excluded molecular surface. See > > > In both cases, be VERY careful to only specify the protein atoms, for example: > > molmap #0&protein 4 gridSpacing 0.5 > - or - > surf #0&protein grid .5 > > ?otherwise all the other atoms (solvent, ligands, etc.) will be assimilated into the blob. Also, these alternative-method surfaces in Chimera aren't automatically associated with atoms, so to get coloring by atom or residue attribute, you have to color the underlying atoms by said attribute, then use the Color Zone tool (or ?scolor? command with zone option) to propagate the atom coloring to nearby surface patches. You can also color them by map values (electrostatic potential, etc.). > > ChimeraX uses the same grid method as mentioned above, but it is more fully integrated and easier to specify/color by atom. However, as you probably know, ChimeraX does not yet have coloring by attribute. > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Aug 3, 2017, at 1:22 PM, Paul van Erp wrote: >> >> Dear chimera users and developers, >> >> Recently I purchased a new laptop. One of the primary uses of this laptop is rendering structures using chimera and running VR simulations of these structures. I've used the new ChimeraX successfully for this. However I also use the old version of chimera for structure visualization, coloring according to attribute lists and I create morph models between structures. The new laptop is unable to calculate virtually any surface. >> >> I've gone through the various troubleshooting pages and tried many things. None seem to be effective. >> >> Is it possible that the surface calculation would be more successful on a different computer? Also would this depend on the hardware? or might a similar computer from a different brand suffice? >> >> Any help you could offer would be greatly appreciated. >> Thanks in advance, >> Regards, >> Paul van Erp > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ch.bilal321 at outlook.com Sun Aug 6 05:01:44 2017 From: ch.bilal321 at outlook.com (Ch Bilal) Date: Sun, 6 Aug 2017 12:01:44 +0000 Subject: [Chimera-users] looking for help in UCSF Chimera Message-ID: Respected Sir/Madam. Its Bilal here and i m doing research on a protein "rstA". I am UCSF Chimera user and i am facing an error while energy minimization i got a pop up windows with this error "No MMKT name of atom "HN1" in standard residue "LYS", please help me out i am attaching my complexes with this mail as well please find the attachment. Thank you! -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: top-2-2242.pdb Type: application/vnd.palm Size: 327060 bytes Desc: top-2-2242.pdb URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: top-3-1610.pdb Type: application/vnd.palm Size: 326535 bytes Desc: top-3-1610.pdb URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: top-4-530.pdb Type: application/vnd.palm Size: 326226 bytes Desc: top-4-530.pdb URL: From a.malay at riken.jp Mon Aug 7 01:42:03 2017 From: a.malay at riken.jp (Ali Malay) Date: Mon, 7 Aug 2017 17:42:03 +0900 Subject: [Chimera-users] Automatically changing rotamers Message-ID: Dear all, I have a large, capsid-sized structure. Is there an easy way (e.g. using a script) to automatically change all of the rotamers of a particular residue type? For example, I would like to modify all cysteine residues such that they all correspond to the Dunbrack rotamer with Chi1= -61; could this be done using the swapaa command? Thank you in advance! Ali From pett at cgl.ucsf.edu Mon Aug 7 15:53:11 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 7 Aug 2017 15:53:11 -0700 Subject: [Chimera-users] Automatically changing rotamers In-Reply-To: References: Message-ID: <9FFE6F06-E05A-4509-9CB4-AE5BB8DFF9CF@cgl.ucsf.edu> Hi Ali, Well, using ?criteria 2? in the swapaa command would use the rotamer with the second-highest probability. You have to keep in mind though that the Dunbrack rotamers are backbone dependent, and therefore unless your residues have exactly the same backbone phi and psi angles, the set of rotamers will differ from residue to residue. What you may want to do is set the chi1 angle directly. These commands will set the chi1 angle of all cysteine residues that aren?t involved in disulfide bonds to -61 degrees: sel disulfide; sel up; setattr r chi1 -61 :CYS & ~sel ?Eric > On Aug 7, 2017, at 1:42 AM, Ali Malay wrote: > > Dear all, > > I have a large, capsid-sized structure. Is there an easy way (e.g. using a script) to automatically change all of the rotamers of a particular residue type? > For example, I would like to modify all cysteine residues such that they all correspond to the Dunbrack rotamer with Chi1= -61; could this be done using the swapaa command? > > Thank you in advance! > Ali > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Aug 7 16:15:12 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 7 Aug 2017 16:15:12 -0700 Subject: [Chimera-users] looking for help in UCSF Chimera In-Reply-To: References: Message-ID: Hi, What created these PDB files? I only looked briefly at the first one (top-2-2242.pdb), but for instance residue 66 in chain A has two copies of every atom (at different coordinates) except for the C and the O. I?m guessing the the original PDB file had alternate-location indicators to differentiate between the atoms, but that those indicators were dropped by whatever program wrote this version of the file. At any rate, Chimera will not be able to perform minimization on such a file. So the first thing you need to do is fix the program that wrote this file so that it outputs a legal PDB file. Once you?ve done that, then I can help you with any further problems you have. You should report errors to chimera-bugs at cgl.ucsf.edu rather than chimera-users. Besides regular email, you can also use Help->Report A Bug in the Chimera menus to do so. --Eric Eric Pettersen UCSF Computer Graphics Lab > On Aug 6, 2017, at 5:01 AM, Ch Bilal wrote: > > Respected Sir/Madam. > > Its Bilal here and i m doing research on a protein "rstA". I am UCSF Chimera user and i am facing an error while energy minimization i got a pop up windows with this error "No MMKT name of atom "HN1" in standard residue "LYS", please help me out i am attaching my complexes with this mail as well please find the attachment. > Thank you! > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From y.turgay at bioc.uzh.ch Tue Aug 8 08:05:16 2017 From: y.turgay at bioc.uzh.ch (y.turgay at bioc.uzh.ch) Date: Tue, 8 Aug 2017 17:05:16 +0200 Subject: [Chimera-users] chimera batch process Message-ID: Dear chimera users, I was wondering if you could help me automate the following procedure in order to batch process all my tomograms. What I want to do is to open a segmented tomogram, apply parameters like surface, the step size (1 of 8) to increase the connectivity of what has been segmented, to hide the dust (size: 50) and to threshold the tomogram to 0.5. Afterwards I would select all remaining objects and open a script to invert the surface and execute "mask #0 sel invert true" using the command line in chimera to substract the background from the tomogram. Finally I would save this as new map. Can anyone help me with the commands I have to write in the Terminal to iterate through 200 tomogram folder and automate and batch process this. Best Yagmur Turgay -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Aug 8 09:27:55 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 8 Aug 2017 09:27:55 -0700 Subject: [Chimera-users] chimera batch process In-Reply-To: References: Message-ID: <0FBB8CB4-C1A7-4B32-B7D0-AC1C27D7B8AD@cgl.ucsf.edu> Dear Yagmur Turgay, You would first see if it?s possible to do all the things you want with Chimera commands, then you could use Python to loop through multiple data sets as described here: >From your description, I can?t really tell if you can do everything with Chimera commands. Certainly you can open data with the ?open? command; set isosurface display, threshold level, and step size with the ?volume? command; hide dust with command ?sop hideDust?; select with ?select?. However, when you say ?segmented tomogram? I don?t know if you mean just the volume data set or some previously calculated segmentation surfaces. The ?volume? command I mentioned would work on the volume data set. Secondarily, it wasn?t clear to me whether you needed to judge the connectivity interactively to decide what step value to use. If so, it would be harder to automate. For details on each command, see: Operations that are GUI-only (that don?t have Chimera commands) could be executed with python, but somebody else would have to advise on the details. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 8, 2017, at 8:05 AM, y.turgay at bioc.uzh.ch wrote: > > Dear chimera users, > I was wondering if you could help me automate the following procedure in order to batch process all my tomograms. > What I want to do is to open a segmented tomogram, apply parameters like surface, the step size (1 of 8) to increase the connectivity of what has been segmented, to hide the dust (size: 50) and to threshold the tomogram to 0.5. Afterwards I would select all remaining objects and open a script to invert the surface and execute "mask #0 sel invert true" using the command line in chimera to substract the background from the tomogram. Finally I would save this as new map. > Can anyone help me with the commands I have to write in the Terminal to iterate through 200 tomogram folder and automate and batch process this. > Best > Yagmur Turgay From gtzotzos at me.com Tue Aug 8 11:37:26 2017 From: gtzotzos at me.com (George Tzotzos) Date: Tue, 08 Aug 2017 20:37:26 +0200 Subject: [Chimera-users] Problem with added ions in Amber Message-ID: In MD movie I loaded complex.prmtop and complex.inpcrd files In Tools/Amber/Add ions I selected Ion types Na+ to neutralise complex.inpcrd using AMBER ff14SB for standard residues and AM1-BCC for other residues (I?m attaching a snapshot showing the Na+ ions in red). I then proceeded to solvate the complex using TIP3PBOX and Box size: 9 NOTE: I unticked the Removed existing ions/solvent box I obtained the following Warning ?Could not determine charges for pre-existing solvent/ions from added solvent/ions for: NA NA I generated complex_solv.prmtop and complex_solv.inpcrd files When I checked the complex_solv.prmtop file in cpptraj, I did not see any of the Na+ions (see below). > resinfo #Res Name First Last Natom #Orig #Mol 1 ASP 1 14 14 1 1 2 THR 15 28 14 2 1 ??????? 250 LEU 3988 4006 19 250 3 251 VAL 4007 4023 17 251 3 252 KBR 4024 4062 39 252 4 253 WAT 4063 4065 3 253 5 ???? 10272 WAT 34084 34086 3 10272 10024 10273 WAT 34087 34089 3 10273 10025 Is this what should be expected? Should I consider the solvated complex charge neutralised? Antechamber generated exactly the corresponding complex_solv.prmtop file with Na+ ions Thank you in advance for any suggestions. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PastedGraphic-1.png Type: image/png Size: 375124 bytes Desc: not available URL: From meng at cgl.ucsf.edu Tue Aug 8 13:02:19 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 8 Aug 2017 13:02:19 -0700 Subject: [Chimera-users] Problem with added ions in Amber In-Reply-To: References: Message-ID: <8CC6645C-0352-423D-AFA1-827CC748F0BF@cgl.ucsf.edu> Hi George, I can?t tell what the charges are or whether it is neutral without having some data files. If you chose the option to neutralize I would guess the system is neutral. In the image you sent, it looks like you already have several ions and the water box. Did you really want to add more solvent after that? Are you saying you saved complex_solv files from the data shown in the image? Is the question why these files don?t have ions? The ions are shown in the image. I don?t know anything about cpptraj or whether it is correct that the complex_solv files don?t have ions. I would open those files in Chimera to see if the ions were included. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 8, 2017, at 11:37 AM, George Tzotzos wrote: > > In MD movie I loaded complex.prmtop and complex.inpcrd files > > In Tools/Amber/Add ions I selected Ion types Na+ to neutralise complex.inpcrd using AMBER ff14SB for standard residues and AM1-BCC for other residues (I?m attaching a snapshot showing the Na+ ions in red). > > I then proceeded to solvate the complex using TIP3PBOX and Box size: 9 > NOTE: I unticked the Removed existing ions/solvent box > > I obtained the following Warning ?Could not determine charges for pre-existing solvent/ions from added solvent/ions for: NA NA > > I generated complex_solv.prmtop and complex_solv.inpcrd files > > When I checked the complex_solv.prmtop file in cpptraj, I did not see any of the Na+ions (see below). > > resinfo > #Res Name First Last Natom #Orig #Mol > 1 ASP 1 14 14 1 1 > 2 THR 15 28 14 2 1 > ??????? > 250 LEU 3988 4006 19 250 3 > 251 VAL 4007 4023 17 251 3 > 252 KBR 4024 4062 39 252 4 > 253 WAT 4063 4065 3 253 5 > ???? > 10272 WAT 34084 34086 3 10272 10024 > 10273 WAT 34087 34089 3 10273 10025 > > Is this what should be expected? Should I consider the solvated complex charge neutralised? > > Antechamber generated exactly the corresponding complex_solv.prmtop file with Na+ ions > > Thank you in advance for any suggestions. > > From gtzotzos at me.com Tue Aug 8 13:19:50 2017 From: gtzotzos at me.com (George Tzotzos) Date: Tue, 08 Aug 2017 22:19:50 +0200 Subject: [Chimera-users] Problem with added ions in Amber In-Reply-To: <8CC6645C-0352-423D-AFA1-827CC748F0BF@cgl.ucsf.edu> References: <8CC6645C-0352-423D-AFA1-827CC748F0BF@cgl.ucsf.edu> Message-ID: <2C88E9DA-09B5-4ABA-9FA3-48CD80D3F0E5@me.com> Hi Elaine, In answer to your questions (a) I saved the complex_solv files from the data shown in the image; (b) I opened the files in Chimera. No ions were included. Best regards George > On 8 Aug 2017, at 22:02, Elaine Meng wrote: > > Hi George, > I can?t tell what the charges are or whether it is neutral without having some data files. If you chose the option to neutralize I would guess the system is neutral. In the image you sent, it looks like you already have several ions and the water box. Did you really want to add more solvent after that? Are you saying you saved complex_solv files from the data shown in the image? Is the question why these files don?t have ions? The ions are shown in the image. I don?t know anything about cpptraj or whether it is correct that the complex_solv files don?t have ions. I would open those files in Chimera to see if the ions were included. > Best, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Aug 8, 2017, at 11:37 AM, George Tzotzos wrote: >> >> In MD movie I loaded complex.prmtop and complex.inpcrd files >> >> In Tools/Amber/Add ions I selected Ion types Na+ to neutralise complex.inpcrd using AMBER ff14SB for standard residues and AM1-BCC for other residues (I?m attaching a snapshot showing the Na+ ions in red). >> >> I then proceeded to solvate the complex using TIP3PBOX and Box size: 9 >> NOTE: I unticked the Removed existing ions/solvent box >> >> I obtained the following Warning ?Could not determine charges for pre-existing solvent/ions from added solvent/ions for: NA NA >> >> I generated complex_solv.prmtop and complex_solv.inpcrd files >> >> When I checked the complex_solv.prmtop file in cpptraj, I did not see any of the Na+ions (see below). >>> resinfo >> #Res Name First Last Natom #Orig #Mol >> 1 ASP 1 14 14 1 1 >> 2 THR 15 28 14 2 1 >> ??????? >> 250 LEU 3988 4006 19 250 3 >> 251 VAL 4007 4023 17 251 3 >> 252 KBR 4024 4062 39 252 4 >> 253 WAT 4063 4065 3 253 5 >> ???? >> 10272 WAT 34084 34086 3 10272 10024 >> 10273 WAT 34087 34089 3 10273 10025 >> >> Is this what should be expected? Should I consider the solvated complex charge neutralised? >> >> Antechamber generated exactly the corresponding complex_solv.prmtop file with Na+ ions >> >> Thank you in advance for any suggestions. >> >> > From meng at cgl.ucsf.edu Tue Aug 8 13:36:52 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 8 Aug 2017 13:36:52 -0700 Subject: [Chimera-users] Problem with added ions in Amber In-Reply-To: <2C88E9DA-09B5-4ABA-9FA3-48CD80D3F0E5@me.com> References: <8CC6645C-0352-423D-AFA1-827CC748F0BF@cgl.ucsf.edu> <2C88E9DA-09B5-4ABA-9FA3-48CD80D3F0E5@me.com> Message-ID: <81BF2EA8-86A1-4699-B9A9-799A4875E3AC@cgl.ucsf.edu> Hi George, It seems wrong if you see the ions and you save the data to a file, but then that data file doesn?t have the ions. You can check net charge by running addcharge again after reopening that data. You could try submitting a bug report from the Help menu but you?d need to attach a session with the solvent and ions in it from which your saving didn?t include the ions. However, it might not be a bug of Chimera itself since it sounds like all the steps used Ambertools. Elaine > On Aug 8, 2017, at 1:19 PM, George Tzotzos wrote: > > Hi Elaine, > > In answer to your questions (a) I saved the complex_solv files from the data shown in the image; (b) I opened the files in Chimera. No ions were included. > > Best regards > > George > >> On 8 Aug 2017, at 22:02, Elaine Meng wrote: >> >> Hi George, >> I can?t tell what the charges are or whether it is neutral without having some data files. If you chose the option to neutralize I would guess the system is neutral. In the image you sent, it looks like you already have several ions and the water box. Did you really want to add more solvent after that? Are you saying you saved complex_solv files from the data shown in the image? Is the question why these files don?t have ions? The ions are shown in the image. I don?t know anything about cpptraj or whether it is correct that the complex_solv files don?t have ions. I would open those files in Chimera to see if the ions were included. >> Best, >> Elaine >> ---------- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >>> On Aug 8, 2017, at 11:37 AM, George Tzotzos wrote: >>> >>> In MD movie I loaded complex.prmtop and complex.inpcrd files >>> >>> In Tools/Amber/Add ions I selected Ion types Na+ to neutralise complex.inpcrd using AMBER ff14SB for standard residues and AM1-BCC for other residues (I?m attaching a snapshot showing the Na+ ions in red). >>> >>> I then proceeded to solvate the complex using TIP3PBOX and Box size: 9 >>> NOTE: I unticked the Removed existing ions/solvent box >>> >>> I obtained the following Warning ?Could not determine charges for pre-existing solvent/ions from added solvent/ions for: NA NA >>> >>> I generated complex_solv.prmtop and complex_solv.inpcrd files >>> >>> When I checked the complex_solv.prmtop file in cpptraj, I did not see any of the Na+ions (see below). >>>> resinfo >>> #Res Name First Last Natom #Orig #Mol >>> 1 ASP 1 14 14 1 1 >>> 2 THR 15 28 14 2 1 >>> ??????? >>> 250 LEU 3988 4006 19 250 3 >>> 251 VAL 4007 4023 17 251 3 >>> 252 KBR 4024 4062 39 252 4 >>> 253 WAT 4063 4065 3 253 5 >>> ???? >>> 10272 WAT 34084 34086 3 10272 10024 >>> 10273 WAT 34087 34089 3 10273 10025 >>> >>> Is this what should be expected? Should I consider the solvated complex charge neutralised? >>> >>> Antechamber generated exactly the corresponding complex_solv.prmtop file with Na+ ions >>> >>> Thank you in advance for any suggestions. >>> >>> >> > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From joel.mackay at sydney.edu.au Wed Aug 9 02:45:07 2017 From: joel.mackay at sydney.edu.au (Joel Mackay) Date: Wed, 9 Aug 2017 09:45:07 +0000 Subject: [Chimera-users] Error in Windows saving a session Message-ID: <648D98026D45B348A892B0F7DAD11DCA021AABB6FC@ex-mbx-pro-06> Hi all Have other people seen (and solved!) this error before (below)? I'm having it crop up pretty much all the time now when I try to save a session (on my Win7 machine - running Chimera 1.11.2. Thanks Joel WindowsError Exception in Tk callback Function: (type: ) Module: (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 264, in Save getattr(self, self.keepEquiv())() File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 704, in OK self.Apply() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 183, in Apply self.command(1, self) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\gui.py", line 41, in _saveCB saveSession(paths[0], **kw) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) WindowsError: [Error 32] The process cannot access the file because it is being used by another process WindowsError: [Error 32] The process cannot access the file because it is being used by another process File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) See reply log for Python traceback. ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay at sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From me.sr1510 at gmail.com Thu Aug 10 06:35:36 2017 From: me.sr1510 at gmail.com (sonal rashmi) Date: Thu, 10 Aug 2017 19:05:36 +0530 Subject: [Chimera-users] Match->Align commandline Message-ID: sir/mam, i want to use chimera Match->Align feature using the commandline or nogui script (python) to align multiple protein sequences (pdb files) to generate the alignment on MultiAlignViewer and save it as clustal (.aln) file. I tried out the python codes posted on the portals but non of them are giving proper alignment. kindly advice as to what i can do? Is there any commandline available for it? Thanking You Sincere User -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Aug 10 09:53:35 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 10 Aug 2017 09:53:35 -0700 Subject: [Chimera-users] Match->Align commandline In-Reply-To: References: Message-ID: Hello, The first thing to understand is that Match->Align requires the protein structures to be superimposed already. That is, you have to superimpose or match the structures (for example, with the ?matchmaker? command) BEFORE you use Match->Align. Here is a discussion of the different ways to superimpose structures: After the structures are superimposed, then you can consider how to use Match->Align with a script, since it doesn?t have a command. For that, see this previous post: If you are only doing pairwise alignments and the structures have fairly similar sequences, another possibility is to just use the sequence alignment created by Matchmaker (or ?matchmaker" command with ?show true?). For that, see this previous post: I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 10, 2017, at 6:35 AM, sonal rashmi wrote: > > sir/mam, > i want to use chimera Match->Align feature using the commandline or nogui script (python) to align multiple protein sequences (pdb files) to generate the alignment on MultiAlignViewer and save it as clustal (.aln) file. > I tried out the python codes posted on the portals but non of them are giving proper alignment. > kindly advice as to what i can do? Is there any commandline available for it? > Thanking You > Sincere User From milo at nmrfam.wisc.edu Thu Aug 10 13:35:05 2017 From: milo at nmrfam.wisc.edu (Milo Westler) Date: Thu, 10 Aug 2017 15:35:05 -0500 Subject: [Chimera-users] command line minimization Message-ID: We are trying to automate the minimization of a series of compounds using the system command line. Since we have quite a few compounds, we are interested in using the Gasteiger method for assigning charges. The command line minimize includes the AM1-BCC method.. Is there a way to run an automatic minimization using the Gasteiger method? Currently we use: chimera --nogui --silent R.mol opt.cmd Where opt.cmd is: minimize write #0 R_min.pdb -- -- Milo =================================================== National Magnetic Resonance Facility at Madison An NIH-Supported Resource Center W. Milo Westler, Ph.D. NMRFAM Director Senior Scientist and Adjunct Professor Department of Biochemistry University of Wisconsin-Madison DeLuca Biochemistry Laboratories 433 Babcock Drive Rm B160D Madison, WI USA 53706-1544 EMAIL: milo at nmrfam.wisc.edu PHONE: (608)-263-9599 FAX: (608)-263-1722 ======================================================================= ======== -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Thu Aug 10 13:55:21 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 10 Aug 2017 13:55:21 -0700 Subject: [Chimera-users] Error in Windows saving a session In-Reply-To: <648D98026D45B348A892B0F7DAD11DCA021AABB6FC@ex-mbx-pro-06> References: <648D98026D45B348A892B0F7DAD11DCA021AABB6FC@ex-mbx-pro-06> Message-ID: Hi Joel, We have had this reported infrequently by other users and have had no success in tracking it down. Can you answer a couple of questions for me? Are you writing a compressed session file? Is the disk you are writing to nearly full? Thanks. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Aug 9, 2017, at 2:45 AM, Joel Mackay wrote: > > Hi all > Have other people seen (and solved!) this error before (below)? I?m having it crop up pretty much all the time now when I try to save a session (on my Win7 machine ? running Chimera 1.11.2. > Thanks > Joel > > > WindowsError Exception in Tk callback > Function: (type: ) > Module: (line: 447) > Args: () > Traceback (innermost last): > File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ > return apply(self.func, args) > File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 449, in command > getattr(s, buttonFuncName(txt))() > File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 264, in Save > getattr(self, self.keepEquiv())() > File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 704, in OK > self.Apply() > File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 183, in Apply > self.command(1, self) > File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\gui.py", line 41, in _saveCB > saveSession(paths[0], **kw) > File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession > os.rename(tsave, filename) > WindowsError: [Error 32] The process cannot access the file because it is being used by another process > > WindowsError: [Error 32] The process cannot access the file because it is being used by another process > > File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession > os.rename(tsave, filename) > > See reply log for Python traceback. > > > ------------------------------------------------------------------------------------------------------------------------------ > Professor Joel Mackay | NHMRC Senior Research Fellow > Chair, Biochemistry, Cellular and Molecular Biology Cluster > School of Life and Environmental Sciences > THE UNIVERSITY OF SYDNEY > > A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave > The University of Sydney | NSW | 2006 | Australia > T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay > E: joel.mackay at sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/ > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Aug 10 15:58:26 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 10 Aug 2017 15:58:26 -0700 Subject: [Chimera-users] command line minimization In-Reply-To: References: Message-ID: <1C3B9609-AD5D-4D1A-A457-348DE34E8326@cgl.ucsf.edu> Hi Milo, In your command script, include the ?addh? and ?addcharge? commands (with whatever options you want) before the ?minimize? command, instead of having the minimization call these steps. You want the addcharge option ?method gas?, see: I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 10, 2017, at 1:35 PM, Milo Westler wrote: > > We are trying to automate the minimization of a series of compounds using the system command line. Since we have quite a few compounds, we are interested in using the Gasteiger method for assigning charges. The command line minimize includes the AM1-BCC method.. Is there a way to run an automatic minimization using the Gasteiger method? > > Currently we use: > chimera --nogui --silent R.mol opt.cmd > > Where opt.cmd is: > minimize > write #0 R_min.pdb > > -- > -- Milo From joel.mackay at sydney.edu.au Thu Aug 10 16:44:24 2017 From: joel.mackay at sydney.edu.au (Joel Mackay) Date: Thu, 10 Aug 2017 23:44:24 +0000 Subject: [Chimera-users] Error in Windows saving a session In-Reply-To: References: <648D98026D45B348A892B0F7DAD11DCA021AABB6FC@ex-mbx-pro-06> Message-ID: <648D98026D45B348A892B0F7DAD11DCA021AAC6D60@ex-mbx-pro-06> Hi Eric Thanks for getting back to me. I?m just trying to save a .py file. Not sure how to save a compressed version? I?ve tried saving in different directories, but that didn?t work either. The session contains 5 PDB files and a single .mrc file (a low resolution EM dataset). The PDB files are 5 ~40 kDa proteins, so not huge. The disk I?m writing to has ~140 GB free out of 500. Sounds like one of those elusive problems? Please let me know if you?d like me to try anything else. Best regards Joel ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay at sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/ From: Eric Pettersen [mailto:pett at cgl.ucsf.edu] Sent: Friday, 11 August 2017 6:55 AM To: Joel Mackay Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Error in Windows saving a session Hi Joel, We have had this reported infrequently by other users and have had no success in tracking it down. Can you answer a couple of questions for me? Are you writing a compressed session file? Is the disk you are writing to nearly full? Thanks. ?Eric Eric Pettersen UCSF Computer Graphics Lab On Aug 9, 2017, at 2:45 AM, Joel Mackay > wrote: Hi all Have other people seen (and solved!) this error before (below)? I?m having it crop up pretty much all the time now when I try to save a session (on my Win7 machine ? running Chimera 1.11.2. Thanks Joel WindowsError Exception in Tk callback Function: (type: ) Module: (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 264, in Save getattr(self, self.keepEquiv())() File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 704, in OK self.Apply() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 183, in Apply self.command(1, self) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\gui.py", line 41, in _saveCB saveSession(paths[0], **kw) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) WindowsError: [Error 32] The process cannot access the file because it is being used by another process WindowsError: [Error 32] The process cannot access the file because it is being used by another process File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) See reply log for Python traceback. ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay at sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/ _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Fri Aug 11 10:04:25 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 11 Aug 2017 10:04:25 -0700 Subject: [Chimera-users] Error in Windows saving a session In-Reply-To: <648D98026D45B348A892B0F7DAD11DCA021AAC6D60@ex-mbx-pro-06> References: <648D98026D45B348A892B0F7DAD11DCA021AABB6FC@ex-mbx-pro-06> <648D98026D45B348A892B0F7DAD11DCA021AAC6D60@ex-mbx-pro-06> Message-ID: <42080C98-435F-4877-964F-92F0297B3594@cgl.ucsf.edu> Could you try rebooting your machine? ?Eric > On Aug 10, 2017, at 4:44 PM, Joel Mackay wrote: > > Hi Eric > Thanks for getting back to me. > I?m just trying to save a .py file. Not sure how to save a compressed version? > I?ve tried saving in different directories, but that didn?t work either. The session contains 5 PDB files and a single .mrc file (a low resolution EM dataset). The PDB files are 5 ~40 kDa proteins, so not huge. > The disk I?m writing to has ~140 GB free out of 500. > Sounds like one of those elusive problems? > Please let me know if you?d like me to try anything else. > Best regards > Joel > > > ------------------------------------------------------------------------------------------------------------------------------ > Professor Joel Mackay | NHMRC Senior Research Fellow > Chair, Biochemistry, Cellular and Molecular Biology Cluster > School of Life and Environmental Sciences > THE UNIVERSITY OF SYDNEY > > A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave > The University of Sydney | NSW | 2006 | Australia > T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay > E: joel.mackay at sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/ > > From: Eric Pettersen [mailto:pett at cgl.ucsf.edu] > Sent: Friday, 11 August 2017 6:55 AM > To: Joel Mackay > Cc: chimera-users at cgl.ucsf.edu > Subject: Re: [Chimera-users] Error in Windows saving a session > > Hi Joel, > We have had this reported infrequently by other users and have had no success in tracking it down. Can you answer a couple of questions for me? Are you writing a compressed session file? Is the disk you are writing to nearly full? Thanks. > > ?Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > On Aug 9, 2017, at 2:45 AM, Joel Mackay > wrote: > > Hi all > Have other people seen (and solved!) this error before (below)? I?m having it crop up pretty much all the time now when I try to save a session (on my Win7 machine ? running Chimera 1.11.2. > Thanks > Joel > > > WindowsError Exception in Tk callback > Function: (type: ) > Module: (line: 447) > Args: () > Traceback (innermost last): > File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ > return apply(self.func, args) > File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 449, in command > getattr(s, buttonFuncName(txt))() > File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 264, in Save > getattr(self, self.keepEquiv())() > File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 704, in OK > self.Apply() > File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 183, in Apply > self.command(1, self) > File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\gui.py", line 41, in _saveCB > saveSession(paths[0], **kw) > File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession > os.rename(tsave, filename) > WindowsError: [Error 32] The process cannot access the file because it is being used by another process > > WindowsError: [Error 32] The process cannot access the file because it is being used by another process > > File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession > os.rename(tsave, filename) > > See reply log for Python traceback. > > > ------------------------------------------------------------------------------------------------------------------------------ > Professor Joel Mackay | NHMRC Senior Research Fellow > Chair, Biochemistry, Cellular and Molecular Biology Cluster > School of Life and Environmental Sciences > THE UNIVERSITY OF SYDNEY > > A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave > The University of Sydney | NSW | 2006 | Australia > T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay > E: joel.mackay at sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/ > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From joel.mackay at sydney.edu.au Fri Aug 11 20:57:46 2017 From: joel.mackay at sydney.edu.au (Joel Mackay) Date: Sat, 12 Aug 2017 03:57:46 +0000 Subject: [Chimera-users] Error in Windows saving a session In-Reply-To: <42080C98-435F-4877-964F-92F0297B3594@cgl.ucsf.edu> References: <648D98026D45B348A892B0F7DAD11DCA021AABB6FC@ex-mbx-pro-06> <648D98026D45B348A892B0F7DAD11DCA021AAC6D60@ex-mbx-pro-06> <42080C98-435F-4877-964F-92F0297B3594@cgl.ucsf.edu> Message-ID: <648D98026D45B348A892B0F7DAD11DCA021AACEB14@ex-mbx-pro-06> No joy ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay at sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/ From: Eric Pettersen [mailto:pett at cgl.ucsf.edu] Sent: Saturday, 12 August 2017 3:04 AM To: Joel Mackay Cc: chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] Error in Windows saving a session Could you try rebooting your machine? ?Eric On Aug 10, 2017, at 4:44 PM, Joel Mackay > wrote: Hi Eric Thanks for getting back to me. I?m just trying to save a .py file. Not sure how to save a compressed version? I?ve tried saving in different directories, but that didn?t work either. The session contains 5 PDB files and a single .mrc file (a low resolution EM dataset). The PDB files are 5 ~40 kDa proteins, so not huge. The disk I?m writing to has ~140 GB free out of 500. Sounds like one of those elusive problems? Please let me know if you?d like me to try anything else. Best regards Joel ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay at sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/ From: Eric Pettersen [mailto:pett at cgl.ucsf.edu] Sent: Friday, 11 August 2017 6:55 AM To: Joel Mackay > Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Error in Windows saving a session Hi Joel, We have had this reported infrequently by other users and have had no success in tracking it down. Can you answer a couple of questions for me? Are you writing a compressed session file? Is the disk you are writing to nearly full? Thanks. ?Eric Eric Pettersen UCSF Computer Graphics Lab On Aug 9, 2017, at 2:45 AM, Joel Mackay > wrote: Hi all Have other people seen (and solved!) this error before (below)? I?m having it crop up pretty much all the time now when I try to save a session (on my Win7 machine ? running Chimera 1.11.2. Thanks Joel WindowsError Exception in Tk callback Function: (type: ) Module: (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 264, in Save getattr(self, self.keepEquiv())() File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 704, in OK self.Apply() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 183, in Apply self.command(1, self) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\gui.py", line 41, in _saveCB saveSession(paths[0], **kw) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) WindowsError: [Error 32] The process cannot access the file because it is being used by another process WindowsError: [Error 32] The process cannot access the file because it is being used by another process File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) See reply log for Python traceback. ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay at sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/ _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From agszabo at outlook.com Mon Aug 14 12:52:04 2017 From: agszabo at outlook.com (Arthur Szabo) Date: Mon, 14 Aug 2017 19:52:04 +0000 Subject: [Chimera-users] biounit Message-ID: When one fetches structures from the PDB data base what is the difference between fetching using the PDB only selection and the pdb biounit selection? Arthur G. Szabo -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Aug 14 13:41:56 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 14 Aug 2017 13:41:56 -0700 Subject: [Chimera-users] biounit In-Reply-To: References: Message-ID: <2108BBD2-0914-4DFE-8225-5BC02B0FEDB4@cgl.ucsf.edu> Hi Arthur, The main PDB fetch is the contents of the crystallographic asymmetric unit, whereas the biological unit is the known or guessed biologically relevant assembly based on that structure. Sometimes they are the same, but often they?re not? this page at the RCSB PDB has a good explanation: I see that the link I had in the Chimera manual to explain ?biounit? no longer works, so I?ll update it to use the link above instead. The current terminology is ?biological assembly,? which makes more sense. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 14, 2017, at 12:52 PM, Arthur Szabo wrote: > > When one fetches structures from the PDB data base what is the difference between fetching using the PDB only selection and the pdb biounit selection? > Arthur G. Szabo From agszabo at outlook.com Mon Aug 14 15:19:07 2017 From: agszabo at outlook.com (Arthur Szabo) Date: Mon, 14 Aug 2017 22:19:07 +0000 Subject: [Chimera-users] biounit In-Reply-To: <2108BBD2-0914-4DFE-8225-5BC02B0FEDB4@cgl.ucsf.edu> References: <2108BBD2-0914-4DFE-8225-5BC02B0FEDB4@cgl.ucsf.edu> Message-ID: Elaine Thank you A follow up question. PDB 4V9D is a structure of a bacterial ribosome. Some 35Mb. Can this be handled, or is the size to large to download. I tried to fetch it by PDB index, but it just seemed to stall or was way too large. Regards arthur -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: Monday, August 14, 2017 4:42 PM To: Arthur Szabo Cc: chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] biounit Hi Arthur, The main PDB fetch is the contents of the crystallographic asymmetric unit, whereas the biological unit is the known or guessed biologically relevant assembly based on that structure. Sometimes they are the same, but often they?re not? this page at the RCSB PDB has a good explanation: I see that the link I had in the Chimera manual to explain ?biounit? no longer works, so I?ll update it to use the link above instead. The current terminology is ?biological assembly,? which makes more sense. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 14, 2017, at 12:52 PM, Arthur Szabo wrote: > > When one fetches structures from the PDB data base what is the difference between fetching using the PDB only selection and the pdb biounit selection? > Arthur G. Szabo From meng at cgl.ucsf.edu Mon Aug 14 15:52:00 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 14 Aug 2017 15:52:00 -0700 Subject: [Chimera-users] biounit In-Reply-To: References: <2108BBD2-0914-4DFE-8225-5BC02B0FEDB4@cgl.ucsf.edu> Message-ID: <25DF4658-AE28-4375-A284-5C78C58E8764@cgl.ucsf.edu> Hi Arthur, It?s probably too big for your computer and/or for reasonable speed of interaction in Chimera (display changes, rotation etc.). The structure is so large that it?s being downloaded in mmCIF format and Chimera is rather slow to open mmCIF. It might load eventually if you waited a really long time (many minutes?), but then rotation etc. would still be slow. Our new software ChimeraX is developed to handle such large structures and mmCIF format much better and faster, but it also depends on having a reasonably up-to-date computer. Download could still be slow depending on the speed of your connection with the database. As for the computer, we recommend using one from the ?last 3 years? although it is certainly possible it might work on older computers too. ChimeraX commands have a lot of similarities with Chimera commands, but there are differences, and most functions are command-only (not in the menu). Nevertheless, should be easy to try downloading the program and seeing if it runs on your computer, and if so, entering command ?open 4v9d? to see how that goes. ChimeraX is still in pre-release but available to download, and it has a lot of display options and image-saving. The ChimeraX home page has links to download and User Guide on the left: The bottom example in the ChimeraX image gallery is a ribosome: I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 14, 2017, at 3:19 PM, Arthur Szabo wrote: > > Elaine > > Thank you > > A follow up question. PDB 4V9D is a structure of a bacterial ribosome. Some 35Mb. > > Can this be handled, or is the size to large to download. > I tried to fetch it by PDB index, but it just seemed to stall or was way too large. > > Regards > > arthur From milo at nmrfam.wisc.edu Wed Aug 16 06:32:33 2017 From: milo at nmrfam.wisc.edu (Milo Westler) Date: Wed, 16 Aug 2017 08:32:33 -0500 Subject: [Chimera-users] command line minimization In-Reply-To: <1C3B9609-AD5D-4D1A-A457-348DE34E8326@cgl.ucsf.edu> References: <1C3B9609-AD5D-4D1A-A457-348DE34E8326@cgl.ucsf.edu> Message-ID: Thanks, I'll try it. On Thu, Aug 10, 2017 at 5:58 PM, Elaine Meng wrote: > Hi Milo, > In your command script, include the ?addh? and ?addcharge? commands (with > whatever options you want) before the ?minimize? command, instead of having > the minimization call these steps. You want the addcharge option ?method > gas?, see: > > > > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Aug 10, 2017, at 1:35 PM, Milo Westler wrote: > > > > We are trying to automate the minimization of a series of compounds > using the system command line. Since we have quite a few compounds, we are > interested in using the Gasteiger method for assigning charges. The command > line minimize includes the AM1-BCC method.. Is there a way to run an > automatic minimization using the Gasteiger method? > > > > Currently we use: > > chimera --nogui --silent R.mol opt.cmd > > > > Where opt.cmd is: > > minimize > > write #0 R_min.pdb > > > > -- > > -- Milo > > -- -- Milo =================================================== National Magnetic Resonance Facility at Madison An NIH-Supported Resource Center W. Milo Westler, Ph.D. NMRFAM Director Senior Scientist and Adjunct Professor Department of Biochemistry University of Wisconsin-Madison DeLuca Biochemistry Laboratories 433 Babcock Drive Rm B160D Madison, WI USA 53706-1544 EMAIL: milo at nmrfam.wisc.edu PHONE: (608)-263-9599 FAX: (608)-263-1722 ======================================================================= ======== -------------- next part -------------- An HTML attachment was scrubbed... URL: From mailmd2011 at gmail.com Tue Aug 15 23:18:25 2017 From: mailmd2011 at gmail.com (Albert) Date: Wed, 16 Aug 2017 08:18:25 +0200 Subject: [Chimera-users] advanced option for WebGL? Message-ID: Hello, I noticed that Chimera can export a scene as HTML file which is based on WebGL. However, we can no longer change the displaying styles through this .html file since there is no any menu or option button in the page. Would it be good if Chimera could provide this function? As far as I know, PyMOL has similar function, but the generated .html provide a menu to change the scene styles. see here https://pymolwiki.org/index.php/Pymol2glmol Thank you very much. Albert From hernando.sosa at einstein.yu.edu Wed Aug 16 06:15:12 2017 From: hernando.sosa at einstein.yu.edu (Hernando J Sosa) Date: Wed, 16 Aug 2017 13:15:12 +0000 Subject: [Chimera-users] Matchmaker & fit map into map In-Reply-To: <25DF4658-AE28-4375-A284-5C78C58E8764@cgl.ucsf.edu> References: <2108BBD2-0914-4DFE-8225-5BC02B0FEDB4@cgl.ucsf.edu> <25DF4658-AE28-4375-A284-5C78C58E8764@cgl.ucsf.edu> Message-ID: Dear Chimera, Is it possible when using Matchmaker to move an associated density map with it? Eg: assuming that atomic model #1 is fitted to density #2 and atomic model #3 is fitted to density #4, is it possible to move/match #3 into #1 moving #4 with it? I know it would be possible to achieve something similar doing Matchmaker first and then fit map into map, but I wonder if the above could be done too as it would be simpler and easier when dealing with many maps with already fitted structures. Thanks Hernando From meng at cgl.ucsf.edu Wed Aug 16 10:54:08 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 16 Aug 2017 10:54:08 -0700 Subject: [Chimera-users] Matchmaker & fit map into map In-Reply-To: References: <2108BBD2-0914-4DFE-8225-5BC02B0FEDB4@cgl.ucsf.edu> <25DF4658-AE28-4375-A284-5C78C58E8764@cgl.ucsf.edu> Message-ID: <971BEFFA-5417-4937-964C-D385379D2E32@cgl.ucsf.edu> Hi Hernando, In our newer software ChimeraX, there is a matchmaker command ?bring? option that does exactly what you describe: However, Chimera does not have this matchmaker option, and things may be more complicated. If the map and its atomic structure are already in the right relationship with each other when you first open their files, it should work to: (1) superimpose the atomic structure (let?s call it model #2) onto another atomic structure (#1) (2) use ?matrixcopy? command to apply rotation/translation matrix from structure #2 to map #3: matrixcopy #2 #3 However, if the map and its structure weren?t in the right relationship when their files were first opened (if you had to move them separately, e.g. fitting), I don?t think that would work. The Chimera ?match? (but not matchmaker) command does have an ?active? option to bring other models that are activated for motion (movable with the mouse) along during the match. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 16, 2017, at 6:15 AM, Hernando J Sosa wrote: > > Dear Chimera, > > Is it possible when using Matchmaker to move an associated density map with it? > Eg: assuming that atomic model #1 is fitted to density #2 and atomic model #3 is fitted to density #4, is it possible to move/match #3 into #1 moving #4 with it? > I know it would be possible to achieve something similar doing Matchmaker first and then fit map into map, but I wonder if the above could be done too as it would be simpler and easier when dealing with many maps with already fitted structures. > > Thanks > Hernando From meng at cgl.ucsf.edu Wed Aug 16 11:10:55 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 16 Aug 2017 11:10:55 -0700 Subject: [Chimera-users] Matchmaker & fit map into map In-Reply-To: <971BEFFA-5417-4937-964C-D385379D2E32@cgl.ucsf.edu> References: <2108BBD2-0914-4DFE-8225-5BC02B0FEDB4@cgl.ucsf.edu> <25DF4658-AE28-4375-A284-5C78C58E8764@cgl.ucsf.edu> <971BEFFA-5417-4937-964C-D385379D2E32@cgl.ucsf.edu> Message-ID: <9830B069-7D64-4EC5-B3A3-392D1944B94A@cgl.ucsf.edu> Sorry, my mistake, this ChimeraX matchmaker command option only brings along atomic models currently. We?ll look into whether it can be expanded to other kinds of models (maps etc.) Elaine > On Aug 16, 2017, at 10:54 AM, Elaine Meng wrote: > > In our newer software ChimeraX, there is a matchmaker command ?bring? option that does exactly what you describe: > From goddard at sonic.net Wed Aug 16 11:56:30 2017 From: goddard at sonic.net (Tom Goddard) Date: Wed, 16 Aug 2017 11:56:30 -0700 Subject: [Chimera-users] Matchmaker & fit map into map In-Reply-To: <971BEFFA-5417-4937-964C-D385379D2E32@cgl.ucsf.edu> References: <2108BBD2-0914-4DFE-8225-5BC02B0FEDB4@cgl.ucsf.edu> <25DF4658-AE28-4375-A284-5C78C58E8764@cgl.ucsf.edu> <971BEFFA-5417-4937-964C-D385379D2E32@cgl.ucsf.edu> Message-ID: Hi Hernando, The trick you want is to use ?matrixcopy? with the ?moving? option to move additional models using the same motion. First matchmaker an extra copy of the atomic model (#5) then move the original copy (#3) and associated density map (#4) to align with it matchmaker #1 #5 matrixcopy #5 #3 moving #4 https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html Tom > On Aug 16, 2017, at 10:54 AM, Elaine Meng wrote: > > Hi Hernando, > In our newer software ChimeraX, there is a matchmaker command ?bring? option that does exactly what you describe: > > > However, Chimera does not have this matchmaker option, and things may be more complicated. > > If the map and its atomic structure are already in the right relationship with each other when you first open their files, it should work to: > > (1) superimpose the atomic structure (let?s call it model #2) onto another atomic structure (#1) > > (2) use ?matrixcopy? command to apply rotation/translation matrix from structure #2 to map #3: > matrixcopy #2 #3 > > > However, if the map and its structure weren?t in the right relationship when their files were first opened (if you had to move them separately, e.g. fitting), I don?t think that would work. > > The Chimera ?match? (but not matchmaker) command does have an ?active? option to bring other models that are activated for motion (movable with the mouse) along during the match. > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Aug 16, 2017, at 6:15 AM, Hernando J Sosa wrote: >> >> Dear Chimera, >> >> Is it possible when using Matchmaker to move an associated density map with it? >> Eg: assuming that atomic model #1 is fitted to density #2 and atomic model #3 is fitted to density #4, is it possible to move/match #3 into #1 moving #4 with it? >> I know it would be possible to achieve something similar doing Matchmaker first and then fit map into map, but I wonder if the above could be done too as it would be simpler and easier when dealing with many maps with already fitted structures. >> >> Thanks >> Hernando > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Aug 16 13:07:57 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 16 Aug 2017 13:07:57 -0700 Subject: [Chimera-users] Matchmaker & fit map into map In-Reply-To: <9830B069-7D64-4EC5-B3A3-392D1944B94A@cgl.ucsf.edu> References: <2108BBD2-0914-4DFE-8225-5BC02B0FEDB4@cgl.ucsf.edu> <25DF4658-AE28-4375-A284-5C78C58E8764@cgl.ucsf.edu> <971BEFFA-5417-4937-964C-D385379D2E32@cgl.ucsf.edu> <9830B069-7D64-4EC5-B3A3-392D1944B94A@cgl.ucsf.edu> Message-ID: As of tomorrow, the ChimeraX matchmaker ?bring? option will be able to bring along any kind of models. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Aug 16, 2017, at 11:10 AM, Elaine Meng wrote: > > Sorry, my mistake, this ChimeraX matchmaker command option only brings along atomic models currently. We?ll look into whether it can be expanded to other kinds of models (maps etc.) > > Elaine > >> On Aug 16, 2017, at 10:54 AM, Elaine Meng wrote: >> >> In our newer software ChimeraX, there is a matchmaker command ?bring? option that does exactly what you describe: >> > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hernando.sosa at einstein.yu.edu Wed Aug 16 15:19:50 2017 From: hernando.sosa at einstein.yu.edu (Hernando J Sosa) Date: Wed, 16 Aug 2017 22:19:50 +0000 Subject: [Chimera-users] Matchmaker & fit map into map In-Reply-To: <971BEFFA-5417-4937-964C-D385379D2E32@cgl.ucsf.edu> References: <2108BBD2-0914-4DFE-8225-5BC02B0FEDB4@cgl.ucsf.edu> <25DF4658-AE28-4375-A284-5C78C58E8764@cgl.ucsf.edu> <971BEFFA-5417-4937-964C-D385379D2E32@cgl.ucsf.edu> Message-ID: Hi Elaine >(2) use ?matrixcopy? command to apply rotation/translation matrix from structure #2 to map #3: >matrixcopy #2 #3 did the trick for me. Thanks! (much better than trying to fit manually map into map each time). I will try ChimeraX later. Best H. -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: Wednesday, August 16, 2017 1:54 PM To: Hernando J Sosa Cc: chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] Matchmaker & fit map into map Hi Hernando, In our newer software ChimeraX, there is a matchmaker command ?bring? option that does exactly what you describe: However, Chimera does not have this matchmaker option, and things may be more complicated. If the map and its atomic structure are already in the right relationship with each other when you first open their files, it should work to: (1) superimpose the atomic structure (let?s call it model #2) onto another atomic structure (#1) (2) use ?matrixcopy? command to apply rotation/translation matrix from structure #2 to map #3: matrixcopy #2 #3 However, if the map and its structure weren?t in the right relationship when their files were first opened (if you had to move them separately, e.g. fitting), I don?t think that would work. The Chimera ?match? (but not matchmaker) command does have an ?active? option to bring other models that are activated for motion (movable with the mouse) along during the match. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 16, 2017, at 6:15 AM, Hernando J Sosa wrote: > > Dear Chimera, > > Is it possible when using Matchmaker to move an associated density map with it? > Eg: assuming that atomic model #1 is fitted to density #2 and atomic model #3 is fitted to density #4, is it possible to move/match #3 into #1 moving #4 with it? > I know it would be possible to achieve something similar doing Matchmaker first and then fit map into map, but I wonder if the above could be done too as it would be simpler and easier when dealing with many maps with already fitted structures. > > Thanks > Hernando From biocjh at gmail.com Thu Aug 17 00:56:50 2017 From: biocjh at gmail.com (C.J.) Date: Thu, 17 Aug 2017 15:56:50 +0800 Subject: [Chimera-users] move different map to the same origin of coordinate Message-ID: Dear specialists, I open a map(#1) and make icosahedron surface(#1) using Tools-> Higher-Order structure->icosahedron surface. But the model #0 and #1 don't have the same center, how could I center them into the origin of same coordinate? Thanks! -- Best regards! Jianhao -------------- next part -------------- An HTML attachment was scrubbed... URL: From catrajen at umail.iu.edu Thu Aug 17 08:09:06 2017 From: catrajen at umail.iu.edu (Catherine Jenifer Rajam Rajendran) Date: Thu, 17 Aug 2017 11:09:06 -0400 Subject: [Chimera-users] Draw Line Message-ID: Hi Eric, Can you please tell me what are the ways to draw an axis. I have a directional vector - x, y, z coordinates (e.g., 0.407 -0.747 0.526) and a point (14.395, 37.07, -12.029). How to draw an axis in chimera tool with these two data? Thanks, Catherine -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Aug 17 09:32:19 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 17 Aug 2017 09:32:19 -0700 Subject: [Chimera-users] Draw Line In-Reply-To: References: Message-ID: <1B6D6E00-620C-46E2-8B3D-84ED0870E561@cgl.ucsf.edu> Hi Catherine, This is another basic geometry question, similar to what you asked before (), and not a Chimera issue. Use geometry (check in a textbook or look online) to figure out the coordinates of the two ends of the line or cylinder you want to display. In your question, you only gave a point and a direction, so there are a infinite number of points along that line and thus an infinite number of choices for the coordinates of the two ends of the cylinder. You would still have to decide which segment of that infinite line you want to depict. Basically the points on the line are your point coordinates plus or minus any multiple (including fractional) of the direction vector values. Now, here is the Chimera question part: Once you figure out the coordinates of the two ends you can put that in a BILD format file to show a cylinder just like we discussed before. The BILD format also allows you to draw an arrow or line instead (see .arrow or .dot + .draw). Or, make a PDB file with two fake atoms with those coordinates connected by a bond, which could be shown as wire or stick. Good luck, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 17, 2017, at 8:09 AM, Catherine Jenifer Rajam Rajendran wrote: > > Hi Eric, > Can you please tell me what are the ways to draw an axis. I have a directional vector - x, y, z coordinates (e.g., 0.407 -0.747 0.526) and a point (14.395, 37.07, -12.029). How to draw an axis in chimera tool with these two data? > Thanks, > Catherine From meng at cgl.ucsf.edu Thu Aug 17 09:55:51 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 17 Aug 2017 09:55:51 -0700 Subject: [Chimera-users] move different map to the same origin of coordinate In-Reply-To: References: Message-ID: Hi Jianhao, Probably what you want is to change the map center, as described in this previous post: I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 17, 2017, at 12:56 AM, C.J. wrote: > > Dear specialists, > I open a map(#1) and make icosahedron surface(#1) using Tools-> Higher-Order structure->icosahedron surface. > But the model #0 and #1 don't have the same center, how could I center them into the origin of same coordinate? > Thanks! > -- > Best regards! > Jianhao From pett at cgl.ucsf.edu Thu Aug 17 11:15:59 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 17 Aug 2017 11:15:59 -0700 Subject: [Chimera-users] advanced option for WebGL? In-Reply-To: References: Message-ID: <47998060-B8CE-4456-8565-D8AF29FC784B@cgl.ucsf.edu> Hi Albert, Unfortunately we are unlikely to enhance Chimera in this fashion, what with our focus on improving the usability of ChimeraX. Our plan is to have ChimeraX interoperate with other web-based molecular viewers to provide this functionality, but that?s quite aways off at this point. I?m sorry I don?t have anything very positive to offer here. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Aug 15, 2017, at 11:18 PM, Albert wrote: > > Hello, > > I noticed that Chimera can export a scene as HTML file which is based on WebGL. However, we can no longer change the displaying styles through this .html file since there is no any menu or option button in the page. Would it be good if Chimera could provide this function? As far as I know, PyMOL has similar function, but the generated .html provide a menu to change the scene styles. see here https://pymolwiki.org/index.php/Pymol2glmol > > Thank you very much. > > Albert > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From biocjh at gmail.com Thu Aug 17 18:11:25 2017 From: biocjh at gmail.com (C.J.) Date: Fri, 18 Aug 2017 09:11:25 +0800 Subject: [Chimera-users] move different map to the same origin of coordinate In-Reply-To: References: Message-ID: Hi Elaine, This really helps, and Thanks! Regards, Jianhao 2017-08-18 0:55 GMT+08:00 Elaine Meng : > Hi Jianhao, > Probably what you want is to change the map center, as described in this > previous post: > > > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Aug 17, 2017, at 12:56 AM, C.J. wrote: > > > > Dear specialists, > > I open a map(#1) and make icosahedron surface(#1) using Tools-> > Higher-Order structure->icosahedron surface. > > But the model #0 and #1 don't have the same center, how could I center > them into the origin of same coordinate? > > Thanks! > > -- > > Best regards! > > Jianhao > > -- Best regards! C.J. -------------- next part -------------- An HTML attachment was scrubbed... URL: From agszabo at outlook.com Thu Aug 17 18:55:51 2017 From: agszabo at outlook.com (Arthur Szabo) Date: Fri, 18 Aug 2017 01:55:51 +0000 Subject: [Chimera-users] biounit In-Reply-To: <25DF4658-AE28-4375-A284-5C78C58E8764@cgl.ucsf.edu> References: <2108BBD2-0914-4DFE-8225-5BC02B0FEDB4@cgl.ucsf.edu> <25DF4658-AE28-4375-A284-5C78C58E8764@cgl.ucsf.edu> Message-ID: Elaine Presumably in order to run ChimeraX one needs to have Windows 10 as an operating system. When I bought this computer three years ago it had Windows 8 on it. I got rid of that and loaded Windows 7. Being in the middle of writing a text with lots of figures I wanted to stay with Windows 7 and not have to learn a new operating system. I could have loaded Windows 10 for free, but for the same reasons I declined. art -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: Monday, August 14, 2017 6:52 PM To: Arthur Szabo Cc: UCSF Chimera Mailing List Subject: Re: [Chimera-users] biounit Hi Arthur, It?s probably too big for your computer and/or for reasonable speed of interaction in Chimera (display changes, rotation etc.). The structure is so large that it?s being downloaded in mmCIF format and Chimera is rather slow to open mmCIF. It might load eventually if you waited a really long time (many minutes?), but then rotation etc. would still be slow. Our new software ChimeraX is developed to handle such large structures and mmCIF format much better and faster, but it also depends on having a reasonably up-to-date computer. Download could still be slow depending on the speed of your connection with the database. As for the computer, we recommend using one from the ?last 3 years? although it is certainly possible it might work on older computers too. ChimeraX commands have a lot of similarities with Chimera commands, but there are differences, and most functions are command-only (not in the menu). Nevertheless, should be easy to try downloading the program and seeing if it runs on your computer, and if so, entering command ?open 4v9d? to see how that goes. ChimeraX is still in pre-release but available to download, and it has a lot of display options and image-saving. The ChimeraX home page has links to download and User Guide on the left: The bottom example in the ChimeraX image gallery is a ribosome: I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 14, 2017, at 3:19 PM, Arthur Szabo wrote: > > Elaine > > Thank you > > A follow up question. PDB 4V9D is a structure of a bacterial ribosome. Some 35Mb. > > Can this be handled, or is the size to large to download. > I tried to fetch it by PDB index, but it just seemed to stall or was way too large. > > Regards > > arthur From nissanabilaabdulrazak at gmail.com Fri Aug 18 00:18:50 2017 From: nissanabilaabdulrazak at gmail.com (Nissa Nabila) Date: Fri, 18 Aug 2017 15:18:50 +0800 Subject: [Chimera-users] I Can't Open My ZDOCK Output File Into Chimera Message-ID: Hello and hi! My name is Nissa Nabila and I am a Chimera user. Recently, I did a docking job on ZDOCK server webpage, and already got all the output files. But then, those output files cannot be opened by Chimera even though the output files are all in PDB format. So, can you please help me to solve this problem? Attached is the ZDOCK output file that need to be viewed by Chimera. Have a review. Thank you in advanced! -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: job.122931.zd3.0.2.out Type: application/octet-stream Size: 94363 bytes Desc: not available URL: From nissanabilaabdulrazak at gmail.com Fri Aug 18 00:20:59 2017 From: nissanabilaabdulrazak at gmail.com (Nissa Nabila) Date: Fri, 18 Aug 2017 15:20:59 +0800 Subject: [Chimera-users] I Can't Open My ZDOCK Output File Into Chimera In-Reply-To: References: Message-ID: And these as well, I missed to upload it earlier. Sorry for the inconvenient! :-( On Fri, Aug 18, 2017 at 3:18 PM, Nissa Nabila < nissanabilaabdulrazak at gmail.com> wrote: > Hello and hi! > > My name is Nissa Nabila and I am a Chimera user. Recently, I did a docking > job on ZDOCK server webpage, and already got all the output files. But > then, those output files cannot be opened by Chimera even though the output > files are all in PDB format. So, can you please help me to solve this > problem? > > Attached is the ZDOCK output file that need to be viewed by Chimera. Have > a review. > > Thank you in advanced! > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lig.job122931.bl.pdb Type: chemical/x-pdb Size: 245597 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rec.job122931.bl.pdb Type: chemical/x-pdb Size: 28054 bytes Desc: not available URL: From meng at cgl.ucsf.edu Fri Aug 18 08:56:03 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 18 Aug 2017 08:56:03 -0700 Subject: [Chimera-users] biounit In-Reply-To: References: <2108BBD2-0914-4DFE-8225-5BC02B0FEDB4@cgl.ucsf.edu> <25DF4658-AE28-4375-A284-5C78C58E8764@cgl.ucsf.edu> Message-ID: Hi Arthur, ChimeraX might work on your Windows 7 system, it?s just not ?guaranteed? ? you would have to try it to find out. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 17, 2017, at 6:55 PM, Arthur Szabo wrote: > > Elaine > > Presumably in order to run ChimeraX one needs to have Windows 10 as an operating system. > > When I bought this computer three years ago it had Windows 8 on it. I got rid of that and loaded Windows 7. Being in the middle of writing a text with lots of figures I wanted to stay with Windows 7 and not have to learn a new operating system. I could have loaded Windows 10 for free, but for the same reasons I declined. > > art > From meng at cgl.ucsf.edu Fri Aug 18 09:21:55 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 18 Aug 2017 09:21:55 -0700 Subject: [Chimera-users] I Can't Open My ZDOCK Output File Into Chimera In-Reply-To: References: Message-ID: Hi Nissa, Well, the ?.out? file is not PDB format or any format that Chimera knows about, and the rec[?]pdb and lig[?]pdb files are not really correct PDB format either. They have some extra stuff after the X,Y,Z coordinates in each line that is different from the standard PDB format. Maybe some other programs tolerate this extra stuff, but Chimera doesn?t. See our ?introduction to PDB format?: ? and here?s a list of the kinds of docking outputs Chimera reads: So if you want to use Chimera to view the PDB files, you would have to edit them to delete the part of each ATOM line after the X,Y,Z coordinate values. I attach edited versions of your two files. You could use whatever text-editing method you prefer. After you did that, you would be able to see the atomic structures, but Chimera still would not know how to read the ZDOCK ?.out? file. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco -------------- next part -------------- A non-text attachment was scrubbed... Name: lig-edited.pdb Type: application/octet-stream Size: 162745 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rec-edited.pdb Type: application/octet-stream Size: 18590 bytes Desc: not available URL: -------------- next part -------------- > On Aug 18, 2017, at 12:20 AM, Nissa Nabila wrote: > > And these as well, I missed to upload it earlier. Sorry for the inconvenient! :-( > > On Fri, Aug 18, 2017 at 3:18 PM, Nissa Nabila wrote: > Hello and hi! > > My name is Nissa Nabila and I am a Chimera user. Recently, I did a docking job on ZDOCK server webpage, and already got all the output files. But then, those output files cannot be opened by Chimera even though the output files are all in PDB format. So, can you please help me to solve this problem? > > Attached is the ZDOCK output file that need to be viewed by Chimera. Have a review. > > Thank you in advanced! > > From hernando.sosa at einstein.yu.edu Sat Aug 19 10:32:26 2017 From: hernando.sosa at einstein.yu.edu (Hernando J Sosa) Date: Sat, 19 Aug 2017 17:32:26 +0000 Subject: [Chimera-users] Chimera-X In-Reply-To: References: Message-ID: Hi, I am trying to use Chimera-X t for solvent-accessible-surface display (in my system surface display fails almost every time in Chimera). I managed to get it to work in Chimer-X once but now when I click the appropriate icon on the top in chimera-X menu this icon and most others (except the one to open files) are inactive. Is there anything that I should do to activate these icons? I am I missing something? I tried selecting the model that was opened but that didn't help. Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sat Aug 19 14:04:05 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 19 Aug 2017 14:04:05 -0700 Subject: [Chimera-users] Chimera-X In-Reply-To: References: Message-ID: Hi Hernando, Not sure I understand this question, because there is no ?inactive? status of the ChimeraX toolbar icons. When I use ChimeraX, these icons always look the same and can be clicked, even when nothing is open. It doesn?t require selecting, unless you want to limit the action to some subset of what is open. I assume you are referring to the icons described here: If you could send a screenshot of the ChimeraX window with this problem, maybe that would help. However, the icons are just shortcuts to commands. After opening your atomic structure, you could try entering the ChimeraX command ?surface? and seeing if that works. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 19, 2017, at 10:32 AM, Hernando J Sosa wrote: > > Hi, > I am trying to use Chimera-X t for solvent-accessible-surface display (in my system surface display fails almost every time in Chimera). I managed to get it to work in Chimer-X once but now when I click the appropriate icon on the top in chimera-X menu this icon and most others (except the one to open files) are inactive. Is there anything that I should do to activate these icons? I am I missing something? I tried selecting the model that was opened but that didn't help. > Thanks. From hernando.sosa at einstein.yu.edu Sat Aug 19 17:27:58 2017 From: hernando.sosa at einstein.yu.edu (Hernando J Sosa) Date: Sun, 20 Aug 2017 00:27:58 +0000 Subject: [Chimera-users] Chimera-X In-Reply-To: References: , Message-ID: Hi Elaine, I figured it out what the problem may be. For some reason the mouse position it is not mapped out correctly in the ChimeraX window. I.e. the icons are active but the cursor has to be placed not on top of the icon but somewhere else close by (below). This occurs with the latest daily build or the latest alpha version. I am running it in a Windows 10 laptop. Best H. ________________________________ Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa at einstein.yu.edu ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Saturday, August 19, 2017 5:04 PM To: Hernando J Sosa Cc: chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] Chimera-X Hi Hernando, Not sure I understand this question, because there is no ?inactive? status of the ChimeraX toolbar icons. When I use ChimeraX, these icons always look the same and can be clicked, even when nothing is open. It doesn?t require selecting, unless you want to limit the action to some subset of what is open. I assume you are referring to the icons described here: If you could send a screenshot of the ChimeraX window with this problem, maybe that would help. However, the icons are just shortcuts to commands. After opening your atomic structure, you could try entering the ChimeraX command ?surface? and seeing if that works. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 19, 2017, at 10:32 AM, Hernando J Sosa wrote: > > Hi, > I am trying to use Chimera-X t for solvent-accessible-surface display (in my system surface display fails almost every time in Chimera). I managed to get it to work in Chimer-X once but now when I click the appropriate icon on the top in chimera-X menu this icon and most others (except the one to open files) are inactive. Is there anything that I should do to activate these icons? I am I missing something? I tried selecting the model that was opened but that didn't help. > Thanks. From cy16f01.dilip at nitk.edu.in Sun Aug 20 10:45:49 2017 From: cy16f01.dilip at nitk.edu.in (Dilip H N) Date: Sun, 20 Aug 2017 23:15:49 +0530 Subject: [Chimera-users] Regarding generating a .pdb file of peptide (Diglycine) Message-ID: Hello, I have install chimers in ubuntu 14.04.. I am finding difficult to get the .pdb format for diglyicne peptide... 1] If in Build Structure i select PubChem CID and type 11163 (Diglycine PubChem CID) i am getting error as:- Error fetching 11163:[Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssi.c:590) 2] I even tried through File - Fetch by ID - Pubchem and typed 1163 (Diglycine PubChem CID).. but in vain..i am getting the same error.. So can anybody kindly help....i am a novice here.. Thank you... -- With Best Regards, DILIP.H.N Ph.D Student Sent with Mailtrack -------------- next part -------------- An HTML attachment was scrubbed... URL: From cy16f01.dilip at nitk.edu.in Sun Aug 20 11:03:53 2017 From: cy16f01.dilip at nitk.edu.in (Dilip H N) Date: Sun, 20 Aug 2017 23:33:53 +0530 Subject: [Chimera-users] Regarding generating a .pdb file of peptide (Diglycine) In-Reply-To: References: Message-ID: Hello, I have installed chimera in ubuntu 14.04.. I am finding difficult to get the .pdb format for diglyicne peptide (and further to create the topology and run the simulation in gromacs)... 1] If in Build Structure i select PubChem CID and type 11163 (Diglycine PubChem CID) i am getting error as:- Error fetching 11163:[Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssi.c:590) 2] I even tried through File - Fetch by ID - Pubchem and typed 1163 (Diglycine PubChem CID).. but in vain..i am getting the same error.. So can anybody kindly help....i am a novice here.. Any suggestions are highly appreciated.. Thank you... Sent with Mailtrack On Sun, Aug 20, 2017 at 11:15 PM, Dilip H N wrote: > Hello, > I have install chimers in ubuntu 14.04.. > I am finding difficult to get the .pdb format for diglyicne peptide... > 1] If in Build Structure i select PubChem CID and type 11163 (Diglycine > PubChem CID) i am getting error as:- > Error fetching 11163:[Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] > certificate verify failed (_ssi.c:590) > 2] I even tried through File - Fetch by ID - Pubchem and typed 1163 > (Diglycine PubChem CID).. but in vain..i am getting the same error.. > > So can anybody kindly help....i am a novice here.. > > Thank you... > -- > With Best Regards, > > DILIP.H.N > Ph.D Student > > > > Sent with Mailtrack > > -- With Best Regards, DILIP.H.N Ph.D Student -------------- next part -------------- An HTML attachment was scrubbed... URL: From nissanabilaabdulrazak at gmail.com Sun Aug 20 19:15:00 2017 From: nissanabilaabdulrazak at gmail.com (Nissa Nabila) Date: Mon, 21 Aug 2017 10:15:00 +0800 Subject: [Chimera-users] I Can't Open My ZDOCK Output File Into Chimera In-Reply-To: References: Message-ID: Alright, thank you for your responses. Have a nice day ahead! :-) On Sat, Aug 19, 2017 at 12:21 AM, Elaine Meng wrote: > Hi Nissa, > Well, the ?.out? file is not PDB format or any format that Chimera knows > about, and the rec[?]pdb and lig[?]pdb files are not really correct PDB > format either. They have some extra stuff after the X,Y,Z coordinates in > each line that is different from the standard PDB format. Maybe some other > programs tolerate this extra stuff, but Chimera doesn?t. > > See our ?introduction to PDB format?: > tutorials/framepdbintro.html> > > ? and here?s a list of the kinds of docking outputs Chimera reads: > framevd.html> > > So if you want to use Chimera to view the PDB files, you would have to > edit them to delete the part of each ATOM line after the X,Y,Z coordinate > values. I attach edited versions of your two files. You could use whatever > text-editing method you prefer. > > After you did that, you would be able to see the atomic structures, but > Chimera still would not know how to read the ZDOCK ?.out? file. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > > > On Aug 18, 2017, at 12:20 AM, Nissa Nabila com> wrote: > > > > And these as well, I missed to upload it earlier. Sorry for the > inconvenient! :-( > > > > On Fri, Aug 18, 2017 at 3:18 PM, Nissa Nabila < > nissanabilaabdulrazak at gmail.com> wrote: > > Hello and hi! > > > > My name is Nissa Nabila and I am a Chimera user. Recently, I did a > docking job on ZDOCK server webpage, and already got all the output files. > But then, those output files cannot be opened by Chimera even though the > output files are all in PDB format. So, can you please help me to solve > this problem? > > > > Attached is the ZDOCK output file that need to be viewed by Chimera. > Have a review. > > > > Thank you in advanced! > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Aug 21 17:44:01 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 21 Aug 2017 17:44:01 -0700 Subject: [Chimera-users] Regarding generating a .pdb file of peptide (Diglycine) In-Reply-To: References: Message-ID: <955A3372-FE2F-44B5-87F4-B8B67AB62522@cgl.ucsf.edu> Hi, We can reproduce the problem you?re having (only occurs on Linux) and are working on a solution. Until we fix it, you have three options: 1) Use a non-Linux machine 2) Since PubChem 11163 is simply a diglycine, use the ?peptide? option in Build Structure with the sequence ?GG?. This will differ slightly from the PubChem structure in that the PubChem one will be protonated as neutral, whereas the Build Structure one (if you later add hydrogens) will be protonated for biological pH. 3) Assuming you installed Chimera in the default location on your Linux box, run it as ?SSL_CERT_DIR=/etc/ssl/certs ~/.local/UCSF-Chimera64-/bin/chimera?. You will have to look in your ~/.local directory and replace with the Chimera version number you see there. Then you should be able to use a PubChem fetch successfully. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Aug 20, 2017, at 11:03 AM, Dilip H N wrote: > > Hello, > I have installed chimera in ubuntu 14.04.. > I am finding difficult to get the .pdb format for diglyicne peptide (and further to create the topology and run the simulation in gromacs)... > 1] If in Build Structure i select PubChem CID and type 11163 (Diglycine PubChem CID) i am getting error as:- > Error fetching 11163:[Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssi.c:590) > 2] I even tried through File - Fetch by ID - Pubchem and typed 1163 (Diglycine PubChem CID).. but in vain..i am getting the same error.. > > So can anybody kindly help....i am a novice here.. > Any suggestions are highly appreciated.. > > Thank you... > > > > ? Sent with Mailtrack > > On Sun, Aug 20, 2017 at 11:15 PM, Dilip H N > wrote: > Hello, > I have install chimers in ubuntu 14.04.. > I am finding difficult to get the .pdb format for diglyicne peptide... > 1] If in Build Structure i select PubChem CID and type 11163 (Diglycine PubChem CID) i am getting error as:- > Error fetching 11163:[Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssi.c:590) > 2] I even tried through File - Fetch by ID - Pubchem and typed 1163 (Diglycine PubChem CID).. but in vain..i am getting the same error.. > > So can anybody kindly help....i am a novice here.. > > Thank you... > -- > With Best Regards, > > DILIP.H.N > Ph.D Student > > > > ? Sent with Mailtrack > > > -- > With Best Regards, > > DILIP.H.N > Ph.D Student > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From biocjh at gmail.com Mon Aug 21 20:51:16 2017 From: biocjh at gmail.com (C.J.) Date: Tue, 22 Aug 2017 11:51:16 +0800 Subject: [Chimera-users] setting surface color of EM map in command-line Message-ID: Dear specialists, I want to color spherical slices of different radius of my EM map in command line/script. How to set the "surface color" dialog in command-line? If anyone could give me a example? Thank you! Best regards! Jianhao -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Aug 22 08:41:48 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 22 Aug 2017 08:41:48 -0700 Subject: [Chimera-users] setting surface color of EM map in command-line In-Reply-To: References: Message-ID: <00D4D98A-4B94-4177-B2A5-B92F27030426@cgl.ucsf.edu> Hi Jianhao, The ?scolor? command does several types of surface coloring, including the radial coloring you describe. See the ?scolor? manual page, ?geometry radial? option. The second example near the top of the page uses this option. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 21, 2017, at 8:51 PM, C.J. wrote: > > Dear specialists, > > I want to color spherical slices of different radius of my EM map in command line/script. How to set the "surface color" dialog in command-line? > If anyone could give me a example? Thank you! > > Best regards! > Jianhao From goddard at sonic.net Tue Aug 22 08:40:47 2017 From: goddard at sonic.net (Tom Goddard) Date: Tue, 22 Aug 2017 08:40:47 -0700 Subject: [Chimera-users] setting surface color of EM map in command-line In-Reply-To: References: Message-ID: <3AD38621-E701-469F-AE1F-5814132DC870@sonic.net> Hi Jianhao, The command equivalent to the surface color is scolor. There are examples using it in the documentation. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html Tom > On Aug 21, 2017, at 8:51 PM, "C.J." wrote: > > Dear specialists, > > I want to color spherical slices of different radius of my EM map in command line/script. How to set the "surface color" dialog in command-line? > If anyone could give me a example? Thank you! > > Best regards! > Jianhao > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From natannoage at gmail.com Tue Aug 22 04:42:12 2017 From: natannoage at gmail.com (natan geier) Date: Tue, 22 Aug 2017 14:42:12 +0300 Subject: [Chimera-users] Helix voxels labeling Message-ID: Hello, I am currently studying the connection between density maps and the secondary structure elements. I have a density map file for a certain protein, giving for each voxel a density value, and what I am missing is a "helix map", giving a binary value for each voxel, representing wether it is a part of a helix or not. In order to build this "helix map", I need to use the .pdb file of that protein, but I am not really sure how to extract an appropriate 3D boolean matrix out of this file. Any suggestions would be greatly appreciated. Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Tue Aug 22 11:06:51 2017 From: goddard at sonic.net (Tom Goddard) Date: Tue, 22 Aug 2017 11:06:51 -0700 Subject: [Chimera-users] Helix voxels labeling In-Reply-To: References: Message-ID: <394D96A9-E214-440B-A879-54A0228902C2@sonic.net> Hi Natan, You can use the molmap and mask commands to get a binary mask around helices, for example, open 3p2i molmap helix 10 grid 2 model #1 vol #1 level 0.25 mask ones #1 volume #1 hide volume #2 save helixmask.mrc These commands open PDB file 3p2i, create a density map at resolution 10 Angstroms with grid spacing 2 Angstroms for the helix atoms calling the resulting map #1, set the surface contour level of that helix map to 0.25, create a 0/1 binary mask with one values within the surface of the helix map, hide the original helix map so you can see the binary mask, and save the binary mask to an MRC file. All the commands are described in great detail in the documentation. Tom > On Aug 22, 2017, at 4:42 AM, natan geier wrote: > > Hello, > I am currently studying the connection between density maps and the secondary structure elements. > I have a density map file for a certain protein, giving for each voxel a density value, and what I am missing is a "helix map", giving a binary value for each voxel, representing wether it is a part of a helix or not. > In order to build this "helix map", I need to use the .pdb file of that protein, but I am not really sure how to extract an appropriate 3D boolean matrix out of this file. > Any suggestions would be greatly appreciated. > > Thanks > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: helixmask.png Type: image/png Size: 314670 bytes Desc: not available URL: From goddard at sonic.net Tue Aug 22 11:11:12 2017 From: goddard at sonic.net (Tom Goddard) Date: Tue, 22 Aug 2017 11:11:12 -0700 Subject: [Chimera-users] Chimera-X In-Reply-To: References: Message-ID: Hi Hernando, This seems like a Qt window toolkit bug. We do not observe this on Windows 10 or any other operating system, although reports on the web suggest Qt can sometimes get confused about the window position if you minimize or maximize the window. Does it fix itself if you manually resize the ChimeraX window or move the window? You can send email to chimerax-bugs at cgl.ucsf.edu to make a bug report. It will be hard for us to do anything about it if we cannot make it happen on one of our machines. Tom > On Aug 19, 2017, at 5:27 PM, Hernando J Sosa wrote: > > Hi Elaine, > > I figured it out what the problem may be. For some reason the mouse position it is not mapped out correctly in the ChimeraX window. I.e. the icons are active but the cursor has to be placed not on top of the icon but somewhere else close by (below). This occurs with the latest daily build or the latest alpha version. I am running it in a Windows 10 laptop. > > Best > > H. > > ________________________________ > Hernando Sosa > Dept. of Physiology and Biophysics > Albert Einstein College of Medicine > 1300 Morris Park Av. > Bronx NY 10461 > phone (718) 430-3456 > FAX (718) 430-8819 > email hernando.sosa at einstein.yu.edu > > ________________________________________ > From: Elaine Meng > Sent: Saturday, August 19, 2017 5:04 PM > To: Hernando J Sosa > Cc: chimera-users at cgl.ucsf.edu BB > Subject: Re: [Chimera-users] Chimera-X > > Hi Hernando, > Not sure I understand this question, because there is no ?inactive? status of the ChimeraX toolbar icons. When I use ChimeraX, these icons always look the same and can be clicked, even when nothing is open. It doesn?t require selecting, unless you want to limit the action to some subset of what is open. I assume you are referring to the icons described here: > > > > If you could send a screenshot of the ChimeraX window with this problem, maybe that would help. > > However, the icons are just shortcuts to commands. After opening your atomic structure, you could try entering the ChimeraX command ?surface? and seeing if that works. > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Aug 19, 2017, at 10:32 AM, Hernando J Sosa wrote: >> >> Hi, >> I am trying to use Chimera-X t for solvent-accessible-surface display (in my system surface display fails almost every time in Chimera). I managed to get it to work in Chimer-X once but now when I click the appropriate icon on the top in chimera-X menu this icon and most others (except the one to open files) are inactive. Is there anything that I should do to activate these icons? I am I missing something? I tried selecting the model that was opened but that didn't help. >> Thanks. > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From biocjh at gmail.com Tue Aug 22 22:28:34 2017 From: biocjh at gmail.com (C.J.) Date: Wed, 23 Aug 2017 13:28:34 +0800 Subject: [Chimera-users] setting surface color of EM map in command-line In-Reply-To: <00D4D98A-4B94-4177-B2A5-B92F27030426@cgl.ucsf.edu> References: <00D4D98A-4B94-4177-B2A5-B92F27030426@cgl.ucsf.edu> Message-ID: Thank you! It really helps! Regards, Jianhao 2017-08-22 23:41 GMT+08:00 Elaine Meng : > > Hi Jianhao, > The ?scolor? command does several types of surface coloring, including the > radial coloring you describe. See the ?scolor? manual page, ?geometry > radial? option. The second example near the top of the page uses this > option. > > > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Aug 21, 2017, at 8:51 PM, C.J. wrote: > > > > Dear specialists, > > > > I want to color spherical slices of different radius of my EM map in > command line/script. How to set the "surface color" dialog in command-line? > > If anyone could give me a example? Thank you! > > > > Best regards! > > Jianhao > > -- Best regards! C.J. -------------- next part -------------- An HTML attachment was scrubbed... URL: From agszabo at outlook.com Wed Aug 23 16:03:20 2017 From: agszabo at outlook.com (Arthur Szabo) Date: Wed, 23 Aug 2017 23:03:20 +0000 Subject: [Chimera-users] sent to a different url Message-ID: I am interested in a structure 1GSG deposited in 1990. The PDB index for this file shows the enzyme Gln tRNA synthetase with the usual ribbon structure, bound to tRNA(Gln). When I fetch 1GSG using either the PDB file number only, or that file number input into PDB biounit, the structure that comes up does not have the helical or ?-sheet secondary structures shown as ribbons. Rather the entire protein backbone is shown without any secondary structure definition. One can see the helical segments in the worm like structure, but not in the form of the usual helical secondary structure. How can I retrieve a structure that is similar to that in the PDB index list. I have enclosed the following: [cid:image001.png at 01D31C42.7C7B48F0] This is what comes up when I fetch the PDB file. [cid:image002.png at 01D31C42.7C7B48F0] Thanks Arthur G. Szabo Professor Emeritus -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 165703 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 66704 bytes Desc: image002.png URL: From meng at cgl.ucsf.edu Wed Aug 23 17:32:02 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 23 Aug 2017 17:32:02 -0700 Subject: [Chimera-users] secondary structure ribbons not drawn for CA-only protein In-Reply-To: References: Message-ID: <7C496DC7-111B-4554-B623-E2FBB586C1E7@cgl.ucsf.edu> Hi Arthur, PDB entry 1gsg contains only 1 atom per residue, CA atoms for the protein and P atoms for the tRNA. Chimera does not draw the secondary-structure ribbons for alpha-carbon-only proteins because it uses the carbonyl oxygens to define the plane of the ribbon. Some other program was used to make the image you see at the RCSB PDB. You could instead try using some other structure that is more complete. Here are all the structures with the same protein as 1gsg, most of which are complexed with tRNA (4jyz, 4jxx, etc.): I got this list by first searching RCSB PDB for 1GSG and going to its page: ? then lower in the page in the Macromolecules section, clicking the link to search for PDB structures with UniprotKB Access Code ?P00962? I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 23, 2017, at 4:03 PM, Arthur Szabo wrote: > > I am interested in a structure 1GSG deposited in 1990. The PDB index for this file shows the enzyme Gln tRNA synthetase with the usual ribbon structure, bound to tRNA(Gln). > > When I fetch 1GSG using either the PDB file number only, or that file number input into PDB biounit, the structure that comes up does not have the helical or ?-sheet secondary structures shown as ribbons. Rather the entire protein backbone is shown without any secondary structure definition. One can see the helical segments in the worm like structure, but not in the form of the usual helical secondary structure. > > How can I retrieve a structure that is similar to that in the PDB index list. > > I have enclosed the following: > > > > This is what comes up when I fetch the PDB file. > > > > Thanks > > Arthur G. Szabo > Professor Emeritus From agszabo at outlook.com Wed Aug 23 19:20:03 2017 From: agszabo at outlook.com (Arthur Szabo) Date: Thu, 24 Aug 2017 02:20:03 +0000 Subject: [Chimera-users] secondary structure ribbons not drawn for CA-only protein In-Reply-To: <7C496DC7-111B-4554-B623-E2FBB586C1E7@cgl.ucsf.edu> References: <7C496DC7-111B-4554-B623-E2FBB586C1E7@cgl.ucsf.edu> Message-ID: Elaine Thank you for your repl;y. I found another structure that is complete 1GTR Thanks for your information. art -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: Wednesday, August 23, 2017 8:32 PM To: Arthur Szabo Cc: chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] secondary structure ribbons not drawn for CA-only protein Hi Arthur, PDB entry 1gsg contains only 1 atom per residue, CA atoms for the protein and P atoms for the tRNA. Chimera does not draw the secondary-structure ribbons for alpha-carbon-only proteins because it uses the carbonyl oxygens to define the plane of the ribbon. Some other program was used to make the image you see at the RCSB PDB. You could instead try using some other structure that is more complete. Here are all the structures with the same protein as 1gsg, most of which are complexed with tRNA (4jyz, 4jxx, etc.): I got this list by first searching RCSB PDB for 1GSG and going to its page: ? then lower in the page in the Macromolecules section, clicking the link to search for PDB structures with UniprotKB Access Code ?P00962? I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 23, 2017, at 4:03 PM, Arthur Szabo wrote: > > I am interested in a structure 1GSG deposited in 1990. The PDB index for this file shows the enzyme Gln tRNA synthetase with the usual ribbon structure, bound to tRNA(Gln). > > When I fetch 1GSG using either the PDB file number only, or that file number input into PDB biounit, the structure that comes up does not have the helical or ?-sheet secondary structures shown as ribbons. Rather the entire protein backbone is shown without any secondary structure definition. One can see the helical segments in the worm like structure, but not in the form of the usual helical secondary structure. > > How can I retrieve a structure that is similar to that in the PDB index list. > > I have enclosed the following: > > > > This is what comes up when I fetch the PDB file. > > > > Thanks > > Arthur G. Szabo > Professor Emeritus From biocjh at gmail.com Wed Aug 23 21:25:59 2017 From: biocjh at gmail.com (C.J.) Date: Thu, 24 Aug 2017 12:25:59 +0800 Subject: [Chimera-users] duplicate a EM map in window by command line Message-ID: Dear specialists, Is there a command line to creat a model copy of a opened EM map in the window? Thank you! Best regards! Jianhao -------------- next part -------------- An HTML attachment was scrubbed... URL: From cy16f01.dilip at nitk.edu.in Thu Aug 24 02:16:15 2017 From: cy16f01.dilip at nitk.edu.in (Dilip H N) Date: Thu, 24 Aug 2017 14:46:15 +0530 Subject: [Chimera-users] Regarding getting the .pdb file of glutamine Message-ID: Hello, 1] I am having difficulties in getting the Glutamine.pdb file in chimera. I tried in Build Structure - Peptide and in peptide sequence if i type GLN, i am getting peptide of glutamine...., but what i want is just glutamine molecule, and not a peptide.. So how can i generate a glutamine molecule in chimera.... 2] Another question in Diglycine peptide, i want to insert CH2 in between the molecule (say in between C=O and CA), How can i insert the methyl group there.. Any suggestions are highly appreciated -- With Best Regards, DILIP.H.N Ph.D Student Sent with Mailtrack -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Aug 24 09:43:29 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 24 Aug 2017 09:43:29 -0700 Subject: [Chimera-users] Regarding getting the .pdb file of glutamine In-Reply-To: References: Message-ID: <7350F2CA-A2F8-4E97-8A11-820422835D00@cgl.ucsf.edu> Hello, (1) Build Structure: peptide uses one-letter codes, as explained in the help (click the Help button on the dialog or use the link below). In one-letter codes, Q = glutamine, GLN = glycine-leucine-asparagine Another way is to open some structure from the PDB that has the residue(s) you want and delete the rest of the atoms. (2) There is no ?insert? in Build Structure, only changing atom types, which also adds hydrogens and allows you to build out gradually atom-by-atom in several steps. In Build Structure, where it says ?Start Structure? near the top of the dialog, change to the ?Modify Structure? section to change atom types. If you can fetch, entering SMILES in the Start Structure section might be easier? but maybe you can?t, due to the pubchem-fetching problem you reported earlier. PubChem also shows SMILES strings. Glycine with an extra ?backbone? CH2 is also called beta-alanine? see Pubmed: ?that page shows its SMILES string: C(CN)C(=O)O There are several structures in the PDB that have this residue (residue name BAL), such as 4xn9. Can you fetch PDB structures? These commands leave me with one beta-alanine residue: open 4xn9 delete ~ :bal You could try building the standard-residue part of your peptide in the ?Start Structure? section of Build Structure, and in a separate model get a beta-alanine residue, and then use the ?Join Models? section of Build Structure to form a peptide bond between those two parts. I tried that just now and it worked. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 24, 2017, at 2:16 AM, Dilip H N wrote: > > Hello, > 1] I am having difficulties in getting the Glutamine.pdb file in chimera. > I tried in Build Structure - Peptide and in peptide sequence if i type GLN, i am getting peptide of glutamine...., but what i want is just glutamine molecule, and not a peptide.. > So how can i generate a glutamine molecule in chimera.... > > 2] Another question in Diglycine peptide, i want to insert CH2 in between the molecule (say in between C=O and CA), How can i insert the methyl group there.. > > Any suggestions are highly appreciated > > -- With Best Regards, > > DILIP.H.N > Ph.D Student From meng at cgl.ucsf.edu Thu Aug 24 09:51:36 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 24 Aug 2017 09:51:36 -0700 Subject: [Chimera-users] duplicate a EM map in window by command line In-Reply-To: References: Message-ID: <309D19A6-E719-4682-9402-269C887E5E80@cgl.ucsf.edu> Dear Jianhao, There is a slightly silly way. The ?vop add? command is really for adding multiple maps together, but I?ve noticed that if you only specify one map, it makes a copy of it. For example, if I already have a map #0, command: vop add #0 ...makes another map #1 that is the same. Its name includes ?resampled? but the histogram looks identical. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 23, 2017, at 9:25 PM, C.J. wrote: > > Dear specialists, > > Is there a command line to creat a model copy of a opened EM map in the window? > Thank you! > > Best regards! > Jianhao From biocjh at gmail.com Thu Aug 24 18:14:55 2017 From: biocjh at gmail.com (C.J.) Date: Fri, 25 Aug 2017 09:14:55 +0800 Subject: [Chimera-users] duplicate a EM map in window by command line In-Reply-To: <309D19A6-E719-4682-9402-269C887E5E80@cgl.ucsf.edu> References: <309D19A6-E719-4682-9402-269C887E5E80@cgl.ucsf.edu> Message-ID: That helps! Thank you for your reply. Regards, Jianhao 2017-08-25 0:51 GMT+08:00 Elaine Meng : > Dear Jianhao, > There is a slightly silly way. The ?vop add? command is really for adding > multiple maps together, but I?ve noticed that if you only specify one map, > it makes a copy of it. For example, if I already have a map #0, command: > > vop add #0 > > ...makes another map #1 that is the same. Its name includes ?resampled? > but the histogram looks identical. > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Aug 23, 2017, at 9:25 PM, C.J. wrote: > > > > Dear specialists, > > > > Is there a command line to creat a model copy of a opened EM map in the > window? > > Thank you! > > > > Best regards! > > Jianhao > > -- Best regards! C.J. -------------- next part -------------- An HTML attachment was scrubbed... URL: From liyixuan1307 at outlook.com Thu Aug 24 19:57:44 2017 From: liyixuan1307 at outlook.com (=?gb2312?B?wO4g0tXQ+w==?=) Date: Fri, 25 Aug 2017 02:57:44 +0000 Subject: [Chimera-users] Molecule Display Message-ID: Dear professor: In the process of using chimera, I encountered some problems. I found Gly residues can not be shown in stick, wire, ball-and-stick and sphere presentation. Can you help me Looking for your reply All the best. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Aug 25 08:46:05 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 25 Aug 2017 08:46:05 -0700 Subject: [Chimera-users] Molecule Display In-Reply-To: References: Message-ID: Hello, My guess is that you are showing ribbons. When you are showing ribbons, by default all the backbone atoms are hidden, and since glycine does not have a sidechain, that means all the atoms of glycine are hidden. You can either hide ribbons and show the atoms, or if you want to show both ribbons and backbone atoms at the same time, enter this command: ribbackbone Then you will still have to display whichever backbone atoms you want, if they weren?t already displayed (but hidden by ribbon). However, because the ribbon path is smoothed, the backbone atoms may be separated in space from the ribbon. This is explained in the manual, along with some possible ways to improve the display: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 24, 2017, at 7:57 PM, ? ?? wrote: > > Dear professor: > In the process of using chimera, I encountered some problems. I found Gly residues can not be shown in stick, wire, ball-and-stick and sphere presentation. Can you help me > Looking for your reply > All the best. From cy16f01.dilip at nitk.edu.in Fri Aug 25 23:17:07 2017 From: cy16f01.dilip at nitk.edu.in (Dilip H N) Date: Sat, 26 Aug 2017 11:47:07 +0530 Subject: [Chimera-users] Regarding getting the .pdb file of glutamine In-Reply-To: <7350F2CA-A2F8-4E97-8A11-820422835D00@cgl.ucsf.edu> References: <7350F2CA-A2F8-4E97-8A11-820422835D00@cgl.ucsf.edu> Message-ID: Thank you very much Elaine Sir, Your valuable suggestions has helped me a lot... Sir, i have few doubts still... Is it possible to to know the list of one letter codes for building amino acids, two letter codes for peptides, three letter code for dipeptides....etc...?? How can i know the one/two/three letter codes to build the molecules....?? since each letter is specific for each molecule...any references..?? Thank you.... Sent with Mailtrack On Thu, Aug 24, 2017 at 10:13 PM, Elaine Meng wrote: > Hello, > (1) Build Structure: peptide uses one-letter codes, as explained in the > help (click the Help button on the dialog or use the link below). > In one-letter codes, Q = glutamine, GLN = glycine-leucine-asparagine > editing.html> > > Another way is to open some structure from the PDB that has the residue(s) > you want and delete the rest of the atoms. > > (2) There is no ?insert? in Build Structure, only changing atom types, > which also adds hydrogens and allows you to build out gradually > atom-by-atom in several steps. In Build Structure, where it says ?Start > Structure? near the top of the dialog, change to the ?Modify Structure? > section to change atom types. If you can fetch, entering SMILES in the > Start Structure section might be easier? but maybe you can?t, due to the > pubchem-fetching problem you reported earlier. > input_line-entry_system> > PubChem also shows SMILES strings. > > Glycine with an extra ?backbone? CH2 is also called beta-alanine? see > Pubmed: > > ?that page shows its SMILES string: C(CN)C(=O)O > > There are several structures in the PDB that have this residue (residue > name BAL), such as 4xn9. Can you fetch PDB structures? These commands > leave me with one beta-alanine residue: > open 4xn9 > delete ~ :bal > > You could try building the standard-residue part of your peptide in the > ?Start Structure? section of Build Structure, and in a separate model get a > beta-alanine residue, and then use the ?Join Models? section of Build > Structure to form a peptide bond between those two parts. I tried that > just now and it worked. > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Aug 24, 2017, at 2:16 AM, Dilip H N > wrote: > > > > Hello, > > 1] I am having difficulties in getting the Glutamine.pdb file in chimera. > > I tried in Build Structure - Peptide and in peptide sequence if i type > GLN, i am getting peptide of glutamine...., but what i want is just > glutamine molecule, and not a peptide.. > > So how can i generate a glutamine molecule in chimera.... > > > > 2] Another question in Diglycine peptide, i want to insert CH2 in > between the molecule (say in between C=O and CA), How can i insert the > methyl group there.. > > > > Any suggestions are highly appreciated > > > > -- With Best Regards, > > > > DILIP.H.N > > Ph.D Student > > -- With Best Regards, DILIP.H.N Ph.D Student -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sat Aug 26 09:39:34 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 26 Aug 2017 09:39:34 -0700 Subject: [Chimera-users] Regarding getting the .pdb file of glutamine In-Reply-To: References: <7350F2CA-A2F8-4E97-8A11-820422835D00@cgl.ucsf.edu> Message-ID: <2439F398-3FC7-4C7A-85CA-3F4AE50B952C@cgl.ucsf.edu> Hi Dilip, The one-letter code is always the same for each amino acid. If you put 3 one-letter codes together you get a tripeptide of those three amino acids, in that order from N-terminus to C-terminus. This is not a Chimera thing, it is simply how protein sequences are notated. The one-letter codes are given in many general references, for example: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 25, 2017, at 11:17 PM, Dilip H N wrote: > > Thank you very much Elaine Sir, > Your valuable suggestions has helped me a lot... > Sir, i have few doubts still... > > Is it possible to to know the list of one letter codes for building amino acids, two letter codes for peptides, three letter code for dipeptides....etc...?? > How can i know the one/two/three letter codes to build the molecules....?? since each letter is specific for each molecule...any references..?? > > Thank you.... > > Sent with Mailtrack > > On Thu, Aug 24, 2017 at 10:13 PM, Elaine Meng wrote: > Hello, > (1) Build Structure: peptide uses one-letter codes, as explained in the help (click the Help button on the dialog or use the link below). > In one-letter codes, Q = glutamine, GLN = glycine-leucine-asparagine > > > Another way is to open some structure from the PDB that has the residue(s) you want and delete the rest of the atoms. > > (2) There is no ?insert? in Build Structure, only changing atom types, which also adds hydrogens and allows you to build out gradually atom-by-atom in several steps. In Build Structure, where it says ?Start Structure? near the top of the dialog, change to the ?Modify Structure? section to change atom types. If you can fetch, entering SMILES in the Start Structure section might be easier? but maybe you can?t, due to the pubchem-fetching problem you reported earlier. > > PubChem also shows SMILES strings. > > Glycine with an extra ?backbone? CH2 is also called beta-alanine? see Pubmed: > > ?that page shows its SMILES string: C(CN)C(=O)O > > There are several structures in the PDB that have this residue (residue name BAL), such as 4xn9. Can you fetch PDB structures? These commands leave me with one beta-alanine residue: > open 4xn9 > delete ~ :bal > > You could try building the standard-residue part of your peptide in the ?Start Structure? section of Build Structure, and in a separate model get a beta-alanine residue, and then use the ?Join Models? section of Build Structure to form a peptide bond between those two parts. I tried that just now and it worked. > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Aug 24, 2017, at 2:16 AM, Dilip H N wrote: > > > > Hello, > > 1] I am having difficulties in getting the Glutamine.pdb file in chimera. > > I tried in Build Structure - Peptide and in peptide sequence if i type GLN, i am getting peptide of glutamine...., but what i want is just glutamine molecule, and not a peptide.. > > So how can i generate a glutamine molecule in chimera.... > > > > 2] Another question in Diglycine peptide, i want to insert CH2 in between the molecule (say in between C=O and CA), How can i insert the methyl group there.. > > > > Any suggestions are highly appreciated > > > > -- With Best Regards, > > > > DILIP.H.N > > Ph.D Student > > > > > -- > With Best Regards, > > DILIP.H.N > Ph.D Student > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From mark.rosenberg at manchester.ac.uk Mon Aug 28 04:51:05 2017 From: mark.rosenberg at manchester.ac.uk (Mark Rosenberg) Date: Mon, 28 Aug 2017 11:51:05 +0000 Subject: [Chimera-users] Rainbow command Message-ID: <129550EA-8DA8-4955-B2BC-EE58DE152C27@manchester.ac.uk> Please can you provide an example of using Rainbow with Command line for a specific chain so I can see how the nomenclature works. It would be so helpful if the Chimera help files could provide more examples like this so one can adapt them to different situations. Thank you. From meng at cgl.ucsf.edu Mon Aug 28 09:53:01 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 28 Aug 2017 09:53:01 -0700 Subject: [Chimera-users] Rainbow command In-Reply-To: <129550EA-8DA8-4955-B2BC-EE58DE152C27@manchester.ac.uk> References: <129550EA-8DA8-4955-B2BC-EE58DE152C27@manchester.ac.uk> Message-ID: <9720843C-6931-48C1-8B2D-F0C309DB9847@cgl.ucsf.edu> Hi Mark, Short answer first and then a longer explanation. The short answer is that ?rainbow? always affects the whole model, i.e. you can?t just apply it to one chain in a model and not the others. So the command is simply rainbow ? or if you had more than one model, specifying the one you want, e.g. rainbow #1 Longer explanation: I know it takes a little getting used to, but the ?Usage? information on each command?s help page describes how to use the command. ( Individual examples are helpful, but often fail to cover the specific thing each user wants to do.) Usage notation: ?rainbow? command help: I? was guessing you want to color the residues in a chain along the rainbow spectrum (one color per residue, not one color per chain). That is the ?residue? level, which is the default, so you don?t have to specify it. If you want the standard rainbow colors starting with blue at N-term and ending with red at C-term, you don?t have to specify any colors either. So the only thing you might want to specify is which atoms to apply the command to, the ?atom-spec? in the usage. In the usage, this links to a separate page because most commands have ?atom-spec? and there are a lot of different ways to specify even the same set of atoms. However, as mentioned in the rainbow help page, it only affects the whole model. For other commands that can apply to some specific chain, the atom-spec part could be something like #0:.a - model 0 chain A :.c - all chains C in all models ? more examples here ... I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 28, 2017, at 4:51 AM, Mark Rosenberg wrote: > > Please can you provide an example of using Rainbow with Command line for a specific chain so I can see how the nomenclature works. > > It would be so helpful if the Chimera help files could provide more examples like this so one can adapt them to different situations. > > Thank you. From mark.rosenberg at manchester.ac.uk Mon Aug 28 09:57:21 2017 From: mark.rosenberg at manchester.ac.uk (Mark Rosenberg) Date: Mon, 28 Aug 2017 16:57:21 +0000 Subject: [Chimera-users] Rainbow command In-Reply-To: <9720843C-6931-48C1-8B2D-F0C309DB9847@cgl.ucsf.edu> References: <129550EA-8DA8-4955-B2BC-EE58DE152C27@manchester.ac.uk> <9720843C-6931-48C1-8B2D-F0C309DB9847@cgl.ucsf.edu> Message-ID: <66EF1EC4-2C45-40F1-AD5E-E89068F0BDFD@manchester.ac.uk> Hi Elaine That is wonderful. Thank you. There is whole depth of logical information for me to follow. Thank you so much. Best Mark > On 28 Aug 2017, at 17:53, Elaine Meng wrote: > > Hi Mark, > Short answer first and then a longer explanation. The short answer is that ?rainbow? always affects the whole model, i.e. you can?t just apply it to one chain in a model and not the others. So the command is simply > > rainbow > > ? or if you had more than one model, specifying the one you want, e.g. > > rainbow #1 > > Longer explanation: > I know it takes a little getting used to, but the ?Usage? information on each command?s help page describes how to use the command. ( Individual examples are helpful, but often fail to cover the specific thing each user wants to do.) > > Usage notation: > > > ?rainbow? command help: > > > I? was guessing you want to color the residues in a chain along the rainbow spectrum (one color per residue, not one color per chain). That is the ?residue? level, which is the default, so you don?t have to specify it. If you want the standard rainbow colors starting with blue at N-term and ending with red at C-term, you don?t have to specify any colors either. So the only thing you might want to specify is which atoms to apply the command to, the ?atom-spec? in the usage. In the usage, this links to a separate page because most commands have ?atom-spec? and there are a lot of different ways to specify even the same set of atoms. > > > > However, as mentioned in the rainbow help page, it only affects the whole model. For other commands that can apply to some specific chain, the atom-spec part could be something like > > #0:.a > - model 0 chain A > > :.c > - all chains C in all models > > ? more examples here ... > > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Aug 28, 2017, at 4:51 AM, Mark Rosenberg wrote: >> >> Please can you provide an example of using Rainbow with Command line for a specific chain so I can see how the nomenclature works. >> >> It would be so helpful if the Chimera help files could provide more examples like this so one can adapt them to different situations. >> >> Thank you. > From goddard at sonic.net Mon Aug 28 10:06:38 2017 From: goddard at sonic.net (Tom Goddard) Date: Mon, 28 Aug 2017 10:06:38 -0700 Subject: [Chimera-users] Rainbow command In-Reply-To: <66EF1EC4-2C45-40F1-AD5E-E89068F0BDFD@manchester.ac.uk> References: <129550EA-8DA8-4955-B2BC-EE58DE152C27@manchester.ac.uk> <9720843C-6931-48C1-8B2D-F0C309DB9847@cgl.ucsf.edu> <66EF1EC4-2C45-40F1-AD5E-E89068F0BDFD@manchester.ac.uk> Message-ID: ChimeraX, our next generation of Chimera, is a bit nicer in that it can rainbow a single chain, for example ?rainbow /b? to color just chain b. Tom > On Aug 28, 2017, at 9:57 AM, Mark Rosenberg wrote: > > Hi Elaine > That is wonderful. Thank you. > There is whole depth of logical information for me to follow. > Thank you so much. > Best > Mark >> On 28 Aug 2017, at 17:53, Elaine Meng wrote: >> >> Hi Mark, >> Short answer first and then a longer explanation. The short answer is that ?rainbow? always affects the whole model, i.e. you can?t just apply it to one chain in a model and not the others. So the command is simply >> >> rainbow >> >> ? or if you had more than one model, specifying the one you want, e.g. >> >> rainbow #1 >> >> Longer explanation: >> I know it takes a little getting used to, but the ?Usage? information on each command?s help page describes how to use the command. ( Individual examples are helpful, but often fail to cover the specific thing each user wants to do.) >> >> Usage notation: >> >> >> ?rainbow? command help: >> >> >> I? was guessing you want to color the residues in a chain along the rainbow spectrum (one color per residue, not one color per chain). That is the ?residue? level, which is the default, so you don?t have to specify it. If you want the standard rainbow colors starting with blue at N-term and ending with red at C-term, you don?t have to specify any colors either. So the only thing you might want to specify is which atoms to apply the command to, the ?atom-spec? in the usage. In the usage, this links to a separate page because most commands have ?atom-spec? and there are a lot of different ways to specify even the same set of atoms. >> >> >> >> However, as mentioned in the rainbow help page, it only affects the whole model. For other commands that can apply to some specific chain, the atom-spec part could be something like >> >> #0:.a >> - model 0 chain A >> >> :.c >> - all chains C in all models >> >> ? more examples here ... >> >> >> I hope this helps, >> Elaine >> ---------- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >>> On Aug 28, 2017, at 4:51 AM, Mark Rosenberg wrote: >>> >>> Please can you provide an example of using Rainbow with Command line for a specific chain so I can see how the nomenclature works. >>> >>> It would be so helpful if the Chimera help files could provide more examples like this so one can adapt them to different situations. >>> >>> Thank you. >> > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From mark.rosenberg at manchester.ac.uk Mon Aug 28 11:18:28 2017 From: mark.rosenberg at manchester.ac.uk (Mark Rosenberg) Date: Mon, 28 Aug 2017 18:18:28 +0000 Subject: [Chimera-users] Rainbow command In-Reply-To: References: <129550EA-8DA8-4955-B2BC-EE58DE152C27@manchester.ac.uk> <9720843C-6931-48C1-8B2D-F0C309DB9847@cgl.ucsf.edu> <66EF1EC4-2C45-40F1-AD5E-E89068F0BDFD@manchester.ac.uk> Message-ID: <2103BA42-88D5-4CB7-B621-3205847C7746@manchester.ac.uk> Wonderful Tom and Elaine. I will try that too. Thank you so much. > On 28 Aug 2017, at 18:06, Tom Goddard wrote: > > ChimeraX, our next generation of Chimera, is a bit nicer in that it can rainbow a single chain, for example ?rainbow /b? to color just chain b. > > Tom > >> On Aug 28, 2017, at 9:57 AM, Mark Rosenberg wrote: >> >> Hi Elaine >> That is wonderful. Thank you. >> There is whole depth of logical information for me to follow. >> Thank you so much. >> Best >> Mark >>> On 28 Aug 2017, at 17:53, Elaine Meng wrote: >>> >>> Hi Mark, >>> Short answer first and then a longer explanation. The short answer is that ?rainbow? always affects the whole model, i.e. you can?t just apply it to one chain in a model and not the others. So the command is simply >>> >>> rainbow >>> >>> ? or if you had more than one model, specifying the one you want, e.g. >>> >>> rainbow #1 >>> >>> Longer explanation: >>> I know it takes a little getting used to, but the ?Usage? information on each command?s help page describes how to use the command. ( Individual examples are helpful, but often fail to cover the specific thing each user wants to do.) >>> >>> Usage notation: >>> >>> >>> ?rainbow? command help: >>> >>> >>> I? was guessing you want to color the residues in a chain along the rainbow spectrum (one color per residue, not one color per chain). That is the ?residue? level, which is the default, so you don?t have to specify it. If you want the standard rainbow colors starting with blue at N-term and ending with red at C-term, you don?t have to specify any colors either. So the only thing you might want to specify is which atoms to apply the command to, the ?atom-spec? in the usage. In the usage, this links to a separate page because most commands have ?atom-spec? and there are a lot of different ways to specify even the same set of atoms. >>> >>> >>> >>> However, as mentioned in the rainbow help page, it only affects the whole model. For other commands that can apply to some specific chain, the atom-spec part could be something like >>> >>> #0:.a >>> - model 0 chain A >>> >>> :.c >>> - all chains C in all models >>> >>> ? more examples here ... >>> >>> >>> I hope this helps, >>> Elaine >>> ---------- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>>> On Aug 28, 2017, at 4:51 AM, Mark Rosenberg wrote: >>>> >>>> Please can you provide an example of using Rainbow with Command line for a specific chain so I can see how the nomenclature works. >>>> >>>> It would be so helpful if the Chimera help files could provide more examples like this so one can adapt them to different situations. >>>> >>>> Thank you. >>> >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > From aconstantinides1 at student.gsu.edu Mon Aug 28 09:00:03 2017 From: aconstantinides1 at student.gsu.edu (Amanda Evans Constantinides) Date: Mon, 28 Aug 2017 16:00:03 +0000 Subject: [Chimera-users] B-Factor Difference Plot Message-ID: Hello, I am plotting the B-factor differences between two similar structures. I do not understand why the plot is almost entirely on the positive side of the X-axis. If I open B factor putty models in PYMOL and in Chimera, there are some visible areas that should translate to negative B-factor differences on a quantitative plot. There is no way one structure is entirely more flexible than the other. Can you help explain this to me? Is there away to adjust the zero point to more accurately reflect these differences on the plot? Thank you, Amanda Constantinides Graduate Research Assistant Georgia State University -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Aug 28 14:37:36 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 28 Aug 2017 14:37:36 -0700 Subject: [Chimera-users] B-Factor Difference Plot In-Reply-To: References: Message-ID: Hi Amanda, Visually comparing the putty models (worms in Chimera) between the two structures is not meaningful unless you are sure you mapped the same value to the same radius in both structures. Even so, it is hard to see in this way. The more direct way is to just look at the PDB file in a text editor and see what the B-factor values are in the corresponding residues. I don?t know how you are calculating the differences, but you would have to make sure your script or whatever is mathematically correct and that it is also correctly pairing the residues between the two structures. I.e. the residue numbering might be different in the two structures. Now, comparing all the atomic values is probably too hard, so you could use Chimera to output the average values per residue so that you have fewer numbers to compare. In the Render by Attribute dialog (the same one used to make the worms display) you could choose File? Save Attributes and then choose to save the attribute of ?residues? named ?average->bfactor? to a file. You would need to do this for each of the two structures. So that it doesn?t include other stuff besides the protein, you could use command ?select protein? and then choose the option to ?Restrict save to current selection? (or alternatively, delete all the stuff you don?t care about for this comparison like solvent before saving the values). Now, if you are sure your script is mathematically correct and also that the correct residues are paired between the two structures, then maybe your question is really how to compare B-factors between two structures when they seem to be on a different scale or systematically offset. The question of whether or how best to normalize the values between different crystal structures is not a Chimera question per se, but a more general biophysical one to which I do not know the answer. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 28, 2017, at 9:00 AM, Amanda Evans Constantinides wrote: > > Hello, > I am plotting the B-factor differences between two similar structures. I do not understand why the plot is almost entirely on the positive side of the X-axis. If I open B factor putty models in PYMOL and in Chimera, there are some visible areas that should translate to negative B-factor differences on a quantitative plot. There is no way one structure is entirely more flexible than the other. Can you help explain this to me? Is there away to adjust the zero point to more accurately reflect these differences on the plot? > Thank you, > Amanda Constantinides > Graduate Research Assistant > Georgia State University From aconstantinides1 at student.gsu.edu Mon Aug 28 15:34:57 2017 From: aconstantinides1 at student.gsu.edu (Amanda Evans Constantinides) Date: Mon, 28 Aug 2017 22:34:57 +0000 Subject: [Chimera-users] B-Factor Difference Plot In-Reply-To: References: , Message-ID: Hi Elaine, Thanks for your detailed reply. I successfully generated Chimera output files containing lists of average B factor values, aligned the residues, plotted residue vs. B factor difference, and saw the graphs existed mainly on one side or the other of the x axis, but were not distributed across the x axis as expected based on what I saw using B putty. I tried also using Baverage in CCP4 and made Main Chain B factor difference plots and saw the same thing. My question, hopefully written more clearly, is how to normalize between the structures in comparison. I am looking at the equation for b-factor to see how I can accomplish this. If you have any ideas or know anyone who does, please send them my way! Best regards, Amanda Constantinides Graduate Research Assistant Georgia State University ________________________________ From: Elaine Meng Sent: Monday, August 28, 2017 5:37:36 PM To: Amanda Evans Constantinides Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] B-Factor Difference Plot Hi Amanda, Visually comparing the putty models (worms in Chimera) between the two structures is not meaningful unless you are sure you mapped the same value to the same radius in both structures. Even so, it is hard to see in this way. The more direct way is to just look at the PDB file in a text editor and see what the B-factor values are in the corresponding residues. I don?t know how you are calculating the differences, but you would have to make sure your script or whatever is mathematically correct and that it is also correctly pairing the residues between the two structures. I.e. the residue numbering might be different in the two structures. Now, comparing all the atomic values is probably too hard, so you could use Chimera to output the average values per residue so that you have fewer numbers to compare. In the Render by Attribute dialog (the same one used to make the worms display) you could choose File? Save Attributes and then choose to save the attribute of ?residues? named ?average->bfactor? to a file. You would need to do this for each of the two structures. So that it doesn?t include other stuff besides the protein, you could use command ?select protein? and then choose the option to ?Restrict save to current selection? (or alternatively, delete all the stuff you don?t care about for this comparison like solvent before saving the values). Now, if you are sure your script is mathematically correct and also that the correct residues are paired between the two structures, then maybe your question is really how to compare B-factors between two structures when they seem to be on a different scale or systematically offset. The question of whether or how best to normalize the values between different crystal structures is not a Chimera question per se, but a more general biophysical one to which I do not know the answer. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 28, 2017, at 9:00 AM, Amanda Evans Constantinides wrote: > > Hello, > I am plotting the B-factor differences between two similar structures. I do not understand why the plot is almost entirely on the positive side of the X-axis. If I open B factor putty models in PYMOL and in Chimera, there are some visible areas that should translate to negative B-factor differences on a quantitative plot. There is no way one structure is entirely more flexible than the other. Can you help explain this to me? Is there away to adjust the zero point to more accurately reflect these differences on the plot? > Thank you, > Amanda Constantinides > Graduate Research Assistant > Georgia State University -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Aug 28 16:09:51 2017 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 28 Aug 2017 16:09:51 -0700 Subject: [Chimera-users] B-Factor Difference Plot In-Reply-To: References: Message-ID: <962C5D9C-0E46-4A16-9037-CE5BC87C9793@cgl.ucsf.edu> Hi Amanda, You could try various types of normalization based on the mean and/or spread of values, but I don?t know what is most appropriate biophysically for comparing B-factors between different crystal structures. You could try asking on some other mailing lists frequented by crystallographers (maybe PDB-L, see https://lists.sdsc.edu/mailman/listinfo/pdb-l or CCP4 bulletin board, see http://www.ccp4.ac.uk/ccp4bb.php ) if you don?t get advice on this list. My only other idea is to find papers that make similar comparisons and read what those authors did, but I don?t have any specific knowledge of such papers. Best, Elaine > On Aug 28, 2017, at 3:34 PM, Amanda Evans Constantinides wrote: > > Hi Elaine, > Thanks for your detailed reply. I successfully generated Chimera output files containing lists of average B factor values, aligned the residues, plotted residue vs. B factor difference, and saw the graphs existed mainly on one side or the other of the x axis, but were not distributed across the x axis as expected based on what I saw using B putty. I tried also using Baverage in CCP4 and made Main Chain B factor difference plots and saw the same thing. My question, hopefully written more clearly, is how to normalize between the structures in comparison. I am looking at the equation for b-factor to see how I can accomplish this. If you have any ideas or know anyone who does, please send them my way! > > Best regards, > > Amanda Constantinides > Graduate Research Assistant > Georgia State University > From: Elaine Meng > Sent: Monday, August 28, 2017 5:37:36 PM > To: Amanda Evans Constantinides > Cc: chimera-users at cgl.ucsf.edu > Subject: Re: [Chimera-users] B-Factor Difference Plot > > Hi Amanda, > Visually comparing the putty models (worms in Chimera) between the two structures is not meaningful unless you are sure you mapped the same value to the same radius in both structures. Even so, it is hard to see in this way. > > The more direct way is to just look at the PDB file in a text editor and see what the B-factor values are in the corresponding residues. I don?t know how you are calculating the differences, but you would have to make sure your script or whatever is mathematically correct and that it is also correctly pairing the residues between the two structures. I.e. the residue numbering might be different in the two structures. > > Now, comparing all the atomic values is probably too hard, so you could use Chimera to output the average values per residue so that you have fewer numbers to compare. In the Render by Attribute dialog (the same one used to make the worms display) you could choose File? Save Attributes and then choose to save the attribute of ?residues? named ?average->bfactor? to a file. You would need to do this for each of the two structures. So that it doesn?t include other stuff besides the protein, you could use command ?select protein? and then choose the option to ?Restrict save to current selection? (or alternatively, delete all the stuff you don?t care about for this comparison like solvent before saving the values). > > > Now, if you are sure your script is mathematically correct and also that the correct residues are paired between the two structures, then maybe your question is really how to compare B-factors between two structures when they seem to be on a different scale or systematically offset. The question of whether or how best to normalize the values between different crystal structures is not a Chimera question per se, but a more general biophysical one to which I do not know the answer. > > Best, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > On Aug 28, 2017, at 9:00 AM, Amanda Evans Constantinides wrote: > > > > Hello, > > I am plotting the B-factor differences between two similar structures. I do not understand why the plot is almost entirely on the positive side of the X-axis. If I open B factor putty models in PYMOL and in Chimera, there are some visible areas that should translate to negative B-factor differences on a quantitative plot. There is no way one structure is entirely more flexible than the other. Can you help explain this to me? Is there away to adjust the zero point to more accurately reflect these differences on the plot? > > Thank you, > > Amanda Constantinides > > Graduate Research Assistant > > Georgia State University > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From gtzotzos at me.com Wed Aug 30 09:00:06 2017 From: gtzotzos at me.com (George Tzotzos) Date: Wed, 30 Aug 2017 19:00:06 +0300 Subject: [Chimera-users] Adding ions with Amber Message-ID: I?ve loaded the prmtop and inpcrd of a protein in complex with a ligand (named DE3). I?ve tried to add ions to the complex using the Amber Tool. I received the following message (see Reply log below). I wonder if I erred, in which case I would be grateful for any suggestions, or there?s a bug in the program. Many thanks in advance George Assigning chain ID A to 125 residues, e.g. ASP Assigning chain ID B to 125 residues, e.g. ASP Model 0 (complex.inpcrd) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. /Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/matplotlib/axes.py:2369: UserWarning: Attempting to set identical left==right results in singular transformations; automatically expanding. left=1, right=1 + 'left=%s, right=%s') % (left, right)) Charge model: AMBER ff14SB Assigning partial charges to residue DE3 (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/hd/94rkn65x0d75wdjf_5xmblp80000gn/T/tmpJfFWs_/ante.in.mol2 -fi mol2 -o /var/folders/hd/94rkn65x0d75wdjf_5xmblp80000gn/T/tmpJfFWs_/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (DE3) (DE3) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (DE3) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (DE3) Reason: image not found (DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (DE3) (DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (DE3) Total number of electrons: 104; net charge: 0 (DE3) (DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (DE3) Error: cannot run "/Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit Failure running ANTECHAMBER for residue DE3 Check reply log for details -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Aug 30 10:35:12 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 30 Aug 2017 10:35:12 -0700 Subject: [Chimera-users] Adding ions with Amber In-Reply-To: References: Message-ID: Hi George, What version of Chimera are you running? This problem: (DE3) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib should be fixed in the 1.11 releases of Chimera. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Aug 30, 2017, at 9:00 AM, George Tzotzos wrote: > > I?ve loaded the prmtop and inpcrd of a protein in complex with a ligand (named DE3). I?ve tried to add ions to the complex using the Amber Tool. > > I received the following message (see Reply log below). I wonder if I erred, in which case I would be grateful for any suggestions, or there?s a bug in the program. > > Many thanks in advance > > George > > Assigning chain ID A to 125 residues, e.g. ASP > Assigning chain ID B to 125 residues, e.g. ASP > Model 0 (complex.inpcrd) appears to be a protein without secondary structure assignments. > Automatically computing assignments using 'ksdssp' and parameter values: > energy cutoff -0.5 > minimum helix length 3 > minimum strand length 3 > Use command 'help ksdssp' for more information. > /Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/matplotlib/axes.py:2369: UserWarning: Attempting to set identical left==right results > in singular transformations; automatically expanding. > left=1, right=1 > + 'left=%s, right=%s') % (left, right)) > Charge model: AMBER ff14SB > Assigning partial charges to residue DE3 (net charge +0) with am1-bcc method > Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/hd/94rkn65x0d75wdjf_5xmblp80000gn/T/tmpJfFWs_/ante.in.mol2 -fi mol2 -o /var/folders/hd/94rkn65x0d75wdjf_5xmblp80000gn/T/tmpJfFWs_/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 > (DE3) > > (DE3) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib > > (DE3) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib > > (DE3) Reason: image not found > > (DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac > > (DE3) > > (DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff > > (DE3) Total number of electrons: 104; net charge: 0 > > (DE3) > > (DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out > > (DE3) Error: cannot run "/Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit > > Failure running ANTECHAMBER for residue DE3 > Check reply log for details > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From jmsstarlight at gmail.com Wed Aug 30 08:40:03 2017 From: jmsstarlight at gmail.com (James Starlight) Date: Wed, 30 Aug 2017 17:40:03 +0200 Subject: [Chimera-users] Batch mode for Chimera Message-ID: Dear Chimera Users! My simple bash script loops the folder with the pdbs and open it in Chimera for pdb in ${output}/xtc_proc/*.pdb ; do name=$(basename "$pdb") echo "I am sending ${name} to Chimera!" chimera $pdb done My question - can I use with chimera some batch file which will apply the following commands to each of the loaded pdbs without opening of Chimera GUI: 1- Apply "publications-2" preset 2 - rangecolor bfactor key 2 blue 30 red 50 yellow # color pdb according to b-factor provided in the pdb file 3- make a screen-shot of the colored cartoon figure in the selected output folder. I thanks so much for the example of batch file and the syntax accepted by chimera from the linux shell. James From danpf at uw.edu Wed Aug 30 11:44:06 2017 From: danpf at uw.edu (Daniel P Farrell) Date: Wed, 30 Aug 2017 11:44:06 -0700 Subject: [Chimera-users] Center on surface at mouse accelerator Message-ID: Hello, I found myself constantly needing to re-center on different regions of EM density maps, and I was originally just dropping spheres on the surface, centering on those, then deleting them. Finally I got sick of that and wrote this. It will center the window on the surface of whatever surface the mouse is currently overlaying. I found this to be a very helpful addition when looking at large EM maps, and was thinking other people might too, after using it for a while I feel as though it could be part of trunk since I use it so much. basically it would require the addition of this to standard_accelerators.py ... other accelerators.. ('zx', 'Center view on surface where mouse is located', center_on_surface_at_mouse), ... zx because it's close to where you rest your hands on the keyboard... def center_on_surface_at_mouse(): from chimera import selection, tkgui hits = [] w = tkgui.app.graphics x = w.winfo_pointerx() - w.winfo_rootx() y = w.winfo_pointery() - w.winfo_rooty() from Surface import surface_models import VolumePath.tracer as tracer hits.extend(tracer.surface_intercepts(x, y, surface_models())) xyz, model = tracer.closest_hit(hits) print(xyz) if xyz: print('cofr %f,%f,%f' % (xyz[0],xyz[1],xyz[2])) chimera.runCommand('cofr %f,%f,%f' % (xyz[0],xyz[1],xyz[2])) chimera.viewer.camera.center = xyz cheers! ~Dan -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Aug 30 13:54:11 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 30 Aug 2017 13:54:11 -0700 Subject: [Chimera-users] Batch mode for Chimera In-Reply-To: References: Message-ID: <40E3FAC5-F2A6-4ECC-ACEF-5D1BD35A8DFB@cgl.ucsf.edu> Hi James, First, if you want to save images without showing the Chimera GUI then you have to use the ?headless? version of Chimera, available on the download page. To do the other things you want, just put the equivalent commands in a file that ends in ?.cmd? and just add that file to your invocation of Chimera, e.g.: chimera $pdb script.cmd The easiest way to handle the image file name is probably to used a fixed name in the Chimera ?copy? command, and then in your bash script move that file to the final name you want. Also, "preset? is the command to apply presets ? ?help preset? in Chimera for more info. Hope this helps. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Aug 30, 2017, at 8:40 AM, James Starlight wrote: > > Dear Chimera Users! > > My simple bash script loops the folder with the pdbs and open it in Chimera > > for pdb in ${output}/xtc_proc/*.pdb ; do > name=$(basename "$pdb") > echo "I am sending ${name} to Chimera!" > chimera $pdb > done > > My question - can I use with chimera some batch file which will > apply the following commands to each of the loaded pdbs without > opening of Chimera GUI: > > 1- Apply "publications-2" preset > > 2 - rangecolor bfactor key 2 blue 30 red 50 yellow # color pdb > according to b-factor provided in the pdb file > > 3- make a screen-shot of the colored cartoon figure in the selected > output folder. > > > I thanks so much for the example of batch file and the syntax accepted > by chimera from the linux shell. > > James > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Wed Aug 30 18:10:25 2017 From: goddard at sonic.net (Tom Goddard) Date: Wed, 30 Aug 2017 18:10:25 -0700 Subject: [Chimera-users] Center on surface at mouse accelerator In-Reply-To: References: Message-ID: <8C27A46F-7827-46DC-BDED-CE8D5E5A7B35@sonic.net> Hi Dan, Thanks for the code. You know ctrl-click with the right mouse button centers on the clicked atoms? It also centers when you click on a surface, but it uses the center of the entire surface instead of the point you clicked on. It seems like it would be more useful to center on the surface point you clicked on so I changed the code to do that ? will be in tonight?s Chimera builds. I think this is better than using a keyboard shortcut since few people enable the keyboard shortcuts. Tom > On Aug 30, 2017, at 11:44 AM, Daniel P Farrell wrote: > > Hello, > > I found myself constantly needing to re-center on different regions of EM density maps, and I was originally just dropping spheres on the surface, centering on those, then deleting them. Finally I got sick of that and wrote this. It will center the window on the surface of whatever surface the mouse is currently overlaying. > > I found this to be a very helpful addition when looking at large EM maps, and was thinking other people might too, after using it for a while I feel as though it could be part of trunk since I use it so much. > > > basically it would require the addition of this to standard_accelerators.py > > ... other accelerators.. > > ('zx', 'Center view on surface where mouse is located', center_on_surface_at_mouse), > > ... zx because it's close to where you rest your hands on the keyboard... > > def center_on_surface_at_mouse(): > from chimera import selection, tkgui > hits = [] > w = tkgui.app.graphics > x = w.winfo_pointerx() - w.winfo_rootx() > y = w.winfo_pointery() - w.winfo_rooty() > from Surface import surface_models > import VolumePath.tracer as tracer > hits.extend(tracer.surface_intercepts(x, y, surface_models())) > xyz, model = tracer.closest_hit(hits) > print(xyz) > if xyz: > print('cofr %f,%f,%f' % (xyz[0],xyz[1],xyz[2])) > chimera.runCommand('cofr %f,%f,%f' % (xyz[0],xyz[1],xyz[2])) > chimera.viewer.camera.center = xyz > > cheers! > ~Dan > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From v.arinkin at fz-juelich.de Thu Aug 31 01:41:51 2017 From: v.arinkin at fz-juelich.de (Vladimir Arinkin) Date: Thu, 31 Aug 2017 10:41:51 +0200 Subject: [Chimera-users] B-Factor Difference Plot In-Reply-To: References: Message-ID: <6936961c-2b30-bc3f-b8d0-71224d21da31@fz-juelich.de> Dear Amanda, you also need to keep in mind one thing when comparing B-factors from different structures. B-factors refined in the structure does not only contain true Atomic Displacement Factors (ADP-factors) but also distortions of the crystal lattice, which are being modeled into the B-factors as one cannot really separate them. Probably for this reason you assume that one structure is more "flexible", it maybe just due to higher crystal lattice distortions. You can try to normalize to mean B-factor of all protein residues in the structure. And the second, make sure that both structures has isotropic B-factors (no ANISOU records in PDB file) otherwise you cannot simply compare numbers. Cheers, Vladimir Arinkin Am 29.08.2017 um 00:34 schrieb Amanda Evans Constantinides: Hi Elaine, Thanks for your detailed reply. I successfully generated Chimera output files containing lists of average B factor values, aligned the residues, plotted residue vs. B factor difference, and saw the graphs existed mainly on one side or the other of the x axis, but were not distributed across the x axis as expected based on what I saw using B putty. I tried also using Baverage in CCP4 and made Main Chain B factor difference plots and saw the same thing. My question, hopefully written more clearly, is how to normalize between the structures in comparison. I am looking at the equation for b-factor to see how I can accomplish this. If you have any ideas or know anyone who does, please send them my way! Best regards, Amanda Constantinides Graduate Research Assistant Georgia State University ________________________________ From: Elaine Meng Sent: Monday, August 28, 2017 5:37:36 PM To: Amanda Evans Constantinides Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] B-Factor Difference Plot Hi Amanda, Visually comparing the putty models (worms in Chimera) between the two structures is not meaningful unless you are sure you mapped the same value to the same radius in both structures. Even so, it is hard to see in this way. The more direct way is to just look at the PDB file in a text editor and see what the B-factor values are in the corresponding residues. I don?t know how you are calculating the differences, but you would have to make sure your script or whatever is mathematically correct and that it is also correctly pairing the residues between the two structures. I.e. the residue numbering might be different in the two structures. Now, comparing all the atomic values is probably too hard, so you could use Chimera to output the average values per residue so that you have fewer numbers to compare. In the Render by Attribute dialog (the same one used to make the worms display) you could choose File? Save Attributes and then choose to save the attribute of ?residues? named ?average->bfactor? to a file. You would need to do this for each of the two structures. So that it doesn?t include other stuff besides the protein, you could use command ?select protein? and then choose the option to ?Restrict save to current selection? (or alternatively, delete all the stuff you don?t care about for this comparison like solvent before saving the values). Now, if you are sure your script is mathematically correct and also that the correct residues are paired between the two structures, then maybe your question is really how to compare B-factors between two structures when they seem to be on a different scale or systematically offset. The question of whether or how best to normalize the values between different crystal structures is not a Chimera question per se, but a more general biophysical one to which I do not know the answer. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 28, 2017, at 9:00 AM, Amanda Evans Constantinides wrote: > > Hello, > I am plotting the B-factor differences between two similar structures. I do not understand why the plot is almost entirely on the positive side of the X-axis. If I open B factor putty models in PYMOL and in Chimera, there are some visible areas that should translate to negative B-factor differences on a quantitative plot. There is no way one structure is entirely more flexible than the other. Can you help explain this to me? Is there away to adjust the zero point to more accurately reflect these differences on the plot? > Thank you, > Amanda Constantinides > Graduate Research Assistant > Georgia State University _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. 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URL: From danpf at uw.edu Wed Aug 30 18:21:53 2017 From: danpf at uw.edu (Daniel P Farrell) Date: Wed, 30 Aug 2017 18:21:53 -0700 Subject: [Chimera-users] Center on surface at mouse accelerator In-Reply-To: <8C27A46F-7827-46DC-BDED-CE8D5E5A7B35@sonic.net> References: <8C27A46F-7827-46DC-BDED-CE8D5E5A7B35@sonic.net> Message-ID: re ctrl-click: yes I was originally using place marker (sorry not sphere) on surface + ctrl-click + delete marker to emulate this behavior, if that makes sense. Anyways, Awesome! Thanks so much, can't wait for the nightly! ~Dan On Wed, Aug 30, 2017 at 6:10 PM, Tom Goddard wrote: > Hi Dan, > > Thanks for the code. You know ctrl-click with the right mouse button > centers on the clicked atoms? It also centers when you click on a surface, > but it uses the center of the entire surface instead of the point you > clicked on. It seems like it would be more useful to center on the surface > point you clicked on so I changed the code to do that ? will be in > tonight?s Chimera builds. I think this is better than using a keyboard > shortcut since few people enable the keyboard shortcuts. > > Tom > > > > On Aug 30, 2017, at 11:44 AM, Daniel P Farrell wrote: > > > > Hello, > > > > I found myself constantly needing to re-center on different regions of > EM density maps, and I was originally just dropping spheres on the surface, > centering on those, then deleting them. Finally I got sick of that and > wrote this. It will center the window on the surface of whatever surface > the mouse is currently overlaying. > > > > I found this to be a very helpful addition when looking at large EM > maps, and was thinking other people might too, after using it for a while I > feel as though it could be part of trunk since I use it so much. > > > > > > basically it would require the addition of this to > standard_accelerators.py > > > > ... other accelerators.. > > > > ('zx', 'Center view on surface where mouse is located', > center_on_surface_at_mouse), > > > > ... zx because it's close to where you rest your hands on the keyboard... > > > > def center_on_surface_at_mouse(): > > from chimera import selection, tkgui > > hits = [] > > w = tkgui.app.graphics > > x = w.winfo_pointerx() - w.winfo_rootx() > > y = w.winfo_pointery() - w.winfo_rooty() > > from Surface import surface_models > > import VolumePath.tracer as tracer > > hits.extend(tracer.surface_intercepts(x, y, surface_models())) > > xyz, model = tracer.closest_hit(hits) > > print(xyz) > > if xyz: > > print('cofr %f,%f,%f' % (xyz[0],xyz[1],xyz[2])) > > chimera.runCommand('cofr %f,%f,%f' % (xyz[0],xyz[1],xyz[2])) > > chimera.viewer.camera.center = xyz > > > > cheers! > > ~Dan > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > > Manage subscription: http://plato.cgl.ucsf.edu/ > mailman/listinfo/chimera-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jmsstarlight at gmail.com Thu Aug 31 01:00:23 2017 From: jmsstarlight at gmail.com (James Starlight) Date: Thu, 31 Aug 2017 10:00:23 +0200 Subject: [Chimera-users] Batch mode for Chimera In-Reply-To: <40E3FAC5-F2A6-4ECC-ACEF-5D1BD35A8DFB@cgl.ucsf.edu> References: <40E3FAC5-F2A6-4ECC-ACEF-5D1BD35A8DFB@cgl.ucsf.edu> Message-ID: Thanks Eric! Everything works fine with the exception of the copy command. On the rendering stage I have: Opened AT1_dry_apo.1rep.step7_1.pdb containing 1 model, 57791 atoms, and 12661 residues Traceback (most recent call last): File "/home/gleb/.local/UCSF-Chimera64-batch/share/chimeraInit.py", line 683, in init chimera.openModels.open(a, prefixableType=1) File "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/__init__.py", line 1951, in open models = func(filename, *args, **kw) File "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/ChimeraExtension.py", line 31, in func processCommandFile(fileName) File "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", line 108, in processCommandFile _processFile(f, emulateRead, filename) File "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", line 143, in _processFile if makeCommand(line): File "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", line 1786, in doRangeColor showKey=key) File "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/__init__.py", line 2526, in rangeColor from Ilabel.gui import IlabelDialog File "/home/gleb/.local/UCSF-Chimera64-batch/share/Ilabel/gui.py", line 13, in from chimera import tkgui, chimage, CLOSE_SESSION File "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/tkgui.py", line 74, in import Togl ImportError: No module named Togl Error while processing /home/gleb/Desktop/Scripts/MegaAnalysis/temp/script_AT1_dry_apo.1rep.step7_1.pdb.cmd: ImportError: No module named Togl File "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/tkgui.py", line 74, in import Togl See reply log for Python traceback. I have found that it is due to some conflict in PYTHONPATH from my bash since I am running Chimera directly from BASH. The people also wrote that Its related to setting transparency- which was not a case there - I did not set in my script. Anyway how to fix it? Thanks you! James 2017-08-30 22:54 GMT+02:00 Eric Pettersen : > Hi James, > First, if you want to save images without showing the Chimera GUI then you > have to use the ?headless? version of Chimera, available on the download > page. To do the other things you want, just put the equivalent commands in > a file that ends in ?.cmd? and just add that file to your invocation of > Chimera, e.g.: > > chimera $pdb script.cmd > > The easiest way to handle the image file name is probably to used a fixed > name in the Chimera ?copy? command, and then in your bash script move that > file to the final name you want. Also, "preset? is the command to apply > presets ? ?help preset? in Chimera for more info. > > Hope this helps. > > ?Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > > > On Aug 30, 2017, at 8:40 AM, James Starlight wrote: > > Dear Chimera Users! > > My simple bash script loops the folder with the pdbs and open it in Chimera > > for pdb in ${output}/xtc_proc/*.pdb ; do > name=$(basename "$pdb") > echo "I am sending ${name} to Chimera!" > chimera $pdb > done > > My question - can I use with chimera some batch file which will > apply the following commands to each of the loaded pdbs without > opening of Chimera GUI: > > 1- Apply "publications-2" preset > > 2 - rangecolor bfactor key 2 blue 30 red 50 yellow # color pdb > according to b-factor provided in the pdb file > > 3- make a screen-shot of the colored cartoon figure in the selected > output folder. > > > I thanks so much for the example of batch file and the syntax accepted > by chimera from the linux shell. > > James > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > From olivercgrant at gmail.com Thu Aug 31 07:18:27 2017 From: olivercgrant at gmail.com (Oliver Grant) Date: Thu, 31 Aug 2017 16:18:27 +0200 Subject: [Chimera-users] 3D-SNFG symbol representation for carbohydrate molecules Message-ID: Dear developers, The carbohydrate community has decided on a standard symbol representation for carbohydrates. The article is here , and the webpage is here . Our group has created a 3D version of the symbols within the software VMD. Here's a video showing both versions. We have also worked with David Sehnal to implement this into LiteMol, here is an example . I wanted to reach out and see if you are interested to implement this representation within Chimera? We can discuss the details if so. Regards, Dr. Oliver Grant Associate Research Scientist Complex Carbohydrate Research Center Athens, GA, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Thu Aug 31 13:04:04 2017 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Thu, 31 Aug 2017 13:04:04 -0700 Subject: [Chimera-users] Batch mode for Chimera In-Reply-To: References: <40E3FAC5-F2A6-4ECC-ACEF-5D1BD35A8DFB@cgl.ucsf.edu> Message-ID: <66d8ea2e-23d9-fa15-e4a1-2fef276169bd@cgl.ucsf.edu> You must have the given the "key" argument to the rangecolor command. That option tries to display the Color Key tool which want you to use the mouse to position the color key in the graphics window. That is not possible in batch mode. You'll need to add the color key afterwards with an image editor if you need it. HTH, Greg On 08/31/2017 01:00 AM, James Starlight wrote: > Thanks Eric! > > Everything works fine with the exception of the copy command. On the > rendering stage I have: > > > Opened AT1_dry_apo.1rep.step7_1.pdb containing 1 model, 57791 atoms, > and 12661 residues > Traceback (most recent call last): > File "/home/gleb/.local/UCSF-Chimera64-batch/share/chimeraInit.py", > line 683, in init > chimera.openModels.open(a, prefixableType=1) > File "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/__init__.py", > line 1951, in open > models = func(filename, *args, **kw) > File "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/ChimeraExtension.py", > line 31, in func > processCommandFile(fileName) > File "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", > line 108, in processCommandFile > _processFile(f, emulateRead, filename) > File "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", > line 143, in _processFile > if makeCommand(line): > File "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", > line 69, in makeCommand > f(c, args) > File "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", > line 1786, in doRangeColor > showKey=key) > File "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/__init__.py", > line 2526, in rangeColor > from Ilabel.gui import IlabelDialog > File "/home/gleb/.local/UCSF-Chimera64-batch/share/Ilabel/gui.py", > line 13, in > from chimera import tkgui, chimage, CLOSE_SESSION > File "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/tkgui.py", > line 74, in > import Togl > ImportError: No module named Togl > > Error while processing > /home/gleb/Desktop/Scripts/MegaAnalysis/temp/script_AT1_dry_apo.1rep.step7_1.pdb.cmd: > ImportError: No module named Togl > > File "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/tkgui.py", > line 74, in > import Togl > > See reply log for Python traceback. > > I have found that it is due to some conflict in PYTHONPATH from my > bash since I am running Chimera directly from BASH. The people also > wrote that Its related to setting transparency- which was not a case > there - I did not set in my script. Anyway how to fix it? > > Thanks you! > > James > > 2017-08-30 22:54 GMT+02:00 Eric Pettersen : >> Hi James, >> First, if you want to save images without showing the Chimera GUI then you >> have to use the ?headless? version of Chimera, available on the download >> page. To do the other things you want, just put the equivalent commands in >> a file that ends in ?.cmd? and just add that file to your invocation of >> Chimera, e.g.: >> >> chimera $pdb script.cmd >> >> The easiest way to handle the image file name is probably to used a fixed >> name in the Chimera ?copy? command, and then in your bash script move that >> file to the final name you want. Also, "preset? is the command to apply >> presets ? ?help preset? in Chimera for more info. >> >> Hope this helps. >> >> ?Eric >> >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >> On Aug 30, 2017, at 8:40 AM, James Starlight wrote: >> >> Dear Chimera Users! >> >> My simple bash script loops the folder with the pdbs and open it in Chimera >> >> for pdb in ${output}/xtc_proc/*.pdb ; do >> name=$(basename "$pdb") >> echo "I am sending ${name} to Chimera!" >> chimera $pdb >> done >> >> My question - can I use with chimera some batch file which will >> apply the following commands to each of the loaded pdbs without >> opening of Chimera GUI: >> >> 1- Apply "publications-2" preset >> >> 2 - rangecolor bfactor key 2 blue 30 red 50 yellow # color pdb >> according to b-factor provided in the pdb file >> >> 3- make a screen-shot of the colored cartoon figure in the selected >> output folder. >> >> >> I thanks so much for the example of batch file and the syntax accepted >> by chimera from the linux shell. >> >> James >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From pett at cgl.ucsf.edu Thu Aug 31 16:22:47 2017 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 31 Aug 2017 16:22:47 -0700 Subject: [Chimera-users] 3D-SNFG symbol representation for carbohydrate molecules In-Reply-To: References: Message-ID: Dear Dr. Grant, We are definitely interested, though we would be more likely to implement it in ChimeraX than Chimera, since most of our new work is in ChimeraX and also ChimeraX has better underlying support for adding new depictions like this. We will discuss this in a meeting on Tuesday and get back to you with further details. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Aug 31, 2017, at 7:18 AM, Oliver Grant wrote: > > Dear developers, > > The carbohydrate community has decided on a standard symbol representation for carbohydrates. The article is here , and the webpage is here . Our group has created a 3D version of the symbols within the software VMD. Here's a video showing both versions. We have also worked with David Sehnal to implement this into LiteMol, here is an example . I wanted to reach out and see if you are interested to implement this representation within Chimera? We can discuss the details if so. > > Regards, > > Dr. Oliver Grant > Associate Research Scientist > Complex Carbohydrate Research Center > Athens, GA, USA. > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: