From conrad at cgl.ucsf.edu Mon Jan 4 12:14:32 2016 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Mon, 4 Jan 2016 12:14:32 -0800 Subject: [Chimera-users] Identify hinges and rigid groups using Morph Conformations? In-Reply-To: <65AC4FC2-5856-4D2D-A989-F69633804E9C@gmail.com> References: <65AC4FC2-5856-4D2D-A989-F69633804E9C@gmail.com> Message-ID: <568AD2A8.1010207@cgl.ucsf.edu> Unfortunately, this is not a simple task. There are actually several layers of heuristics beyond the referenced procedures, mainly to handle small segments and chain identifiers, so the results may not be as clean as one would expect. Also, we would then have to come up with some sort of naming/attribute scheme so that different parts can be referenced. This may fall more in the ChimeraX realm at this point. Sorry. Conrad On 12/18/2015 1:06 PM, Oliver Clarke wrote: > Hi, > > I gather from reading the documentation for ?Morph Conformations? > (https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html) > that Chimera identifies hinge regions and rigid groups as part of the > procedure (as per > http://nar.oxfordjournals.org/content/28/8/1665.long). > > Would it be possible to expose these to the user (or maybe this is > already possible?), such that one can color/label the hinges and > rigid entities as desired? This would be helpful for visual > simplification of complex conformational changes. > > Cheers, Oliver. _______________________________________________ > Chimera-users mailing list Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From Rebecca_Swett at vrtx.com Mon Jan 4 12:09:08 2016 From: Rebecca_Swett at vrtx.com (Rebecca Swett) Date: Mon, 4 Jan 2016 20:09:08 +0000 Subject: [Chimera-users] Drawing shapes given coordinates Message-ID: Hi all, I'm trying to add some 3d shapes to a visualization. I was wondering if it would be possible to draw either a cylinder or tube given starting and ending coordinates rather than atom names/numbers or centroid? For example, if I had this coordinate pair: 6.17 1.10 -15.33 20.82 -0.70 -8.39 What would be the best way to go about drawing a line of some sort between those two points? I have dozens of pairs of coordinates so something command line would be ideal. Cheers, Rebecca This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Jan 4 14:20:45 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 4 Jan 2016 14:20:45 -0800 Subject: [Chimera-users] Drawing shapes given coordinates In-Reply-To: References: Message-ID: <24E0F8EF-2B53-42B6-9211-183EBBABC170@cgl.ucsf.edu> Hi Rebecca, There are two approaches for adding cylinders independent of atoms? but I don?t know if either will be satisfactory: (1) ?shape cylinder? is command-line and doesn?t require using atoms as endpoints, but it doesn?t allow specifying endpoint coordinates directly. A cylinder is specified by only its center, height, radius, and a rotation angle. I don?t think it is easy to figure out what angle gives the desired endpoint coordinates. (We?ve discussed the need to improve this, but it may be deferred to our next-generation software in development.) (2) BILD-format input allows specifying endpoint coordinates of a cylinder, but it is not a command. You generate a BILD text file describing the objects and read it in to Chimera. BILD format is very simple, however: The objects created with ?shape? are surface models, so you can change their colors afterward. The BILD objects are not surface models and cannot be recolored and do not work well with transparency. There are two approaches that depend on atoms: (1) pseudobonds can be created with the ?distance? command (or atom pairs can be read in from a file with Pseudobond Reader), but pseudobonds require atoms as endpoints. (2) the ?define? command (or Axes/Planes/Centroids) tool will show cylindrical axes that are best fits to specified sets of atoms. However, there is currently little control over length? it is automatically determined from the atomic coordinates. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 4, 2016, at 12:09 PM, Rebecca Swett wrote: > > Hi all, > I'm trying to add some 3d shapes to a visualization. I was wondering if it would be possible to draw either a cylinder or tube given starting and ending coordinates rather than atom names/numbers or centroid? For example, if I had this coordinate pair: > 6.17 1.10 -15.33 20.82 -0.70 -8.39 > > What would be the best way to go about drawing a line of some sort between those two points? I have dozens of pairs of coordinates so something command line would be ideal. > Cheers, > Rebecca From olibclarke at gmail.com Mon Jan 4 15:06:12 2016 From: olibclarke at gmail.com (Oliver Clarke) Date: Mon, 4 Jan 2016 18:06:12 -0500 Subject: [Chimera-users] Identify hinges and rigid groups using Morph Conformations? In-Reply-To: <568AD2A8.1010207@cgl.ucsf.edu> References: <65AC4FC2-5856-4D2D-A989-F69633804E9C@gmail.com> <568AD2A8.1010207@cgl.ucsf.edu> Message-ID: Makes sense, thanks for checking it out. Cheers, Oliver. On Mon, Jan 4, 2016 at 3:14 PM, Conrad Huang wrote: > Unfortunately, this is not a simple task. There are actually several > layers of heuristics beyond the referenced procedures, mainly to handle > small segments and chain identifiers, so the results may not be as clean as > one would expect. Also, we would then have to come up with some sort of > naming/attribute scheme so that different parts can be referenced. This may > fall more in the ChimeraX realm at this point. Sorry. > > Conrad > > > On 12/18/2015 1:06 PM, Oliver Clarke wrote: > >> Hi, >> >> I gather from reading the documentation for ?Morph Conformations? >> ( >> https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html >> ) >> that Chimera identifies hinge regions and rigid groups as part of the >> procedure (as per >> http://nar.oxfordjournals.org/content/28/8/1665.long). >> >> Would it be possible to expose these to the user (or maybe this is >> already possible?), such that one can color/label the hinges and >> rigid entities as desired? This would be helpful for visual >> simplification of complex conformational changes. >> >> Cheers, Oliver. _______________________________________________ >> Chimera-users mailing list Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Rebecca_Swett at vrtx.com Tue Jan 5 05:37:16 2016 From: Rebecca_Swett at vrtx.com (Rebecca Swett) Date: Tue, 5 Jan 2016 13:37:16 +0000 Subject: [Chimera-users] Drawing shapes given coordinates In-Reply-To: <24E0F8EF-2B53-42B6-9211-183EBBABC170@cgl.ucsf.edu> Message-ID: Thank you! Theoretically if I was to create dummy atoms with coordinates at the locations where I want the cylinders to end, I could connect them with pseudobonds. I can easily shape my data that way, and if it doesn't work the BILD files will probably be fine. Thanks for the help! Cheers, Rebecca On 1/4/16, 5:20 PM, "Elaine Meng" wrote: >Hi Rebecca, >There are two approaches for adding cylinders independent of atoms? but I >don?t know if either will be satisfactory: > >(1) ?shape cylinder? is command-line and doesn?t require using atoms as >endpoints, but it doesn?t allow specifying endpoint coordinates directly. > A cylinder is specified by only its center, height, radius, and a >rotation angle. I don?t think it is easy to figure out what angle gives >the desired endpoint coordinates. (We?ve discussed the need to improve >this, but it may be deferred to our next-generation software in >development.) >mera_docs_UsersGuide_midas_shape.html-23cylinder&d=CwIFaQ&c=TzEZu9LIcihmW3 >7vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd >4eXf6HdP_BL9dt0gv_zz3oMdq8&s=9vZCIh2K2i-8UrGF7HkSZwZwT7CRFcS9RUZsHUsson4&e >= > > >(2) BILD-format input allows specifying endpoint coordinates of a >cylinder, but it is not a command. You generate a BILD text file >describing the objects and read it in to Chimera. BILD format is very >simple, however: >mera_docs_UsersGuide_bild.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r=Z2BqCMu >wlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_BL9dt0gv_ >zz3oMdq8&s=2A5wPT06BJ7QN1TDyA4kS36ILONzhA703a7xRpdnJKY&e= > > >The objects created with ?shape? are surface models, so you can change >their colors afterward. The BILD objects are not surface models and >cannot be recolored and do not work well with transparency. > >There are two approaches that depend on atoms: > >(1) pseudobonds can be created with the ?distance? command (or atom pairs >can be read in from a file with Pseudobond Reader), but pseudobonds >require atoms as endpoints. >mera_docs_UsersGuide_midas_distance.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w >&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP >_BL9dt0gv_zz3oMdq8&s=tUGhl0z5yTsTqr2tyEgexdraCTB8o2JtwjuJZTgMwvo&e= > >mera_docs_ContributedSoftware_pbreader_pbreader.html&d=CwIFaQ&c=TzEZu9LIci >hmW37vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH >6akd4eXf6HdP_BL9dt0gv_zz3oMdq8&s=nRvWQ2FPg5n33Obqd9Bee1ovSNmgCCdbaT1EH6Uc1 >I8&e= > > >(2) the ?define? command (or Axes/Planes/Centroids) tool will show >cylindrical axes that are best fits to specified sets of atoms. However, >there is currently little control over length? it is automatically >determined from the atomic coordinates. >mera_docs_UsersGuide_midas_define.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r >=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_B >L9dt0gv_zz3oMdq8&s=t9I-WC_-VvEvmTfphtU3ey2GT0sMRiFtO62hFkRj7Rk&e= > > >I hope this helps, >Elaine >---------- >Elaine C. Meng, Ph.D. >UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >Department of Pharmaceutical Chemistry >University of California, San Francisco > >> On Jan 4, 2016, at 12:09 PM, Rebecca Swett >>wrote: >> >> Hi all, >> I'm trying to add some 3d shapes to a visualization. I was wondering if >>it would be possible to draw either a cylinder or tube given starting >>and ending coordinates rather than atom names/numbers or centroid? For >>example, if I had this coordinate pair: >> 6.17 1.10 -15.33 20.82 -0.70 -8.39 >> >> What would be the best way to go about drawing a line of some sort >>between those two points? I have dozens of pairs of coordinates so >>something command line would be ideal. >> Cheers, >> Rebecca > This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you. From meng at cgl.ucsf.edu Tue Jan 5 10:45:23 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 5 Jan 2016 10:45:23 -0800 Subject: [Chimera-users] Drawing shapes given coordinates In-Reply-To: References: Message-ID: You?re welcome! If going the pseudobond route, just make sure you can get the kind of display you want. If you just want solid cylinders, that can be achived with the stick drawmode, and you can also set color and radius as desired. If you make a file for Pseudobond Reader you can also specify the colors and (optional) text labels in the file. Otherwise you can control pseudobond attributes collectively or individually with ?setattr p? and ?setattr g? commands. For example, you could hide all distance labels with command: setattr p label '' (that?s two single quote marks in a row) and the same command except plus ?sel? at the end will do it for only the pseudobonds with both end atoms selected. You could also give the atom names. Best, Elaine > On Jan 5, 2016, at 5:37 AM, Rebecca Swett wrote: > > Thank you! Theoretically if I was to create dummy atoms with coordinates > at the locations where I want the cylinders to end, I could connect them > with pseudobonds. I can easily shape my data that way, and if it doesn't > work the BILD files will probably be fine. Thanks for the help! > Cheers, > Rebecca > > On 1/4/16, 5:20 PM, "Elaine Meng" wrote: > >> Hi Rebecca, >> There are two approaches for adding cylinders independent of atoms? but I >> don?t know if either will be satisfactory: >> >> (1) ?shape cylinder? is command-line and doesn?t require using atoms as >> endpoints, but it doesn?t allow specifying endpoint coordinates directly. >> A cylinder is specified by only its center, height, radius, and a >> rotation angle. I don?t think it is easy to figure out what angle gives >> the desired endpoint coordinates. (We?ve discussed the need to improve >> this, but it may be deferred to our next-generation software in >> development.) >> > mera_docs_UsersGuide_midas_shape.html-23cylinder&d=CwIFaQ&c=TzEZu9LIcihmW3 >> 7vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd >> 4eXf6HdP_BL9dt0gv_zz3oMdq8&s=9vZCIh2K2i-8UrGF7HkSZwZwT7CRFcS9RUZsHUsson4&e >> = > >> >> (2) BILD-format input allows specifying endpoint coordinates of a >> cylinder, but it is not a command. You generate a BILD text file >> describing the objects and read it in to Chimera. BILD format is very >> simple, however: >> > mera_docs_UsersGuide_bild.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r=Z2BqCMu >> wlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_BL9dt0gv_ >> zz3oMdq8&s=2A5wPT06BJ7QN1TDyA4kS36ILONzhA703a7xRpdnJKY&e= > >> >> The objects created with ?shape? are surface models, so you can change >> their colors afterward. The BILD objects are not surface models and >> cannot be recolored and do not work well with transparency. >> >> There are two approaches that depend on atoms: >> >> (1) pseudobonds can be created with the ?distance? command (or atom pairs >> can be read in from a file with Pseudobond Reader), but pseudobonds >> require atoms as endpoints. >> > mera_docs_UsersGuide_midas_distance.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w >> &r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP >> _BL9dt0gv_zz3oMdq8&s=tUGhl0z5yTsTqr2tyEgexdraCTB8o2JtwjuJZTgMwvo&e= > >> > mera_docs_ContributedSoftware_pbreader_pbreader.html&d=CwIFaQ&c=TzEZu9LIci >> hmW37vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH >> 6akd4eXf6HdP_BL9dt0gv_zz3oMdq8&s=nRvWQ2FPg5n33Obqd9Bee1ovSNmgCCdbaT1EH6Uc1 >> I8&e= > >> >> (2) the ?define? command (or Axes/Planes/Centroids) tool will show >> cylindrical axes that are best fits to specified sets of atoms. However, >> there is currently little control over length? it is automatically >> determined from the atomic coordinates. >> > mera_docs_UsersGuide_midas_define.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r >> =Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_B >> L9dt0gv_zz3oMdq8&s=t9I-WC_-VvEvmTfphtU3ey2GT0sMRiFtO62hFkRj7Rk&e= > >> >> I hope this helps, >> Elaine >> ---------- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >>> On Jan 4, 2016, at 12:09 PM, Rebecca Swett >>> wrote: >>> >>> Hi all, >>> I'm trying to add some 3d shapes to a visualization. I was wondering if >>> it would be possible to draw either a cylinder or tube given starting >>> and ending coordinates rather than atom names/numbers or centroid? For >>> example, if I had this coordinate pair: >>> 6.17 1.10 -15.33 20.82 -0.70 -8.39 >>> >>> What would be the best way to go about drawing a line of some sort >>> between those two points? I have dozens of pairs of coordinates so >>> something command line would be ideal. >>> Cheers, >>> Rebecca From edberg at ucsc.edu Tue Jan 5 14:45:33 2016 From: edberg at ucsc.edu (Eric Berg) Date: Tue, 5 Jan 2016 14:45:33 -0800 Subject: [Chimera-users] Suggested Improvement of Command Line Message-ID: Hello, I have noticed that when giving the command line a list of residue indexes using the "select" function, the inclusion of white space will cause an error (see attachment). This is technically a pretty small quibble, but it may be beneficial in these instances to include something to filter out white space prior to parsing. Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- Example of correct input: $ select: 1,5,7,8,9 Example of incorrect input: $ select: 1, 5, 7, 8, 9 From wouter.vanputte at gmail.com Wed Jan 6 06:37:56 2016 From: wouter.vanputte at gmail.com (Wouter Van Putte) Date: Wed, 6 Jan 2016 15:37:56 +0100 Subject: [Chimera-users] Chimera and imod isosurface (*.mod files) and 'volume eraser' Message-ID: <568D26C4.9070900@gmail.com> Dear, I would like to use chimera for removing some densities manually of an isosurface generated with imod. I've loaded the map/model (.mod) and already used the function 'hide dust' to remove most of the noise. I now would like to use 'volume eraser' to remove the other noise manually. This however doesn't work, probably due to the file format (.mod). I thought saving in another file format would help, but it gave me errors when opening the file. How should I proceed? best wishes, Wouter From wouter.vanputte at gmail.com Wed Jan 6 06:39:39 2016 From: wouter.vanputte at gmail.com (Wouter Van Putte) Date: Wed, 6 Jan 2016 15:39:39 +0100 Subject: [Chimera-users] volume eraser and imod isosurface Message-ID: <568D272B.40105@gmail.com> Dear, I would like to use chimera for removing some densities manually of an isosurface generated with imod. I've loaded the map/model (.mod) and already used the function 'hide dust' to remove most of the noise. I now would like to use 'volume eraser' to remove the other noise manually. This however doesn't work, probably due to the file format (.mod). I thought saving in another file format would help, but it gave me errors when opening the file. How should I proceed? best wishes, Wouter From meng at cgl.ucsf.edu Wed Jan 6 09:07:20 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 6 Jan 2016 09:07:20 -0800 Subject: [Chimera-users] volume eraser and imod isosurface In-Reply-To: <568D272B.40105@gmail.com> References: <568D272B.40105@gmail.com> Message-ID: <9A3754F1-C198-4D28-B825-731E814F14BA@cgl.ucsf.edu> Dear Wouter, The issue is that an IMOD file makes surfaces in Chimera, not a volume model (map or density grid with associated values at each grid point). Volume Eraser only works with volume models, formats listed here: Maybe your original data was or could be written in one of those formats? Also, Hide Dust only hides small surface bits; it does not delete any data. I hope this makes it clearer, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. appears to be a duplicate question, I?ll just answer this one On Jan 6, 2016, at 6:39 AM, Wouter Van Putte wrote: > Dear, > > I would like to use chimera for removing some densities manually of an isosurface generated with imod. I've loaded the map/model (.mod) and already used the function 'hide dust' to remove most of the noise. I now would like to use 'volume eraser' to remove the other noise manually. This however doesn't work, probably due to the file format (.mod). I thought saving in another file format would help, but it gave me errors when opening the file. How should I proceed? > > best wishes, > > Wouter From goddard at sonic.net Wed Jan 6 11:14:42 2016 From: goddard at sonic.net (Tom Goddard) Date: Wed, 6 Jan 2016 11:14:42 -0800 Subject: [Chimera-users] volume eraser and imod isosurface In-Reply-To: <9A3754F1-C198-4D28-B825-731E814F14BA@cgl.ucsf.edu> References: <568D272B.40105@gmail.com> <9A3754F1-C198-4D28-B825-731E814F14BA@cgl.ucsf.edu> Message-ID: <05CDF6AF-F339-4E4E-8ECE-1D8D125A8576@sonic.net> Hi Wouter, To add some more info to what Elaine said, there are two kinds of IMOD files read by Chimera, density maps which often have file suffix *.rec (for reconstruction) or *.mrc, and segmentation files with suffix *.mod. The segmentation files just contain surfaces, not the density map data. Since Volume Eraser erases density values and doesn?t do anything with surfaces it doesn?t work with the *.mod files. There isn?t a tool for erasing parts of surfaces in Chimera. You found ?Hide Dust? that can hide the small connected surface blobs. It is also possible to by hand hide other connected surface blobs with the ?sop split? command to make a copy of the surface where each blob is selectable, then select any blobs and use menu Actions / Surface / Hide to undisplay those. One last trick, the Chimera Surface Zone tool or ?sop zone? command can display just the parts of a surface within some distance of a set of markers, and the Color Zone tool could color surfaces to be completely transparent within a zone around markers, and the Volume Tracer tool can place markers. So that is another route to hide certain parts of a surface. Tom > On Jan 6, 2016, at 9:07 AM, Elaine Meng wrote: > > Dear Wouter, > The issue is that an IMOD file makes surfaces in Chimera, not a volume model (map or density grid with associated values at each grid point). > > > Volume Eraser only works with volume models, formats listed here: > > > Maybe your original data was or could be written in one of those formats? > > Also, Hide Dust only hides small surface bits; it does not delete any data. > > I hope this makes it clearer, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > P.S. appears to be a duplicate question, I?ll just answer this one > > On Jan 6, 2016, at 6:39 AM, Wouter Van Putte wrote: > >> Dear, >> >> I would like to use chimera for removing some densities manually of an isosurface generated with imod. I've loaded the map/model (.mod) and already used the function 'hide dust' to remove most of the noise. I now would like to use 'volume eraser' to remove the other noise manually. This however doesn't work, probably due to the file format (.mod). I thought saving in another file format would help, but it gave me errors when opening the file. How should I proceed? >> >> best wishes, >> >> Wouter > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From pett at cgl.ucsf.edu Wed Jan 6 17:24:24 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 6 Jan 2016 17:24:24 -0800 Subject: [Chimera-users] Suggested Improvement of Command Line In-Reply-To: References: Message-ID: <99123093-1F7C-45A5-9FFA-E023EB8F4879@cgl.ucsf.edu> Hi Eric, I was mildly shocked that ?select:? even works, I would have thought you would need a space after ?select?. Nonetheless, I agree that it?s a little weird that you can put spaces almost anywhere in an atom spec but you can?t put them after a comma. So I changed the parser to allow this. Now the parser code is extremely arcane, so it was significantly harder to do that than you would expect, but ultimately I prevailed. :-) It will be available in the next daily build. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Jan 5, 2016, at 2:45 PM, Eric Berg wrote: > > Hello, > > I have noticed that when giving the command line a list of residue indexes using the "select" function, the inclusion of white space will cause an error (see attachment). This is technically a pretty small quibble, but it may be beneficial in these instances to include something to filter out white space prior to parsing. > > Eric > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From olibclarke at gmail.com Thu Jan 7 08:49:13 2016 From: olibclarke at gmail.com (Oliver Clarke) Date: Thu, 7 Jan 2016 11:49:13 -0500 Subject: [Chimera-users] Drawing shapes given coordinates Message-ID: Dear Rebecca, I have used Elaine's suggestion before, and it works well, as in the following alias: alias ^pbond dist sel; setattr p label "" sel; setattr p drawMode 1 sel; setattr p radius 0.03 sel which places a thin black cylinder between two selected atoms. To make invisible dummy atoms at arbitrary coordinates, I would use the "mc" accelerator ("ac mc" on the command line), which places and selects a dummy atom at the center of rotation. So something like: cofr x1,y1,z1; ac mc; namesel atom1; cofr x2,y2,z2; ac mc; namesel atom2; sel atom1|atom2; pbond; vdwdefine 0.01 sel; transparency 100,a sel should work. Cheers, Oli. ------------------------------ Thank you! Theoretically if I was to create dummy atoms with coordinates at the locations where I want the cylinders to end, I could connect them with pseudobonds. I can easily shape my data that way, and if it doesn't work the BILD files will probably be fine. Thanks for the help! Cheers, Rebecca On 1/4/16, 5:20 PM, "Elaine Meng" > wrote: >*Hi Rebecca, *>*There are two approaches for adding cylinders independent of atoms? but I *>*don?t know if either will be satisfactory: *>>*(1) ?shape cylinder? is command-line and doesn?t require using atoms as *>*endpoints, but it doesn?t allow specifying endpoint coordinates directly. *>* A cylinder is specified by only its center, height, radius, and a *>*rotation angle. I don?t think it is easy to figure out what angle gives *>*the desired endpoint coordinates. (We?ve discussed the need to improve *>*this, but it may be deferred to our next-generation software in *>*development.) *>* *>*mera_docs_UsersGuide_midas_shape.html-23cylinder&d=CwIFaQ&c=TzEZu9LIcihmW3 *>*7vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd *>*4eXf6HdP_BL9dt0gv_zz3oMdq8&s=9vZCIh2K2i-8UrGF7HkSZwZwT7CRFcS9RUZsHUsson4&e *>*= > *>>*(2) BILD-format input allows specifying endpoint coordinates of a *>*cylinder, but it is not a command. You generate a BILD text file *>*describing the objects and read it in to Chimera. BILD format is very *>*simple, however: *>* *>*mera_docs_UsersGuide_bild.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r=Z2BqCMu *>*wlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_BL9dt0gv_ *>*zz3oMdq8&s=2A5wPT06BJ7QN1TDyA4kS36ILONzhA703a7xRpdnJKY&e= > *>>*The objects created with ?shape? are surface models, so you can change *>*their colors afterward. The BILD objects are not surface models and *>*cannot be recolored and do not work well with transparency. *>>*There are two approaches that depend on atoms: *>>*(1) pseudobonds can be created with the ?distance? command (or atom pairs *>*can be read in from a file with Pseudobond Reader), but pseudobonds *>*require atoms as endpoints. *>* *>*mera_docs_UsersGuide_midas_distance.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w *>*&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP *>*_BL9dt0gv_zz3oMdq8&s=tUGhl0z5yTsTqr2tyEgexdraCTB8o2JtwjuJZTgMwvo&e= > *>* *>*mera_docs_ContributedSoftware_pbreader_pbreader.html&d=CwIFaQ&c=TzEZu9LIci *>*hmW37vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH *>*6akd4eXf6HdP_BL9dt0gv_zz3oMdq8&s=nRvWQ2FPg5n33Obqd9Bee1ovSNmgCCdbaT1EH6Uc1 *>*I8&e= > *>>*(2) the ?define? command (or Axes/Planes/Centroids) tool will show *>*cylindrical axes that are best fits to specified sets of atoms. However, *>*there is currently little control over length? it is automatically *>*determined from the atomic coordinates. *>* *>*mera_docs_UsersGuide_midas_define.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r *>*=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_B *>*L9dt0gv_zz3oMdq8&s=t9I-WC_-VvEvmTfphtU3ey2GT0sMRiFtO62hFkRj7Rk&e= > *>>*I hope this helps, *>*Elaine *>*---------- *>*Elaine C. Meng, Ph.D. *>*UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab *>*Department of Pharmaceutical Chemistry *>*University of California, San Francisco *>>>* On Jan 4, 2016, at 12:09 PM, Rebecca Swett > *>>*wrote: *>>>>* Hi all, *>>* I'm trying to add some 3d shapes to a visualization. I was wondering if *>>*it would be possible to draw either a cylinder or tube given starting *>>*and ending coordinates rather than atom names/numbers or centroid? For *>>*example, if I had this coordinate pair: *>>* 6.17 1.10 -15.33 20.82 -0.70 -8.39 *>>>>* What would be the best way to go about drawing a line of some sort *>>*between those two points? I have dozens of pairs of coordinates so *>>*something command line would be ideal. *>>* Cheers, *>>* Rebecca *> This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Thu Jan 7 11:27:33 2016 From: goddard at sonic.net (Tom Goddard) Date: Thu, 7 Jan 2016 11:27:33 -0800 Subject: [Chimera-users] [chimera-dev] Volume Eraser: Recentering the eraser In-Reply-To: <5936F79A-8A06-4C25-AD99-710E1832F60B@cgl.ucsf.edu> References: <5936F79A-8A06-4C25-AD99-710E1832F60B@cgl.ucsf.edu> Message-ID: <540C42BA-965C-45C1-8EA6-86D93C88EF9F@sonic.net> Hi Mohan, Here are a few more details about how to erase the density inside the capsid of a virus density map. The trick as you?ve seen is getting the sphere centered at the center of the virus and having the correct radius. Here?s how I do this. First I adjust the volume eraser sphere radius so it visually looks about the same radius as the outside of the virus map. Then I move the sphere with the mouse to try to center it on the virus. I rotate to look at it from different view angles and center with the mouse at each view direction. It helps if the radius of the sphere is set so that just a little bit of the density pokes through so you can visually see whether the same amount of density is poking through on all sides. Now I have the right centering and I try to get the radius I want. For this it helps to clip the map and sphere using menu Favorites / Side View and move the left vertical yellow line to the right to clip the models. I move the clip plane to cut through near the center of the virus, then adjust the sphere radius. In this view you can see the sphere size relative to the concentric layers of density. It helps here to make the sphere not transparent by clicking the color square in the Volume Eraser dialog and setting the A (opacity) channel to 1. I?ve attached a pickture. To do this in a more precise way I create a sphere and mask using it with commands shape sphere radius 240 center 0,0,0 coordinateSystem #0 color blue mask #0 #2 invert true This requires that the origin of the map is set to the center of the virus capsid. You can choose this center grid point using Volume Viewer menu Features / Coordinates setting the Origin Index. Tom > On Jan 7, 2016, at 9:38 AM, Elaine Meng wrote: > > Hello Mohan, > If you read the Help for Volume Eraser (press the Help button on the dialog to see it), it explains how to move and resize the eraser sphere. Or, you can see this information on our website: > > > > Basically you can set which mouse button will be used to move the sphere, and then use the mouse to move it to where you want, including with Shift to move in Z (toward or away from you). There isn?t a feature to automatically put it at the center of the capsid. > > For user questions, the better address is chimera-users at cgl.ucsf.edu (not this address chimera-dev, which is more for programming questions). > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On Jan 6, 2016, at 9:01 AM, Mohan Sudabattula wrote: >> >> Hello, >> >> My name is Mohan Sudabattula, I am fairly new at using Chimera so please excuse my lack of understanding the program. >> >> I am currently utilizing the Volume Eraser tool and am trying to employ it erase the internal structure of a viral capsid. Upon opening the Volume Eraser it always seems to orient itself to the "frontmost face of the current display region". This is problematic because it is now only partially erasing what I am needing to be erased. >> >> Instead I am looking to have it oriented so that it is in the center of my virus. Is there any way to reorient the eraser so that this may be the case? >> >> ?Thank you!? >> Mohan Sudabattula >> > > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: erasesphere.png Type: image/png Size: 379711 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 801 bytes Desc: Message signed with OpenPGP using GPGMail URL: From matthewd at bcm.edu Thu Jan 7 14:58:27 2016 From: matthewd at bcm.edu (Dougherty, Matthew T) Date: Thu, 7 Jan 2016 22:58:27 +0000 Subject: [Chimera-users] save command Message-ID: The FILE pull down menu allows for "save" and "save as". The command "save" allows for two options: with or without a session_name. Without a session_name, a dialog box is presented and effectively I am doing the "save as" in the FILE menu at that point. With a session_name, it functions as a 'save as' without the dialog box. How do I create the same effect as FILE pull down menu "save", using the save command? Looking for a generic approach for any session, not knowing the file/session name apriori, & having to type the session name everytime. I suppose there is a python method to get the session filename & path, then build the command string. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= -------------- next part -------------- An HTML attachment was scrubbed... URL: From maozhouhe at 163.com Fri Jan 8 22:34:52 2016 From: maozhouhe at 163.com (maozhouhe) Date: Sat, 9 Jan 2016 14:34:52 +0800 Subject: [Chimera-users] header intact Message-ID: <4170b152.11ff7.152251842be.Coremail.maozhouhe@163.com> confirm 4cb1de59074527102f482c8970f4d33506347705 -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Mon Jan 11 19:01:32 2016 From: goddard at sonic.net (Tom Goddard) Date: Mon, 11 Jan 2016 19:01:32 -0800 Subject: [Chimera-users] save command In-Reply-To: References: Message-ID: <578DAD23-2414-451B-9D7B-D5E3DC2B76C1@sonic.net> Hi Matt, The 2 letter keyboard shorcuts are your friends. Shortcut ?Ss? which can be invoked with command ?ac Ss? saves the current state using the current session file name. Unfortunately I see that if there is no current session file name it throws an error. But maybe this is still useful to you. If not and you need it to show a dialog in the cases when there is no current session file name, I can fix that in the daily build. Tom > On Jan 7, 2016, at 2:58 PM, Dougherty, Matthew T wrote: > > The FILE pull down menu allows for "save" and "save as". > > The command "save" allows for two options: with or without a session_name. > > Without a session_name, a dialog box is presented and effectively I am doing the "save as" in the FILE menu at that point. > > With a session_name, it functions as a 'save as' without the dialog box. > > How do I create the same effect as FILE pull down menu "save", using the save command? > > Looking for a generic approach for any session, not knowing the file/session name apriori, & having to type the session name everytime. > > I suppose there is a python method to get the session filename & path, then build the command string. > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > ================================================= > ================================================= > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > 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: signature.asc Type: application/pgp-signature Size: 801 bytes Desc: Message signed with OpenPGP using GPGMail URL: From m.kadlof at cent.uw.edu.pl Wed Jan 13 06:28:45 2016 From: m.kadlof at cent.uw.edu.pl (=?utf-8?Q?Micha=C5=82?= Kadlof) Date: Wed, 13 Jan 2016 15:28:45 +0100 (CET) Subject: [Chimera-users] importing xyz file In-Reply-To: <1019877736.4702624.1452695049618.JavaMail.javamailuser@localhost> Message-ID: <1705258525.4704544.1452695325447.JavaMail.javamailuser@localhost> Hello, I would like to visualize in chimera objects (not exactly atoms) from my XYZ file. I can import them ans see as scattered balls but I would like to see them connected to each other in order that they are appear in file. The distances are much larger than usual inter atoms interactions. Is it possible? -- best Micha? Kadlof From meng at cgl.ucsf.edu Wed Jan 13 09:58:12 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 13 Jan 2016 09:58:12 -0800 Subject: [Chimera-users] importing xyz file In-Reply-To: <1705258525.4704544.1452695325447.JavaMail.javamailuser@localhost> References: <1705258525.4704544.1452695325447.JavaMail.javamailuser@localhost> Message-ID: <5A3BFFCE-89D5-4A84-AC27-292C7589DEA6@cgl.ucsf.edu> Hello Micha?, The XYZ format does not specify bonds directly. Normally if the points are atoms with reasonable bond lengths, Chimera can guess where the bonds are based on the elements and coordinates. If they are not atomic structures and the bonds are of arbitrary length, here are some possibilities of what you could do: (1) after reading in the XYZ file, add bonds manually yourself, for example, select two ?atoms? (Ctrl-click, Shift-Ctrl-click) and then use command ?bond sel?. Repeat. This could be tedious if you have a lot of bonds to add. You could also use atom names instead of selecting, for example ?bond @c1,c2?. Although the XYZ file doesn?t contain atom names, ?atoms? of the same ?element? will be named in Chimera according to element with a sequential number appended (the first C is named C1, the second C is named C2, etc.). - OR - (2) convert XYZ file into some other format that specifies bonds, for example a PDB file with CONECT lines. This would also take some effort to script a process (which could involve other people?s programs, say Babel to convert to PDB but then you would still need to add your CONECT lines), but once you had that done, it could be applied to a large file or multiple files. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 13, 2016, at 6:28 AM, Micha? Kadlof wrote: > Hello, > I would like to visualize in chimera objects (not exactly atoms) from my XYZ file. I can import them ans see as scattered balls but I would like to see them connected to each other in order that they are appear in file. The distances are much larger than usual inter atoms interactions. Is it possible? > -- > best > Micha? Kadlof From meng at cgl.ucsf.edu Wed Jan 13 09:59:48 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 13 Jan 2016 09:59:48 -0800 Subject: [Chimera-users] importing xyz file In-Reply-To: <5A3BFFCE-89D5-4A84-AC27-292C7589DEA6@cgl.ucsf.edu> References: <1705258525.4704544.1452695325447.JavaMail.javamailuser@localhost> <5A3BFFCE-89D5-4A84-AC27-292C7589DEA6@cgl.ucsf.edu> Message-ID: <371BAD09-BD7F-4DB2-AF5A-60A2F8DD8DF0@cgl.ucsf.edu> Additional alternative formats are BILD objects and Chimera marker files, see: Elaine On Jan 13, 2016, at 9:58 AM, Elaine Meng wrote: > Hello Micha?, > The XYZ format does not specify bonds directly. Normally if the points are atoms with reasonable bond lengths, Chimera can guess where the bonds are based on the elements and coordinates. If they are not atomic structures and the bonds are of arbitrary length, here are some possibilities of what you could do: > > (1) after reading in the XYZ file, add bonds manually yourself, for example, select two ?atoms? (Ctrl-click, Shift-Ctrl-click) and then use command ?bond sel?. Repeat. This could be tedious if you have a lot of bonds to add. You could also use atom names instead of selecting, for example ?bond @c1,c2?. Although the XYZ file doesn?t contain atom names, ?atoms? of the same ?element? will be named in Chimera according to element with a sequential number appended (the first C is named C1, the second C is named C2, etc.). > > > - OR - > > (2) convert XYZ file into some other format that specifies bonds, for example a PDB file with CONECT lines. > > This would also take some effort to script a process (which could involve other people?s programs, say Babel to convert to PDB but then you would still need to add your CONECT lines), but once you had that done, it could be applied to a large file or multiple files. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jan 13, 2016, at 6:28 AM, Micha? Kadlof wrote: > >> Hello, >> I would like to visualize in chimera objects (not exactly atoms) from my XYZ file. I can import them ans see as scattered balls but I would like to see them connected to each other in order that they are appear in file. The distances are much larger than usual inter atoms interactions. Is it possible? >> -- >> best >> Micha? Kadlof > From pett at cgl.ucsf.edu Wed Jan 13 10:03:32 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 13 Jan 2016 10:03:32 -0800 Subject: [Chimera-users] importing xyz file In-Reply-To: <5A3BFFCE-89D5-4A84-AC27-292C7589DEA6@cgl.ucsf.edu> References: <1705258525.4704544.1452695325447.JavaMail.javamailuser@localhost> <5A3BFFCE-89D5-4A84-AC27-292C7589DEA6@cgl.ucsf.edu> Message-ID: <027CDA6D-5C65-413B-857C-227AFF42E3A5@cgl.ucsf.edu> > On Jan 13, 2016, at 9:58 AM, Elaine Meng wrote: > > (1) after reading in the XYZ file, add bonds manually yourself, for example, select two ?atoms? (Ctrl-click, Shift-Ctrl-click) and then use command ?bond sel?. Repeat. This could be tedious if you have a lot of bonds to add. You could also use atom names instead of selecting, for example ?bond @c1,c2?. Although the XYZ file doesn?t contain atom names, ?atoms? of the same ?element? will be named in Chimera according to element with a sequential number appended (the first C is named C1, the second C is named C2, etc.). > > And the above could be combined into a script, e.g.: open myfile.xyz bond @c1,c2 bond @c1,c7 ? That script file could then be opening with a single command in Chimera: ?open myscript.cmd?. ?Eric Eric Pettersen UCSF Computer Graphics Lab -------------- next part -------------- An HTML attachment was scrubbed... URL: From conrad at cgl.ucsf.edu Wed Jan 13 11:21:56 2016 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Wed, 13 Jan 2016 11:21:56 -0800 Subject: [Chimera-users] importing xyz file In-Reply-To: <5A3BFFCE-89D5-4A84-AC27-292C7589DEA6@cgl.ucsf.edu> References: <1705258525.4704544.1452695325447.JavaMail.javamailuser@localhost> <5A3BFFCE-89D5-4A84-AC27-292C7589DEA6@cgl.ucsf.edu> Message-ID: <5696A3D4.7080305@cgl.ucsf.edu> Attached is a Chimera script that you can open immediately after opening your XYZ file. It connects consecutive "atoms" in the last opened model. You can even use it on the command line like: chimera methane.xyz connectxyz.py Obviously something bad may happen if there is already connectivity within the model. Conrad On 1/13/2016 9:58 AM, Elaine Meng wrote: > Hello Micha?, > The XYZ format does not specify bonds directly. Normally if the points are atoms with reasonable bond lengths, Chimera can guess where the bonds are based on the elements and coordinates. If they are not atomic structures and the bonds are of arbitrary length, here are some possibilities of what you could do: > > (1) after reading in the XYZ file, add bonds manually yourself, for example, select two ?atoms? (Ctrl-click, Shift-Ctrl-click) and then use command ?bond sel?. Repeat. This could be tedious if you have a lot of bonds to add. You could also use atom names instead of selecting, for example ?bond @c1,c2?. Although the XYZ file doesn?t contain atom names, ?atoms? of the same ?element? will be named in Chimera according to element with a sequential number appended (the first C is named C1, the second C is named C2, etc.). > > > - OR - > > (2) convert XYZ file into some other format that specifies bonds, for example a PDB file with CONECT lines. > > This would also take some effort to script a process (which could involve other people?s programs, say Babel to convert to PDB but then you would still need to add your CONECT lines), but once you had that done, it could be applied to a large file or multiple files. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jan 13, 2016, at 6:28 AM, Micha? Kadlof wrote: > >> Hello, >> I would like to visualize in chimera objects (not exactly atoms) from my XYZ file. I can import them ans see as scattered balls but I would like to see them connected to each other in order that they are appear in file. The distances are much larger than usual inter atoms interactions. Is it possible? >> -- >> best >> Micha? Kadlof > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: connectxyz.py Type: text/x-python Size: 126 bytes Desc: not available URL: From agszabo at bell.net Thu Jan 14 13:59:56 2016 From: agszabo at bell.net (A G Szabo) Date: Thu, 14 Jan 2016 16:59:56 -0500 Subject: [Chimera-users] question Message-ID: <002801d14f16$e7ac5240$b704f6c0$@bell.net> I have to admit that my understanding of the various commands to use for very specific functions in Chimera is difficult for me to find the correct command. I know how to color a specific residue using the sequence table and the color chart. So how do I color a specific atom in a residue. For example I am interested in coloring the nitrogen of the Asn amide side chain say color red. How can I do this? When I highlight a residue and visualize it as a ball and stick, then color it different from the color of the helix, the color of that part of the helix changes to the color of the ball and stick, different from the color of the rest of the helix. How can I reset the color of the helix location of that residue, leaving the ball and stick as another color. Thank you Arthur Szabo Professor Emeritus Chemistry and Biochemistry Wilfrid Laurier University Waterloo Canada. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Jan 14 16:13:14 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 14 Jan 2016 16:13:14 -0800 Subject: [Chimera-users] coloring only specific atoms, or atoms but not ribbon In-Reply-To: <002801d14f16$e7ac5240$b704f6c0$@bell.net> References: <002801d14f16$e7ac5240$b704f6c0$@bell.net> Message-ID: Hi Arthur, If you are coloring your selection with the menu, choose menu: Actions? Color? all options (it?s at the bottom of the menu). That will open a separate Color Actions dialog, in which you could set the ?Color applies to? to ?atoms/bonds? to color atoms/bonds only, or ?ribbons? to color ribbon segment only, etc. (default is ?all of the above?). If you first display the atoms of the residue, you can Ctrl-click to select a specific atom instead of the whole residue. If you are using the ?color" command, you control which types of displays are affected by putting some text right after the color name. For example: color red,a sel ?. which colors atoms/bonds only, indicated by the ?,a? (no space before it!!), and instead of selecting and using ?sel? you can give residue and atom information directly: color red,a :55.A at ND1 ? to color atom ND1 of residue 55 in chain A, or color hot pink,r :55.A ? to color ribbon-only (indicated by ?,r?) of residue 55 in chain A The getting-started tutorials include examples of these, but I know it can be hard to find exactly what you want. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 14, 2016, at 1:59 PM, A G Szabo wrote: > > I have to admit that my understanding of the various commands to use for very specific functions in Chimera is difficult for me to find the correct command. > > I know how to color a specific residue using the sequence table and the color chart. > So how do I color a specific atom in a residue. For example I am interested in coloring the nitrogen of the Asn amide side chain say color red. How can I do this? > When I highlight a residue and visualize it as a ball and stick, then color it different from the color of the helix, the color of that part of the helix changes to the color of the ball and stick, different from the color of the rest of the helix. > > How can I reset the color of the helix location of that residue, leaving the ball and stick as another color. > Thank you > > Arthur Szabo > Professor Emeritus > Chemistry and Biochemistry > Wilfrid Laurier University > Waterloo Canada. From agszabo at bell.net Thu Jan 14 18:27:13 2016 From: agszabo at bell.net (A G Szabo) Date: Thu, 14 Jan 2016 21:27:13 -0500 Subject: [Chimera-users] coloring only specific atoms, or atoms but not ribbon In-Reply-To: References: <002801d14f16$e7ac5240$b704f6c0$@bell.net> Message-ID: <003201d14f3c$3e832830$bb897890$@bell.net> Elaine Thank you for your prompt reply. I should probably ask another question going through the generic question email. But In the structure I am working with there is a 25 amino acid segment that is flexible and not represented in the crystal structure. In the Chimera structure it is represented by a series of dashed lines. How can I increase the thickness of those branched lines and even change their color from the rest of the protein. Thank you Arthur -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: January-14-16 7:13 PM To: A G Szabo Cc: chimera-users at cgl.ucsf.edu Subject: coloring only specific atoms, or atoms but not ribbon Hi Arthur, If you are coloring your selection with the menu, choose menu: Actions? Color? all options (it?s at the bottom of the menu). That will open a separate Color Actions dialog, in which you could set the ?Color applies to? to ?atoms/bonds? to color atoms/bonds only, or ?ribbons? to color ribbon segment only, etc. (default is ?all of the above?). If you first display the atoms of the residue, you can Ctrl-click to select a specific atom instead of the whole residue. If you are using the ?color" command, you control which types of displays are affected by putting some text right after the color name. For example: color red,a sel ?. which colors atoms/bonds only, indicated by the ?,a? (no space before it!!), and instead of selecting and using ?sel? you can give residue and atom information directly: color red,a :55.A at ND1 ? to color atom ND1 of residue 55 in chain A, or color hot pink,r :55.A ? to color ribbon-only (indicated by ?,r?) of residue 55 in chain A The getting-started tutorials include examples of these, but I know it can be hard to find exactly what you want. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 14, 2016, at 1:59 PM, A G Szabo wrote: > > I have to admit that my understanding of the various commands to use for very specific functions in Chimera is difficult for me to find the correct command. > > I know how to color a specific residue using the sequence table and the color chart. > So how do I color a specific atom in a residue. For example I am interested in coloring the nitrogen of the Asn amide side chain say color red. How can I do this? > When I highlight a residue and visualize it as a ball and stick, then color it different from the color of the helix, the color of that part of the helix changes to the color of the ball and stick, different from the color of the rest of the helix. > > How can I reset the color of the helix location of that residue, leaving the ball and stick as another color. > Thank you > > Arthur Szabo > Professor Emeritus > Chemistry and Biochemistry > Wilfrid Laurier University > Waterloo Canada. From tobias.eilert at uni-ulm.de Thu Jan 14 23:36:45 2016 From: tobias.eilert at uni-ulm.de (tobias.eilert at uni-ulm.de) Date: Fri, 15 Jan 2016 08:36:45 +0100 Subject: [Chimera-users] Geometric Center Message-ID: <20160115083645.mo2objrkgc048s8g@imap.uni-ulm.de> Hello, I want to translocate a protein such that its geometric center is the origin. Finally I want to save this new configuration in a pdb-file, so it is conserved like this. Do you have any suggestions? With kind regards Tobias Eilert From meng at cgl.ucsf.edu Fri Jan 15 11:06:57 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 15 Jan 2016 11:06:57 -0800 Subject: [Chimera-users] changing appearance of dashed lines In-Reply-To: <003201d14f3c$3e832830$bb897890$@bell.net> References: <002801d14f16$e7ac5240$b704f6c0$@bell.net> <003201d14f3c$3e832830$bb897890$@bell.net> Message-ID: <852574A0-74CB-4B96-A760-4AD20C5A6E5B@cgl.ucsf.edu> Hi Arthur, Those dashed lines are ?pseudobonds? (like H-bond and distance-measuring lines). You can Ctrl-click to select one and then click the green magnifying glass icon near the bottom right of the Chimera window to show the Selection Inspector. In the Selection Inspector, you can Inspect ?Pseudobond? and change its color by: (1) turning ?halfbond mode? to ?off?, AND (2) clicking on the square color-well and using the resulting Color Editor dialog to choose a color. The color will not be visible in the display unless you turn halfbond mode off. To change line thickness, Inspect ?Pseudobond group? (click on the ?Pseudobond? and you can see it is a menu where you can change to ?Pseudobond group? instead) and then change the ?line width? value. Or, you could do all these things with the ?setattr? command ?of which there are a few examples in these previous posts: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 14, 2016, at 6:27 PM, A G Szabo wrote: > Elaine > Thank you for your prompt reply. > I should probably ask another question going through the generic question email. But > > In the structure I am working with there is a 25 amino acid segment that is flexible and not represented in the crystal structure. In the Chimera structure it is represented by a series of dashed lines. How can I increase the thickness of those branched lines and even change their color from the rest of the protein. > > Thank you > Arthur > From meng at cgl.ucsf.edu Fri Jan 15 11:31:06 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 15 Jan 2016 11:31:06 -0800 Subject: [Chimera-users] Geometric Center In-Reply-To: <20160115083645.mo2objrkgc048s8g@imap.uni-ulm.de> References: <20160115083645.mo2objrkgc048s8g@imap.uni-ulm.de> Message-ID: <1F936E3C-5BD5-4AC2-BBE8-08CD66B8FF72@cgl.ucsf.edu> Hi Tobias, Basically you would first calculate the center of the set of atoms, then subtract its coordinates by translating along X,Y,Z, and then saving the transformed coordinates. For calculating the center, you can do mass-weighting or not, and you can specify exactly which set of atoms you want, using the same Chimera ?atomspec? syntax as in other commands. For example, commands like: define centroid mass false define centroid mass true measure center ? where the latter does mass weighting and can be any Chimera atomspec such as: #1 (all atoms of model 1, which would include any solvent, ions, ligands ...) protein (all protein atoms) #1 & protein (all protein atoms in model 1) etc. The coordinates of the center will be reported in the Reply Log (open from Favorites menu). Then, command ?reset? will remove any mouse rotations/translations you might have done. Without moving the structure at all with the mouse, use the ?move? command to subtract out the coordinates of the center. For example, if center is reported as: centroid name, ID, center: centroid: c3 ( 35.247, 30.064, 49.104) I would use commands: move x -35.247 move y -30.064 move z -49.104 then File? Save PDB, uncheck ?Use transformed coordinates? since you want the transformed coordinates. Or, you can save PDB with the ?write? command. I checked by reading the new PDB back in and calculating center again with the same set of atoms. The coordinates weren?t exactly zero, I guess because of rounding issues, but close: -0.03, -0.01, -0.01). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 14, 2016, at 11:36 PM, tobias.eilert at uni-ulm.de wrote: > Hello, > I want to translocate a protein such that its geometric center is the origin. Finally I want to save this new configuration in a pdb-file, so it is conserved like this. > Do you have any suggestions? > With kind regards > Tobias Eilert From agszabo at bell.net Fri Jan 15 12:37:18 2016 From: agszabo at bell.net (A G Szabo) Date: Fri, 15 Jan 2016 15:37:18 -0500 Subject: [Chimera-users] changing appearance of dashed lines In-Reply-To: <852574A0-74CB-4B96-A760-4AD20C5A6E5B@cgl.ucsf.edu> References: <002801d14f16$e7ac5240$b704f6c0$@bell.net> <003201d14f3c$3e832830$bb897890$@bell.net> <852574A0-74CB-4B96-A760-4AD20C5A6E5B@cgl.ucsf.edu> Message-ID: <004e01d14fd4$872fc190$958f44b0$@bell.net> Elaine Once again you have been very helpful. Thank you very much. It worked. I`ll Have to remember to send you a copy of the book when it is completed. arthur -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: January-15-16 2:07 PM To: A G Szabo Cc: chimera-users at cgl.ucsf.edu Subject: changing appearance of dashed lines Hi Arthur, Those dashed lines are "pseudobonds" (like H-bond and distance-measuring lines). You can Ctrl-click to select one and then click the green magnifying glass icon near the bottom right of the Chimera window to show the Selection Inspector. In the Selection Inspector, you can Inspect "Pseudobond" and change its color by: (1) turning "halfbond mode" to "off", AND (2) clicking on the square color-well and using the resulting Color Editor dialog to choose a color. The color will not be visible in the display unless you turn halfbond mode off. To change line thickness, Inspect "Pseudobond group" (click on the "Pseudobond" and you can see it is a menu where you can change to "Pseudobond group" instead) and then change the "line width" value. Or, you could do all these things with the "setattr" command .of which there are a few examples in these previous posts: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 14, 2016, at 6:27 PM, A G Szabo wrote: > Elaine > Thank you for your prompt reply. > I should probably ask another question going through the generic > question email. But > > In the structure I am working with there is a 25 amino acid segment that is flexible and not represented in the crystal structure. In the Chimera structure it is represented by a series of dashed lines. How can I increase the thickness of those branched lines and even change their color from the rest of the protein. > > Thank you > Arthur > From meng at cgl.ucsf.edu Fri Jan 15 13:12:31 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 15 Jan 2016 13:12:31 -0800 Subject: [Chimera-users] changing appearance of dashed lines In-Reply-To: <004e01d14fd4$872fc190$958f44b0$@bell.net> References: <002801d14f16$e7ac5240$b704f6c0$@bell.net> <003201d14f3c$3e832830$bb897890$@bell.net> <852574A0-74CB-4B96-A760-4AD20C5A6E5B@cgl.ucsf.edu> <004e01d14fd4$872fc190$958f44b0$@bell.net> Message-ID: You?re welcome! I didn?t realize (or forgot if you told me) that you were working on figures for a book? always a big project! Yes, we would be interested in seeing the results. Best, Elaine On Jan 15, 2016, at 12:37 PM, A G Szabo wrote: > Elaine > > Once again you have been very helpful. Thank you very much. It worked. > > I`ll Have to remember to send you a copy of the book when it is completed. > > arthur > > -----Original Message----- > From: Elaine Meng [mailto:meng at cgl.ucsf.edu] > Sent: January-15-16 2:07 PM > To: A G Szabo > Cc: chimera-users at cgl.ucsf.edu > Subject: changing appearance of dashed lines > > Hi Arthur, > Those dashed lines are "pseudobonds" (like H-bond and distance-measuring > lines). You can Ctrl-click to select one and then click the green > magnifying glass icon near the bottom right of the Chimera window to show > the Selection Inspector. > > > In the Selection Inspector, you can Inspect "Pseudobond" and change its > color by: > (1) turning "halfbond mode" to "off", AND > (2) clicking on the square color-well and using the resulting Color Editor > dialog to choose a color. The color will not be visible in the display > unless you turn halfbond mode off. > > To change line thickness, Inspect "Pseudobond group" (click on the > "Pseudobond" and you can see it is a menu where you can change to > "Pseudobond group" instead) and then change the "line width" value. > > Or, you could do all these things with the "setattr" command > > .of which there are a few examples in these previous posts: > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of > Pharmaceutical Chemistry University of California, San Francisco > > On Jan 14, 2016, at 6:27 PM, A G Szabo wrote: > >> Elaine >> Thank you for your prompt reply. >> I should probably ask another question going through the generic >> question email. But >> >> In the structure I am working with there is a 25 amino acid segment that > is flexible and not represented in the crystal structure. In the Chimera > structure it is represented by a series of dashed lines. How can I increase > the thickness of those branched lines and even change their color from the > rest of the protein. >> >> Thank you >> Arthur >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From olibclarke at gmail.com Tue Jan 19 13:59:15 2016 From: olibclarke at gmail.com (Oliver Clarke) Date: Tue, 19 Jan 2016 16:59:15 -0500 Subject: [Chimera-users] Select residues with missing atoms? Message-ID: Hello, Is there any way to select/color all protein residues with incomplete sidechains? This would be very helpful when looking at a structure and deciding whether it is necessary to run dock prep to fill them in prior to performing other calculations (e.g. sometimes I am only concerned with what is going on around a ligand binding site). Cheers, Oliver. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Jan 19 14:20:39 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 19 Jan 2016 14:20:39 -0800 Subject: [Chimera-users] Select residues with missing atoms? In-Reply-To: References: Message-ID: Hi Oliver, Attached is a script that Eric made me years ago to select all the incomplete residues. I just did a spot-check on 5BTR and opening this script did select all the residues with missing atoms that were listed in the PDB header. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco -------------- next part -------------- A non-text attachment was scrubbed... Name: findIncomplete.py Type: text/x-python-script Size: 565 bytes Desc: not available URL: -------------- next part -------------- P.S. I don?t see it listed in this Chimera Python-scripts page, will add it soon? > On Jan 19, 2016, at 1:59 PM, Oliver Clarke wrote: > > Hello, > > Is there any way to select/color all protein residues with incomplete sidechains? > > This would be very helpful when looking at a structure and deciding whether it is necessary to run dock prep to fill them in prior to performing other calculations (e.g. sometimes I am only concerned with what is going on around a ligand binding site). > > Cheers, > Oliver. > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From olibclarke at gmail.com Tue Jan 19 14:25:27 2016 From: olibclarke at gmail.com (Oliver Clarke) Date: Tue, 19 Jan 2016 17:25:27 -0500 Subject: [Chimera-users] Select residues with missing atoms? In-Reply-To: References: Message-ID: Thanks Elaine! That looks like it'll do the trick nicely :) Oli. On Tue, Jan 19, 2016 at 5:20 PM, Elaine Meng wrote: > Hi Oliver, > Attached is a script that Eric made me years ago to select all the > incomplete residues. I just did a spot-check on 5BTR and opening this > script did select all the residues with missing atoms that were listed in > the PDB header. > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > P.S. I don?t see it listed in this Chimera Python-scripts page, will add > it soon? > > > > > On Jan 19, 2016, at 1:59 PM, Oliver Clarke wrote: > > > > Hello, > > > > Is there any way to select/color all protein residues with incomplete > sidechains? > > > > This would be very helpful when looking at a structure and deciding > whether it is necessary to run dock prep to fill them in prior to > performing other calculations (e.g. sometimes I am only concerned with what > is going on around a ligand binding site). > > > > Cheers, > > Oliver. > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From 21620101152414 at xmu.edu.cn Fri Jan 22 05:00:19 2016 From: 21620101152414 at xmu.edu.cn (=?utf-8?B?5p2O5pm65rW3?=) Date: Fri, 22 Jan 2016 21:00:19 +0800 Subject: [Chimera-users] the fastest way to convert a pdb to density map Message-ID: <93777716-FA67-452D-AC05-E7D16DEE8562@stu.xmu.edu.cn> Hi, Here I want to calculate a model-to-map FSC curve. If I am not wrong, firstly I am supposed to convert the pdb file to a density map. So I was just wondering in Chimera, how to use command molmap to generated a map with the same pixel size and dimensions as the corresponding map? Any help will be high appreciated. Best, Zhihai Li -------------- next part -------------- An HTML attachment was scrubbed... URL: From 21620101152414 at xmu.edu.cn Fri Jan 22 05:25:36 2016 From: 21620101152414 at xmu.edu.cn (=?utf-8?B?5p2O5pm65rW3?=) Date: Fri, 22 Jan 2016 21:25:36 +0800 Subject: [Chimera-users] the fastest way to convert a pdb to density map In-Reply-To: <93777716-FA67-452D-AC05-E7D16DEE8562@stu.xmu.edu.cn> References: <93777716-FA67-452D-AC05-E7D16DEE8562@stu.xmu.edu.cn> Message-ID: Maybe now I find the answer to my own question, the command combinations molmap onGrid and vop resample can solve my problem. Zhihai > On Jan 22, 2016, at 9:00 PM, ??? <21620101152414 at STU.XMU.EDU.CN> wrote: > > Hi, > > Here I want to calculate a model-to-map FSC curve. If I am not wrong, firstly I am supposed to convert the pdb file to a density map. So I was just wondering in Chimera, how to use command molmap to generated a map with the same pixel size and dimensions as the corresponding map? > > Any help will be high appreciated. > > Best, > > Zhihai Li > -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Fri Jan 22 11:19:18 2016 From: goddard at sonic.net (Tom Goddard) Date: Fri, 22 Jan 2016 11:19:18 -0800 Subject: [Chimera-users] the fastest way to convert a pdb to density map In-Reply-To: References: <93777716-FA67-452D-AC05-E7D16DEE8562@stu.xmu.edu.cn> Message-ID: <3169F229-A952-4603-8B44-E4E101680F74@sonic.net> Hi Zhihai, Yes use molmap then vop resample. If your atomic model is #0 and experimental map is #1 with resolution 5 Angstroms use molmap #0 5 vop resample #2 ongrid #1 For computing FSC it should not matter what resolution you use with molmap because that resolution value will just scale the Fourier shells and should not alter the correlation with a shell. But I would test to make sure this is the case. Also if you are at very high resolution (3 - 4 Angstroms) I am not sure the molmap map is good enough an approximation since it simply puts a Gaussian at each atom position with all Gaussians having the same standard deviation. Tom > On Jan 22, 2016, at 5:25 AM, ??? < wrote: > > Maybe now I find the answer to my own question, the command combinations molmap onGrid and vop resample can solve my problem. > > Zhihai >> On Jan 22, 2016, at 9:00 PM, ??? wrote: >> >> Hi, >> >> Here I want to calculate a model-to-map FSC curve. If I am not wrong, firstly I am supposed to convert the pdb file to a density map. So I was just wondering in Chimera, how to use command molmap to generated a map with the same pixel size and dimensions as the corresponding map? >> >> Any help will be high appreciated. >> >> Best, >> >> Zhihai Li >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > 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: signature.asc Type: application/pgp-signature Size: 801 bytes Desc: Message signed with OpenPGP using GPGMail URL: From helge.paternoga at googlemail.com Fri Jan 22 17:18:31 2016 From: helge.paternoga at googlemail.com (Helge) Date: Sat, 23 Jan 2016 02:18:31 +0100 Subject: [Chimera-users] rendering of custom annotation Message-ID: <56A2D4E7.10707@googlemail.com> Dear Chimera users, I have some data, which contains numbers of hits for each given residue of a chain (in my case the 25S rRNA). The data consists of a table with two columns: residues and corresponding hits. I would now like to color each residue in Chimera, relative to the amount of hits, with the highest number always getting a defined color. Is this possible? best regards, Helge From lluis.blancafort at udg.edu Mon Jan 25 09:00:10 2016 From: lluis.blancafort at udg.edu (Lluis Blancafort) Date: Mon, 25 Jan 2016 18:00:10 +0100 Subject: [Chimera-users] Add Charges failure (libquadmath) Message-ID: Hi, I?m running Chimera alpha version 1.11 on Mac OSX El Capitan 10.11.2 The Add Charges tool does not work for non-standard residues with AM1-BCC. The Reply Log reports a problem with libquadmath and later with sqm utility (see below). I don?t have libquadmath.0.dylib installed. Can anybody help? Thanks! Llu?s Blancafort Institut de Qu?mica Computacional i Cat?lisi Universitat de Girona 17071 Girona Spain (1) Charge model: AMBER ff14SB Assigning partial charges to residue SGA (net charge -1) with am1-bcc method Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/6j/nf071g8n2b5csd0rdcm8n5sc0000gn/T/tmpKi57P0/ante.in.mol2 -fi mol2 -o /var/folders/6j/nf071g8n2b5csd0rdcm8n5sc0000gn/T/tmpKi57P0/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 (SGA) (SGA) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (SGA) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (SGA) Reason: image not found SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (SGA) (SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (SGA) Total number of electrons: 136; net charge: -1 (SGA) (SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (SGA) 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 From yanli.li at e-campus.uab.cat Mon Jan 25 09:07:03 2016 From: yanli.li at e-campus.uab.cat (Yanli Li) Date: Mon, 25 Jan 2016 18:07:03 +0100 Subject: [Chimera-users] my question Message-ID: Dear sirs/madams, I am a PhD student in Universitat Aut?noma de Barcelona. I am working on the Porcine Reproductive and Respiratory Syndrome Virus (PRRSV). I have got differences of cytokine profiles and phenotype regulation of antigen presenting cells by different isolates through the lab work. Now I intend to predict the structure of the whole or some parts of the viral particle with UCSF CHIMERA. However, there are only three relevant structures(nucleocapsid, nsp1, nsp4) that have been published. Is it possible to realize it? If yes, can you tell me the method in brief? Thanks a lot! Waiting for your reply. Best wishes, Yanli LI -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Jan 25 11:17:31 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 25 Jan 2016 11:17:31 -0800 Subject: [Chimera-users] rendering of custom annotation In-Reply-To: <56A2D4E7.10707@googlemail.com> References: <56A2D4E7.10707@googlemail.com> Message-ID: Dear Helge, Yes, you would only need to reformat your data slightly to make the ?attribute file? text format that can be read by Chimera. Reading that file will assign the values as a residue attribute, and then you can easily color the residues (ribbons and/or atoms and/or surfaces) to show the values with either the Render by Attribute graphical interface or the ?rangecolor? command. Attribute file format and example files: There are a few information lines at the top to say it is a residue attribute and what you want to name it, and the rest is just two columns preceded by tabs. The first column will be residue identifiers just like you could use in the command line (for example :26 for residue 26, :26.a for residue 26 of chain A, etc. ) and the second column the value, in your case the number of hits. Render by Attribute: You would start Define Attribute (in menu under Tools? Structure Analysis) or use command ?defattr? to read in your attribute file, and then the Render tool appears automatically, but you can also open it from the menu. ?rangecolor? command: For example, if you?d named your attribute ?nhits?, you could use something like the following: rangecol nhits min purple mid orange max yellow (you can try this with ?bfactor? instead of ?nhits? if you haven?t made your attribute yet). You can also give specific values instead of min/mid/max and lots of color names are shown here: I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 22, 2016, at 5:18 PM, Helge wrote: > > Dear Chimera users, > > I have some data, which contains numbers of hits for each given residue of a chain (in my case the 25S rRNA). The data consists of a table with two columns: residues and corresponding hits. I would now like to color each residue in Chimera, relative to the amount of hits, with the highest number always getting a defined color. > > Is this possible? > > best regards, > > Helge From meng at cgl.ucsf.edu Mon Jan 25 11:35:03 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 25 Jan 2016 11:35:03 -0800 Subject: [Chimera-users] my question In-Reply-To: References: Message-ID: <37086BFD-7D62-4222-ACFF-F7F7A907E1DC@cgl.ucsf.edu> Dear Yanli Li, Chimera does not predict structures. If the solved parts already have symmetry matrix information in their files, Chimera can use these matrices to assemble their multimers (see Multiscale Models tool or ?sym? command). You could also interactively assemble parts in Chimera with the mouse based on your own knowledge such as information from the literature, known homologous structures and related viruses, or data such as an EM map into which you could semi-manually fit the crystal structures. As far as I understand it, ?nsp? means nonstructural protein, so you would mainly be interested in the nucleocapsid structure. I searched the RCSB PDB and found this structure 1p65 ? but it is only a fragment, and it does not contain the symmetry information that would be needed to build up a whole particle. So you would probably need to try to figure out if there are other similar viruses or known homologous proteins with more complete structure information, and think about whether they are similar enough to help you model PRRSV. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 25, 2016, at 9:07 AM, Yanli Li wrote: > > Dear sirs/madams, > > I am a PhD student in Universitat Aut?noma de Barcelona. I am working on the Porcine Reproductive and Respiratory Syndrome Virus (PRRSV). I have got differences of cytokine profiles and phenotype regulation of antigen presenting cells by different isolates through the lab work. Now I intend to predict the structure of the whole or some parts of the viral particle with UCSF CHIMERA. However, there are only three relevant structures(nucleocapsid, nsp1, nsp4) that have been published. Is it possible to realize it? If yes, can you tell me the method in brief? Thanks a lot! > > Waiting for your reply. > > Best wishes, > > Yanli LI From David.Bhella at glasgow.ac.uk Mon Jan 25 12:37:15 2016 From: David.Bhella at glasgow.ac.uk (David Bhella) Date: Mon, 25 Jan 2016 20:37:15 +0000 Subject: [Chimera-users] my question In-Reply-To: <37086BFD-7D62-4222-ACFF-F7F7A907E1DC@cgl.ucsf.edu> References: , <37086BFD-7D62-4222-ACFF-F7F7A907E1DC@cgl.ucsf.edu> Message-ID: <93A24617-ECB4-4BC9-B6EF-3F8E1DE42861@glasgow.ac.uk> I think I answered a similar enquiry on this mailing list a few years back. PRRSV is not thought to be an icosahedral virus, so far as I know so it will not be possible to assemble a virion model from pdb files. Terje Dokland published a paper on this by tomography. Reviewed here http://www.ncbi.nlm.nih.gov/m/pubmed/20692304 Sent from my iPhone > On 25 Jan 2016, at 19:42, Elaine Meng wrote: > > Dear Yanli Li, > Chimera does not predict structures. If the solved parts already have symmetry matrix information in their files, Chimera can use these matrices to assemble their multimers (see Multiscale Models tool or ?sym? command). You could also interactively assemble parts in Chimera with the mouse based on your own knowledge such as information from the literature, known homologous structures and related viruses, or data such as an EM map into which you could semi-manually fit the crystal structures. > > As far as I understand it, ?nsp? means nonstructural protein, so you would mainly be interested in the nucleocapsid structure. I searched the RCSB PDB and found this structure 1p65 > > > ? but it is only a fragment, and it does not contain the symmetry information that would be needed to build up a whole particle. So you would probably need to try to figure out if there are other similar viruses or known homologous proteins with more complete structure information, and think about whether they are similar enough to help you model PRRSV. > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On Jan 25, 2016, at 9:07 AM, Yanli Li wrote: >> >> Dear sirs/madams, >> >> I am a PhD student in Universitat Aut?noma de Barcelona. I am working on the Porcine Reproductive and Respiratory Syndrome Virus (PRRSV). I have got differences of cytokine profiles and phenotype regulation of antigen presenting cells by different isolates through the lab work. Now I intend to predict the structure of the whole or some parts of the viral particle with UCSF CHIMERA. However, there are only three relevant structures(nucleocapsid, nsp1, nsp4) that have been published. Is it possible to realize it? If yes, can you tell me the method in brief? Thanks a lot! >> >> Waiting for your reply. >> >> Best wishes, >> >> Yanli LI > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From pett at cgl.ucsf.edu Mon Jan 25 15:48:08 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 25 Jan 2016 15:48:08 -0800 Subject: [Chimera-users] Add Charges failure (libquadmath) In-Reply-To: References: Message-ID: <599F2D18-8BAD-4510-AC52-7A9E8922EAB5@cgl.ucsf.edu> Hi Lluis, Thanks for reporting the problem. After some detective work, we?ve discovered that it is only a problem in the 32-bit version of the daily build. We will try to have a fix in for tomorrow?s daily build but in the meantime if you use the 64-bit version then things will work. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Jan 25, 2016, at 9:00 AM, Lluis Blancafort wrote: > > Hi, > > I?m running Chimera alpha version 1.11 on Mac OSX El Capitan 10.11.2 > > The Add Charges tool does not work for non-standard residues with AM1-BCC. The Reply Log reports a problem with libquadmath and later with sqm utility (see below). I don?t have libquadmath.0.dylib installed. > > Can anybody help? > > Thanks! > > Llu?s Blancafort > Institut de Qu?mica Computacional i Cat?lisi > Universitat de Girona > 17071 Girona > Spain > > (1) Charge model: AMBER ff14SB > Assigning partial charges to residue SGA (net charge -1) with am1-bcc method > Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/6j/nf071g8n2b5csd0rdcm8n5sc0000gn/T/tmpKi57P0/ante.in.mol2 -fi mol2 -o /var/folders/6j/nf071g8n2b5csd0rdcm8n5sc0000gn/T/tmpKi57P0/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 > (SGA) > > (SGA) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib > > (SGA) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib > > (SGA) Reason: image not found > > SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac > > (SGA) > > (SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff > > (SGA) Total number of electrons: 136; net charge: -1 > > (SGA) > > (SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out > > (SGA) 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 > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Jan 26 09:33:30 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 26 Jan 2016 09:33:30 -0800 Subject: [Chimera-users] rendering of custom annotation In-Reply-To: References: <56A2D4E7.10707@googlemail.com> Message-ID: A couple more notes: You can also draw a ?color key? to explain the coloring scheme, as shown in the B-factor coloring tutorial: There are more coloring examples in the attributes tutorial: Elaine > On Jan 25, 2016, at 11:17 AM, Elaine Meng wrote: > > Dear Helge, > Yes, you would only need to reformat your data slightly to make the ?attribute file? text format that can be read by Chimera. Reading that file will assign the values as a residue attribute, and then you can easily color the residues (ribbons and/or atoms and/or surfaces) to show the values with either the Render by Attribute graphical interface or the ?rangecolor? command. > > Attribute file format and example files: > > > There are a few information lines at the top to say it is a residue attribute and what you want to name it, and the rest is just two columns preceded by tabs. The first column will be residue identifiers just like you could use in the command line (for example :26 for residue 26, :26.a for residue 26 of chain A, etc. ) and the second column the value, in your case the number of hits. > > Render by Attribute: > > > You would start Define Attribute (in menu under Tools? Structure Analysis) or use command ?defattr? to read in your attribute file, and then the Render tool appears automatically, but you can also open it from the menu. > > ?rangecolor? command: > > > For example, if you?d named your attribute ?nhits?, you could use something like the following: > > rangecol nhits min purple mid orange max yellow > > (you can try this with ?bfactor? instead of ?nhits? if you haven?t made your attribute yet). You can also give specific values instead of min/mid/max and lots of color names are shown here: > > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Jan 22, 2016, at 5:18 PM, Helge wrote: >> >> Dear Chimera users, >> >> I have some data, which contains numbers of hits for each given residue of a chain (in my case the 25S rRNA). The data consists of a table with two columns: residues and corresponding hits. I would now like to color each residue in Chimera, relative to the amount of hits, with the highest number always getting a defined color. >> >> Is this possible? >> >> best regards, >> >> Helge From jingchuan at gmail.com Mon Jan 25 14:14:58 2016 From: jingchuan at gmail.com (Jingchuan Sun) Date: Mon, 25 Jan 2016 17:14:58 -0500 Subject: [Chimera-users] Tool:Structure Editing:Model:Refine loops Message-ID: Hello, When I tried MODEL plugin to model loop, the changes in result model is not just the selected loop to be modelled. It renumbered residues. There are several missing residues outside the selected loop in my old model. They become connected (in not accepting way) in returned models. Could I disable this "over-reach"? I only need to model the selected loop, no change to other places or renumbering. Best, Jingchuan -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Jan 26 10:49:04 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 26 Jan 2016 10:49:04 -0800 Subject: [Chimera-users] Tool:Structure Editing:Model:Refine loops In-Reply-To: References: Message-ID: <1112666E-F5C4-45B3-B4A8-2EE9C5A99032@cgl.ucsf.edu> Dear Jingchuan, The modeling that you can do with this interface is only single-chain. So, using the whole sequence, you can?t just ask to model part of the missing loop and get a free (disconnected) end. Instead it will always try to connect to the residues before and after the modeled segment even if there are really more residues missing. I assume you are using the ?active region? option and have drawn a box around the sequence of the residues you want to model. You CAN do it but only by editing the input sequence so that it ends right after the residues you want to model (if you want to model only the first part of a loop and leave its C-term free) or starts with the residues you want to model (if you want to model only the second part of a loop and leave its N-term free). You can show the original sequence (Favorites? Sequence) and save it to a fasta text file (from the sequence window menu), then use a text-editor outside of Chimera to delete part of the sequence, then main menu File? Open to open the edited sequence. If it is not automatically associated to your structure, tell it to associate (Structure? Associations in the menu of the edited sequence) and then draw a box around the residues in the sequence and model them (Structure? Modeller (loops/refinement) in the menu of the edited sequence). I just tried this whole procedure on a test structure to make sure it worked. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 25, 2016, at 2:14 PM, Jingchuan Sun wrote: > > Hello, > When I tried MODEL plugin to model loop, the changes in result model is not just the selected loop to be modelled. It renumbered residues. There are several missing residues outside the selected loop in my old model. They become connected (in not accepting way) in returned models. > > Could I disable this "over-reach"? I only need to model the selected loop, no change to other places or renumbering. > Best, > Jingchuan From ignatiou at gmail.com Thu Jan 28 10:09:54 2016 From: ignatiou at gmail.com (T-I) Date: Thu, 28 Jan 2016 18:09:54 +0000 Subject: [Chimera-users] Question from PhD student Message-ID: Dear Chimera, I would like to know exactly how to enclose my EM density map within a cube of specified size (where x, y and z have equal dimensions, i.e x,y,z = 150 pixels). It seems that when I place a marker (from volume tracer) on my map and then specify the padding number a rectangular cube is produced instead. I there a simple command to do this or can it be done from the GUI? Many thanks T.I PhD student, London -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Thu Jan 28 12:33:47 2016 From: goddard at sonic.net (Tom Goddard) Date: Thu, 28 Jan 2016 12:33:47 -0800 Subject: [Chimera-users] Question from PhD student In-Reply-To: References: Message-ID: Hi T.I, The ?vop boxes? command is intended to do this but ends of giving box dimensions that differ by 1 grid point (like 149 by 149 by 150). A few other people have asked about this recently. So I?ve fixed vop boxes in tonight?s Chimera daily build so you can say vop boxes #0 #1 isize 150 where #0 is the density map and #1 are the markers and ?isize 150? means extract a map for each marker that is 150 by 150 by 150 grid points. This ?isize? option is new. The previous option ?size? still exists but is specified in Angstroms. If you use that option it will also give cubes, but depending on where the marker is centered between grid points, the cube sizes could differ by 1 grid point for different markers. So I added the isize option so you could get exactly the same number of grid points for each marker. This isn?t exactly true ? you don?t always get cubes ? if the marker is too close to the edge of the density map so the box would go outside the map, then the extracted region is not a cube. Would be nice if it could fill it with zeros and make it a cube but it doesn?t do this now. Tom > On Jan 28, 2016, at 10:09 AM, T-I wrote: > > Dear Chimera, > > I would like to know exactly how to enclose my EM density map within a cube of specified size (where x, y and z have equal dimensions, i.e x,y,z = 150 pixels). > > It seems that when I place a marker (from volume tracer) on my map and then specify the padding number a rectangular cube is produced instead. > > I there a simple command to do this or can it be done from the GUI? > > > > Many thanks > T.I > > PhD student, London > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > 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: signature.asc Type: application/pgp-signature Size: 801 bytes Desc: Message signed with OpenPGP using GPGMail URL: From kyle.lauersen at uni-bielefeld.de Fri Jan 29 05:33:18 2016 From: kyle.lauersen at uni-bielefeld.de (Kyle J. Lauersen) Date: Fri, 29 Jan 2016 14:33:18 +0100 Subject: [Chimera-users] Joining models question Message-ID: <2DEB2776-F671-477F-87F2-76976EB8183B@uni-bielefeld.de> Hello, I am trying to join the two models attached to this sequence. I have used the sequence selection code in atom specifier: #1:559.a at C #0:2.a at N Where model #0 is YFP and #1 is PcPs. When I go to join models, the Apply button is not accessible. Can you indicate if I am doing something incorrect in the selection of the C and N atoms? Thank you for your time. Kyle Dr. Kyle J. Lauersen Algae Biotechnology & Bioenergy Center for Biotechnology Bielefeld University p: +49 (0) 521 106 12289 e: kyle.lauersen at uni-bielefeld.de -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: YFP.pdb Type: application/octet-stream Size: 157063 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PcPs.pdb Type: application/octet-stream Size: 362759 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Jan 29 11:43:02 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 29 Jan 2016 11:43:02 -0800 Subject: [Chimera-users] Joining models question In-Reply-To: <2DEB2776-F671-477F-87F2-76976EB8183B@uni-bielefeld.de> References: <2DEB2776-F671-477F-87F2-76976EB8183B@uni-bielefeld.de> Message-ID: Hi Kyle, The following works for me: I opened YFP and PcPs in that order, then: commands: ~ribbon disp @n,ca,c sel #1:559.a at C #0:2.a at N menu: Tools?.Structure Editing? Build Structure, change to Join Models section of the resulting dialog. Then I chose the ?C-N peptide bond? option and clicked Apply, and the join appears to take place successfully. However, I see your point that something weird is going on: I repeated the process several times, and sometimes (but not always!!) if I didn?t change from ribbon to atom display, the Apply button was grayed out. We should look into why that is happening. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 29, 2016, at 5:33 AM, Kyle J. Lauersen wrote: > Hello, > > I am trying to join the two models attached to this sequence. > > I have used the sequence selection code in atom specifier: #1:559.a at C #0:2.a at N > > Where model #0 is YFP and #1 is PcPs. > > When I go to join models, the Apply button is not accessible. > > Can you indicate if I am doing something incorrect in the selection of the C and N atoms? > > Thank you for your time. > > Kyle > > > > > Dr. Kyle J. Lauersen > Algae Biotechnology & Bioenergy > Center for Biotechnology > Bielefeld University > p: +49 (0) 521 106 12289 > e: kyle.lauersen at uni-bielefeld.de > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From kyle.lauersen at uni-bielefeld.de Fri Jan 29 11:56:21 2016 From: kyle.lauersen at uni-bielefeld.de (Kyle J. Lauersen) Date: Fri, 29 Jan 2016 20:56:21 +0100 Subject: [Chimera-users] Joining models question In-Reply-To: References: <2DEB2776-F671-477F-87F2-76976EB8183B@uni-bielefeld.de> Message-ID: <7938EA6F-F3B0-458D-B11A-A855AD9ED3DF@uni-bielefeld.de> Thanks Elaine. I was omitting the .A. Since they only had one chain I didn't think it was required. But it's working now. Best, Kyle Dr. Kyle J. Lauersen Algae Biotechnology & Bioenergy Center for Biotechnology Bielefeld University p: +49 (0) 521 106 12261 e: kyle.lauersen at uni-bielefeld.de > On 29.01.2016, at 20:43, Elaine Meng wrote: > > Hi Kyle, > The following works for me: > > I opened YFP and PcPs in that order, then: > > commands: > ~ribbon > disp @n,ca,c > sel #1:559.a at C #0:2.a at N > > menu: Tools?.Structure Editing? Build Structure, change to Join Models section of the resulting dialog. > > Then I chose the ?C-N peptide bond? option and clicked Apply, and the join appears to take place successfully. > > However, I see your point that something weird is going on: I repeated the process several times, and sometimes (but not always!!) if I didn?t change from ribbon to atom display, the Apply button was grayed out. We should look into why that is happening. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > >> On Jan 29, 2016, at 5:33 AM, Kyle J. Lauersen wrote: >> >> Hello, >> >> I am trying to join the two models attached to this sequence. >> >> I have used the sequence selection code in atom specifier: #1:559.a at C #0:2.a at N >> >> Where model #0 is YFP and #1 is PcPs. >> >> When I go to join models, the Apply button is not accessible. >> >> Can you indicate if I am doing something incorrect in the selection of the C and N atoms? >> >> Thank you for your time. >> >> Kyle >> >> >> >> >> Dr. Kyle J. Lauersen >> Algae Biotechnology & Bioenergy >> Center for Biotechnology >> Bielefeld University >> p: +49 (0) 521 106 12289 >> e: kyle.lauersen at uni-bielefeld.de >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Jan 29 12:31:52 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 29 Jan 2016 12:31:52 -0800 Subject: [Chimera-users] Joining models question In-Reply-To: <7938EA6F-F3B0-458D-B11A-A855AD9ED3DF@uni-bielefeld.de> References: <2DEB2776-F671-477F-87F2-76976EB8183B@uni-bielefeld.de> <7938EA6F-F3B0-458D-B11A-A855AD9ED3DF@uni-bielefeld.de> Message-ID: <7B7C57FE-2473-4E78-82F7-6F916EF4EA87@cgl.ucsf.edu> Hi Kyle, I don?t think that was the problem, since I could repeat the same except omitting the ?.a? from both places in the select command. It still selected just 2 atoms. If there is only one residue with that number in that structure, it should not matter. Elaine On Jan 29, 2016, at 11:56 AM, Kyle J. Lauersen wrote: > Thanks Elaine. > > I was omitting the .A. Since they only had one chain I didn't think it was required. But it's working now. > > Best, > > Kyle > > Dr. Kyle J. Lauersen > Algae Biotechnology & Bioenergy > Center for Biotechnology > Bielefeld University > p: +49 (0) 521 106 12261 > e: kyle.lauersen at uni-bielefeld.de > > > > > On 29.01.2016, at 20:43, Elaine Meng wrote: > >> Hi Kyle, >> The following works for me: >> >> I opened YFP and PcPs in that order, then: >> >> commands: >> ~ribbon >> disp @n,ca,c >> sel #1:559.a at C #0:2.a at N >> >> menu: Tools?.Structure Editing? Build Structure, change to Join Models section of the resulting dialog. >> >> Then I chose the ?C-N peptide bond? option and clicked Apply, and the join appears to take place successfully. >> >> However, I see your point that something weird is going on: I repeated the process several times, and sometimes (but not always!!) if I didn?t change from ribbon to atom display, the Apply button was grayed out. We should look into why that is happening. >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >> >> On Jan 29, 2016, at 5:33 AM, Kyle J. Lauersen wrote: >> >>> Hello, >>> >>> I am trying to join the two models attached to this sequence. >>> >>> I have used the sequence selection code in atom specifier: #1:559.a at C #0:2.a at N >>> >>> Where model #0 is YFP and #1 is PcPs. >>> >>> When I go to join models, the Apply button is not accessible. >>> >>> Can you indicate if I am doing something incorrect in the selection of the C and N atoms? >>> >>> Thank you for your time. >>> >>> Kyle >>> >>> >>> >>> >>> Dr. Kyle J. Lauersen >>> Algae Biotechnology & Bioenergy >>> Center for Biotechnology >>> Bielefeld University >>> p: +49 (0) 521 106 12289 >>> e: kyle.lauersen at uni-bielefeld.de >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From olibclarke at gmail.com Sat Jan 30 03:44:01 2016 From: olibclarke at gmail.com (Oliver Clarke) Date: Sat, 30 Jan 2016 12:44:01 +0100 Subject: [Chimera-users] Running out of memory when recording movies Message-ID: Hello, I am consistently running out of memory when recording long-ish movies (using the Animation tool) on a Macbook pro with 16GB RAM. Admittedly there are a lot of atoms in the model I am using (~120,000), but most are not displayed (only ribbons). Chimera is consistently crashing at about the 300 frame mark and looking at the activity monitor during the recording I can see memory pressure gradually increasing until Chimera freezes (which is generally not recoverable). Is there any way to reduce the amount of memory required for movie recording? Will deleting all undisplayed atoms help? Is there some way to perform these operations on disk rather than in memory (most likely a silly question)? Cheers, Oli. -------------- next part -------------- An HTML attachment was scrubbed... URL: From olibclarke at gmail.com Sat Jan 30 10:16:31 2016 From: olibclarke at gmail.com (Oliver Clarke) Date: Sat, 30 Jan 2016 19:16:31 +0100 Subject: [Chimera-users] Morph groups of maps? Message-ID: Hello, In a situation where I have maps for two conformations, and I've extracted out domain specific maps in both cases, is it possible to run morph maps on both groups of maps simultaneously? Or is there any way to apply color zone to the trajectory generated by morph maps? I would like to generate a morph map movie where the map is colored by domain throughout the morph, and can't figure out how to do so. Cheers, Oli -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sat Jan 30 12:23:17 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 30 Jan 2016 12:23:17 -0800 Subject: [Chimera-users] Morph groups of maps? In-Reply-To: References: Message-ID: Hi Oliver, I haven?t tried these things in a situation similar to yours, but some initial ideas are: (1) use two ?vop morph? commands separated by only a semicolon so that (if it is possible to run two map-morphs concurrently), they will start at the same frame (2) use ?perframe? (possibly with ?alias?) to specify running ?scolor" zone command(s) at each frame I would try those things one at a time, for example, perframe scolor with a single vop morph. Even in that case, I?m not sure it will work. We may be able to come up with better answer or at least a more definite answer of whether it is possible next week. In the meanwhile, these are just some things to look into. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 30, 2016, at 10:16 AM, Oliver Clarke wrote: > Hello, > > In a situation where I have maps for two conformations, and I've extracted out domain specific maps in both cases, is it possible to run morph maps on both groups of maps simultaneously? Or is there any way to apply color zone to the trajectory generated by morph maps? I would like to generate a morph map movie where the map is colored by domain throughout the morph, and can't figure out how to do so. > > Cheers, > Oli From olibclarke at gmail.com Sat Jan 30 13:44:08 2016 From: olibclarke at gmail.com (Oliver Clarke) Date: Sat, 30 Jan 2016 22:44:08 +0100 Subject: [Chimera-users] Morph groups of maps? In-Reply-To: References: Message-ID: Thanks for the helpful suggestions Elaine! I will look into them and see where it gets me - I have a feeling I have tried the perframe/scolor idea in the past without success but I may be misremembering. One other thing - I'd like a one command way to convert a full atom model to a Calpha model, keeping the helix/sheet records at the start intact. This would be very helpful when running morphs of a large protein (where often I do not need to display sidechains, just ribbon), because it makes the calculations much faster (e.g. rather than 120,000 atoms I have ~17000 using CAs only). Currently what I do is I delete all the non-CA atoms in chimera, save the pdb, remove all the TER flags chimera has added between each CA atom using grep, and then replace the HELIX/SHEET records with those from the original file (because they get corrupted for some reason in the process. This works fine but it would be nice to have a one liner in chimera to handle the same at some point (although I realize it is a pretty niche functionality and maybe not worth it). (alternatively a "coarse grained" morph where parameters for each residue only take into account the CA would accomplish the same thing I guess.) Cheers, Oli On Sat, Jan 30, 2016 at 9:23 PM, Elaine Meng wrote: > Hi Oliver, > I haven?t tried these things in a situation similar to yours, but some > initial ideas are: > > (1) use two ?vop morph? commands separated by only a semicolon so that (if > it is possible to run two map-morphs concurrently), they will start at the > same frame > > (2) use ?perframe? (possibly with ?alias?) to specify running ?scolor" > zone command(s) at each frame > > I would try those things one at a time, for example, perframe scolor with > a single vop morph. Even in that case, I?m not sure it will work. We may > be able to come up with better answer or at least a more definite answer of > whether it is possible next week. In the meanwhile, these are just some > things to look into. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jan 30, 2016, at 10:16 AM, Oliver Clarke wrote: > > > Hello, > > > > In a situation where I have maps for two conformations, and I've > extracted out domain specific maps in both cases, is it possible to run > morph maps on both groups of maps simultaneously? Or is there any way to > apply color zone to the trajectory generated by morph maps? I would like > to generate a morph map movie where the map is colored by domain throughout > the morph, and can't figure out how to do so. > > > > Cheers, > > Oli > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From olibclarke at gmail.com Sat Jan 30 14:04:50 2016 From: olibclarke at gmail.com (Oliver Clarke) Date: Sat, 30 Jan 2016 23:04:50 +0100 Subject: [Chimera-users] Running out of memory when recording movies In-Reply-To: References: Message-ID: Also, I've noticed that if I try to record another movie in the same session of chimera after having recorded one already, I run out of memory very fast, whereas if I restart chimera and immediately reload the same session, I am able to record the same movie without a problem - I wonder if maybe there is a memory leak of some sort? Cheers, Oli On Sat, Jan 30, 2016 at 12:44 PM, Oliver Clarke wrote: > Hello, > > I am consistently running out of memory when recording long-ish movies > (using the Animation tool) on a Macbook pro with 16GB RAM. Admittedly there > are a lot of atoms in the model I am using (~120,000), but most are not > displayed (only ribbons). > > Chimera is consistently crashing at about the 300 frame mark and looking > at the activity monitor during the recording I can see memory pressure > gradually increasing until Chimera freezes (which is generally not > recoverable). > > Is there any way to reduce the amount of memory required for movie > recording? Will deleting all undisplayed atoms help? Is there some way to > perform these operations on disk rather than in memory (most likely a silly > question)? > > Cheers, > Oli. > -------------- next part -------------- An HTML attachment was scrubbed... URL: