From hatuey.hack at gmail.com Mon Dec 2 02:02:14 2013 From: hatuey.hack at gmail.com (Hatuey Hack) Date: Mon, 2 Dec 2013 08:02:14 -0200 Subject: [Chimera-users] << measuring areas >> Message-ID: Hellos ChimeraUsers, It could be possible to measure different parts of a surface according to a given parameter? For example, from the electrostatic potential surface, I would like to know the respective area surface with positive and/or negative values. Best regards, Hatuey -------------- next part -------------- An HTML attachment was scrubbed... URL: From antonvila.s at gmail.com Mon Dec 2 07:37:52 2013 From: antonvila.s at gmail.com (=?ISO-8859-1?Q?Ant=F3n_Vila_Sanjurjo?=) Date: Mon, 2 Dec 2013 16:37:52 +0100 Subject: [Chimera-users] translation matrix Message-ID: Hi, I'm trying to get a translation matrix for two different crystal structures of ribisomal subunits. I've been trying to use the "measure rotation" command but I can only get it to display the following message "rotation angle is near zero (0 degrees)". I was wondering whether the command might be failing due to the fact that the ribosome contains numerous chains, or perhaps because the command does not deal with RNA. At any rate, how would one go about obtaining a translation matrix that can be applied to any model? best, Ant?n -- Ant?n Vila-Sanjurjo, PhD Marie Curie fellow Grupo QOSBIOS, Dept. Qu?mica Fundamental Facultade de Ciencias Universidade de A Coru?a (UDC) Campus Zapateira, s/n 15.071 - A Coru?a - Espa?a (Spain). tlf: (34) 981-167000 ext:2659 e-mail: antonvila.s at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Dec 2 08:29:52 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 2 Dec 2013 08:29:52 -0800 Subject: [Chimera-users] translation matrix In-Reply-To: References: Message-ID: <01ACA02E-0592-42EF-BB20-CC6B0B6E9863@cgl.ucsf.edu> Hi Ant?n, You would first need to superimpose the two structures yourself. I.e. "measure rotation" simply measures the transformation of one structure relative to another, after you have done something that moves it. That command does not figure out how they should be moved. Maybe superimposing the structures was your goal in the first place. Ways to superimpose structures in Chimera are listed here: Of the methods mentioned in the above, you might want to use Matchmaker but instead of defaults (trying all chains against all chains, which would take a REALLY long time for ribosomal subunits), choosing the option to specify exactly which chain(s) to use. 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 Dec 2, 2013, at 7:37 AM, Ant?n Vila Sanjurjo wrote: > Hi, > I'm trying to get a translation matrix for two different crystal structures of ribisomal subunits. I've been trying to use the "measure rotation" command but I can only get it to display the following message "rotation angle is near zero (0 degrees)". I was wondering whether the command might be failing due to the fact that the ribosome contains numerous chains, or perhaps because the command does not deal with RNA. At any rate, how would one go about obtaining a translation matrix that can be applied to any model? > best, > Ant?n > From antonvila.s at gmail.com Mon Dec 2 08:45:13 2013 From: antonvila.s at gmail.com (=?ISO-8859-1?Q?Ant=F3n_Vila_Sanjurjo?=) Date: Mon, 2 Dec 2013 17:45:13 +0100 Subject: [Chimera-users] translation matrix In-Reply-To: <01ACA02E-0592-42EF-BB20-CC6B0B6E9863@cgl.ucsf.edu> References: <01ACA02E-0592-42EF-BB20-CC6B0B6E9863@cgl.ucsf.edu> Message-ID: Hi Elaine, thanks for your reply. I'm not interested in of superimposing structures per se, Matchmaker does this beautifully, however it does not provide me with the translation matrix used for the superposition. Since ribosome pdb files are split in subunits, due to their large size, after I superpose one of the subunits, I would like to have the translation matrix to superpose the other. Does this make sense? I could get this information from other pieces of software, of course, but I was wondering whether chimera could do it as well. best, Anton On Mon, Dec 2, 2013 at 5:29 PM, Elaine Meng wrote: > Hi Ant?n, > You would first need to superimpose the two structures yourself. I.e. > "measure rotation" simply measures the transformation of one structure > relative to another, after you have done something that moves it. That > command does not figure out how they should be moved. > < > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation > > > > Maybe superimposing the structures was your goal in the first place. Ways > to superimpose structures in Chimera are listed here: > > > Of the methods mentioned in the above, you might want to use Matchmaker > but instead of defaults (trying all chains against all chains, which would > take a REALLY long time for ribosomal subunits), choosing the option to > specify exactly which chain(s) to use. > > 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 Dec 2, 2013, at 7:37 AM, Ant?n Vila Sanjurjo > wrote: > > > Hi, > > I'm trying to get a translation matrix for two different crystal > structures of ribisomal subunits. I've been trying to use the "measure > rotation" command but I can only get it to display the following message > "rotation angle is near zero (0 degrees)". I was wondering whether the > command might be failing due to the fact that the ribosome contains > numerous chains, or perhaps because the command does not deal with RNA. At > any rate, how would one go about obtaining a translation matrix that can be > applied to any model? > > best, > > Ant?n > > > > -- Ant?n Vila-Sanjurjo, PhD Marie Curie fellow Grupo QOSBIOS, Dept. Qu?mica Fundamental Facultade de Ciencias Universidade de A Coru?a (UDC) Campus Zapateira, s/n 15.071 - A Coru?a - Espa?a (Spain). tlf: (34) 981-167000 ext:2659 e-mail: antonvila.s at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Dec 2 08:54:46 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 2 Dec 2013 08:54:46 -0800 Subject: [Chimera-users] << measuring areas >> In-Reply-To: References: Message-ID: Hi Hatuey, Well?. yes and no. If you can select the desired set of atoms, you can then sum their surface areas. However, you cannot select surface triangles directly. Further complications are (A) values are associated with surface points, not triangles, but points don't have areas (B) electrostatic potential (ESP) coloring by default shows the potential not exactly at the surface but 1.4 angstroms farther out. In other words, the solvent-excluded surface (SES) is displayed, but colored by the potential at the larger solvent-accessible surface (SAS). So, you could select the *atoms* at which ESP is positive (or negative) and then get the total SAS and/or SES area for those atoms, but it would *not* be the same as the area of the surface with positive potential. I don't know of any way to get the latter. To do the former, after opening the structure and the ESP map and showing the surface, you would: (1) use Values at Atom Positions (under Tools? Volume Data) to map ESP values onto atoms; this automatically opens Render/Select by Attribute (2) in Render/Select by Attribute, use the Select tab and select the desired set of atoms based on their potential values. It will be difficult, however, to decide what set of values to choose. This will select both buried and surface atoms, but buried atoms will not contribute to the total surface area calculated in the next step. (3) use Attribute Calculator (under Tools? Structure Analysis) to sum areaSAS or areaSES for atoms over the whole model. For example, calculate attribute "totalSESpositive" for "molecules" (which really means models) with formula: sum(atom.areaSES) and making sure to "restrict formula domain to current selection, if any" so that the sum will only include the selected atoms. Sorry it isn't exactly what you wanted to do. It's the closest thing I could come up with, however. 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 Dec 2, 2013, at 2:02 AM, Hatuey Hack wrote: > Hellos ChimeraUsers, > It could be possible to measure different parts of a surface according to a given parameter? > For example, from the electrostatic potential surface, I would like to know the respective area surface with positive and/or negative values. > Best regards, > Hatuey From meng at cgl.ucsf.edu Mon Dec 2 09:05:29 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 2 Dec 2013 09:05:29 -0800 Subject: [Chimera-users] translation matrix In-Reply-To: References: <01ACA02E-0592-42EF-BB20-CC6B0B6E9863@cgl.ucsf.edu> Message-ID: Sorry, I was only guessing that you hadn't superimposed the structures. Now that you said more about what you were doing, I have a much easier solution: just use the "matrixcopy" command to apply the transformation of one model to another! Best, Elaine On Dec 2, 2013, at 8:45 AM, Ant?n Vila Sanjurjo wrote: > Hi Elaine, > > thanks for your reply. I'm not interested in of superimposing structures per se, Matchmaker does this beautifully, however it does not provide me with the translation matrix used for the superposition. Since ribosome pdb files are split in subunits, due to their large size, after I superpose one of the subunits, I would like to have the translation matrix to superpose the other. Does this make sense? I could get this information from other pieces of software, of course, but I was wondering whether chimera could do it as well. > > best, > > Anton > > > On Mon, Dec 2, 2013 at 5:29 PM, Elaine Meng wrote: > Hi Ant?n, > You would first need to superimpose the two structures yourself. I.e. "measure rotation" simply measures the transformation of one structure relative to another, after you have done something that moves it. That command does not figure out how they should be moved. > > > Maybe superimposing the structures was your goal in the first place. Ways to superimpose structures in Chimera are listed here: > > > Of the methods mentioned in the above, you might want to use Matchmaker but instead of defaults (trying all chains against all chains, which would take a REALLY long time for ribosomal subunits), choosing the option to specify exactly which chain(s) to use. > > 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 Dec 2, 2013, at 7:37 AM, Ant?n Vila Sanjurjo wrote: > > > Hi, > > I'm trying to get a translation matrix for two different crystal structures of ribisomal subunits. I've been trying to use the "measure rotation" command but I can only get it to display the following message "rotation angle is near zero (0 degrees)". I was wondering whether the command might be failing due to the fact that the ribosome contains numerous chains, or perhaps because the command does not deal with RNA. At any rate, how would one go about obtaining a translation matrix that can be applied to any model? > > best, > > Ant?n > > > > > > > -- > Ant?n Vila-Sanjurjo, PhD > Marie Curie fellow > Grupo QOSBIOS, Dept. Qu?mica Fundamental > Facultade de Ciencias > Universidade de A Coru?a (UDC) > Campus Zapateira, s/n > 15.071 - A Coru?a - Espa?a (Spain). > > tlf: (34) 981-167000 ext:2659 > e-mail: antonvila.s at gmail.com > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at sonic.net Mon Dec 2 10:17:28 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 2 Dec 2013 10:17:28 -0800 Subject: [Chimera-users] << measuring areas >> In-Reply-To: References: Message-ID: Hi Hatuey, Some Python code could calculate this -- Chimera has the underlying funtions to find the electrostatic potential at surface points and give an area for each surface point (1/3 of the areas of all the surface triangles that have a corner at that point). But the details are important - what surface? and how do you want ESP calculated? I think the most sensible surface to use would be the solvent accessible surface, but Chimera does not calculate that type of surface. ESP could be computed by Coulombic approximation or APBS or other external programs that use Poisson-Boltzman to handle solvent dielectric better. Tom On Dec 2, 2013, at 2:02 AM, Hatuey Hack wrote: > Hellos ChimeraUsers, > > It could be possible to measure different parts of a surface according to a given parameter? > > For example, from the electrostatic potential surface, I would like to know the respective area surface with positive and/or negative values. > > Best regards, > > > Hatuey > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at sonic.net Mon Dec 2 10:05:41 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 2 Dec 2013 10:05:41 -0800 Subject: [Chimera-users] translation matrix In-Reply-To: References: Message-ID: <9165429C-5646-4982-BB87-F72554EA0C70@sonic.net> Hi Ant?n, The "measure rotation" command gives the rotation and translation in the Reply Log dialog (menu Favorites / Reply Log). It only reports the rotation angle in the status line at the bottom of the main window. Keep in mind that "measure rotation #0 #1" measures the difference between the coordinate systems for the two models. If you simply open any two PDB models and use measure rotation it will give zero rotation and translation because they start out with the same coordinate systems. If you use Match Maker or the match command it will move the coordinate system of one model relative to the other to achieve the alignment and then measure rotation will give a non-zero rotation and translation. Tom On Dec 2, 2013, at 7:37 AM, Ant?n Vila Sanjurjo wrote: > Hi, > > I'm trying to get a translation matrix for two different crystal structures of ribisomal subunits. I've been trying to use the "measure rotation" command but I can only get it to display the following message "rotation angle is near zero (0 degrees)". I was wondering whether the command might be failing due to the fact that the ribosome contains numerous chains, or perhaps because the command does not deal with RNA. At any rate, how would one go about obtaining a translation matrix that can be applied to any model? > > best, > > Ant?n > > -- > Ant?n Vila-Sanjurjo, PhD > Marie Curie fellow > Grupo QOSBIOS, Dept. Qu?mica Fundamental > Facultade de Ciencias > Universidade de A Coru?a (UDC) > Campus Zapateira, s/n > 15.071 - A Coru?a - Espa?a (Spain). > > tlf: (34) 981-167000 ext:2659 > e-mail: antonvila.s at gmail.com > _______________________________________________ > 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 goddard at sonic.net Mon Dec 2 10:46:53 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 2 Dec 2013 10:46:53 -0800 Subject: [Chimera-users] Query about increasing resolution for vrml export In-Reply-To: References: Message-ID: <593BC2F0-51A7-42BE-B2D6-C04DAE0BE873@sonic.net> Hi Darren, There are two options in the Chimera Volume Viewer dialog in the Surface and Mesh Options panel (menu Features / Surface and Mesh Options), one called "Subdivide surface N times" and the other "Surface smoothing iterations 2, factor 0.3". Turning the first one on will divide every surface triangle into 4 triangles. And turning the second one on will move the surface vertices a little bit to give a smoother appearance. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#surf-options The finer surface will be export to VRML. Also, be sure to make sure the "Step" size is set to 1 above the histogram in the volume viewer dialog since step > 1 subsamples the data and shows fewer triangles. A nicer smoother appearance would be achieved by interpolating the density map on a finer grid but Chimera does not have an easy way to do that. Tom On Nov 29, 2013, at 5:52 AM, Darren Gowers wrote: > Dear Chimera community, > > Sorry to bother. I'm very interested in trying to increase the vrml export resolution (of any pdb model) so that more polygons are used to describe the curvature of the electron density more smoothly. There is a command in PyMol that does the equivalent (I think it is 'surface_quality'), but I'd rather use Chimera to generate vrml files! > > Does anyone have any suggestions how to make molecular surfaces much smoother please? > > Many thanks, > > Darren > -- > Dr Darren Gowers > Senior Lecturer in Biochemistry > School of Biological Sciences > University of Portsmouth > PO1 2DY > +44(0)2392 842057 > _______________________________________________ > 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 Mon Dec 2 12:14:41 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 2 Dec 2013 12:14:41 -0800 Subject: [Chimera-users] solvent-accessible surface area In-Reply-To: <000001ceec9d$581058d0$08310a70$@gmail.com> References: <000001ceec9d$581058d0$08310a70$@gmail.com> Message-ID: <3DDD7761-D354-475C-A82B-DD3EA14795DA@cgl.ucsf.edu> Hi Amit, Your message did go to the list (you just emailed the address chimera-users at cgl.ucsf.edu)!! I don't know of any standard, commonly used surface area value to use as the cutoff between buried and exposed. Often people will use a percentage normalized by the area of that same amino acid type in some model of the completely exposed state. For example, they might decide that an amino acid is buried if its surface area in the protein is less than 10% of the surface area of that same type of amino acid in a Gly-X-Gly tripeptide. However, Chimera does not do such a normalization, nor provide surface areas of completely exposed states. You either have to use your own judgement as to what surface area cutoff you want to use, or use some other program such as getArea that does provide normalization: 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 Nov 28, 2013, at 4:52 PM, "Amit Goyal" wrote: > Hi Elaine, > Today I subscribe to Chimera mailing list, but unable to get the proper way to post a query on it. So I am sending the query this way. > > I have been reading this post about how to get the areaSAS and areaSES values for any residues. > http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002617.html > > Still, I think, is there any specific values/range for the areas AS to decide whether a particular amino acid residues is buried or exposed to the solvent. > Hoping for > Thanks for your help. > Sincerely, > AMIT From meng at cgl.ucsf.edu Mon Dec 2 12:30:00 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 2 Dec 2013 12:30:00 -0800 Subject: [Chimera-users] Chimera- Imod file size problems In-Reply-To: <4FE1F428-8867-4B65-A0C3-7B769A72184C@caltech.edu> References: <4FE1F428-8867-4B65-A0C3-7B769A72184C@caltech.edu> Message-ID: <36A79A4A-B6A7-415B-871E-A2A8DFCBE5DD@cgl.ucsf.edu> Hi Ariane, I only know how to do it for "volume data" like MRC files and other density maps, but not for IMOD segmentation mesh (You said "imod mrc" but then it sounded like you meant a segmentation file instead.) If it's a density map, you can adjust voxel size in the Volume Viewer (choose Features? Coordinates to show those settings) The same thing can also be done with the volume command, see "dimension and scale options": Unless data are private, please send Chimera questions to chimera-users at cgl.ucsf.edu instead of only to me. Then If I don't know the answer or am away from work, others can respond. Thanks, 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 Dec 2, 2013, at 10:45 AM, Ariane Briegel wrote: > Dear Elaine, > I have a question you might have a quick answer to. I am trying to open a model file I generated with the IMOD program. > Generally, when I open Imod mrc files in chimera the pixel size is correct in both programs. With this model the size is way off in chimera (I have never used an imod model in chimera before, just mrc files so far). > See screenshots below- the first one shows that the model has the correct pixel size when opened in IMOD, the second shows the wrong size in chimera (the blue and green layers should have the same height as the crystal structures below), and the last screenshot shows how the data opened in chimera (as a mesh). Is there a way for me to manually adjust the pixel size of a mesh? > If you have any idea how I can fix this issue I would be very grateful! > Thank you! > Ariane > > ???????????????????????????? > Ariane Briegel, Ph.D. > California Institute of Technology > Broad Center, MC 114-96 > 1200 E. California Blvd. > Pasadena, CA 91125 > > Tel: 626-395-8848 > Fax: 626-395-5730 > ???????????????????????????? > > > From meng at cgl.ucsf.edu Mon Dec 2 13:48:11 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 2 Dec 2013 13:48:11 -0800 Subject: [Chimera-users] Query about increasing resolution for vrml export In-Reply-To: <593BC2F0-51A7-42BE-B2D6-C04DAE0BE873@sonic.net> References: <593BC2F0-51A7-42BE-B2D6-C04DAE0BE873@sonic.net> Message-ID: <0B56FAA7-D8CE-434D-827C-BB8103AABE16@cgl.ucsf.edu> Hi Darren, Tom described what to do for density map isosurfaces. However, if you are instead talking about molecular surfaces, it is a separate parameter, "vertex density" ? this can be changed in the Selection Inspector or with command "setattr," for example: setattr s density 8 The default vertex density is 2. This setattr command will only affect the molecular surfaces that already exist. If you want to change the setting for subsequently calculated molecular surfaces, it can be done in the Preferences, category: New Surfaces; remember to click Save if you want your change to apply to future uses of Chimera. 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 Dec 2, 2013, at 10:46 AM, Tom Goddard wrote: > Hi Darren, > > There are two options in the Chimera Volume Viewer dialog in the Surface and Mesh Options panel (menu Features / Surface and Mesh Options), one called "Subdivide surface N times" and the other "Surface smoothing iterations 2, factor 0.3". Turning the first one on will divide every surface triangle into 4 triangles. And turning the second one on will move the surface vertices a little bit to give a smoother appearance. > > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#surf-options > > The finer surface will be export to VRML. Also, be sure to make sure the "Step" size is set to 1 above the histogram in the volume viewer dialog since step > 1 subsamples the data and shows fewer triangles. > > A nicer smoother appearance would be achieved by interpolating the density map on a finer grid but Chimera does not have an easy way to do that. > > Tom > > On Nov 29, 2013, at 5:52 AM, Darren Gowers wrote: > >> Dear Chimera community, >> >> Sorry to bother. I'm very interested in trying to increase the vrml export resolution (of any pdb model) so that more polygons are used to describe the curvature of the electron density more smoothly. There is a command in PyMol that does the equivalent (I think it is 'surface_quality'), but I'd rather use Chimera to generate vrml files! >> >> Does anyone have any suggestions how to make molecular surfaces much smoother please? >> >> Many thanks, >> >> Darren >> -- >> Dr Darren Gowers >> Senior Lecturer in Biochemistry >> School of Biological Sciences >> University of Portsmouth >> PO1 2DY >> +44(0)2392 842057 >> _______________________________________________ >> 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 goddard at sonic.net Mon Dec 2 14:12:29 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 2 Dec 2013 14:12:29 -0800 Subject: [Chimera-users] Chimera- Imod file size problems In-Reply-To: <36A79A4A-B6A7-415B-871E-A2A8DFCBE5DD@cgl.ucsf.edu> References: <4FE1F428-8867-4B65-A0C3-7B769A72184C@caltech.edu> <36A79A4A-B6A7-415B-871E-A2A8DFCBE5DD@cgl.ucsf.edu> Message-ID: Hi Ariane, Might be a bug in the Chimera IMOD mesh file reader. When Chimera reads an IMOD mesh file it prints to the Chimera Reply Log (menu Favorites) the "pixel size" and x,y,z scale factors it found in the IMOD file. What does it say for your file? Can you check these parameters in IMOD? (I don't know how to do that in IMOD.) Seems like the problem is that z-scale is probably one, but to match your molecule it needs to be much larger. Your images show the x and y sizes of the mesh match the molecule, but not the z size. You could submit a Chimera bug report (menu Help / Report a Bug?). I would need the IMOD mesh file in order to understand what went wrong. Tom On Dec 2, 2013, at 12:30 PM, Elaine Meng wrote: > Hi Ariane, > I only know how to do it for "volume data" like MRC files and other density maps, but not for IMOD segmentation mesh (You said "imod mrc" but then it sounded like you meant a segmentation file instead.) > > > > If it's a density map, you can adjust voxel size in the Volume Viewer (choose Features? Coordinates to show those settings) > > > The same thing can also be done with the volume command, see "dimension and scale options": > > > Unless data are private, please send Chimera questions to chimera-users at cgl.ucsf.edu instead of only to me. Then If I don't know the answer or am away from work, others can respond. > Thanks, > 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 Dec 2, 2013, at 10:45 AM, Ariane Briegel < wrote: > >> Dear Elaine, >> I have a question you might have a quick answer to. I am trying to open a model file I generated with the IMOD program. >> Generally, when I open Imod mrc files in chimera the pixel size is correct in both programs. With this model the size is way off in chimera (I have never used an imod model in chimera before, just mrc files so far). >> See screenshots below- the first one shows that the model has the correct pixel size when opened in IMOD, the second shows the wrong size in chimera (the blue and green layers should have the same height as the crystal structures below), and the last screenshot shows how the data opened in chimera (as a mesh). Is there a way for me to manually adjust the pixel size of a mesh? >> If you have any idea how I can fix this issue I would be very grateful! >> Thank you! >> Ariane >> >> ???????????????????????????? >> Ariane Briegel, Ph.D. >> California Institute of Technology >> Broad Center, MC 114-96 >> 1200 E. California Blvd. >> Pasadena, CA 91125 >> >> Tel: 626-395-8848 >> Fax: 626-395-5730 >> ???????????????????????????? >> >> >> > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From meng at cgl.ucsf.edu Mon Dec 2 14:33:59 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 2 Dec 2013 14:33:59 -0800 Subject: [Chimera-users] Information In-Reply-To: References: Message-ID: Hello Mabel, Generally "multimer" refers to multiple copies of a monomer that are not bonded to each other. If you have a monomer and you want to make the multimer, it depends on whether there is symmetry information in the original PDB file, and what kind of information. In Chimera you could try: (A) Model Panel (in menu under Favorites) - choose your model on the left, then click "biological unit" on the right. That requires BIOMT information in the PDB file. If the PDB file doesn't have that kind of information nothing will happen. (B) Next, you could try using other types of information with Unit Cell (in menu under Tools? Higher-Order Structure) If neither of those make the hexamer, your PDB file lacks the needed information. In that case, it will be more difficult. If there is a similar protein that you already have in hexamer form, you could open that structure and then 6 copies of your protein and match each copy of your protein to one of the chains in the other structure. If your PDB file is depositied in the Protein Data Bank, another possibility is to see if other databases such as PISA have predicted the hexamer. You may be able to download the hexamer from one of those other databases. 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 Nov 29, 2013, at 12:38 PM, Mabel Guzman Rodriguez wrote: > Hello! > I few days ago I tried to use your program Chimera, the reason is because I try to make a structure of a multimer protein but I need to know how can I bond the single subunits of the protein to make an hexamer. I hope you can help me. > Greetings > Mabel G. From hatuey.hack at gmail.com Tue Dec 3 07:18:10 2013 From: hatuey.hack at gmail.com (Hatuey Hack) Date: Tue, 3 Dec 2013 13:18:10 -0200 Subject: [Chimera-users] << measuring areas >> In-Reply-To: References: Message-ID: Thank you very much! I will try the suggestions. []'s, Camps On Mon, Dec 2, 2013 at 4:17 PM, Tom Goddard wrote: > Hi Hatuey, > > Some Python code could calculate this -- Chimera has the underlying > funtions to find the electrostatic potential at surface points and give an > area for each surface point (1/3 of the areas of all the surface triangles > that have a corner at that point). But the details are important - what > surface? and how do you want ESP calculated? I think the most sensible > surface to use would be the solvent accessible surface, but Chimera does > not calculate that type of surface. ESP could be computed by Coulombic > approximation or APBS or other external programs that use Poisson-Boltzman > to handle solvent dielectric better. > > Tom > > > > On Dec 2, 2013, at 2:02 AM, Hatuey Hack wrote: > > > Hellos ChimeraUsers, > > > > It could be possible to measure different parts of a surface according > to a given parameter? > > > > For example, from the electrostatic potential surface, I would like to > know the respective area surface with positive and/or negative values. > > > > Best regards, > > > > > > Hatuey > > _______________________________________________ > > 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 duncant at upstate.edu Tue Dec 3 07:47:33 2013 From: duncant at upstate.edu (Tom Duncan) Date: Tue, 3 Dec 2013 10:47:33 -0500 Subject: [Chimera-users] reading PDB-format alignment files Message-ID: Can Chimera read sequence alignments from PDB-format alignment files, such as those generated by the I-Tasser modeling server? Or are there scripts to convert them? I have attached an example file. Thanks Tom ----------------------------------------------------- Thomas M. Duncan, Ph.D. Associate Professor Dept Biochemistry & Molecular Biology SUNY Upstate Medical University Syracuse, NY -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: threading1.pdb Type: application/octet-stream Size: 6978 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Tue Dec 3 11:27:02 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 3 Dec 2013 11:27:02 -0800 Subject: [Chimera-users] reading PDB-format alignment files In-Reply-To: References: Message-ID: <9EF6E8D1-3C93-4C30-AD51-2B110CF5C813@cgl.ucsf.edu> On Dec 3, 2013, at 7:47 AM, Tom Duncan wrote: > Can Chimera read sequence alignments from PDB-format alignment files, such as those generated by the I-Tasser modeling server? Or are there scripts to convert them? I have attached an example file. Hi Tom, Well, this "PDB" file doesn't conform to the PDB standard in a variety of ways, but the one you care about is the extra two columns on the ATOM records. The presence of those columns causes Chimera to skip those records. If you simply edit them out then Chimera displays the structure. I've attached an edited version of your file. I will open an enhancement-request ticket in our bug-tracking database for having Chimera ignore non-standard columns past the coordinate records (there are some standard columns that are supposed to be there!) and put you on the notification list for that ticket. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: threading2.pdb Type: chemical/x-pdb Size: 6250 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From duncant at upstate.edu Tue Dec 3 12:28:40 2013 From: duncant at upstate.edu (Tom Duncan) Date: Tue, 3 Dec 2013 15:28:40 -0500 Subject: [Chimera-users] reading PDB-format alignment files In-Reply-To: References: Message-ID: Eric, It's not the structural info I want to extract - just the sequence alignment info. See the remarks in the file header. Thanks, Tom ----------------------------------------------------- Thomas M. Duncan, Ph.D. Associate Professor Dept Biochemistry & Molecular Biology SUNY Upstate Medical University Syracuse, NY On Dec 3, 2013, at 3:00 PM, chimera-users-request at cgl.ucsf.edu wrote: > Date: Tue, 3 Dec 2013 11:27:02 -0800 > From: Eric Pettersen > To: Tom Duncan > Cc: chimera-users BB > Subject: Re: [Chimera-users] reading PDB-format alignment files > Message-ID: <9EF6E8D1-3C93-4C30-AD51-2B110CF5C813 at cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > On Dec 3, 2013, at 7:47 AM, Tom Duncan wrote: > >> Can Chimera read sequence alignments from PDB-format alignment files, such as those generated by the I-Tasser modeling server? Or are there scripts to convert them? I have attached an example file. > > Hi Tom, > Well, this "PDB" file doesn't conform to the PDB standard in a variety of ways, but the one you care about is the extra two columns on the ATOM records. The presence of those columns causes Chimera to skip those records. If you simply edit them out then Chimera displays the structure. I've attached an edited version of your file. I will open an enhancement-request ticket in our bug-tracking database for having Chimera ignore non-standard columns past the coordinate records (there are some standard columns that are supposed to be there!) and put you on the notification list for that ticket. > > --Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Tue Dec 3 13:08:40 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 3 Dec 2013 13:08:40 -0800 Subject: [Chimera-users] reading PDB-format alignment files In-Reply-To: References: Message-ID: <773664F9-A73E-49F8-B00D-51B4D3D259A8@cgl.ucsf.edu> Okay, though in your example file the alignment is kind of trivial since the query and template are identical. Nonetheless, here is a simple Python script that will read I-Tasser PDB files and show the alignment. You run the script by giving Chimera the startup command-line arguments: --script "tasser.py threading1.pdb" (assuming both the script and the PDB file are in the folder you are currently in). You can also provide more than one of the PDB files if you want it to show several alignments. For more info about starting Chimera from the command line, go to this page: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/startup.html --Eric On Dec 3, 2013, at 12:28 PM, Tom Duncan wrote: > Eric, > > It's not the structural info I want to extract - just the sequence alignment info. > See the remarks in the file header. > > Thanks, > Tom > ----------------------------------------------------- > Thomas M. Duncan, Ph.D. > Associate Professor > Dept Biochemistry & Molecular Biology > SUNY Upstate Medical University > Syracuse, NY > > On Dec 3, 2013, at 3:00 PM, chimera-users-request at cgl.ucsf.edu wrote: > >> Date: Tue, 3 Dec 2013 11:27:02 -0800 >> From: Eric Pettersen >> To: Tom Duncan >> Cc: chimera-users BB >> Subject: Re: [Chimera-users] reading PDB-format alignment files >> Message-ID: <9EF6E8D1-3C93-4C30-AD51-2B110CF5C813 at cgl.ucsf.edu> >> Content-Type: text/plain; charset="us-ascii" >> >> On Dec 3, 2013, at 7:47 AM, Tom Duncan wrote: >> >>> Can Chimera read sequence alignments from PDB-format alignment files, such as those generated by the I-Tasser modeling server? Or are there scripts to convert them? I have attached an example file. >> >> Hi Tom, >> Well, this "PDB" file doesn't conform to the PDB standard in a variety of ways, but the one you care about is the extra two columns on the ATOM records. The presence of those columns causes Chimera to skip those records. If you simply edit them out then Chimera displays the structure. I've attached an edited version of your file. I will open an enhancement-request ticket in our bug-tracking database for having Chimera ignore non-standard columns past the coordinate records (there are some standard columns that are supposed to be there!) and put you on the notification list for that ticket. >> >> --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: -------------- next part -------------- A non-text attachment was scrubbed... Name: tasser.py Type: text/x-python-script Size: 438 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From homeira.a at gmail.com Tue Dec 3 13:11:57 2013 From: homeira.a at gmail.com (Aani Homeira) Date: Tue, 3 Dec 2013 13:11:57 -0800 Subject: [Chimera-users] request for removal from mailing list Message-ID: Thanks . . . . . . . . . . . . . . . . . . . A n i . H o m e i r a . A m i r k h a n i . -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Dec 3 14:40:35 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 3 Dec 2013 14:40:35 -0800 Subject: [Chimera-users] request for removal from mailing list In-Reply-To: References: Message-ID: You can unsubscribe by clicking the link at the bottom of any chimera-users email message and following the instructions to unsubscribe. Elaine On Dec 3, 2013, at 1:11 PM, Aani Homeira wrote: > Thanks > . > . . . . . . > . . . . . . . . . . . . > A n i . H o m e i r a . A m i r k h a n i . > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From matsuo.tatsuhito at jaea.go.jp Mon Dec 2 18:31:53 2013 From: matsuo.tatsuhito at jaea.go.jp (Tatsuhito Matsuo) Date: Tue, 3 Dec 2013 11:31:53 +0900 Subject: [Chimera-users] Electrostatic potential values at each residue Message-ID: <36DA22D5-4E1D-442E-A207-1AC7E8381C1D@jaea.go.jp> Dear All, I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy? Thank you very much in advance, T.M. -------------- next part -------------- A non-text attachment was scrubbed... Name: ubiquitin.py Type: text/x-python-script Size: 292870 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ubiquitin.pyc Type: application/octet-stream Size: 283415 bytes Desc: not available URL: From goddard at sonic.net Tue Dec 3 19:19:32 2013 From: goddard at sonic.net (Tom Goddard) Date: Tue, 3 Dec 2013 19:19:32 -0800 Subject: [Chimera-users] Electrostatic potential values at each residue In-Reply-To: <36DA22D5-4E1D-442E-A207-1AC7E8381C1D@jaea.go.jp> References: <36DA22D5-4E1D-442E-A207-1AC7E8381C1D@jaea.go.jp> Message-ID: <61001B9A-92F8-4D0A-A5FB-AD88EB9F5846@sonic.net> Hi T.M., I think you've left out details about what you have done -- how did you get this value_Coulombic_ESP attribute? Did you use values at atom positions? Did you use the "compute grid" option in the Coulombic Surface Coloring dialog? I guess you did that. And you say you use Attributes of Residues -- is that an average of the atom attribute obtained from the values at atom positions dialog? I can't be sure what you've done, but here's a guess at what your problem is. The Chimera Coulombic Surface Coloring dialog computes the potential at points 1.4 Angstroms out from the solvent excluded molecular surface and colors the surface points using that value. If you instead use a potential value interpolated at the center of an atom, that will give a much different value -- in fact it should tend to give an extremely large value because if the atom is charged the potential at the atom center is infinite using the simple Coulomb calculation. But because you are (I think) using a value interpolated from a grid you don't get an infinite value, just a very large value. So I think your problem is you are not considering that the electrostatic potential varies rapidly in space and you are comparing colors using potential values at different positions in space. Tom On Dec 2, 2013, at 6:31 PM, Tatsuhito Matsuo wrote: > Dear All, > > I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy? > > Thank you very much in advance, > > T.M. > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From emailanindito at yahoo.co.in Tue Dec 3 23:10:39 2013 From: emailanindito at yahoo.co.in (Anindito Sen) Date: Wed, 4 Dec 2013 15:10:39 +0800 (SGT) Subject: [Chimera-users] Problem of Launching Chimera Remotely on a Mac Message-ID: <1386141039.20817.YahooMailNeo@web193004.mail.sg3.yahoo.com> Dear All, I am having difficulty to launch Chimera remotely with the following Error message on my Mac. I understand that the current OS X (version 10.8.5) and the latest Xcode has some issues and cannot handle the process ?!? Is there a way out of this ? Thanks and Best Wishes Andy [andy@****** ~]$ chimera Xlib: ?extension "NV-GLX" missing on display "localhost:15.0". Xlib: ?extension "NV-GLX" missing on display "localhost:15.0". X Error of failed request: ?GLXBadCurrentWindow ? Major opcode of failed request: ?149 (GLX) ? Minor opcode of failed request: ?5 (X_GLXMakeCurrent) ? Serial number of failed request: ?1354 ? Current serial number in output stream: ?1354 ? Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Dec 4 09:37:29 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 4 Dec 2013 09:37:29 -0800 Subject: [Chimera-users] Electrostatic potential values at each residue In-Reply-To: <36DA22D5-4E1D-442E-A207-1AC7E8381C1D@jaea.go.jp> References: <36DA22D5-4E1D-442E-A207-1AC7E8381C1D@jaea.go.jp> Message-ID: <14A5FA93-5A7F-4850-BAF5-3F5925E336C6@cgl.ucsf.edu> Dear TM, The values are for different locations: the attributes are values mapped to atomic centers, whereas the surface coloring shows the potential values farther out, at the surface or beyond (even farther from the atom centers). By default in Chimera, Coulombic or other electrostatic surface coloring shows the values at points 1.4 angstroms outward from the displayed (solvent-excluded) surface, approximating the values at the larger solvent-accessible surface, which is not displayed. This is the "Distance from surface" parameter in the Coulombic surface coloring dialog, and there is a similar option in the Surface Color tool. Using the Coulombic coloring tool does not automatically create attributes. I'm guessing you used the option to create a grid, then read in the grid, and then used Values at Atom Positions to get the attributes assigned. (Your session cannot be restored because it also requires the grid file.) To summarize, however, you would not expect the values to be the same because the locations where the potential is evaluated are quite different. 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 Dec 2, 2013, at 6:31 PM, Tatsuhito Matsuo wrote: > Dear All, > > I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy? > > Thank you very much in advance, > > T.M. From goddard at sonic.net Wed Dec 4 09:46:04 2013 From: goddard at sonic.net (Tom Goddard) Date: Wed, 4 Dec 2013 09:46:04 -0800 Subject: [Chimera-users] Problem of Launching Chimera Remotely on a Mac In-Reply-To: <1386141039.20817.YahooMailNeo@web193004.mail.sg3.yahoo.com> References: <1386141039.20817.YahooMailNeo@web193004.mail.sg3.yahoo.com> Message-ID: <39DF3860-93B5-4CD4-B303-05FE08F55AAD@sonic.net> Hi Andy, Your error message means the two machines you are using cannot remotely display OpenGL using X windows because of incompatible graphics drivers. It has nothing to do with Chimera. Specifically the error says the NV-GLX (nvidia glx) extension is missing on the server. X windows remote display is a nearly dead technology, poorly supported, only in rare cases does the OpenGL work. Why are you trying to do this instead of using a modern desktop sharing protocol? Tom On Dec 3, 2013, at 11:10 PM, Anindito Sen wrote: > Dear All, > > I am having difficulty to launch Chimera remotely with the following Error message on my Mac. I understand that the current OS X (version 10.8.5) and the latest Xcode has some issues and cannot handle the process ?! > > Is there a way out of this ? > > Thanks and Best Wishes > > Andy > > > [andy@****** ~]$ chimera > Xlib: extension "NV-GLX" missing on display "localhost:15.0". > Xlib: extension "NV-GLX" missing on display "localhost:15.0". > X Error of failed request: GLXBadCurrentWindow > Major opcode of failed request: 149 (GLX) > Minor opcode of failed request: 5 (X_GLXMakeCurrent) > Serial number of failed request: 1354 > Current serial number in output stream: 1354 > > >> Dr. Anindito Sen (Ph.D) >> Department of Cell Biology & Anatomy >> Graduate School of Medicine >> University of Tokyo >> Tel & fax: +81-3-5841-3339 > > _______________________________________________ > 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 goddard at sonic.net Wed Dec 4 10:41:10 2013 From: goddard at sonic.net (Tom Goddard) Date: Wed, 4 Dec 2013 10:41:10 -0800 Subject: [Chimera-users] Surface area with positive electrostatic potential In-Reply-To: <96572196-0C31-4FC6-A8CB-4D9D22885A72@jaea.go.jp> References: <36DA22D5-4E1D-442E-A207-1AC7E8381C1D@jaea.go.jp> <61001B9A-92F8-4D0A-A5FB-AD88EB9F5846@sonic.net> <96572196-0C31-4FC6-A8CB-4D9D22885A72@jaea.go.jp> Message-ID: <3C48E55D-65E1-494D-96D0-157A8C8673D2@sonic.net> Hi T.M., To find the surface area with positive electrostatic potential would require computing the potential at surface points. Chimera does not compute solvent accessible surface (SAS) points (although it does compute total area). So there is no simple way to get the SAS area for positive potential points. Chimera does compute the solvent excluded surface (SES) using menu Actions / Surface or command "surface". For an SES surface a little Python code can give the fraction of the surface area colored red. I've attached that Python code red_area.py. You color the surface using the normal red-blue electrostatic coloring. The red_area.py code adds a command called "redarea" that computes the area of the surface that is more red than blue. Here's an example from the header of the red_area.py file. # Example use. # # menu File / Open..., red_area.py, Creates the new redarea command. # # open 1a0m # surface # coulombic -10 red 0 white 10 blue #0 # redarea #0 # # menu Favorites / Reply Log # -> "Surface MSMS main surface of 1a0m, red area 1400, total area 1888, ratio 0.7414" This script and other odd Python code for doing computations is on the Chimera developer web site: http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts Tom -------------- next part -------------- A non-text attachment was scrubbed... Name: red_area.py Type: text/x-python-script Size: 1315 bytes Desc: not available URL: -------------- next part -------------- On Dec 3, 2013, at 9:05 PM, Tatsuhito Matsuo wrote: > Dear Tom, > > Thank you very much for the reply and I'm sorry for inadequate information on what I've done (your guess is completely right). What I'd like to know is the ratio of the solvent accessible surface (SAS) with positive (or negative) potential values to the total SAS. The total SAS value is automatically calculated by the surface plot, and I need the value of SAS having positive/negative potential values. > At first, I thought the ESP value of "Attributes of Residues" is relevant to the one at the corresponding protein surface area. I now understand that this was wrong. Could you teach me how to get the SAS having positive/negative potential values? > > Best regards, > > T.M. > > On 2013/12/04, at 12:19, Tom Goddard wrote: > >> Hi T.M., >> >> I think you've left out details about what you have done -- how did you get this value_Coulombic_ESP attribute? Did you use values at atom positions? Did you use the "compute grid" option in the Coulombic Surface Coloring dialog? I guess you did that. And you say you use Attributes of Residues -- is that an average of the atom attribute obtained from the values at atom positions dialog? I can't be sure what you've done, but here's a guess at what your problem is. The Chimera Coulombic Surface Coloring dialog computes the potential at points 1.4 Angstroms out from the solvent excluded molecular surface and colors the surface points using that value. If you instead use a potential value interpolated at the center of an atom, that will give a much different value -- in fact it should tend to give an extremely large value because if the atom is charged the potential at the atom center is infinite using the simple Coulomb calculation. But because you are (I think) using a value interpolated from a grid you don't get an infinite value, just a very large value. So I think your problem is you are not considering that the electrostatic potential varies rapidly in space and you are comparing colors using potential values at different positions in space. >> >> Tom >> >> >> >> On Dec 2, 2013, at 6:31 PM, Tatsuhito Matsuo wrote: >> >>> Dear All, >>> >>> I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy? >>> >>> Thank you very much in advance, >>> >>> T.M. >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > From miguel.ortiz-lombardia at afmb.univ-mrs.fr Thu Dec 5 00:00:22 2013 From: miguel.ortiz-lombardia at afmb.univ-mrs.fr (=?UTF-8?B?TWlndWVsIE9ydGl6IExvbWJhcmTDrWE=?=) Date: Thu, 05 Dec 2013 09:00:22 +0100 Subject: [Chimera-users] Problem of Launching Chimera Remotely on a Mac In-Reply-To: <52A02BA1.6020603@afmb.univ-mrs.fr> References: <1386141039.20817.YahooMailNeo@web193004.mail.sg3.yahoo.com> <39DF3860-93B5-4CD4-B303-05FE08F55AAD@sonic.net> <52A02BA1.6020603@afmb.univ-mrs.fr> Message-ID: <52A03296.8040006@afmb.univ-mrs.fr> Forgot to mention : the main problem with remote desktop sharing in OSX (up to 10.6, which still many of us use) is that you share the "physical" desktop... i.e. that only one person can use the desktop on the remote machine, whereas with X11 several people can run multiple graphical sessions on the remote server. That changed in OSX 10.7 (Lion) but the performance was still really bad, as far as I could see. I don't know for 10.8 or the new 10.9. Cheers, Miguel Ortiz Lombard?a Architecture et Fonction des Macromol?cules Biologiques (UMR7257) CNRS, Aix-Marseille Universit? Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 86 44 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia at afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia Le 05/12/13 08:30, Miguel Ortiz Lombard?a a ?crit : > Hi Tom, > > I'm very sad to learn about the announced death of X windows remote > display after so many years. I have never had problems using OpenGL on > remote X windows when communicating between Linux machines. Anyway, IMO > remote desktop sharing is not an option with OSX machines : far too slow > and very low quality. Unless you know of an option other than the remote > desktop service shipped with OSX, which I would be very interested in. > > With best regards, > > Miguel Ortiz Lombard?a > > Architecture et Fonction des Macromol?cules Biologiques (UMR7257) > CNRS, Aix-Marseille Universit? > Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France > Tel: +33(0) 491 82 86 44 > Fax: +33(0) 491 26 67 20 > mailto:miguel.ortiz-lombardia at afmb.univ-mrs.fr > http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia > > Le 04/12/13 18:46, Tom Goddard a ?crit : >> Hi Andy, >> >> Your error message means the two machines you are using cannot >> remotely display OpenGL using X windows because of incompatible graphics >> drivers. It has nothing to do with Chimera. Specifically the error >> says the NV-GLX (nvidia glx) extension is missing on the server. X >> windows remote display is a nearly dead technology, poorly supported, >> only in rare cases does the OpenGL work. Why are you trying to do this >> instead of using a modern desktop sharing protocol? >> >> Tom >> >> >> On Dec 3, 2013, at 11:10 PM, Anindito Sen wrote: >> >>> Dear All, >>> >>> I am having difficulty to launch Chimera remotely with the following >>> Error message on my Mac. I understand that the current OS X (version >>> 10.8.5) and the latest Xcode has some issues and cannot handle the >>> process ?! >>> >>> Is there a way out of this ? >>> >>> Thanks and Best Wishes >>> >>> Andy >>> >>> >>> [andy@****** ~]$ chimera >>> Xlib: extension "NV-GLX" missing on display "localhost:15.0". >>> Xlib: extension "NV-GLX" missing on display "localhost:15.0". >>> X Error of failed request: GLXBadCurrentWindow >>> Major opcode of failed request: 149 (GLX) >>> Minor opcode of failed request: 5 (X_GLXMakeCurrent) >>> Serial number of failed request: 1354 >>> Current serial number in output stream: 1354 >>> >>> >>> * >>>> *Dr. Anindito Sen (Ph.D)* >>>> *Department of Cell Biology & Anatomy* >>>> *Graduate School of Medicine* >>>> *University of Tokyo* >>>> *Tel & fax: +81-3-5841-3339* >>> * >>> * >>> * >>> _______________________________________________ >>> 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 miguel.ortiz-lombardia at afmb.univ-mrs.fr Wed Dec 4 23:30:41 2013 From: miguel.ortiz-lombardia at afmb.univ-mrs.fr (=?UTF-8?B?TWlndWVsIE9ydGl6IExvbWJhcmTDrWE=?=) Date: Thu, 05 Dec 2013 08:30:41 +0100 Subject: [Chimera-users] Problem of Launching Chimera Remotely on a Mac In-Reply-To: <39DF3860-93B5-4CD4-B303-05FE08F55AAD@sonic.net> References: <1386141039.20817.YahooMailNeo@web193004.mail.sg3.yahoo.com> <39DF3860-93B5-4CD4-B303-05FE08F55AAD@sonic.net> Message-ID: <52A02BA1.6020603@afmb.univ-mrs.fr> Hi Tom, I'm very sad to learn about the announced death of X windows remote display after so many years. I have never had problems using OpenGL on remote X windows when communicating between Linux machines. Anyway, IMO remote desktop sharing is not an option with OSX machines : far too slow and very low quality. Unless you know of an option other than the remote desktop service shipped with OSX, which I would be very interested in. With best regards, Miguel Ortiz Lombard?a Architecture et Fonction des Macromol?cules Biologiques (UMR7257) CNRS, Aix-Marseille Universit? Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 86 44 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia at afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia Le 04/12/13 18:46, Tom Goddard a ?crit : > Hi Andy, > > Your error message means the two machines you are using cannot > remotely display OpenGL using X windows because of incompatible graphics > drivers. It has nothing to do with Chimera. Specifically the error > says the NV-GLX (nvidia glx) extension is missing on the server. X > windows remote display is a nearly dead technology, poorly supported, > only in rare cases does the OpenGL work. Why are you trying to do this > instead of using a modern desktop sharing protocol? > > Tom > > > On Dec 3, 2013, at 11:10 PM, Anindito Sen wrote: > >> Dear All, >> >> I am having difficulty to launch Chimera remotely with the following >> Error message on my Mac. I understand that the current OS X (version >> 10.8.5) and the latest Xcode has some issues and cannot handle the >> process ?! >> >> Is there a way out of this ? >> >> Thanks and Best Wishes >> >> Andy >> >> >> [andy@****** ~]$ chimera >> Xlib: extension "NV-GLX" missing on display "localhost:15.0". >> Xlib: extension "NV-GLX" missing on display "localhost:15.0". >> X Error of failed request: GLXBadCurrentWindow >> Major opcode of failed request: 149 (GLX) >> Minor opcode of failed request: 5 (X_GLXMakeCurrent) >> Serial number of failed request: 1354 >> Current serial number in output stream: 1354 >> >> >> * >>> *Dr. Anindito Sen (Ph.D)* >>> *Department of Cell Biology & Anatomy* >>> *Graduate School of Medicine* >>> *University of Tokyo* >>> *Tel & fax: +81-3-5841-3339* >> * >> * >> * >> _______________________________________________ >> 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 bala.biophysics at gmail.com Thu Dec 5 07:58:59 2013 From: bala.biophysics at gmail.com (Bala subramanian) Date: Thu, 5 Dec 2013 16:58:59 +0100 Subject: [Chimera-users] calculate buried surface area Message-ID: Friends, I have a dimer protein (say monomers 1,2). I have calculated the electrostatic potential of monomer 1 using apbs. I used volume viewer to display the electrostatic surface. I see that the elect. surface of one monomer 1, touches the vdw surface of monomer 2 at a contour level of 1. I want to calculate the total surface area of monomer 2 that is exposed/buried within the elec. surface of monomer 1. Is there any simple. If not suggestion how i can do it with a python script perhaps. Thanks, Bala -- C. Balasubramanian -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Dec 5 09:12:41 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 5 Dec 2013 09:12:41 -0800 Subject: [Chimera-users] calculate buried surface area In-Reply-To: References: Message-ID: <4C48A4DF-7F0C-4544-82AE-4EC0665BC6F5@cgl.ucsf.edu> Hi Bala, I can't think of any (noncoding) way in Chimera for looking at surfaces geometrically and getting the area of the monomer 2 molecular surface that is inside the ESP isosurface from monomer 1. However, it sounds like it just boils down to getting the surface area of monomer 2 at which the ESP from monomer 1 is above (or below) some value. In that case, you could color the monomer 2 molecular surface by the ESP from monomer 1 and then use the script that was posted yesterday to get surface area based on color. Since in this case you want the coloring to reflect the ESP right at the surface instead of 1.4 angstroms outward, when coloring be sure to turn OFF the option for "Surface offset" in Electrostatic Surface Coloring. 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 Dec 5, 2013, at 7:58 AM, Bala subramanian wrote: > Friends, > > I have a dimer protein (say monomers 1,2). I have calculated the electrostatic potential of monomer 1 using apbs. I used volume viewer to display the electrostatic surface. > > I see that the elect. surface of one monomer 1, touches the vdw surface of monomer 2 at a contour level of 1. I want to calculate the total surface area of monomer 2 that is exposed/buried within the elec. surface of monomer 1. Is there any simple. If not suggestion how i can do it with a python script perhaps. > > Thanks, > Bala From meng at cgl.ucsf.edu Thu Dec 5 09:25:06 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 5 Dec 2013 09:25:06 -0800 Subject: [Chimera-users] calculate buried surface area In-Reply-To: <4C48A4DF-7F0C-4544-82AE-4EC0665BC6F5@cgl.ucsf.edu> References: <4C48A4DF-7F0C-4544-82AE-4EC0665BC6F5@cgl.ucsf.edu> Message-ID: <6D584A96-A0C2-4396-99B6-D7A203C0A99C@cgl.ucsf.edu> Or, maybe you do want the values 1.4 angstroms outward. Either way, be aware of how it works and make a conscious decision about which values you want the coloring to reflect. Elaine On Dec 5, 2013, at 9:12 AM, Elaine Meng wrote: > > Since in this case you want the coloring to reflect the ESP right at the surface instead of 1.4 angstroms outward, when coloring be sure to turn OFF the option for "Surface offset" in Electrostatic Surface Coloring. > From goddard at sonic.net Thu Dec 5 10:25:59 2013 From: goddard at sonic.net (Tom Goddard) Date: Thu, 5 Dec 2013 10:25:59 -0800 Subject: [Chimera-users] calculate buried surface area In-Reply-To: <6D584A96-A0C2-4396-99B6-D7A203C0A99C@cgl.ucsf.edu> References: <4C48A4DF-7F0C-4544-82AE-4EC0665BC6F5@cgl.ucsf.edu> <6D584A96-A0C2-4396-99B6-D7A203C0A99C@cgl.ucsf.edu> Message-ID: <954EECD7-5018-42FE-AB91-6D2810902CA2@sonic.net> Hi Bala, One more little detail about using the redarea command to do this measurement. The command measures the area of the surface points where the red color component is greater than or equal to the blue color component. So you should use the surface color dialog to color the molecular surface by volume where it is red at values above a certain potential, e.g. above 5, and blue below 5. To do this you would use two colors for example blue with level 4.999 and red with level 5.001. If you choose other colors like white and red, then every surface point will have the red component greater than or equal to the blue component and you won't measure what you want. Tom On Dec 5, 2013, at 9:25 AM, Elaine Meng wrote: > Or, maybe you do want the values 1.4 angstroms outward. Either way, be aware of how it works and make a conscious decision about which values you want the coloring to reflect. > Elaine > > On Dec 5, 2013, at 9:12 AM, Elaine Meng wrote: > >> >> Since in this case you want the coloring to reflect the ESP right at the surface instead of 1.4 angstroms outward, when coloring be sure to turn OFF the option for "Surface offset" in Electrostatic Surface Coloring. >> > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From bala.biophysics at gmail.com Thu Dec 5 12:03:32 2013 From: bala.biophysics at gmail.com (Bala subramanian) Date: Thu, 5 Dec 2013 21:03:32 +0100 Subject: [Chimera-users] calculate buried surface area In-Reply-To: <954EECD7-5018-42FE-AB91-6D2810902CA2@sonic.net> References: <4C48A4DF-7F0C-4544-82AE-4EC0665BC6F5@cgl.ucsf.edu> <6D584A96-A0C2-4396-99B6-D7A203C0A99C@cgl.ucsf.edu> <954EECD7-5018-42FE-AB91-6D2810902CA2@sonic.net> Message-ID: Elaine, Tom, Thank you for the information. Just a clarification, I coloured the surface of monomer 2 with the electrostatic potential of monomer 1 with a threshold of -0.5 to 0.5 and the colour range goes from red-white-blue. What i see is that some portion of monomer 2 surface is out of this colour range (and are coloured in dim gray). Does it mean this portion is out of the electrostatic grid of monomer 1 ? Thanks, Bala On Thu, Dec 5, 2013 at 7:25 PM, Tom Goddard wrote: > Hi Bala, > > One more little detail about using the redarea command to do this > measurement. The command measures the area of the surface points where the > red color component is greater than or equal to the blue color component. > So you should use the surface color dialog to color the molecular surface > by volume where it is red at values above a certain potential, e.g. above > 5, and blue below 5. To do this you would use two colors for example blue > with level 4.999 and red with level 5.001. If you choose other colors like > white and red, then every surface point will have the red component greater > than or equal to the blue component and you won't measure what you want. > > Tom > > > On Dec 5, 2013, at 9:25 AM, Elaine Meng wrote: > > > Or, maybe you do want the values 1.4 angstroms outward. Either way, be > aware of how it works and make a conscious decision about which values you > want the coloring to reflect. > > Elaine > > > > On Dec 5, 2013, at 9:12 AM, Elaine Meng wrote: > > > >> > >> Since in this case you want the coloring to reflect the ESP right at > the surface instead of 1.4 angstroms outward, when coloring be sure to turn > OFF the option for "Surface offset" in Electrostatic Surface Coloring. > >> < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html > > > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > -- C. Balasubramanian -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Dec 5 12:08:28 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 5 Dec 2013 12:08:28 -0800 Subject: [Chimera-users] calculate buried surface area In-Reply-To: References: <4C48A4DF-7F0C-4544-82AE-4EC0665BC6F5@cgl.ucsf.edu> <6D584A96-A0C2-4396-99B6-D7A203C0A99C@cgl.ucsf.edu> <954EECD7-5018-42FE-AB91-6D2810902CA2@sonic.net> Message-ID: <49CE28F8-6919-4EE4-AC1C-3BD5BB729423@cgl.ucsf.edu> Probably: the "color outside volume" is one of the options in the Surface Color (Electrostatic Surface Coloring) dialog. Elaine On Dec 5, 2013, at 12:03 PM, Bala subramanian wrote: > Elaine, Tom, > > Thank you for the information. Just a clarification, I coloured the surface of monomer 2 with the electrostatic potential of monomer 1 with a threshold of -0.5 to 0.5 and the colour range goes from red-white-blue. What i see is that some portion of monomer 2 surface is out of this colour range (and are coloured in dim gray). Does it mean this portion is out of the electrostatic grid of monomer 1 ? > > Thanks, > Bala > > > On Thu, Dec 5, 2013 at 7:25 PM, Tom Goddard wrote: > Hi Bala, > > One more little detail about using the redarea command to do this measurement. The command measures the area of the surface points where the red color component is greater than or equal to the blue color component. So you should use the surface color dialog to color the molecular surface by volume where it is red at values above a certain potential, e.g. above 5, and blue below 5. To do this you would use two colors for example blue with level 4.999 and red with level 5.001. If you choose other colors like white and red, then every surface point will have the red component greater than or equal to the blue component and you won't measure what you want. > > Tom > > > On Dec 5, 2013, at 9:25 AM, Elaine Meng wrote: > > > Or, maybe you do want the values 1.4 angstroms outward. Either way, be aware of how it works and make a conscious decision about which values you want the coloring to reflect. > > Elaine > > > > On Dec 5, 2013, at 9:12 AM, Elaine Meng wrote: > > > >> > >> Since in this case you want the coloring to reflect the ESP right at the surface instead of 1.4 angstroms outward, when coloring be sure to turn OFF the option for "Surface offset" in Electrostatic Surface Coloring. > >> > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > > -- > C. Balasubramanian > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From matsuo.tatsuhito at jaea.go.jp Wed Dec 4 18:56:53 2013 From: matsuo.tatsuhito at jaea.go.jp (Tatsuhito Matsuo) Date: Thu, 5 Dec 2013 11:56:53 +0900 Subject: [Chimera-users] Electrostatic potential values at each residue In-Reply-To: <14A5FA93-5A7F-4850-BAF5-3F5925E336C6@cgl.ucsf.edu> References: <36DA22D5-4E1D-442E-A207-1AC7E8381C1D@jaea.go.jp> <14A5FA93-5A7F-4850-BAF5-3F5925E336C6@cgl.ucsf.edu> Message-ID: <5ED304E8-8D86-4DAF-81CD-888A7FE4C67D@jaea.go.jp> Dear Dr. Meng, Thank you very much for the reply and I'm sorry for lacking of the necessary file to open the session I attached. My question was solved thanks to your clear explanation and I now see that I misunderstood the ESP attributes. Thank you so much for your help. Best wishes, T.M. On 2013/12/05, at 2:37, Elaine Meng wrote: > Dear TM, > The values are for different locations: the attributes are values mapped to atomic centers, whereas the surface coloring shows the potential values farther out, at the surface or beyond (even farther from the atom centers). By default in Chimera, Coulombic or other electrostatic surface coloring shows the values at points 1.4 angstroms outward from the displayed (solvent-excluded) surface, approximating the values at the larger solvent-accessible surface, which is not displayed. This is the "Distance from surface" parameter in the Coulombic surface coloring dialog, and there is a similar option in the Surface Color tool. > > Using the Coulombic coloring tool does not automatically create attributes. I'm guessing you used the option to create a grid, then read in the grid, and then used Values at Atom Positions to get the attributes assigned. (Your session cannot be restored because it also requires the grid file.) > > To summarize, however, you would not expect the values to be the same because the locations where the potential is evaluated are quite different. > > 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 Dec 2, 2013, at 6:31 PM, Tatsuhito Matsuo wrote: > >> Dear All, >> >> I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy? >> >> Thank you very much in advance, >> >> T.M. > From lp212 at cam.ac.uk Thu Dec 5 04:58:22 2013 From: lp212 at cam.ac.uk (Luca Pellegrini) Date: Thu, 5 Dec 2013 12:58:22 +0000 Subject: [Chimera-users] Silhouette toggle Message-ID: <80CE1197-0FC6-4B6F-B317-3170A8A371B2@cam.ac.uk> Hi, I have set Silhouette ON in the Effects tab of the Viewing panel, and now I would like to toggle it off for one specific object. However, the Attributes window from Model Panel does not show the Silhouette option (it should feature between 'ribbon spline' and 'stick scale'). Can anyone please advice? I am using Chimera 1.9 (build 39137) for Mac . Kind regards, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212 at cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59 From pett at cgl.ucsf.edu Thu Dec 5 16:42:45 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 5 Dec 2013 16:42:45 -0800 Subject: [Chimera-users] Silhouette toggle In-Reply-To: <80CE1197-0FC6-4B6F-B317-3170A8A371B2@cam.ac.uk> References: <80CE1197-0FC6-4B6F-B317-3170A8A371B2@cam.ac.uk> Message-ID: <02154E6B-CFB7-4724-89B1-B9D816C95C43@cgl.ucsf.edu> Hi Luca, The per-model control of silhouette edges was added by SVN commit 39254, so you have to get a daily build newer than the one you have to get the control you want. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Dec 5, 2013, at 4:58 AM, Luca Pellegrini wrote: > Hi, > > I have set Silhouette ON in the Effects tab of the Viewing panel, and now I would like to toggle it off for one specific object. However, the Attributes window from Model Panel does not show the Silhouette option (it should feature between 'ribbon spline' and 'stick scale'). > > Can anyone please advice? I am using Chimera 1.9 (build 39137) for Mac . > > Kind regards, > Luca From goddard at sonic.net Thu Dec 5 17:47:54 2013 From: goddard at sonic.net (Tom Goddard) Date: Thu, 5 Dec 2013 17:47:54 -0800 Subject: [Chimera-users] Silhouette toggle In-Reply-To: <02154E6B-CFB7-4724-89B1-B9D816C95C43@cgl.ucsf.edu> References: <80CE1197-0FC6-4B6F-B317-3170A8A371B2@cam.ac.uk> <02154E6B-CFB7-4724-89B1-B9D816C95C43@cgl.ucsf.edu> Message-ID: <035ADBFA-3A32-4F78-ADEC-DA4253410FA2@sonic.net> Also the per-model silhouette edges is controlled using the setattr command, there is no button in Model Panel for this, as described in a previous mailing list message: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-November/009279.html Tom On Dec 5, 2013, at 4:42 PM, Eric Pettersen wrote: > Hi Luca, > The per-model control of silhouette edges was added by SVN commit 39254, so you have to get a daily build newer than the one you have to get the control you want. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Dec 5, 2013, at 4:58 AM, Luca Pellegrini wrote: > >> Hi, >> >> I have set Silhouette ON in the Effects tab of the Viewing panel, and now I would like to toggle it off for one specific object. However, the Attributes window from Model Panel does not show the Silhouette option (it should feature between 'ribbon spline' and 'stick scale'). >> >> Can anyone please advice? I am using Chimera 1.9 (build 39137) for Mac . >> >> Kind regards, >> Luca > > > > _______________________________________________ > 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 Thu Dec 5 19:04:56 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 5 Dec 2013 19:04:56 -0800 Subject: [Chimera-users] Silhouette toggle In-Reply-To: <035ADBFA-3A32-4F78-ADEC-DA4253410FA2@sonic.net> References: <80CE1197-0FC6-4B6F-B317-3170A8A371B2@cam.ac.uk> <02154E6B-CFB7-4724-89B1-B9D816C95C43@cgl.ucsf.edu> <035ADBFA-3A32-4F78-ADEC-DA4253410FA2@sonic.net> Message-ID: <4FA3D0DF-DA03-45BC-91D9-E42B85A96303@cgl.ucsf.edu> Though there is no button in the Model Panel's button list, as per Luca's message it does/should appear in the Model Panel's model attribute inspector, in exactly the same way it appears in the selection inspector. --Eric On Dec 5, 2013, at 5:47 PM, Tom Goddard wrote: > Also the per-model silhouette edges is controlled using the setattr command, there is no button in Model Panel for this, as described in a previous mailing list message: > > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-November/009279.html > > Tom > > On Dec 5, 2013, at 4:42 PM, Eric Pettersen wrote: > >> Hi Luca, >> The per-model control of silhouette edges was added by SVN commit 39254, so you have to get a daily build newer than the one you have to get the control you want. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> On Dec 5, 2013, at 4:58 AM, Luca Pellegrini wrote: >> >>> Hi, >>> >>> I have set Silhouette ON in the Effects tab of the Viewing panel, and now I would like to toggle it off for one specific object. However, the Attributes window from Model Panel does not show the Silhouette option (it should feature between 'ribbon spline' and 'stick scale'). >>> >>> Can anyone please advice? I am using Chimera 1.9 (build 39137) for Mac . >>> >>> Kind regards, >>> Luca >> >> >> >> _______________________________________________ >> 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 zhouming2 at mail.nih.gov Mon Dec 9 10:34:56 2013 From: zhouming2 at mail.nih.gov (Zhou, Ming (NIH/NCI) [C]) Date: Mon, 9 Dec 2013 18:34:56 +0000 Subject: [Chimera-users] select all side chains Message-ID: <569DA31B3A88DF45B8C32535B604812C1F2164A8@MLBXv02.nih.gov> Dear Elaine: I have a quick question for you. How should I select all the amino acid side chains in a protein but not the backbone (without CA/C1/N/O). How should I write this command? Thanks Ming Zhou -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Dec 9 11:29:13 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 9 Dec 2013 11:29:13 -0800 Subject: [Chimera-users] select all side chains In-Reply-To: <569DA31B3A88DF45B8C32535B604812C1F2164A8@MLBXv02.nih.gov> References: <569DA31B3A88DF45B8C32535B604812C1F2164A8@MLBXv02.nih.gov> Message-ID: <206FE855-5AA6-4E38-9E4C-2B575FF08B1D@cgl.ucsf.edu> Dear Ming Zhou, There are a few different ways, but one is to select protein atoms that are NOT backbone, e.g.: select protein & ~@n,ca,c,o Another way is with the command: select side chain/base.without CA/C1' ... or the shorter version: select without CA/C1' This is because you can use various Select menu entries exactly as they appear in the menu to specify atoms in the command line. The menu includes "Select... Structure... side chain/base... without CA/C1'" For more details on which menu items can be used in this way, see the section on "built-in classifications": If there was also DNA/RNA in the structure, you could then use an additional command to de-select just that part: ~select nucleic acid There is also a "with CA/C1'" (instead of "without") for example if you wanted to use the selection to display the side chains connected to ribbons instead of floating in space. 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 Dec 9, 2013, at 10:34 AM, Zhou, Ming (NIH/NCI) [C] wrote: > Dear Elaine: > I have a quick question for you. How should I select all the amino acid side chains in a protein but not the backbone (without CA/C1/N/O). How should I write this command? > Thanks > Ming Zhou From meng at cgl.ucsf.edu Mon Dec 9 11:39:36 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 9 Dec 2013 11:39:36 -0800 Subject: [Chimera-users] select all side chains In-Reply-To: <206FE855-5AA6-4E38-9E4C-2B575FF08B1D@cgl.ucsf.edu> References: <569DA31B3A88DF45B8C32535B604812C1F2164A8@MLBXv02.nih.gov> <206FE855-5AA6-4E38-9E4C-2B575FF08B1D@cgl.ucsf.edu> Message-ID: <99DAAC55-4D27-4255-8D14-F53E249CBA7A@cgl.ucsf.edu> Another note: If you are using this for coloring, even though only the sidechain atoms are selected, the ribbon for those residues would still also be colored unless you use ",a" in the coloring command, or if using the Actions menu, choose "Actions... Color... all options" and in the resulting dialog set "Coloring applies to" to "atoms/bonds" instead of "all of the above." (I noticed a question you had asked earlier and it reminded me of this issue!) Elaine On Dec 9, 2013, at 11:29 AM, Elaine Meng wrote: > Dear Ming Zhou, > There are a few different ways, but one is to select protein atoms that are NOT backbone, e.g.: > > select protein & ~@n,ca,c,o > > Another way is with the command: > select side chain/base.without CA/C1' > > ... or the shorter version: > select without CA/C1' > > This is because you can use various Select menu entries exactly as they appear in the menu to specify atoms in the command line. The menu includes "Select... Structure... side chain/base... without CA/C1'" For more details on which menu items can be used in this way, see the section on "built-in classifications": > > > If there was also DNA/RNA in the structure, you could then use an additional command to de-select just that part: > ~select nucleic acid > > There is also a "with CA/C1'" (instead of "without") for example if you wanted to use the selection to display the side chains connected to ribbons instead of floating in space. > > 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 Dec 9, 2013, at 10:34 AM, Zhou, Ming (NIH/NCI) [C] wrote: > >> Dear Elaine: >> I have a quick question for you. How should I select all the amino acid side chains in a protein but not the backbone (without CA/C1/N/O). How should I write this command? >> Thanks >> Ming Zhou > From zhouming2 at mail.nih.gov Mon Dec 9 11:48:55 2013 From: zhouming2 at mail.nih.gov (Zhou, Ming (NIH/NCI) [C]) Date: Mon, 9 Dec 2013 19:48:55 +0000 Subject: [Chimera-users] select all side chains In-Reply-To: <99DAAC55-4D27-4255-8D14-F53E249CBA7A@cgl.ucsf.edu> References: <569DA31B3A88DF45B8C32535B604812C1F2164A8@MLBXv02.nih.gov> <206FE855-5AA6-4E38-9E4C-2B575FF08B1D@cgl.ucsf.edu> <99DAAC55-4D27-4255-8D14-F53E249CBA7A@cgl.ucsf.edu> Message-ID: <569DA31B3A88DF45B8C32535B604812C1F216519@MLBXv02.nih.gov> Hi Elaine, thank you so much for your quick response. I actually is trying to do a simple energy minimization on the side chains. I can't combine the minimize command and the spec-atom command in the command line. Is there a way to do that? Minimize spec #0: The command line won't take the spec-atom selection I put in after : Thanks Ming -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: Monday, December 09, 2013 2:40 PM To: UCSF Chimera Mailing List Cc: Zhou, Ming (NIH/NCI) [C] Subject: Re: [Chimera-users] select all side chains Another note: If you are using this for coloring, even though only the sidechain atoms are selected, the ribbon for those residues would still also be colored unless you use ",a" in the coloring command, or if using the Actions menu, choose "Actions... Color... all options" and in the resulting dialog set "Coloring applies to" to "atoms/bonds" instead of "all of the above." (I noticed a question you had asked earlier and it reminded me of this issue!) Elaine On Dec 9, 2013, at 11:29 AM, Elaine Meng wrote: > Dear Ming Zhou, > There are a few different ways, but one is to select protein atoms that are NOT backbone, e.g.: > > select protein & ~@n,ca,c,o > > Another way is with the command: > select side chain/base.without CA/C1' > > ... or the shorter version: > select without CA/C1' > > This is because you can use various Select menu entries exactly as they appear in the menu to specify atoms in the command line. The menu includes "Select... Structure... side chain/base... without CA/C1'" For more details on which menu items can be used in this way, see the section on "built-in classifications": > .html> > > If there was also DNA/RNA in the structure, you could then use an additional command to de-select just that part: > ~select nucleic acid > > There is also a "with CA/C1'" (instead of "without") for example if you wanted to use the selection to display the side chains connected to ribbons instead of floating in space. > > 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 Dec 9, 2013, at 10:34 AM, Zhou, Ming (NIH/NCI) [C] wrote: > >> Dear Elaine: >> I have a quick question for you. How should I select all the amino acid side chains in a protein but not the backbone (without CA/C1/N/O). How should I write this command? >> Thanks >> Ming Zhou > From meng at cgl.ucsf.edu Mon Dec 9 13:30:53 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 9 Dec 2013 13:30:53 -0800 Subject: [Chimera-users] select all side chains In-Reply-To: <569DA31B3A88DF45B8C32535B604812C1F216519@MLBXv02.nih.gov> References: <569DA31B3A88DF45B8C32535B604812C1F2164A8@MLBXv02.nih.gov> <206FE855-5AA6-4E38-9E4C-2B575FF08B1D@cgl.ucsf.edu> <99DAAC55-4D27-4255-8D14-F53E249CBA7A@cgl.ucsf.edu> <569DA31B3A88DF45B8C32535B604812C1F216519@MLBXv02.nih.gov> Message-ID: <339A634A-EFE8-499E-8197-DDB13CFAE289@cgl.ucsf.edu> Hi Ming, Did you try enclosing the atom spec string in quotation marks? That's required if it contains spaces. Elaine On Dec 9, 2013, at 11:48 AM, Zhou, Ming (NIH/NCI) [C] wrote: > Hi Elaine, thank you so much for your quick response. I actually is trying to do a simple energy minimization on the side chains. I can't combine the minimize command and the spec-atom command in the command line. Is there a way to do that? > > Minimize spec #0: > > The command line won't take the spec-atom selection I put in after : > > Thanks > > Ming > > -----Original Message----- > From: Elaine Meng [mailto:meng at cgl.ucsf.edu] > Sent: Monday, December 09, 2013 2:40 PM > To: UCSF Chimera Mailing List > Cc: Zhou, Ming (NIH/NCI) [C] > Subject: Re: [Chimera-users] select all side chains > > Another note: > If you are using this for coloring, even though only the sidechain atoms are selected, the ribbon for those residues would still also be colored unless you use ",a" in the coloring command, or if using the Actions menu, choose "Actions... Color... all options" and in the resulting dialog set "Coloring applies to" to "atoms/bonds" instead of "all of the above." > > (I noticed a question you had asked earlier and it reminded me of this issue!) > > Elaine > > On Dec 9, 2013, at 11:29 AM, Elaine Meng wrote: > >> Dear Ming Zhou, >> There are a few different ways, but one is to select protein atoms that are NOT backbone, e.g.: >> >> select protein & ~@n,ca,c,o >> >> Another way is with the command: >> select side chain/base.without CA/C1' >> >> ... or the shorter version: >> select without CA/C1' >> >> This is because you can use various Select menu entries exactly as they appear in the menu to specify atoms in the command line. The menu includes "Select... Structure... side chain/base... without CA/C1'" For more details on which menu items can be used in this way, see the section on "built-in classifications": >> > .html> >> >> If there was also DNA/RNA in the structure, you could then use an additional command to de-select just that part: >> ~select nucleic acid >> >> There is also a "with CA/C1'" (instead of "without") for example if you wanted to use the selection to display the side chains connected to ribbons instead of floating in space. >> >> 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 Dec 9, 2013, at 10:34 AM, Zhou, Ming (NIH/NCI) [C] wrote: >> >>> Dear Elaine: >>> I have a quick question for you. How should I select all the amino acid side chains in a protein but not the backbone (without CA/C1/N/O). How should I write this command? >>> Thanks >>> Ming Zhou >> > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From news at compchem.net Wed Dec 11 04:34:14 2013 From: news at compchem.net (CompChem News) Date: Wed, 11 Dec 2013 14:34:14 +0200 Subject: [Chimera-users] Journal of Organic and Biomolecular Simulations: Full page charge waiver Message-ID: <2756366709064170231488@CompChem> An HTML attachment was scrubbed... URL: From olibclarke at gmail.com Tue Dec 10 18:34:32 2013 From: olibclarke at gmail.com (Oliver Clarke) Date: Tue, 10 Dec 2013 21:34:32 -0500 Subject: [Chimera-users] Color by ramachandran probability? Or molprobity overlap? In-Reply-To: References: Message-ID: <72DEDDAF-7BC8-4D04-B215-E3CBE9F00900@gmail.com> Hi all, Quick question, just wondering if there is any way to color a structure by Ramachandran probability? Or by steric overlap scores for each atom as generated by mol probity? Either of these would be very handy as a way of getting a quick graphical overview of trouble spots in a structure. It seems like Chimera ?knows about? Ramachandran plot data, (as one can generate such plots from the model panel) but I can?t find any convenient way to display this data on the structure. Many thanks, Oliver. From meng at cgl.ucsf.edu Wed Dec 11 10:55:57 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 11 Dec 2013 10:55:57 -0800 Subject: [Chimera-users] Color by ramachandran probability? Or molprobity overlap? In-Reply-To: <72DEDDAF-7BC8-4D04-B215-E3CBE9F00900@gmail.com> References: <72DEDDAF-7BC8-4D04-B215-E3CBE9F00900@gmail.com> Message-ID: <6A1A9274-9B91-4E9E-BA15-313BCF83AA27@cgl.ucsf.edu> Hi Oliver, There is no automatic way (without doing some of your own processing), but if you can calculate the values, it is fairly easy to assign them as attributes. Then you can use the Chimera "Render by Attribute" tool or "rangecolor" command to map the values to colors on the structure. Custom attributes are assigned by reading in an "attribute assignment file," which is basically a tab-separated columns text file with some control lines at the top. The format is described here, and several example files are provided: Amino acid residue phi and psi angles are already attributes, but there is no automatic assessment of how well they agree with a Ramachandran map in Chimera other than actually displaying the map with the values plotted (which can be done via the Model Panel, as you saw). Your processing would need to compare the phi and psi values with Ramachandran plot contours and distill that into some value that could be assigned as a residue attribute (analogously you could take the molprobity output values and assign them as atom attributes), then generate a corresponding attribute assignment file. After reading your custom attribute in, you could use Chimera's existing coloring-by-attribute features, as mentioned above. 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 Dec 10, 2013, at 6:34 PM, Oliver Clarke wrote: > Hi all, > Quick question, just wondering if there is any way to color a structure by Ramachandran probability? Or by steric overlap scores for each atom as generated by mol probity? > > Either of these would be very handy as a way of getting a quick graphical overview of trouble spots in a structure. It seems like Chimera ?knows about? Ramachandran plot data, (as one can generate such plots from the model panel) but I can?t find any convenient way to display this data on the structure. > > Many thanks, > Oliver. From darrellh at niaid.nih.gov Wed Dec 11 11:15:34 2013 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Wed, 11 Dec 2013 19:15:34 +0000 Subject: [Chimera-users] Launch external program from Chimera python script? Message-ID: Hi Chimera friends, I am thinking of writing a script for Chimera that allows the user to map lipophilicity to the surface of protein. There are a few algorithms out there, but the easiest that I've found to use is "pyMLP": http://code.google.com/p/pymlp/ I see two ways to do this: (1) Write a wrapper script (shell, Python, etc.) to first run pyMLP to generate a DX file and then launch Chimera with its own script to generate the surface and do the mapping. (2) Write a Chimera Python script to launch pyMLP to get the DX file, generate the surface, and do the mapping. For my purposes, it might be easier in the long run to choose option 2, but that seems a little trickier starting out. Can you advise me on the best way to proceed? Also, I know that you aren't looking to add new functionality to Chimera v1, but the generation of a lipophilicity map might be a nice feature to add to Chimera at some point and pyMLP seems relatively easy to package with Chimera? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From goddard at sonic.net Wed Dec 11 11:50:30 2013 From: goddard at sonic.net (Tom Goddard) Date: Wed, 11 Dec 2013 11:50:30 -0800 Subject: [Chimera-users] Launch external program from Chimera python script? In-Reply-To: <76BA7643-2416-4162-8645-DF0A5A0269A7@sonic.net> References: <76BA7643-2416-4162-8645-DF0A5A0269A7@sonic.net> Message-ID: <903FD40F-E04D-4816-82AF-130DC3B2BA9F@sonic.net> Hi Darrell, Another problem with making this run within Chimera is that the calculation may take a very long time. Don't know without trying it. Tom On Dec 11, 2013, at 11:46 AM, Tom Goddard wrote: > Hi Darrell, > > The pyMLP code is a single 600 line Python file. > > http://code.google.com/p/pymlp/source/browse/trunk/pyMLP.py > > If you are familiar with Python you could probably turn that directly into a Chimera extension that could compute the lipophilic potential in Chimera without running a separate program, without reading PDB files or writing DX files. To use a PDB model already opened in Chimera would require some knowledge of how to get the molecule data and then put it into the format pyMLP.py wants. To use the calculated potential map without writing a DX files you'd need to know a bit about how to make a density map model in Chimera in memory. These are pretty easy tasks but since we don't have good Chimera programming documentation we would need to show you the way. Your first option of just running pyMLP and Chimera with a script would require less knowledge, and no need to use Python. That would be easier. Your second option is also easier than what I described above, because you still could just use PDB and DX files to pass data between pyMLP and Chimera. I guess my advice would be to do the easiest approach first. Then if that is somehow not convenient to use, do the next harder solution. If that is not convenient to use, then do the still harder solution. > > If you think this is a valuable feature for many users, we could add it to Chimera. My quick look suggests it would be a 1 day effort. The pyMLP code has a BSD license so there are no issues there. The pyMLP code handles only standard amino acids, and I'm not sure if its limitations would cause trouble for users. > > Tom > > > > On Dec 11, 2013, at 11:15 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: > >> Hi Chimera friends, >> >> I am thinking of writing a script for Chimera that allows the user to map lipophilicity to the surface of protein. There are a few algorithms out there, but the easiest that I've found to use is "pyMLP": >> http://code.google.com/p/pymlp/ >> >> I see two ways to do this: >> >> (1) Write a wrapper script (shell, Python, etc.) to first run pyMLP to generate a DX file and then launch Chimera with its own script to generate the surface and do the mapping. >> >> (2) Write a Chimera Python script to launch pyMLP to get the DX file, generate the surface, and do the mapping. >> >> For my purposes, it might be easier in the long run to choose option 2, but that seems a little trickier starting out. Can you advise me on the best way to proceed? >> >> Also, I know that you aren't looking to add new functionality to Chimera v1, but the generation of a lipophilicity map might be a nice feature to add to Chimera at some point and pyMLP seems relatively easy to package with Chimera? >> >> Thanks, >> Darrell >> >> -- >> Darrell Hurt, Ph.D. >> Section Head, Computational Biology >> Bioinformatics and Computational Biosciences Branch (BCBB) >> OCICB/OSMO/OD/NIAID/NIH >> >> 31 Center Drive, Room 3B62B, MSC 2135 >> Bethesda, MD 20892-2135 >> Office: 301-402-0095 >> Mobile: 301-758-3559 >> Web: BCBB Home Page >> Twitter: @niaidbioit >> >> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > From goddard at sonic.net Wed Dec 11 11:46:30 2013 From: goddard at sonic.net (Tom Goddard) Date: Wed, 11 Dec 2013 11:46:30 -0800 Subject: [Chimera-users] Launch external program from Chimera python script? In-Reply-To: References: Message-ID: <76BA7643-2416-4162-8645-DF0A5A0269A7@sonic.net> Hi Darrell, The pyMLP code is a single 600 line Python file. http://code.google.com/p/pymlp/source/browse/trunk/pyMLP.py If you are familiar with Python you could probably turn that directly into a Chimera extension that could compute the lipophilic potential in Chimera without running a separate program, without reading PDB files or writing DX files. To use a PDB model already opened in Chimera would require some knowledge of how to get the molecule data and then put it into the format pyMLP.py wants. To use the calculated potential map without writing a DX files you'd need to know a bit about how to make a density map model in Chimera in memory. These are pretty easy tasks but since we don't have good Chimera programming documentation we would need to show you the way. Your first option of just running pyMLP and Chimera with a script would require less knowledge, and no need to use Python. That would be easier. Your second option is also easier than what I described above, because you still could just use PDB and DX files to pass data between pyMLP and Chimera. I guess my advice would be to do the easiest approach first. Then if that is somehow not convenient to use, do the next harder solution. If that is not convenient to use, then do the still harder solution. If you think this is a valuable feature for many users, we could add it to Chimera. My quick look suggests it would be a 1 day effort. The pyMLP code has a BSD license so there are no issues there. The pyMLP code handles only standard amino acids, and I'm not sure if its limitations would cause trouble for users. Tom On Dec 11, 2013, at 11:15 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: > Hi Chimera friends, > > I am thinking of writing a script for Chimera that allows the user to map lipophilicity to the surface of protein. There are a few algorithms out there, but the easiest that I've found to use is "pyMLP": > http://code.google.com/p/pymlp/ > > I see two ways to do this: > > (1) Write a wrapper script (shell, Python, etc.) to first run pyMLP to generate a DX file and then launch Chimera with its own script to generate the surface and do the mapping. > > (2) Write a Chimera Python script to launch pyMLP to get the DX file, generate the surface, and do the mapping. > > For my purposes, it might be easier in the long run to choose option 2, but that seems a little trickier starting out. Can you advise me on the best way to proceed? > > Also, I know that you aren't looking to add new functionality to Chimera v1, but the generation of a lipophilicity map might be a nice feature to add to Chimera at some point and pyMLP seems relatively easy to package with Chimera? > > Thanks, > Darrell > > -- > Darrell Hurt, Ph.D. > Section Head, Computational Biology > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > > 31 Center Drive, Room 3B62B, MSC 2135 > Bethesda, MD 20892-2135 > Office: 301-402-0095 > Mobile: 301-758-3559 > Web: BCBB Home Page > Twitter: @niaidbioit > > Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From darrellh at niaid.nih.gov Wed Dec 11 12:17:36 2013 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Wed, 11 Dec 2013 20:17:36 +0000 Subject: [Chimera-users] Launch external program from Chimera python script? In-Reply-To: <76BA7643-2416-4162-8645-DF0A5A0269A7@sonic.net> References: <76BA7643-2416-4162-8645-DF0A5A0269A7@sonic.net> Message-ID: Hi Tom, This is a great answer. Thanks for checking out the code of pyMLP. You are always going above and beyond! You're right about pyMLP handling only standard amino acids; my script would have to control for that. The code does take some time to run. It isn't the fastest thing in the world. It takes me about 2 minutes to calculate a DX file for a 350-AA protein. As for its utility for many users, I can only say that I've been looking for this functionality for years in open-source software and only recently found pyMLP after searching the literature and finding an old Italian paper. This functionality exists in SYBYL and it was at least one reason we have been hanging onto that license. It seems that the Schrodinger, Open Eye, and Accelrys suites also have this functionality (or something similar). I can't find any information about MOE. Adding it to Chimera may enhance its attractiveness as an open-source alternative to these commercial packages. For now, I think I'll go with option 1. I know a little Perl and shell; I'm learning Python by crash course. Easy is good for now! As an aside, it is important to remember that lipophilicity and hydrophobicity are often used interchangeably, but they are not synonyms. So the "render by attribute" using the Kyte-Doolittle hydrophobicity scale is a nice orthogonal check on pyMLP mappings. Thanks! Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: Tom Goddard > Date: Wednesday, December 11, 2013 2:46 PM To: Darrell Hurt > Cc: "chimera-users at cgl.ucsf.edu" > Subject: Re: [Chimera-users] Launch external program from Chimera python script? Hi Darrell, The pyMLP code is a single 600 line Python file. http://code.google.com/p/pymlp/source/browse/trunk/pyMLP.py If you are familiar with Python you could probably turn that directly into a Chimera extension that could compute the lipophilic potential in Chimera without running a separate program, without reading PDB files or writing DX files. To use a PDB model already opened in Chimera would require some knowledge of how to get the molecule data and then put it into the format pyMLP.py wants. To use the calculated potential map without writing a DX files you'd need to know a bit about how to make a density map model in Chimera in memory. These are pretty easy tasks but since we don't have good Chimera programming documentation we would need to show you the way. Your first option of just running pyMLP and Chimera with a script would require less knowledge, and no need to use Python. That would be easier. Your second option is also easier than what I described above, because you still could just use PDB and DX files to pass data between pyMLP and Chimera. I guess my advice would be to do the easiest approach first. Then if that is somehow not convenient to use, do the next harder solution. If that is not convenient to use, then do the still harder solution. If you think this is a valuable feature for many users, we could add it to Chimera. My quick look suggests it would be a 1 day effort. The pyMLP code has a BSD license so there are no issues there. The pyMLP code handles only standard amino acids, and I'm not sure if its limitations would cause trouble for users. Tom On Dec 11, 2013, at 11:15 AM, "Hurt, Darrell (NIH/NIAID) [E]" > wrote: Hi Chimera friends, I am thinking of writing a script for Chimera that allows the user to map lipophilicity to the surface of protein. There are a few algorithms out there, but the easiest that I've found to use is "pyMLP": http://code.google.com/p/pymlp/ I see two ways to do this: (1) Write a wrapper script (shell, Python, etc.) to first run pyMLP to generate a DX file and then launch Chimera with its own script to generate the surface and do the mapping. (2) Write a Chimera Python script to launch pyMLP to get the DX file, generate the surface, and do the mapping. For my purposes, it might be easier in the long run to choose option 2, but that seems a little trickier starting out. Can you advise me on the best way to proceed? Also, I know that you aren't looking to add new functionality to Chimera v1, but the generation of a lipophilicity map might be a nice feature to add to Chimera at some point and pyMLP seems relatively easy to package with Chimera? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From danilo.dimaio at gmail.com Thu Dec 12 10:31:06 2013 From: danilo.dimaio at gmail.com (Danilo Di Maio) Date: Thu, 12 Dec 2013 19:31:06 +0100 Subject: [Chimera-users] (no subject) Message-ID: danilo.dimaio at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From bala.biophysics at gmail.com Thu Dec 12 10:58:03 2013 From: bala.biophysics at gmail.com (Bala subramanian) Date: Thu, 12 Dec 2013 19:58:03 +0100 Subject: [Chimera-users] changing the rgb for stereo images Message-ID: Friends, I have a glass with a red-cyan color. When i use the Chimera stereo mode (red-cyan) under view controls. I still see some ghost images. I would like to know if there is any possibility to add a features something like a box where i can give the rgb (the light frequencies) values of the images to match my glass. Thank you, Bala -- C. Balasubramanian -------------- next part -------------- An HTML attachment was scrubbed... URL: From cmurin at scripps.edu Thu Dec 12 13:26:01 2013 From: cmurin at scripps.edu (Daniel Murin) Date: Thu, 12 Dec 2013 13:26:01 -0800 Subject: [Chimera-users] chimera slow Message-ID: <83025BE3F3B8D644AA9F8CAA21F264080236B05AB856@EXCH-CCR01.lj.ad.scripps.edu> Hi, I have been trying to use the Unit Cell function on Chimera. It works, but the graphic is so large that moving it around is nearly impossible because the program is running so slowly. It is rendered in ribbon. Is there a way to lower the quality in order to manipulate the graphic faster? Thanks! Charles Daniel Murin Ph.D. Candidate - Ward/Ollmann Saphire Labs Integrative Structural and Computational Biology Immunology and Microbial Science Kellogg School of Science and Technology The Scripps Research Institute 10550 North Torrey Pines Road, CimBio 105 La Jolla, CA 92037 Office: 858.784.3326 Lab: 858.784.7170 Fax: 858.784.8218 email: cmurin at scripps.edu From meng at cgl.ucsf.edu Thu Dec 12 14:00:02 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 12 Dec 2013 14:00:02 -0800 Subject: [Chimera-users] chimera slow In-Reply-To: <83025BE3F3B8D644AA9F8CAA21F264080236B05AB856@EXCH-CCR01.lj.ad.scripps.edu> References: <83025BE3F3B8D644AA9F8CAA21F264080236B05AB856@EXCH-CCR01.lj.ad.scripps.edu> Message-ID: <3BA4BE82-5CE9-45C7-AB52-67F95425B60B@cgl.ucsf.edu> Hi Daniel, It depends on how you want to use the results. You could try instead using Multiscale Models (by default creates low-res surfaces of the extra copies instead of full atomic representations), or the command "sym" with "surfaces true" to do the same thing. If you do need to look at atomic detail in some of the copies, the Multiscale Models interface allows selecting those specific copies and then choosing one of the more detailed kinds of display. Or, if you really did need ribbons and/or atoms for all of the copies, you can decrease their display quality generally by decreasing "subdivision quality," in the Effects tool or with the set command, e.g.: set subdivision .5 ? but low values are pretty hideous. Default is 1.5. Also, I'm not sure how much this would help. Another possibility is to hide ribbons and show backbone trace, maybe as sticks or even wire. 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 Dec 12, 2013, at 1:26 PM, Daniel Murin wrote: > Hi, > I have been trying to use the Unit Cell function on Chimera. It works, but the graphic is so large that moving it around is nearly impossible because the program is running so slowly. It is rendered in ribbon. Is there a way to lower the quality in order to manipulate the graphic faster? > Thanks! From a.vaitinadapoule at gmail.com Fri Dec 13 10:11:41 2013 From: a.vaitinadapoule at gmail.com (Aurore Vaitinadapoule) Date: Fri, 13 Dec 2013 19:11:41 +0100 Subject: [Chimera-users] Modeling with cryo-EM Message-ID: Dear all, I'm would like tu use this following script to model with cryo-EM: from modeller import * log.verbose() env = environ() struct='./M60_9.pdb' map='new_map.mrc' resolution=10.2 box_size=48 # how to define the box size ?? apix=1.88 x=90; y=63; z=23 #origin steps=20 # Read in cryo-EM density map den = density(env, file=map, em_density_format='MRC', voxel_size=apix, resolution=resolution, em_map_size=box_size, density_type='GAUSS', px=x,py=y,pz=z) # Fit the PDB file into the map by MC simulated annealing den.grid_search(em_density_format='MRC', num_structures=1, em_pdb_name=struct, chains_num=[1], start_type='CENTER', number_of_steps=steps, angular_step_size=30., temperature=100., best_docked_models=1, translate_type='RANDOM', em_fit_output_file='modem.log') But i got this error message: _modeller.ModellerError: read_mrc_h_E> Density map must be cubic, and of dimension em_map_size (48): actual dimensions (40, 40, 36) What is exactly the box size? And how to define it? Thank's Aurore -- Aurore G. VA?TINADAPOUL? aurore .vaitinadapoule at inserm.fr a.vaitinadapoule at gmail.com PhD Student in Bioinformatics INSERM UMR-S665, DSIMB Team, Dynamique des Structures et des Interactions des Macromol?cules Biologiques Mobile phone: +33(0) 778 18 52 07 -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Fri Dec 13 11:27:46 2013 From: goddard at sonic.net (Tom Goddard) Date: Fri, 13 Dec 2013 11:27:46 -0800 Subject: [Chimera-users] Modeling with cryo-EM In-Reply-To: References: Message-ID: <9DA37E25-638F-4E02-9647-997B2B151BD9@sonic.net> This is a question about Modeller and appears to have nothing to do with Chimera. Tom On Dec 13, 2013, at 10:11 AM, Aurore Vaitinadapoule wrote: > Dear all, > > I'm would like tu use this following script to model with cryo-EM: > > from modeller import * > > log.verbose() > env = environ() > > struct='./M60_9.pdb' > map='new_map.mrc' > resolution=10.2 > box_size=48 # how to define the box size ?? > apix=1.88 > x=90; y=63; z=23 #origin > steps=20 > > # Read in cryo-EM density map > den = density(env, file=map, em_density_format='MRC', > voxel_size=apix, resolution=resolution, em_map_size=box_size, > density_type='GAUSS', px=x,py=y,pz=z) > > # Fit the PDB file into the map by MC simulated annealing > den.grid_search(em_density_format='MRC', num_structures=1, > em_pdb_name=struct, chains_num=[1], > start_type='CENTER', number_of_steps=steps, > angular_step_size=30., temperature=100., > best_docked_models=1, translate_type='RANDOM', > em_fit_output_file='modem.log') > > > But i got this error message: > _modeller.ModellerError: read_mrc_h_E> Density map must be cubic, and of dimension em_map_size (48): actual dimensions (40, 40, 36) > > > What is exactly the box size? And how to define it? > > Thank's > > Aurore > > -- > Aurore G. VA?TINADAPOUL? > > > PhD Student in Bioinformatics > INSERM UMR-S665, DSIMB Team, > Dynamique des Structures et > des Interactions des Macromol?cules Biologiques > > Mobile phone: +33(0) 778 18 52 07 > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From darrellh at niaid.nih.gov Fri Dec 13 12:16:10 2013 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Fri, 13 Dec 2013 20:16:10 +0000 Subject: [Chimera-users] Dynamic scolor custom cmap? Message-ID: Hi Chimera friends, I have a volumetric potential file loaded that I want to map onto a molecular surface. For my application, I want the color mapping to use a custom palette of at least three colors that spans the full range of surface values. I know that I can do this by simply specifying the custom colors in the Surface Color panel and then clicking "Set full range of surface values". That works for me. However, I want to do this via command line. The following line works for me (I've omitted "cmapRange full" because that is the default setting): scolor #0 volume #1 offset 1.4 cmap cyanmaroon My problem become if I want to set a custom palette: scolor #0 volume #1 offset 1.4 cmap -10,yellow:0,white:10,green This line also works, but for values lower or higher than ?10 or +10, the color ramp "plateaus". And this line only works because the extents of this particular mapping happen to go from ?29 to +17. Is it possible to obtain the values for the full range and specify them for a custom palette? Or is it possible to assign a custom palette and call it like the default palettes? I'm happy to clarify if needed. Thanks! Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From goddard at sonic.net Fri Dec 13 13:10:21 2013 From: goddard at sonic.net (Tom Goddard) Date: Fri, 13 Dec 2013 13:10:21 -0800 Subject: [Chimera-users] Dynamic scolor custom cmap? In-Reply-To: References: Message-ID: <9DBCED9A-A0C0-469E-85FE-67A25BC63C0D@sonic.net> Hi Darrell, There is a tricky undocumented feature that solves your problem. If you specify the scolor option "cmapRange full" and you also specify the cmap option like "cmap 0,red:0.6,yellow:1,blue" or "cmap 0.2,green:0.8,yellow" then values from 0 to 1 in the cmap spec will be mapped linearly to the minimum to maximum full range values. The documentation says the "full" is the default for the cmapRange option but that is not true. Not using cmapRange simply does no range mapping on your specified cmap. I wrote this code and didn't adequately explain it to Elaine who wrote the documentation. We will fix the documentation. Tom On Dec 13, 2013, at 12:16 PM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: > Hi Chimera friends, > > I have a volumetric potential file loaded that I want to map onto a molecular surface. For my application, I want the color mapping to use a custom palette of at least three colors that spans the full range of surface values. > > I know that I can do this by simply specifying the custom colors in the Surface Color panel and then clicking "Set full range of surface values". That works for me. > > However, I want to do this via command line. The following line works for me (I've omitted "cmapRange full" because that is the default setting): > > scolor #0 volume #1 offset 1.4 cmap cyanmaroon > > My problem become if I want to set a custom palette: > > scolor #0 volume #1 offset 1.4 cmap -10,yellow:0,white:10,green > > This line also works, but for values lower or higher than ?10 or +10, the color ramp "plateaus". And this line only works because the extents of this particular mapping happen to go from ?29 to +17. > > Is it possible to obtain the values for the full range and specify them for a custom palette? Or is it possible to assign a custom palette and call it like the default palettes? > > I'm happy to clarify if needed. > > Thanks! > Darrell > > -- > Darrell Hurt, Ph.D. > Section Head, Computational Biology > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > > 31 Center Drive, Room 3B62B, MSC 2135 > Bethesda, MD 20892-2135 > Office: 301-402-0095 > Mobile: 301-758-3559 > Web: BCBB Home Page > Twitter: @niaidbioit > > Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From darrellh at niaid.nih.gov Fri Dec 13 13:15:33 2013 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Fri, 13 Dec 2013 21:15:33 +0000 Subject: [Chimera-users] Dynamic scolor custom cmap? In-Reply-To: <9DBCED9A-A0C0-469E-85FE-67A25BC63C0D@sonic.net> Message-ID: <624EEF8436486C438E2C9E71C4879E6E152647@MLBXV06.nih.gov> Hi Tom, This is perfect. I think this will work well for me. Thanks for the quick reply and the fix. Every time I think there might be a deficiency in Chimera, you all prove me wrong. And it is usually because you've already solved the problem before I ever thought there might be one! Cheers, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office? 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ----- Original Message ----- From: Tom Goddard [mailto:goddard at sonic.net] Sent: Friday, December 13, 2013 04:10 PM To: Hurt, Darrell (NIH/NIAID) [E] Cc: Chimera-users at cgl.ucsf.edu List Subject: Re: [Chimera-users] Dynamic scolor custom cmap? Hi Darrell, There is a tricky undocumented feature that solves your problem. If you specify the scolor option "cmapRange full" and you also specify the cmap option like "cmap 0,red:0.6,yellow:1,blue" or "cmap 0.2,green:0.8,yellow" then values from 0 to 1 in the cmap spec will be mapped linearly to the minimum to maximum full range values. The documentation says the "full" is the default for the cmapRange option but that is not true. Not using cmapRange simply does no range mapping on your specified cmap. I wrote this code and didn't adequately explain it to Elaine who wrote the documentation. We will fix the documentation. Tom On Dec 13, 2013, at 12:16 PM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: > Hi Chimera friends, > > I have a volumetric potential file loaded that I want to map onto a molecular surface. For my application, I want the color mapping to use a custom palette of at least three colors that spans the full range of surface values. > > I know that I can do this by simply specifying the custom colors in the Surface Color panel and then clicking "Set full range of surface values". That works for me. > > However, I want to do this via command line. The following line works for me (I've omitted "cmapRange full" because that is the default setting): > > scolor #0 volume #1 offset 1.4 cmap cyanmaroon > > My problem become if I want to set a custom palette: > > scolor #0 volume #1 offset 1.4 cmap -10,yellow:0,white:10,green > > This line also works, but for values lower or higher than ?10 or +10, the color ramp "plateaus". And this line only works because the extents of this particular mapping happen to go from ?29 to +17. > > Is it possible to obtain the values for the full range and specify them for a custom palette? Or is it possible to assign a custom palette and call it like the default palettes? > > I'm happy to clarify if needed. > > Thanks! > Darrell > > -- > Darrell Hurt, Ph.D. > Section Head, Computational Biology > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > > 31 Center Drive, Room 3B62B, MSC 2135 > Bethesda, MD 20892-2135 > Office: 301-402-0095 > Mobile: 301-758-3559 > Web: BCBB Home Page > Twitter: @niaidbioit > > Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From gregc at cgl.ucsf.edu Fri Dec 13 13:57:20 2013 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Fri, 13 Dec 2013 13:57:20 -0800 Subject: [Chimera-users] changing the rgb for stereo images In-Reply-To: References: Message-ID: <52AB82C0.1070505@cgl.ucsf.edu> Hi Bala, It is not possible for for chimera to set the RGB frequencies, those are determined by your display. But there are several things that can be done to reduce and/or eliminate the ghosting you see: 1. Don't use any saturated colors: you'll get the best effect with gray-scale images. 2. Get better red-cyan glasses: In general, paper glasses are blurry compared to plastic glasses. But some plastic glasses do a better job than others -- you'll need to do some research. 3. Reduce the amount of parallax in the image -- have (most) everything behind the focal plane. Reducing the eye separation might help too. 4. Not likely, but you might need to turn off any color correction that your display is doing. Chimera does not use any color management, so an image in just the red channel should only be shown with the display's red light, but is possible that your display or operating system is remapping the colors to match a particular ICC color profile, e.g., the sRGB profile, and that might cause ghosting. The effect should be too small to notice though. HTH, Greg P.S. Researching this I came across magenta-green stereo which is supposed to be better than red-cyan stereo. Since you can buy magenta-green glasses, I will add support into the daily build. Note that magneta-green are right-left colors, unlike red-cyan which are left-right colors. On 12/12/2013 10:58 AM, Bala subramanian wrote: > Friends, > > I have a glass with a red-cyan color. When i use the Chimera stereo > mode (red-cyan) under view controls. I still see some ghost images. > > I would like to know if there is any possibility to add a features > something like a box where i can give the rgb (the light frequencies) > values of the images to match my glass. > > Thank you, > Bala > > > > -- > C. Balasubramanian > > > _______________________________________________ > 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 darrellh at niaid.nih.gov Mon Dec 16 06:05:39 2013 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Mon, 16 Dec 2013 14:05:39 +0000 Subject: [Chimera-users] Local execution of pdb2pqr and APBS Message-ID: Hi Chimera friends, Sorry to bother you again with so many questions. I'm trying to use PDB2PQR and APBS in a script to calculate an EP map. I know how to specify a local executable location for these external applications if I use the graphics interface, but the documentation that I can find does not indicate how to do this via the command line. Is it possible? How do I do it? Thanks! Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From rswett at chem.wayne.edu Mon Dec 16 08:13:19 2013 From: rswett at chem.wayne.edu (rswett at chem.wayne.edu) Date: Mon, 16 Dec 2013 11:13:19 -0500 Subject: [Chimera-users] Setting selection mode command line Message-ID: <20131216111319.14020s87h2i5ydnj@chem.wayne.edu> Hi all, I'm interested in putting together a script that will open several large pdb files, select some very specific pieces of those files and save the output to another file. The problem is that they are large files and unwieldy in a graphics window. I have no problem generating the commands to select the regions I'm interested in, but I still need to be able to switch selection modes in between commands. Is there a way to change the selection mode at the command line without navigating the selection menu? Rebecca From cjhirschmugl at gmail.com Sat Dec 14 15:47:15 2013 From: cjhirschmugl at gmail.com (Carol J Hirschmugl) Date: Sat, 14 Dec 2013 17:47:15 -0600 Subject: [Chimera-users] import binary format .raw file Message-ID: <36A127E0-0654-49A4-89AC-6876D59DDAB9@gmail.com> Hello, I am new to chimera, but have seen its capabilities for rendering 3D images of complex data sets, and think that this will be an appropriate program for excellent image analysis for my 3D tomography data sets. My data sets are in general binary format, (.raw file), 32 float, big endian, x fastest order for an x,y,z data set of 128 x 128 x 128 voxels of grey scale information. I am using AVIZO and FIJI at present. Avizo is expensive, and fiji is slow and reduces the data to 8 bit before rendering it, which I find unacceptable. TO move to Chimera - I found the web page in the Users Manual that suggested ADDING A FILE TYPE But I am lost by the description of how to proceed since I do not have prior knowledge of python and how to do the mapping to CHIMERA (x,y,z) that is suggested. I gather I need to write a python code - or numpy code maybe. Can you help or provide more context or a self-tutorial link so I can fill in the details? Thank you, Carol -------------- next part -------------- An HTML attachment was scrubbed... URL: From conrad at cgl.ucsf.edu Mon Dec 16 09:51:08 2013 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Mon, 16 Dec 2013 09:51:08 -0800 Subject: [Chimera-users] Local execution of pdb2pqr and APBS In-Reply-To: References: Message-ID: <52AF3D8C.7010002@cgl.ucsf.edu> Ah. Well. Ermmm. It's not possible right now due to an oversight on my part. Although the functionality was all implemented, there is no way to invoke it. I've added some code to the command lines for apbs, pdb2pqr and vina. There are now three additional optional arguments to those commands: - backend = "opal" | "local" - service = Opal service name | path to executable - url = Opal URL | unused So a command like: apbs backend local service /tmp/myapbs should initiate a local computation process. I say "should" because I've not installed APBS on my machine and am a little too busy to do it today. However, when I test the above command, it does tell me that /tmp/myapbs is not an executable file, so the code at least somewhat works. I thought I'd make that available in the daily build for tomorrow and let someone "volunteer" to test it. :-) If you do have a chance to test it, please let me know whether it works. I'll install and test it with apbs on my machine in the next couple days in any case. Conrad On 12/16/2013 6:05 AM, Hurt, Darrell (NIH/NIAID) [E] wrote: > Hi Chimera friends, > > Sorry to bother you again with so many questions. > > I'm trying to use PDB2PQR and APBS in a script to calculate an EP > map. I know how to specify a local executable location for these > external applications if I use the graphics interface, but the > documentation that I can find does not indicate how to do this via > the command line. Is it possible? How do I do it? > > Thanks! Darrell > > -- Darrell Hurt, Ph.D. Section Head, Computational Biology > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > > 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: > 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home > Page > > Twitter: @niaidbioit > > Disclaimer: The information in this e-mail and any of its attachments > is confidential and may contain sensitive information. It should not > be used by anyone who is not the original intended recipient. If you > have received this e-mail in error please inform the sender and > delete it from your mailbox or any other storage devices. National > Institute of Allergy and Infectious Diseases shall not accept > liability for any statements made that are sender's own and not > expressly made on behalf of the NIAID by one of its representatives. > > _______________________________________________ Chimera-users mailing > list Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From meng at cgl.ucsf.edu Mon Dec 16 09:51:46 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Dec 2013 09:51:46 -0800 Subject: [Chimera-users] Setting selection mode command line In-Reply-To: <20131216111319.14020s87h2i5ydnj@chem.wayne.edu> References: <20131216111319.14020s87h2i5ydnj@chem.wayne.edu> Message-ID: <2F976A33-ED2D-4B21-B2AB-A71BA1AA9C85@cgl.ucsf.edu> Hi Rebecca, As far as I know, you cannot change the selection mode in a command. However, with commands you can often circumvent selection entirely, or in the few cases where you can't easily do that (for example, the "findhbond" command uses selections), there are sometimes alternative routes to achieving the same result. In the command line, you can make a selection and then use ~select to deselect only part of it. Sometimes instead of selections you can use aliases and combinations of aliases. For writing a subset of the coordinates, you could undisplay the unwanted atoms and use the corresponding option to the "write" command to exclude them from the output. Or, depending on exactly what you are doing, you could just delete the unwanted atoms before saving to a file. Avoiding selection may be one of the advantages of commands, since (as you found) drawing the selection outlines can make things slow. 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 Dec 16, 2013, at 8:13 AM, rswett at chem.wayne.edu wrote: > Hi all, > I'm interested in putting together a script that will open several large pdb files, select some very specific pieces of those files and save the output to another file. The problem is that they are large files and unwieldy in a graphics window. I have no problem generating the commands to select the regions I'm interested in, but I still need to be able to switch selection modes in between commands. Is there a way to change the selection mode at the command line without navigating the selection menu? > Rebecca From darrellh at niaid.nih.gov Mon Dec 16 09:55:05 2013 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Mon, 16 Dec 2013 17:55:05 +0000 Subject: [Chimera-users] Local execution of pdb2pqr and APBS In-Reply-To: <52AF3D8C.7010002@cgl.ucsf.edu> References: <52AF3D8C.7010002@cgl.ucsf.edu> Message-ID: Hi Conrad, I think it will be OK in my scripts for now, but eventually I will need this functionality for a web server we're developing. I think it unlikely that we'll get permission from our security folks to have our web server send jobs to an external web server and retrieve those results. This is why I need to do it locally. I'll download the daily build and give this a try. I'll let you know ASAP. Thanks! Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: Conrad Huang > Date: Monday, December 16, 2013 12:51 PM To: Darrell Hurt >, "'chimera-users at cgl.ucsf.edu'" > Subject: Re: [Chimera-users] Local execution of pdb2pqr and APBS Ah. Well. Ermmm. It's not possible right now due to an oversight on my part. Although the functionality was all implemented, there is no way to invoke it. I've added some code to the command lines for apbs, pdb2pqr and vina. There are now three additional optional arguments to those commands: - backend = "opal" | "local" - service = Opal service name | path to executable - url = Opal URL | unused So a command like: apbs backend local service /tmp/myapbs should initiate a local computation process. I say "should" because I've not installed APBS on my machine and am a little too busy to do it today. However, when I test the above command, it does tell me that /tmp/myapbs is not an executable file, so the code at least somewhat works. I thought I'd make that available in the daily build for tomorrow and let someone "volunteer" to test it. :-) If you do have a chance to test it, please let me know whether it works. I'll install and test it with apbs on my machine in the next couple days in any case. Conrad On 12/16/2013 6:05 AM, Hurt, Darrell (NIH/NIAID) [E] wrote: Hi Chimera friends, Sorry to bother you again with so many questions. I'm trying to use PDB2PQR and APBS in a script to calculate an EP map. I know how to specify a local executable location for these external applications if I use the graphics interface, but the documentation that I can find does not indicate how to do this via the command line. Is it possible? How do I do it? Thanks! Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at sonic.net Mon Dec 16 10:24:49 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 16 Dec 2013 10:24:49 -0800 Subject: [Chimera-users] import binary format .raw file In-Reply-To: <36A127E0-0654-49A4-89AC-6876D59DDAB9@gmail.com> References: <36A127E0-0654-49A4-89AC-6876D59DDAB9@gmail.com> Message-ID: Hi Carol, I think your best approach is to convert your raw EM map data to another file format that contains a header with the size of the map, value type, byte order, grid plane spacing. The problem with the raw data is that it cannot be interpreted without specifying additional parameters like the grid size. Chimera currently doesn't have a method to ask the user for extra information about how to interpret data in a file. So it isn't a simple matter to add a file format. Data in raw format is likely to become worthless very quickly when no one remembers the extra parameters, so I strongly encourage avoiding raw format. I don't know of a program to recommend to convert raw data, but since you generated the data somehow, maybe the program you used can export a more usable file format. Tom On Dec 14, 2013, at 3:47 PM, Carol J Hirschmugl wrote: > Hello, > > I am new to chimera, but have seen its capabilities for rendering 3D images of complex data sets, > and think that this will be an appropriate program for excellent image analysis for my 3D tomography data sets. > > My data sets are in general binary format, (.raw file), 32 float, big endian, x fastest order for an x,y,z > data set of 128 x 128 x 128 voxels of grey scale information. I am using AVIZO and FIJI at present. Avizo > is expensive, and fiji is slow and reduces the data to 8 bit before rendering it, which I find unacceptable. > > TO move to Chimera - I found the web page in the Users Manual that suggested > ADDING A FILE TYPE > > But I am lost by the description of how to proceed since I do not have prior knowledge of python and how to do the mapping to CHIMERA (x,y,z) that is suggested. > I gather I need to write a python code - or numpy code maybe. Can you help or provide more context or a self-tutorial link so I can fill in the details? > > Thank you, > Carol > > _______________________________________________ > 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 darrellh at niaid.nih.gov Mon Dec 16 10:55:36 2013 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Mon, 16 Dec 2013 18:55:36 +0000 Subject: [Chimera-users] Export options for x3d2stl Message-ID: Hi Chimera friends, Here's the second question of the day. Thanks for your patience with me. When I export the scene as an STL (for 3D printing), I think what happens is that Chimera outputs first an X3D file and then runs the utility program "x3d2stl" to create the STL. The X3D file is about 5 MB, but the STL is about 100 MB. I understand that much of this size inflation is because the "primitives" in X3D have to be converted to mesh objects for STL. However, when I look at the STL file, the meshes derived from the primitives are finer than I really need. I find that I can "get away with" a coarser meshification by using x3d2stl on the command line: x3d2stl -c -r 2 -o sticks.stl < sticks.x3d If I want to export the scene via the command line within Blender, is there any way to issue options to x3d2stl? Or should I just run x3d2stl outside of Blender? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From rswett at chem.wayne.edu Mon Dec 16 11:44:51 2013 From: rswett at chem.wayne.edu (rswett at chem.wayne.edu) Date: Mon, 16 Dec 2013 14:44:51 -0500 Subject: [Chimera-users] Setting selection mode command line In-Reply-To: <2F976A33-ED2D-4B21-B2AB-A71BA1AA9C85@cgl.ucsf.edu> References: <20131216111319.14020s87h2i5ydnj@chem.wayne.edu> <2F976A33-ED2D-4B21-B2AB-A71BA1AA9C85@cgl.ucsf.edu> Message-ID: <20131216144451.13252kc57nks820j@chem.wayne.edu> Alright, thanks. I was hoping to be able to manipulate some excessively large pdb files using chimera commandline only with the --nogui option to get around the display problem. I had intended to open three files, one protein, one solvated system and one standalone ligand. Align the protein to the solvated system and use the zone selection to carve out a sphere around the standalone ligand, saving that portion of the solvated system and the entirety of both progtein structures into a single file. If you have any suggestions let me know. I'll start looking int aliasing if you think that would help bet around the gui. As it stands, I can't get it to work with the --nogui flag on windows anyway. I'm using the command chimera --nogui block.cmd where block.cmd simply opens the solvated system and ligand, selects a zone around the ligand and saves the selected atoms to a file, but I get no output and it runs too fast to be actually reading in the structures. Suggestions? I'm using the 1.8.1 build Quoting Elaine Meng : > Hi Rebecca, > As far as I know, you cannot change the selection mode in a command. > However, with commands you can often circumvent selection entirely, > or in the few cases where you can't easily do that (for example, the > "findhbond" command uses selections), there are sometimes > alternative routes to achieving the same result. In the command > line, you can make a selection and then use ~select to deselect only > part of it. Sometimes instead of selections you can use aliases and > combinations of aliases. For writing a subset of the coordinates, > you could undisplay the unwanted atoms and use the corresponding > option to the "write" command to exclude them from the output. Or, > depending on exactly what you are doing, you could just delete the > unwanted atoms before saving to a file. > > > > > > Avoiding selection may be one of the advantages of commands, since > (as you found) drawing the selection outlines can make things slow. > > 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 Dec 16, 2013, at 8:13 AM, rswett at chem.wayne.edu wrote: > >> Hi all, >> I'm interested in putting together a script that will open several >> large pdb files, select some very specific pieces of those files >> and save the output to another file. The problem is that they are >> large files and unwieldy in a graphics window. I have no problem >> generating the commands to select the regions I'm interested in, >> but I still need to be able to switch selection modes in between >> commands. Is there a way to change the selection mode at the >> command line without navigating the selection menu? >> Rebecca > From meng at cgl.ucsf.edu Mon Dec 16 11:56:40 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Dec 2013 11:56:40 -0800 Subject: [Chimera-users] Setting selection mode command line In-Reply-To: <20131216144451.13252kc57nks820j@chem.wayne.edu> References: <20131216111319.14020s87h2i5ydnj@chem.wayne.edu> <2F976A33-ED2D-4B21-B2AB-A71BA1AA9C85@cgl.ucsf.edu> <20131216144451.13252kc57nks820j@chem.wayne.edu> Message-ID: <64B21110-5678-4E1B-A9A4-735138CA912F@cgl.ucsf.edu> Hi Rebecca, I don't know much about nogui, maybe others can say something about that. I don't know if that would buy you that much time, even if it was working the way you intended. However, you can specify zones in commands without selecting anything. For example: color red ligand z<8 ?and do more complicated combinations, for example: delete solvent & #1 & ligand z>8 (delete solvent residues in model 1 that don't have any atoms within 8 ang of ligand? or ~display instead of delete). Doesn't sound like you'd need aliases. See zones and combinations in the atomspec page. zr and z are for residue-based cutoff, za for atom-based Elaine On Dec 16, 2013, at 11:44 AM, rswett at chem.wayne.edu wrote: > Alright, thanks. > I was hoping to be able to manipulate some excessively large pdb files using chimera commandline only with the --nogui option to get around the display problem. I had intended to open three files, one protein, one solvated system and one standalone ligand. Align the protein to the solvated system and use the zone selection to carve out a sphere around the standalone ligand, saving that portion of the solvated system and the entirety of both progtein structures into a single file. If you have any suggestions let me know. I'll start looking int aliasing if you think that would help bet around the gui. > > As it stands, I can't get it to work with the --nogui flag on windows anyway. I'm using the command > chimera --nogui block.cmd > where block.cmd simply opens the solvated system and ligand, selects a zone around the ligand and saves the selected atoms to a file, but I get no output and it runs too fast to be actually reading in the structures. Suggestions? I'm using the 1.8.1 build > > > Quoting Elaine Meng : > >> Hi Rebecca, >> As far as I know, you cannot change the selection mode in a command. However, with commands you can often circumvent selection entirely, or in the few cases where you can't easily do that (for example, the "findhbond" command uses selections), there are sometimes alternative routes to achieving the same result. In the command line, you can make a selection and then use ~select to deselect only part of it. Sometimes instead of selections you can use aliases and combinations of aliases. For writing a subset of the coordinates, you could undisplay the unwanted atoms and use the corresponding option to the "write" command to exclude them from the output. Or, depending on exactly what you are doing, you could just delete the unwanted atoms before saving to a file. >> >> >> >> >> >> Avoiding selection may be one of the advantages of commands, since (as you found) drawing the selection outlines can make things slow. >> >> 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 Dec 16, 2013, at 8:13 AM, rswett at chem.wayne.edu wrote: >> >>> Hi all, >>> I'm interested in putting together a script that will open several large pdb files, select some very specific pieces of those files and save the output to another file. The problem is that they are large files and unwieldy in a graphics window. I have no problem generating the commands to select the regions I'm interested in, but I still need to be able to switch selection modes in between commands. Is there a way to change the selection mode at the command line without navigating the selection menu? >>> Rebecca >> > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From darrellh at niaid.nih.gov Mon Dec 16 11:59:34 2013 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Mon, 16 Dec 2013 19:59:34 +0000 Subject: [Chimera-users] Attribute Calculator by command line? Message-ID: Hi Chimera friends, I'm trying to calculate convexity as demonstrated in the Attributes tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html I can do it with the graphical tools without a problem, but when I try to do it via the command line, I run into trouble. I cannot find any documentation on running the Attributes Calculator on the command line. I've tried using "setattr": setattr a convexity atom.areaSAS/atom.areaSES This command generates a new atom attribute called "convexity" for every atom, but the value of this attribute for every atom is literally "atom.areaSAS/atom.areaSES" instead of the calculated value. Is there a way to calculate a new attribute value on the command line within Chimera? Sorry to be so demanding? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From gregc at cgl.ucsf.edu Mon Dec 16 12:06:17 2013 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 16 Dec 2013 12:06:17 -0800 Subject: [Chimera-users] Export options for x3d2stl In-Reply-To: References: Message-ID: <52AF5D39.9020307@cgl.ucsf.edu> I assume you meant just run outside of Chimera. x3d2stl would presumably always be run outside of Blender. And to answer your question, right now there is no way within chimera to give options to x3d2stl, nor any of the other converters -- X3D output is the only completely native format. So you need to first export the X3D output, then run x3d2stl separately with the options you require. As you may have deduced, the -r option sets the tessellation resolution, roughly the number of vertices per unit area, and -c says to cap all primitives. Since the sphere and cylinders intersect that chimera generates to represent atoms and bonds, the STL triangles also intersect. And intersecting triangles cause problems for some 3D printer software, so you might need to limit the output to just surfaces. Some 3D printer software takes VRML input, so for those printers, I'd recommend using Chimera VRML output, and let the 3D printer software do the conversion to STL. HTH, Greg On 12/16/2013 10:55 AM, Hurt, Darrell (NIH/NIAID) [E] wrote: > Hi Chimera friends, > > Here's the second question of the day. Thanks for your patience with me. > > When I export the scene as an STL (for 3D printing), I think what happens is that Chimera outputs first an X3D file and then runs the utility program "x3d2stl" to create the STL. The X3D file is about 5 MB, but the STL is about 100 MB. I understand that much of this size inflation is because the "primitives" in X3D have to be converted to mesh objects for STL. However, when I look at the STL file, the meshes derived from the primitives are finer than I really need. > > I find that I can "get away with" a coarser meshification by using x3d2stl on the command line: > > x3d2stl -c -r 2 -o sticks.stl < sticks.x3d > > If I want to export the scene via the command line within Blender, is there any way to issue options to x3d2stl? Or should I just run x3d2stl outside of Blender? > > Thanks, > Darrell > > -- > Darrell Hurt, Ph.D. > Section Head, Computational Biology > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > > 31 Center Drive, Room 3B62B, MSC 2135 > Bethesda, MD 20892-2135 > Office: 301-402-0095 > Mobile: 301-758-3559 > Web: BCBB Home Page > Twitter: @niaidbioit > > Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. > > _______________________________________________ > 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 Dec 16 12:11:10 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 16 Dec 2013 12:11:10 -0800 Subject: [Chimera-users] Setting selection mode command line In-Reply-To: <64B21110-5678-4E1B-A9A4-735138CA912F@cgl.ucsf.edu> References: <20131216111319.14020s87h2i5ydnj@chem.wayne.edu> <2F976A33-ED2D-4B21-B2AB-A71BA1AA9C85@cgl.ucsf.edu> <20131216144451.13252kc57nks820j@chem.wayne.edu> <64B21110-5678-4E1B-A9A4-735138CA912F@cgl.ucsf.edu> Message-ID: Yeah, the primary thing is that you can pretty much emulate selection modes with operators in the command line: | (vertical bar): 'or' [union] ("#1 | ligand" is everything in model 1 and all ligands) &: 'and' [intersection] (""#1 & ligand" is the ligands in model 1) ~: 'not' [negation] ("#1 & ~ligand" is everything in model 1 that is not ligand) If you find it getting too complicated for you, you can instead build up a selection in piecemeal fashion with the 'sel' command: sel ligand & #1 (selection the ligand in model 1) sel sel z<5 (select everything within 5 angstroms of that) sel sel & #2 (keep only the part in model 2) then whatever command you wanted (e.g. "color red sel"). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Dec 16, 2013, at 11:56 AM, Elaine Meng wrote: > Hi Rebecca, > I don't know much about nogui, maybe others can say something about that. I don't know if that would buy you that much time, even if it was working the way you intended. > > However, you can specify zones in commands without selecting anything. For example: > > color red ligand z<8 > > ?and do more complicated combinations, for example: > > delete solvent & #1 & ligand z>8 > > (delete solvent residues in model 1 that don't have any atoms within 8 ang of ligand? or ~display instead of delete). Doesn't sound like you'd need aliases. > > See zones and combinations in the atomspec page. zr and z are for residue-based cutoff, za for atom-based > > > > Elaine > > On Dec 16, 2013, at 11:44 AM, rswett at chem.wayne.edu wrote: > >> Alright, thanks. >> I was hoping to be able to manipulate some excessively large pdb files using chimera commandline only with the --nogui option to get around the display problem. I had intended to open three files, one protein, one solvated system and one standalone ligand. Align the protein to the solvated system and use the zone selection to carve out a sphere around the standalone ligand, saving that portion of the solvated system and the entirety of both progtein structures into a single file. If you have any suggestions let me know. I'll start looking int aliasing if you think that would help bet around the gui. >> >> As it stands, I can't get it to work with the --nogui flag on windows anyway. I'm using the command >> chimera --nogui block.cmd >> where block.cmd simply opens the solvated system and ligand, selects a zone around the ligand and saves the selected atoms to a file, but I get no output and it runs too fast to be actually reading in the structures. Suggestions? I'm using the 1.8.1 build >> >> >> Quoting Elaine Meng : >> >>> Hi Rebecca, >>> As far as I know, you cannot change the selection mode in a command. However, with commands you can often circumvent selection entirely, or in the few cases where you can't easily do that (for example, the "findhbond" command uses selections), there are sometimes alternative routes to achieving the same result. In the command line, you can make a selection and then use ~select to deselect only part of it. Sometimes instead of selections you can use aliases and combinations of aliases. For writing a subset of the coordinates, you could undisplay the unwanted atoms and use the corresponding option to the "write" command to exclude them from the output. Or, depending on exactly what you are doing, you could just delete the unwanted atoms before saving to a file. >>> >>> >>> >>> >>> >>> Avoiding selection may be one of the advantages of commands, since (as you found) drawing the selection outlines can make things slow. >>> >>> 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 Dec 16, 2013, at 8:13 AM, rswett at chem.wayne.edu wrote: >>> >>>> Hi all, >>>> I'm interested in putting together a script that will open several large pdb files, select some very specific pieces of those files and save the output to another file. The problem is that they are large files and unwieldy in a graphics window. I have no problem generating the commands to select the regions I'm interested in, but I still need to be able to switch selection modes in between commands. Is there a way to change the selection mode at the command line without navigating the selection menu? >>>> Rebecca >>> >> >> >> >> _______________________________________________ >> 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 darrellh at niaid.nih.gov Mon Dec 16 12:15:43 2013 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Mon, 16 Dec 2013 20:15:43 +0000 Subject: [Chimera-users] Export options for x3d2stl In-Reply-To: <52AF5D39.9020307@cgl.ucsf.edu> References: <52AF5D39.9020307@cgl.ucsf.edu> Message-ID: Hi Greg, Thanks for your quick reply. You're certainly right about the problems with overlapping triangles and 3D printers. No problem. I just wanted to see if there might be some (as yet) undocumented way to control the export. I'll do it outside of Chimera through a wrapper script. (Sorry about the Blender slip-up ? I've got a bunch of things whirling through my head right now?). Cheers, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: Greg Couch > Date: Monday, December 16, 2013 3:06 PM To: Darrell Hurt >, "chimera-users at cgl.ucsf.edu List" > Subject: Re: [Chimera-users] Export options for x3d2stl I assume you meant just run outside of Chimera. x3d2stl would presumably always be run outside of Blender. And to answer your question, right now there is no way within chimera to give options to x3d2stl, nor any of the other converters -- X3D output is the only completely native format. So you need to first export the X3D output, then run x3d2stl separately with the options you require. As you may have deduced, the -r option sets the tessellation resolution, roughly the number of vertices per unit area, and -c says to cap all primitives. Since the sphere and cylinders intersect that chimera generates to represent atoms and bonds, the STL triangles also intersect. And intersecting triangles cause problems for some 3D printer software, so you might need to limit the output to just surfaces. Some 3D printer software takes VRML input, so for those printers, I'd recommend using Chimera VRML output, and let the 3D printer software do the conversion to STL. HTH, Greg On 12/16/2013 10:55 AM, Hurt, Darrell (NIH/NIAID) [E] wrote: Hi Chimera friends, Here's the second question of the day. Thanks for your patience with me. When I export the scene as an STL (for 3D printing), I think what happens is that Chimera outputs first an X3D file and then runs the utility program "x3d2stl" to create the STL. The X3D file is about 5 MB, but the STL is about 100 MB. I understand that much of this size inflation is because the "primitives" in X3D have to be converted to mesh objects for STL. However, when I look at the STL file, the meshes derived from the primitives are finer than I really need. I find that I can "get away with" a coarser meshification by using x3d2stl on the command line: x3d2stl -c -r 2 -o sticks.stl < sticks.x3d If I want to export the scene via the command line within Blender, is there any way to issue options to x3d2stl? Or should I just run x3d2stl outside of Blender? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Mon Dec 16 13:26:09 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Dec 2013 13:26:09 -0800 Subject: [Chimera-users] Attribute Calculator by command line? In-Reply-To: References: Message-ID: Hi Darrell, As you found, there isn't a command version of Attribute Calculator, sorry! Maybe one of the others can suggest a python solution? Best, Eliane ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 16, 2013, at 11:59 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: > Hi Chimera friends, > > I'm trying to calculate convexity as demonstrated in the Attributes tutorial: > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html > > I can do it with the graphical tools without a problem, but when I try to do it via the command line, I run into trouble. I cannot find any documentation on running the Attributes Calculator on the command line. I've tried using "setattr": > > setattr a convexity atom.areaSAS/atom.areaSES > > This command generates a new atom attribute called "convexity" for every atom, but the value of this attribute for every atom is literally "atom.areaSAS/atom.areaSES" instead of the calculated value. > > Is there a way to calculate a new attribute value on the command line within Chimera? Sorry to be so demanding? > > Thanks, > Darrell From darrellh at niaid.nih.gov Mon Dec 16 13:33:31 2013 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Mon, 16 Dec 2013 21:33:31 +0000 Subject: [Chimera-users] Attribute Calculator by command line? In-Reply-To: References: Message-ID: Too bad! If someone has a solution, I'd be happy to hear it, but if not, that's OK, too. Thanks Elaine! -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page Twitter: @niaidbioit Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: Elaine Meng > Reply-To: "chimera-users at cgl.ucsf.edu List" > Date: Monday, December 16, 2013 4:26 PM To: Darrell Hurt > Cc: "chimera-users at cgl.ucsf.edu List" > Subject: Re: [Chimera-users] Attribute Calculator by command line? Hi Darrell, As you found, there isn't a command version of Attribute Calculator, sorry! Maybe one of the others can suggest a python solution? Best, Eliane ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 16, 2013, at 11:59 AM, "Hurt, Darrell (NIH/NIAID) [E]" > wrote: Hi Chimera friends, I'm trying to calculate convexity as demonstrated in the Attributes tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html I can do it with the graphical tools without a problem, but when I try to do it via the command line, I run into trouble. I cannot find any documentation on running the Attributes Calculator on the command line. I've tried using "setattr": setattr a convexity atom.areaSAS/atom.areaSES This command generates a new atom attribute called "convexity" for every atom, but the value of this attribute for every atom is literally "atom.areaSAS/atom.areaSES" instead of the calculated value. Is there a way to calculate a new attribute value on the command line within Chimera? Sorry to be so demanding? Thanks, Darrell From meng at cgl.ucsf.edu Mon Dec 16 13:38:30 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Dec 2013 13:38:30 -0800 Subject: [Chimera-users] Setting selection mode command line In-Reply-To: <64B21110-5678-4E1B-A9A4-735138CA912F@cgl.ucsf.edu> References: <20131216111319.14020s87h2i5ydnj@chem.wayne.edu> <2F976A33-ED2D-4B21-B2AB-A71BA1AA9C85@cgl.ucsf.edu> <20131216144451.13252kc57nks820j@chem.wayne.edu> <64B21110-5678-4E1B-A9A4-735138CA912F@cgl.ucsf.edu> Message-ID: P.S. back on the topic of making things faster, you could try setting your "New Molecules" Preferences so that structures are just shown as wire when you open them (assuming your other New Molecules settings are defaults, just set smart initial display: false, click Save if you want this to apply to subsequent uses of Chimera). Display would be uglier but less computationally taxing. Elaine On Dec 16, 2013, at 11:56 AM, Elaine Meng wrote: > Hi Rebecca, > I don't know much about nogui, maybe others can say something about that. I don't know if that would buy you that much time, even if it was working the way you intended. > > However, you can specify zones in commands without selecting anything. For example: > > color red ligand z<8 > > ?and do more complicated combinations, for example: > > delete solvent & #1 & ligand z>8 > > (delete solvent residues in model 1 that don't have any atoms within 8 ang of ligand? or ~display instead of delete). Doesn't sound like you'd need aliases. > > See zones and combinations in the atomspec page. zr and z are for residue-based cutoff, za for atom-based > > > > Elaine > > On Dec 16, 2013, at 11:44 AM, rswett at chem.wayne.edu wrote: > >> Alright, thanks. >> I was hoping to be able to manipulate some excessively large pdb files using chimera commandline only with the --nogui option to get around the display problem. I had intended to open three files, one protein, one solvated system and one standalone ligand. Align the protein to the solvated system and use the zone selection to carve out a sphere around the standalone ligand, saving that portion of the solvated system and the entirety of both progtein structures into a single file. If you have any suggestions let me know. I'll start looking int aliasing if you think that would help bet around the gui. >> >> As it stands, I can't get it to work with the --nogui flag on windows anyway. I'm using the command >> chimera --nogui block.cmd >> where block.cmd simply opens the solvated system and ligand, selects a zone around the ligand and saves the selected atoms to a file, but I get no output and it runs too fast to be actually reading in the structures. Suggestions? I'm using the 1.8.1 build >> >> >> Quoting Elaine Meng : >> >>> Hi Rebecca, >>> As far as I know, you cannot change the selection mode in a command. However, with commands you can often circumvent selection entirely, or in the few cases where you can't easily do that (for example, the "findhbond" command uses selections), there are sometimes alternative routes to achieving the same result. In the command line, you can make a selection and then use ~select to deselect only part of it. Sometimes instead of selections you can use aliases and combinations of aliases. For writing a subset of the coordinates, you could undisplay the unwanted atoms and use the corresponding option to the "write" command to exclude them from the output. Or, depending on exactly what you are doing, you could just delete the unwanted atoms before saving to a file. >>> >>> >>> >>> >>> >>> Avoiding selection may be one of the advantages of commands, since (as you found) drawing the selection outlines can make things slow. >>> >>> 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 Dec 16, 2013, at 8:13 AM, rswett at chem.wayne.edu wrote: >>> >>>> Hi all, >>>> I'm interested in putting together a script that will open several large pdb files, select some very specific pieces of those files and save the output to another file. The problem is that they are large files and unwieldy in a graphics window. I have no problem generating the commands to select the regions I'm interested in, but I still need to be able to switch selection modes in between commands. Is there a way to change the selection mode at the command line without navigating the selection menu? >>>> Rebecca >>> >> >> >> >> _______________________________________________ >> 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 pett at cgl.ucsf.edu Mon Dec 16 14:50:33 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 16 Dec 2013 14:50:33 -0800 Subject: [Chimera-users] Attribute Calculator by command line? In-Reply-To: References: Message-ID: <05AAFC13-72F9-4294-9769-1A18CD2E70E3@cgl.ucsf.edu> Hi Darrell, The command line is not a programming language. It has no conditional tests/execution, no math operators, no variables. You have to resort to Chimera's Python interface to do such things. That said, the script to compute and assign the attribute you want is pretty simple. If you put the lines below in a file that ends in ".py" and open that file with "open whatever.py" the attribute would be assigned and could be used in subsequent commands? from Chimera import openModels, Molecule for m in openModels.list(modelTypes=[Molecule]): for a in m.atoms: if a.areaSES == 0.0: continue a.convexity = a.areasSAS / a.areaSES In Python indentation is significant, so make sure it is preserved in the file you create. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Dec 16, 2013, at 1:33 PM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: > Too bad! If someone has a solution, I'd be happy to hear it, but if not, that's OK, too. > > Thanks Elaine! > > -- > Darrell Hurt, Ph.D. > Section Head, Computational Biology > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > > 31 Center Drive, Room 3B62B, MSC 2135 > Bethesda, MD 20892-2135 > Office: 301-402-0095 > Mobile: 301-758-3559 > Web: BCBB Home Page > Twitter: @niaidbioit > > Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. > > From: Elaine Meng > > Reply-To: "chimera-users at cgl.ucsf.edu List" > > Date: Monday, December 16, 2013 4:26 PM > To: Darrell Hurt > > Cc: "chimera-users at cgl.ucsf.edu List" > > Subject: Re: [Chimera-users] Attribute Calculator by command line? > > Hi Darrell, > As you found, there isn't a command version of Attribute Calculator, sorry! Maybe one of the others can suggest a python solution? > Best, > Eliane > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Dec 16, 2013, at 11:59 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: > > Hi Chimera friends, > I'm trying to calculate convexity as demonstrated in the Attributes tutorial: > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html > I can do it with the graphical tools without a problem, but when I try to do it via the command line, I run into trouble. I cannot find any documentation on running the Attributes Calculator on the command line. I've tried using "setattr": > setattr a convexity atom.areaSAS/atom.areaSES > This command generates a new atom attribute called "convexity" for every atom, but the value of this attribute for every atom is literally "atom.areaSAS/atom.areaSES" instead of the calculated value. > Is there a way to calculate a new attribute value on the command line within Chimera? Sorry to be so demanding? > Thanks, > Darrell > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From darrellh at niaid.nih.gov Mon Dec 16 15:19:14 2013 From: darrellh at niaid.nih.gov (Hurt, Darrell (NIH/NIAID) [E]) Date: Mon, 16 Dec 2013 23:19:14 +0000 Subject: [Chimera-users] Attribute Calculator by command line? In-Reply-To: <05AAFC13-72F9-4294-9769-1A18CD2E70E3@cgl.ucsf.edu> Message-ID: <624EEF8436486C438E2C9E71C4879E6E15D1F7@MLBXV06.nih.gov> Hi Eric, This is great! Thanks! Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office? 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ----- Original Message ----- From: Eric Pettersen [mailto:pett at cgl.ucsf.edu] Sent: Monday, December 16, 2013 05:50 PM To: Hurt, Darrell (NIH/NIAID) [E] Cc: chimera-users at cgl.ucsf.edu List Subject: Re: [Chimera-users] Attribute Calculator by command line? Hi Darrell, The command line is not a programming language. It has no conditional tests/execution, no math operators, no variables. You have to resort to Chimera's Python interface to do such things. That said, the script to compute and assign the attribute you want is pretty simple. If you put the lines below in a file that ends in ".py" and open that file with "open whatever.py" the attribute would be assigned and could be used in subsequent commands? from Chimera import openModels, Molecule for m in openModels.list(modelTypes=[Molecule]): for a in m.atoms: if a.areaSES == 0.0: continue a.convexity = a.areasSAS / a.areaSES In Python indentation is significant, so make sure it is preserved in the file you create. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Dec 16, 2013, at 1:33 PM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: > Too bad! If someone has a solution, I'd be happy to hear it, but if not, that's OK, too. > > Thanks Elaine! > > -- > Darrell Hurt, Ph.D. > Section Head, Computational Biology > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > > 31 Center Drive, Room 3B62B, MSC 2135 > Bethesda, MD 20892-2135 > Office: 301-402-0095 > Mobile: 301-758-3559 > Web: BCBB Home Page > Twitter: @niaidbioit > > Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. > > From: Elaine Meng > > Reply-To: "chimera-users at cgl.ucsf.edu List" > > Date: Monday, December 16, 2013 4:26 PM > To: Darrell Hurt > > Cc: "chimera-users at cgl.ucsf.edu List" > > Subject: Re: [Chimera-users] Attribute Calculator by command line? > > Hi Darrell, > As you found, there isn't a command version of Attribute Calculator, sorry! Maybe one of the others can suggest a python solution? > Best, > Eliane > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Dec 16, 2013, at 11:59 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: > > Hi Chimera friends, > I'm trying to calculate convexity as demonstrated in the Attributes tutorial: > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html > I can do it with the graphical tools without a problem, but when I try to do it via the command line, I run into trouble. I cannot find any documentation on running the Attributes Calculator on the command line. I've tried using "setattr": > setattr a convexity atom.areaSAS/atom.areaSES > This command generates a new atom attribute called "convexity" for every atom, but the value of this attribute for every atom is literally "atom.areaSAS/atom.areaSES" instead of the calculated value. > Is there a way to calculate a new attribute value on the command line within Chimera? Sorry to be so demanding? > Thanks, > Darrell > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From wanxiaobo at nibs.ac.cn Sat Dec 14 06:03:15 2013 From: wanxiaobo at nibs.ac.cn (wanxiaobo at nibs.ac.cn) Date: Sat, 14 Dec 2013 22:03:15 +0800 (GMT+08:00) Subject: [Chimera-users] question Message-ID: <663778.9034.142f16b1497.Coremail.wanxiaobo@nibs.ac.cn> Dear chimera team / users, I was looking for a way to save the content of Axis/plane/centroid information, not only the radii via command line, because I want to analyze the structure movement from MD trajectory. It is not convenient to save the information manually for each frame. Thanks Xiaobo -------------- next part -------------- An HTML attachment was scrubbed... URL: From thrabe at sanfordburnham.org Tue Dec 17 12:03:34 2013 From: thrabe at sanfordburnham.org (Thomas Hrabe) Date: Tue, 17 Dec 2013 20:03:34 +0000 Subject: [Chimera-users] Command line export to webgl Message-ID: <47A3D6AE-4757-4E79-B8F0-2345E1B14D73@sanfordburnham.org> Dear Chimera Team, I was curious if there was a functionality to export chimera scenes to webgl through the command line, without having to open the chimera window. Is there a set of python script commands that would do it? Thank you for your support, Thomas From gregc at cgl.ucsf.edu Tue Dec 17 13:53:50 2013 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 17 Dec 2013 13:53:50 -0800 Subject: [Chimera-users] Command line export to webgl In-Reply-To: <47A3D6AE-4757-4E79-B8F0-2345E1B14D73@sanfordburnham.org> References: <47A3D6AE-4757-4E79-B8F0-2345E1B14D73@sanfordburnham.org> Message-ID: <52B0C7EE.9070405@cgl.ucsf.edu> To export 3D data from chimera, you either (a) need a chimera window (can be minimized) or (b) need to use the headless version of chimera (only available for Linux). On the command line, if you export to a file that is named with a .html suffix, it will use WebGL, e.g., export filename.html From Python: from chimera import exports exports.doCommand('WebGL', 'filename.html') We still consider the WebGL support experimental, and it has problems with large structures, but please check it out. HTH, Greg On 12/17/2013 12:03 PM, Thomas Hrabe wrote: > Dear Chimera Team, > > I was curious if there was a functionality to export chimera scenes to webgl through the command line, without having to open the chimera window. > Is there a set of python script commands that would do it? > > Thank you for your support, > Thomas > From pett at cgl.ucsf.edu Tue Dec 17 16:57:01 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 17 Dec 2013 16:57:01 -0800 Subject: [Chimera-users] question In-Reply-To: <663778.9034.142f16b1497.Coremail.wanxiaobo@nibs.ac.cn> References: <663778.9034.142f16b1497.Coremail.wanxiaobo@nibs.ac.cn> Message-ID: <62635DDE-85B0-41AC-BF2C-4E54F246CB62@cgl.ucsf.edu> On Dec 14, 2013, at 6:03 AM, wanxiaobo at nibs.ac.cn wrote: > > Dear chimera team / users, > > I was looking for a way to save the content of Axis/plane/centroid information, not only the radii via command line, because I want to analyze the structure movement from MD trajectory. It is not convenient to save the information manually for each frame. > Thanks > > Xiaobo Hi Xiaobo, You are right that compiling that information in the context of an MD trajectory is far too difficult. Therefore, I have added code to Chimera to log all the pertinent info for axes/planes/centroids as they are created. This means you can run through the trajectory once and then save the reply log to a file to save the relevant info. I assume you are using a per-frame script to create the geometric objects. You may want to add an "echo " to the start of your per-frame script so it is easy to tell which frame the objects belong to. The changes were just committed, so you will have to download a daily build dated Dec. 18th or later to get them. Such a build should show up on the download page in about 12 hours (if the build succeeds). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From tatianad at scripps.edu Wed Dec 18 05:52:37 2013 From: tatianad at scripps.edu (Tatiana Domitrovic) Date: Wed, 18 Dec 2013 05:52:37 -0800 Subject: [Chimera-users] display of improper peptide bond Message-ID: <97CC6820A5866948B18B7C7B0887B7990102E893E681@EXCH-CCR01.lj.ad.scripps.edu> Hi, I am trying to get rid of an improper bond that chimera is displaying between two nearby segments that are actually cleaved. The bond is distorted, creating long CACB bonds if B-spline mode is active. I tried to turn off the auto-chaining, but didn?t work. Because PYmol can properly display these segments as independent polypetides, I was wondering if there is other adjustment that I can try before manually deleting the bond. The PDB is 1ohf and the bond is between residue 570 and 571. Cheers, From meng at cgl.ucsf.edu Wed Dec 18 09:16:35 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 18 Dec 2013 09:16:35 -0800 Subject: [Chimera-users] display of improper peptide bond In-Reply-To: <97CC6820A5866948B18B7C7B0887B7990102E893E681@EXCH-CCR01.lj.ad.scripps.edu> References: <97CC6820A5866948B18B7C7B0887B7990102E893E681@EXCH-CCR01.lj.ad.scripps.edu> Message-ID: Hi Tatiana, You could delete the bond with a command, e.g. ~bond :570 at c :571 at n Based on the ATOM records and PDB format specifications, they would be considered as connected (consecutive standard residues with same chain ID, no TER, ...), so it should be an unusual case. Chimera doesn't distance-test in these "standard residue" situations. 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 Dec 18, 2013, at 5:52 AM, Tatiana Domitrovic wrote: > Hi, > I am trying to get rid of an improper bond that chimera is displaying between two nearby segments that are actually cleaved. The bond is distorted, creating long CACB bonds if B-spline mode is active. I tried to turn off the auto-chaining, but didn?t work. > Because PYmol can properly display these segments as independent polypetides, I was wondering if there is other adjustment that I can try before manually deleting the bond. The PDB is 1ohf and the bond is between residue 570 and 571. > Cheers, From pett at cgl.ucsf.edu Wed Dec 18 11:06:38 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 18 Dec 2013 11:06:38 -0800 Subject: [Chimera-users] display of improper peptide bond In-Reply-To: References: <97CC6820A5866948B18B7C7B0887B7990102E893E681@EXCH-CCR01.lj.ad.scripps.edu> Message-ID: If you look at the sequence for that chain you can see there is a 34-residue segment missing between residues 570 and 571, which is confirmed in the PDB file REMARK records with: REMARK 400 ALL CHAINS ARE AUTOCATALYTICALLY CLEAVED BETWEEN RESIDUES REMARK 400 570 AND 571 I guess I find it surprising that they decided to keep the numbering consecutive instead of numbering to account for the missing residues (or possibly changing chain IDs), but that's why Chimera shows a regular bond between those residues instead of a "missing structure" dashed line, and therefore why the ribbon tries to connect the residues. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Dec 18, 2013, at 9:16 AM, Elaine Meng wrote: > Hi Tatiana, > You could delete the bond with a command, e.g. > > ~bond :570 at c :571 at n > > Based on the ATOM records and PDB format specifications, they would be considered as connected (consecutive standard residues with same chain ID, no TER, ...), so it should be an unusual case. Chimera doesn't distance-test in these "standard residue" situations. > > 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 Dec 18, 2013, at 5:52 AM, Tatiana Domitrovic wrote: > >> Hi, >> I am trying to get rid of an improper bond that chimera is displaying between two nearby segments that are actually cleaved. The bond is distorted, creating long CACB bonds if B-spline mode is active. I tried to turn off the auto-chaining, but didn?t work. >> Because PYmol can properly display these segments as independent polypetides, I was wondering if there is other adjustment that I can try before manually deleting the bond. The PDB is 1ohf and the bond is between residue 570 and 571. >> Cheers, > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From olibclarke at gmail.com Thu Dec 19 08:13:37 2013 From: olibclarke at gmail.com (Oliver Clarke) Date: Thu, 19 Dec 2013 11:13:37 -0500 Subject: [Chimera-users] Color by ramachandran probability? Or molprobity overlap? In-Reply-To: <6A1A9274-9B91-4E9E-BA15-313BCF83AA27@cgl.ucsf.edu> References: <72DEDDAF-7BC8-4D04-B215-E3CBE9F00900@gmail.com> <6A1A9274-9B91-4E9E-BA15-313BCF83AA27@cgl.ucsf.edu> Message-ID: Hi Elaine, Apologies for the late response, and thank you very much for taking the time to reply. Yes, I could do that with some effort, but I was thinking of this more as a routine tool for checking out problematic regions of a structure either while building my own structures, or when inspecting structures in the PDB that I want to interpret - there is no good way that I am aware of at the moment to globally display Ramachandran outliers on a structure, without doing the sort of scripting you describe. Chimera is may favorite tool for visualizing protein structures and making figures, so it would be wonderful to have such functionality - it would also be useful when preparing validation figures, for example to show reviewers that the only geometric outliers in your structure lie in high b-factor, relatively mobile loops. Thanks again, Oliver. On Dec 11, 2013, at 1:55 PM, Elaine Meng wrote: > Hi Oliver, > There is no automatic way (without doing some of your own processing), but if you can calculate the values, it is fairly easy to assign them as attributes. Then you can use the Chimera "Render by Attribute" tool or "rangecolor" command to map the values to colors on the structure. > > Custom attributes are assigned by reading in an "attribute assignment file," which is basically a tab-separated columns text file with some control lines at the top. The format is described here, and several example files are provided: > > > Amino acid residue phi and psi angles are already attributes, but there is no automatic assessment of how well they agree with a Ramachandran map in Chimera other than actually displaying the map with the values plotted (which can be done via the Model Panel, as you saw). Your processing would need to compare the phi and psi values with Ramachandran plot contours and distill that into some value that could be assigned as a residue attribute (analogously you could take the molprobity output values and assign them as atom attributes), then generate a corresponding attribute assignment file. After reading your custom attribute in, you could use Chimera's existing coloring-by-attribute features, as mentioned above. > > > > > 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 Dec 10, 2013, at 6:34 PM, Oliver Clarke wrote: > >> Hi all, >> Quick question, just wondering if there is any way to color a structure by Ramachandran probability? Or by steric overlap scores for each atom as generated by mol probity? >> >> Either of these would be very handy as a way of getting a quick graphical overview of trouble spots in a structure. It seems like Chimera ?knows about? Ramachandran plot data, (as one can generate such plots from the model panel) but I can?t find any convenient way to display this data on the structure. >> >> Many thanks, >> Oliver. > From goddard at sonic.net Thu Dec 19 11:48:19 2013 From: goddard at sonic.net (Tom Goddard) Date: Thu, 19 Dec 2013 11:48:19 -0800 Subject: [Chimera-users] Running Segger from a script In-Reply-To: References: <4FF76447.4080200@sonic.net> <500ED9A3.4090605@sonic.net> <500EF4DE.5040802@sonic.net> <5052542F.1010908@sonic.net> <21D922ED-5CD4-4C3C-B6E4-9050BE7BBB0B@sonic.net> Message-ID: <4A61CEBA-D8A2-40C1-A5E7-95A562F6C94D@sonic.net> Hi Rakesh, There is not Chimera command to run Segger, only a dialog. So you would have to use Python to run it and write out map files for each masked region if you wanted to script it. Segger uses several Chimera features such as Gaussian filtering, and watershed calculations that are in written in C++ and compiled against the Chimera Python. While you can get those to run in another Python if it has an identical version (e.g. 2.7.3), setting up the environment variables to find all the needed libraries is a difficult process. So I suggest using the Chimera Python. You can run Chimera scripts without the graphical interface by starting it from a shell "chimera --nogui myscript.py". The Segger Python functions are not documented so you would need to study the (complex and messy) code found in chimera/share/Segger or on Mac in Chimera.app/Contents/Resources/share/Segger Tom On Dec 18, 2013, at 5:54 PM, rakesh ramachandram wrote: > Hi, > > I would like to know if I can run Segger in a script in an automated fashion and then obtain the individual segmented regions as separate density maps. Is there a way to run chimera scripts from command line directly without using the chimera's python interpreter but using the default python interpreter after importing its libraries. > > Regards > Rakesh > From meng at cgl.ucsf.edu Thu Dec 19 15:23:37 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 19 Dec 2013 15:23:37 -0800 Subject: [Chimera-users] Color by ramachandran probability? Or molprobity overlap? In-Reply-To: References: <72DEDDAF-7BC8-4D04-B215-E3CBE9F00900@gmail.com> <6A1A9274-9B91-4E9E-BA15-313BCF83AA27@cgl.ucsf.edu> Message-ID: <65E09B8B-DE62-4D31-9E9F-CC003B6FD558@cgl.ucsf.edu> Hi Oliver, I agree it would be useful. I wouldn't be the one doing the implementation, so it depends on how developer time is triaged, but your request has been entered into our tracking database as report #12711. Your email address is already on the report for automatic notification of comments or changes related to the request. We're glad you like Chimera, and thanks for the suggestion! 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 Dec 19, 2013, at 8:13 AM, Oliver Clarke wrote: > Hi Elaine, > > Apologies for the late response, and thank you very much for taking the time to reply. > > Yes, I could do that with some effort, but I was thinking of this more as a routine tool for checking out problematic regions of a structure either while building my own structures, or when inspecting structures in the PDB that I want to interpret - there is no good way that I am aware of at the moment to globally display Ramachandran outliers on a structure, without doing the sort of scripting you describe. > > Chimera is may favorite tool for visualizing protein structures and making figures, so it would be wonderful to have such functionality - it would also be useful when preparing validation figures, for example to show reviewers that the only geometric outliers in your structure lie in high b-factor, relatively mobile loops. > > Thanks again, > Oliver. From fujisawa at gifu-u.ac.jp Fri Dec 20 01:58:11 2013 From: fujisawa at gifu-u.ac.jp (Tetsuro Fujisawa) Date: Fri, 20 Dec 2013 01:58:11 -0800 Subject: [Chimera-users] saving coords from script Message-ID: <201312200958.rBK9wBW1033144@plato.cgl.ucsf.edu> The following bug report has been submitted: Platform: windows Chimera Version: 1.8.1 Description Hi, I found some strange behavior in saving pdb file by script file. I tried to modify the orientation of pdb file ?tst.pdb? (#1) in reference to axis coordinate (#0), then save the atomic coordinates in pdb file. When I typed in the commands through either command line window or IDLE, transformed coordinates were saved. It worked fine. However, the exact identical commands (inside the brancket) or lines (rc(?..?)) were run by script file shown in below, the untransformed coordinates were saved. This is also the case for ?Midas.write method?. I wondered this might be a bug. Regards, Tetsuro Sample.py: ---------------------------------------------- from chimera import runCommand as rc rc('open axis.bild') rc('open tst.pdb') rc('rock y 60 1 center #1 coord #0 models #1') # orientation of tst.pdb was modified rc('focus') rc('write relative #0 #1 tstA.pdb') # write current coordinates to tstA.pdb rc('open tstA.pdb') # opened tstA has original untransformed orientation ----------------------------------------------- From pett at cgl.ucsf.edu Mon Dec 23 15:59:16 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 23 Dec 2013 15:59:16 -0800 Subject: [Chimera-users] saving coords from script In-Reply-To: <201312200958.rBK9wBW1033144@plato.cgl.ucsf.edu> References: <201312200958.rBK9wBW1033144@plato.cgl.ucsf.edu> Message-ID: <04B15E0C-844B-4594-8AE6-760588744D85@cgl.ucsf.edu> On Dec 20, 2013, at 1:58 AM, Tetsuro Fujisawa wrote: > Hi, > > I found some strange behavior in saving pdb file by script file. > I tried to modify the orientation of pdb file ?tst.pdb? (#1) in reference to axis coordinate (#0), then save the atomic coordinates in pdb file. > When I typed in the commands through either command line window or IDLE, transformed coordinates were saved. It worked fine. However, the exact identical commands (inside the brancket) or lines (rc(?..?)) were run by script file shown in below, the untransformed coordinates were saved. This is also the case for ?Midas.write method?. > I wondered this might be a bug. > > Regards, > Tetsuro > > Sample.py: > ---------------------------------------------- > from chimera import runCommand as rc > > rc('open axis.bild') > rc('open tst.pdb') > rc('rock y 60 1 center #1 coord #0 models #1') > # orientation of tst.pdb was modified > rc('focus') > rc('write relative #0 #1 tstA.pdb') > # write current coordinates to tstA.pdb > rc('open tstA.pdb') > # opened tstA has original untransformed orientation > ----------------------------------------------- Hi Tetsuro, The issue is that unlike using the command line or IDLE or running a chimera-command script, no frames get drawn during the execution of a Python script unless explicitly requested and therefore the "rock" command in your script doesn't actually do anything until after the entire script runs, and by that time your coordinate file has already been written. To get the rock command to complete before proceeding with the rest of the script you need to append "; wait" or "; wait 1" (since you are rocking for 1 frame) to the end of your rock command. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From htjou at kiost.ac Thu Dec 26 15:10:45 2013 From: htjou at kiost.ac (Hyeong-Tae Jou) Date: Fri, 27 Dec 2013 08:10:45 +0900 Subject: [Chimera-users] Movie for various clipping In-Reply-To: <97CC6820A5866948B18B7C7B0887B7990102E893E681@EXCH-CCR01.lj.ad.scripps.edu> References: <97CC6820A5866948B18B7C7B0887B7990102E893E681@EXCH-CCR01.lj.ad.scripps.edu> Message-ID: Hi, I am trying to animate some clipping motion in volume data. I only find very simple clipping method using plane. I'd like to make a movie for clipping motion using prism or 3-D box (the clipping gear gradually moving deeper into volume data). I have tried mask (by inverse masking) using 3-D box, but it was very inconvenient, and took too much time to make a movie. Are there any other way to make an animation for some fancy clipping? Many thanks, Hyeong-Tae ----------------- Hyeong-Tae Jou KIOST From meng at cgl.ucsf.edu Thu Dec 26 16:37:26 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 26 Dec 2013 16:37:26 -0800 Subject: [Chimera-users] Movie for various clipping In-Reply-To: References: <97CC6820A5866948B18B7C7B0887B7990102E893E681@EXCH-CCR01.lj.ad.scripps.edu> Message-ID: <78E30479-CB6C-4101-AF36-F6FEE88841C3@cgl.ucsf.edu> Dear Hyeong-Tae, I'm not the expert in this area, but will try to list the possibilities that I know about. Other people may have better ideas when they return from the holiday break. (a) single plane or slab perpendicular to viewer, front-back motion ("global clipping") (b) single plane or slab per model, at any angle to viewer ("per-model clipping") ? commands and more details here ... ( c) moving orthogonal planes through the data, for example the "Herpes virus slices" movie about halfway down the Animation Gallery page. Example command file is linked there. (d) showing the volume values with coloring on a surface, where that surface can grow/shrink, for example the movie at the very bottom of the Animation Gallery, "Rice Dwarf Virus". Certain shapes of surfaces (sphere, icosahedron, etc.) can be created with the "shape" command, and the surfaces can be colored by volume data value with the "scolor" command. I don't think there is a shape command option to automatically replace a previous shape, so it may be a bit tedious to create new surface, close old surface, color new surface (repeat). It was probably done with python rather than commands, but that is beyond my skills, sorry. 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 Dec 26, 2013, at 3:10 PM, "Hyeong-Tae Jou" wrote: > Hi, > > I am trying to animate some clipping motion in volume data. > I only find very simple clipping method using plane. > > I'd like to make a movie for clipping motion using prism or 3-D box > (the clipping gear gradually moving deeper into volume data). > > I have tried mask (by inverse masking) using 3-D box, > but it was very inconvenient, and took too much time to make a movie. > Are there any other way to make an animation for some fancy clipping? > > Many thanks, > > Hyeong-Tae > ----------------- > Hyeong-Tae Jou > KIOST From meng at cgl.ucsf.edu Thu Dec 26 16:50:08 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 26 Dec 2013 16:50:08 -0800 Subject: [Chimera-users] Movie for various clipping In-Reply-To: <78E30479-CB6C-4101-AF36-F6FEE88841C3@cgl.ucsf.edu> References: <97CC6820A5866948B18B7C7B0887B7990102E893E681@EXCH-CCR01.lj.ad.scripps.edu> <78E30479-CB6C-4101-AF36-F6FEE88841C3@cgl.ucsf.edu> Message-ID: Ah, I see that the "sop transform" command can be used to grow/shrink an existing surface shape. It's the last example in the "Clipping and Slicing" (bottom) section of the video mini-examples page: There is also a volume planes animation example. Elaine On Dec 26, 2013, at 4:37 PM, Elaine Meng wrote: > Dear Hyeong-Tae, > I'm not the expert in this area, but will try to list the possibilities that I know about. Other people may have better ideas when they return from the holiday break. > > (a) single plane or slab perpendicular to viewer, front-back motion ("global clipping") > (b) single plane or slab per model, at any angle to viewer ("per-model clipping") > ? commands and more details here ... > > > ( c) moving orthogonal planes through the data, for example the "Herpes virus slices" movie about halfway down the Animation Gallery page. Example command file is linked there. > > > (d) showing the volume values with coloring on a surface, where that surface can grow/shrink, for example the movie at the very bottom of the Animation Gallery, "Rice Dwarf Virus". > > Certain shapes of surfaces (sphere, icosahedron, etc.) can be created with the "shape" command, and the surfaces can be colored by volume data value with the "scolor" command. I don't think there is a shape command option to automatically replace a previous shape, so it may be a bit tedious to create new surface, close old surface, color new surface (repeat). It was probably done with python rather than commands, but that is beyond my skills, sorry. > > > > 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 Dec 26, 2013, at 3:10 PM, "Hyeong-Tae Jou" wrote: > >> Hi, >> >> I am trying to animate some clipping motion in volume data. >> I only find very simple clipping method using plane. >> >> I'd like to make a movie for clipping motion using prism or 3-D box >> (the clipping gear gradually moving deeper into volume data). >> >> I have tried mask (by inverse masking) using 3-D box, >> but it was very inconvenient, and took too much time to make a movie. >> Are there any other way to make an animation for some fancy clipping? >> >> Many thanks, >> >> Hyeong-Tae >> ----------------- >> Hyeong-Tae Jou >> KIOST > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From htjou at kiost.ac Thu Dec 26 17:37:41 2013 From: htjou at kiost.ac (Hyeong-Tae Jou) Date: Fri, 27 Dec 2013 10:37:41 +0900 Subject: [Chimera-users] Movie for various clipping In-Reply-To: References: <97CC6820A5866948B18B7C7B0887B7990102E893E681@EXCH-CCR01.lj.ad.scripps.edu> <78E30479-CB6C-4101-AF36-F6FEE88841C3@cgl.ucsf.edu> Message-ID: <3CA88FA8C0EC48EBADE7D4D36D26A2A1@joux64> Hi Elaine, Many thanks for your quick reply. I'll try some of your suggestions while waiting for other's ideas. It's holiday season, and I'll take time to get the good solution. I wish you a Happy New Year. Hyeong-Tae. -----?? ???----- From: Elaine Meng Sent: Friday, December 27, 2013 9:50 AM To: Hyeong-Tae Jou Cc: chimera-users at cgl.ucsf.edu List Subject: Re: [Chimera-users] Movie for various clipping Ah, I see that the "sop transform" command can be used to grow/shrink an existing surface shape. It's the last example in the "Clipping and Slicing" (bottom) section of the video mini-examples page: There is also a volume planes animation example. Elaine On Dec 26, 2013, at 4:37 PM, Elaine Meng wrote: > Dear Hyeong-Tae, > I'm not the expert in this area, but will try to list the possibilities > that I know about. Other people may have better ideas when they return > from the holiday break. > > (a) single plane or slab perpendicular to viewer, front-back motion > ("global clipping") > (b) single plane or slab per model, at any angle to viewer ("per-model > clipping") > ? commands and more details here ... > > > ( c) moving orthogonal planes through the data, for example the "Herpes > virus slices" movie about halfway down the Animation Gallery page. > Example command file is linked there. > > > (d) showing the volume values with coloring on a surface, where that > surface can grow/shrink, for example the movie at the very bottom of the > Animation Gallery, "Rice Dwarf Virus". > > Certain shapes of surfaces (sphere, icosahedron, etc.) can be created with > the "shape" command, and the surfaces can be colored by volume data value > with the "scolor" command. I don't think there is a shape command option > to automatically replace a previous shape, so it may be a bit tedious to > create new surface, close old surface, color new surface (repeat). It was > probably done with python rather than commands, but that is beyond my > skills, sorry. > > > > 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 Dec 26, 2013, at 3:10 PM, "Hyeong-Tae Jou" wrote: > >> Hi, >> >> I am trying to animate some clipping motion in volume data. >> I only find very simple clipping method using plane. >> >> I'd like to make a movie for clipping motion using prism or 3-D box >> (the clipping gear gradually moving deeper into volume data). >> >> I have tried mask (by inverse masking) using 3-D box, >> but it was very inconvenient, and took too much time to make a movie. >> Are there any other way to make an animation for some fancy clipping? >> >> Many thanks, >> >> Hyeong-Tae >> ----------------- >> Hyeong-Tae Jou >> KIOST > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From jug25 at psu.edu Fri Dec 27 08:08:41 2013 From: jug25 at psu.edu (Jian Guan) Date: Fri, 27 Dec 2013 11:08:41 -0500 Subject: [Chimera-users] Find pseudo 2-fold axes relating heavy and light chain Message-ID: <000c01cf031d$e98e8480$bcab8d80$@psu.edu> Dear all, I am trying to find pseudo 2-fold axes relating heavy and light chains in the constant domain and variable domain respectively in Fab. I tried Define Axes, it failed. And I made artificial double heavy chain, it failed again. I can only get axis which is horizontal passing through both light chain and heavy chain. It is not what I want. Can anyone help to give some clues? Thanks Jian From meng at cgl.ucsf.edu Fri Dec 27 10:11:08 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 27 Dec 2013 10:11:08 -0800 Subject: [Chimera-users] Find pseudo 2-fold axes relating heavy and light chain In-Reply-To: <000c01cf031d$e98e8480$bcab8d80$@psu.edu> References: <000c01cf031d$e98e8480$bcab8d80$@psu.edu> Message-ID: Hi Jian, Define Axes creates a best-fit axis to the atoms you specify. It is not meant to find axes of symmetry or pseudosymmetry. I would recommend opening two copies of your structure, then superimposing them based on the parts that are pseudosymmetric (the parts that are pseudoequivalent), then using command "measure rotation" with option "showAxis true" (or maybe "showSlabs true") to show the axis of rotation between the two copies: Ways to superimpose structures are discussed here: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 27, 2013, at 8:08 AM, Jian Guan wrote: > Dear all, > I am trying to find pseudo 2-fold axes relating heavy and light chains in > the constant domain and variable domain respectively in Fab. > I tried Define Axes, it failed. > And I made artificial double heavy chain, it failed again. I can only get > axis which is horizontal passing through both light chain and heavy chain. > It is not what I want. > Can anyone help to give some clues? > Thanks > Jian From jug25 at psu.edu Fri Dec 27 10:40:27 2013 From: jug25 at psu.edu (Jian Guan) Date: Fri, 27 Dec 2013 13:40:27 -0500 Subject: [Chimera-users] Find pseudo 2-fold axes relating heavy and light chain In-Reply-To: References: <000c01cf031d$e98e8480$bcab8d80$@psu.edu> Message-ID: <000d01cf0333$1d491d20$57db5760$@psu.edu> Hi Elaine, Thank you so much for your reply. I did what you said in the letter. However the return is "Rotation angle is near zero". Then no axis came out. What I want to do is to get the elbow angle of the Fab. The elbow angle is the angle between pseudo 2-fold axes relating heavy and light chains in the variable domain and heavy and light chains in the constant domain. So I have to make two axes for variable and constant domain respectively. Then measure the angles. Looking forward to your reply. Thanks, Jian -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: 2013?12?27? 13:11 To: Jian Guan Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Find pseudo 2-fold axes relating heavy and light chain Hi Jian, Define Axes creates a best-fit axis to the atoms you specify. It is not meant to find axes of symmetry or pseudosymmetry. I would recommend opening two copies of your structure, then superimposing them based on the parts that are pseudosymmetric (the parts that are pseudoequivalent), then using command "measure rotation" with option "showAxis true" (or maybe "showSlabs true") to show the axis of rotation between the two copies: Ways to superimpose structures are discussed 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 Dec 27, 2013, at 8:08 AM, Jian Guan wrote: > Dear all, > I am trying to find pseudo 2-fold axes relating heavy and light chains > in the constant domain and variable domain respectively in Fab. > I tried Define Axes, it failed. > And I made artificial double heavy chain, it failed again. I can only > get axis which is horizontal passing through both light chain and heavy chain. > It is not what I want. > Can anyone help to give some clues? > Thanks > Jian From jug25 at psu.edu Fri Dec 27 10:50:19 2013 From: jug25 at psu.edu (Jian Guan) Date: Fri, 27 Dec 2013 13:50:19 -0500 Subject: [Chimera-users] How to get central cross section which pass through two asigned cross axis Message-ID: <000e01cf0334$7d78b880$786a2980$@psu.edu> Dear all, I have a density map of virus-Fab complex. I want to make a central cross section which pass through the Fab pseudo-symmetry 2-fold axis. I have measure the angle of Fab relative to the capsid. Hope someone can help me. Thank you so much. Sincerely yours, Jian -----Original Message----- From: chimera-users-bounces at cgl.ucsf.edu [mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of chimera-users-request at cgl.ucsf.edu Sent: 2013?12?24? 15:00 To: chimera-users at cgl.ucsf.edu Subject: Chimera-users Digest, Vol 128, Issue 25 Send Chimera-users mailing list submissions to chimera-users at cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request at cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner at cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: saving coords from script (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Dec 2013 15:59:16 -0800 From: Eric Pettersen To: Tetsuro Fujisawa Cc: "chimera-users at cgl.ucsf.edu Mailing List" Subject: Re: [Chimera-users] saving coords from script Message-ID: <04B15E0C-844B-4594-8AE6-760588744D85 at cgl.ucsf.edu> Content-Type: text/plain; charset="windows-1252" On Dec 20, 2013, at 1:58 AM, Tetsuro Fujisawa wrote: > Hi, > > I found some strange behavior in saving pdb file by script file. > I tried to modify the orientation of pdb file ?tst.pdb? (#1) in reference to axis coordinate (#0), then save the atomic coordinates in pdb file. > When I typed in the commands through either command line window or IDLE, transformed coordinates were saved. It worked fine. However, the exact identical commands (inside the brancket) or lines (rc(?..?)) were run by script file shown in below, the untransformed coordinates were saved. This is also the case for ?Midas.write method?. > I wondered this might be a bug. > > Regards, > Tetsuro > > Sample.py: > ---------------------------------------------- > from chimera import runCommand as rc > > rc('open axis.bild') > rc('open tst.pdb') > rc('rock y 60 1 center #1 coord #0 models #1') # orientation of > tst.pdb was modified > rc('focus') > rc('write relative #0 #1 tstA.pdb') > # write current coordinates to tstA.pdb rc('open tstA.pdb') # opened > tstA has original untransformed orientation > ----------------------------------------------- Hi Tetsuro, The issue is that unlike using the command line or IDLE or running a chimera-command script, no frames get drawn during the execution of a Python script unless explicitly requested and therefore the "rock" command in your script doesn't actually do anything until after the entire script runs, and by that time your coordinate file has already been written. To get the rock command to complete before proceeding with the rest of the script you need to append "; wait" or "; wait 1" (since you are rocking for 1 frame) to the end of your rock command. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 128, Issue 25 ********************************************** From meng at cgl.ucsf.edu Fri Dec 27 11:48:17 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 27 Dec 2013 11:48:17 -0800 Subject: [Chimera-users] Find pseudo 2-fold axes relating heavy and light chain In-Reply-To: <000d01cf0333$1d491d20$57db5760$@psu.edu> References: <000c01cf031d$e98e8480$bcab8d80$@psu.edu> <000d01cf0333$1d491d20$57db5760$@psu.edu> Message-ID: <81A69E8B-54BA-48D1-854A-8058BC8D5411@cgl.ucsf.edu> Hi Jian, Most important is to make sure you have superimposed the correct (pseudoequivalent) parts. My earlier answer was for calculating one pseudosymmetry axis. From what you say, and also from this descriptive page I found, you need to calculate two of those, and then measure the angle between them. I was able to do it in Chimera and reproduce the result for the example structure 1bbd in that page. My calculation gave 53 degrees (because the axes in the calculation don't have a direction), whereas the real answer is 180 - 53 = 127 degrees as stated in that page. You can see by just looking at the structure whether it is 53 or 127. (1) open two copies, superimpose V-H of one copy onto V-L of the other copy, use "measure rotation" to show that pseudo 2-fold axis. The tricky part is only using the V (variable) parts of the chains instead of the whole H and L chains when superimposing the structures. More detail on that below. (2) next superimpose the C-H of one copy onto C-L of the other copy, use "measure rotation" to show that pseudo 2-fold axis. (3) now you have two axes, but they are defined as marker sets by the "measure" command and there is no direct way to get the angle between them... so it is necessary to use Define Axes to copy them as axes that can be used in measurements. My Fab copies were models #0,1 and the axes from measure were models #2,3. I selected #2 (for example, command: select #2) and then used define axis for the selected atoms (markers are fake atoms), then selected #3 and used define axis again for the selected atoms, making sure to turn OFF the option to replace the existing define-axis. (4) then in the table of Axes/Planes/Centroids, two axes are listed. Use the mouse to choose those two rows in the table, which automatically reports the axes' angle of intersection near the bottom of that dialog. Image of what I had then is attached below. OK, now the detail about how to only use parts of the chains in the matches. I opened 1bba two times, so it was models #0 and #1. Each model has chains H (heavy) and L (light). I just used Ctrl-drag in the Chimera window to drag a selection box only around the variable domains. Then in MatchMaker I chose "Chain pairing: Specific chain(s) in reference structure with specific chain(s) in match structure" with reference chain #0 chain L and chain to match #1 chain H, and also checked the box "Further restrict matching to current selection." Thus I could superimpose #0 and #1 using only V-H and V-L. After using "measure rotation" to generate the first axis, I chose from the main Chimera menu "Select... Invert (selected models)" so now only the constant parts are selected, and used Matchmaker again without changing any of the settings in that dialog. Then used "measure rotation" ... etc. The main thing is to draw the first selection box carefully. It doesn't matter if you draw it around variable or constant, because the other one will be calculated after you invert selection. I don't have any ideas about what to do if the angle is near zero, but if you really superimposed the structures correctly, my guess is it should not be near zero. Well, now I've learned a lot (too much?) about Fab structures! Elaine -------------- next part -------------- A non-text attachment was scrubbed... Name: grab.tiff Type: image/tiff Size: 207626 bytes Desc: not available URL: -------------- next part -------------- On Dec 27, 2013, at 10:40 AM, Jian Guan wrote: > Hi Elaine, > Thank you so much for your reply. > I did what you said in the letter. However the return is "Rotation angle is > near zero". Then no axis came out. > What I want to do is to get the elbow angle of the Fab. The elbow angle is > the angle between pseudo 2-fold axes relating heavy and light chains in the > variable domain and heavy and light chains in the constant domain. So I have > to make two axes for variable and constant domain respectively. Then measure > the angles. > Looking forward to your reply. > Thanks, > Jian From meng at cgl.ucsf.edu Fri Dec 27 11:56:35 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 27 Dec 2013 11:56:35 -0800 Subject: [Chimera-users] How to get central cross section which pass through two asigned cross axis In-Reply-To: <000e01cf0334$7d78b880$786a2980$@psu.edu> References: <000e01cf0334$7d78b880$786a2980$@psu.edu> Message-ID: Hi Jian, If you have the axes already displayed, you can just use Per-Model Clipping (in menu under Tools... Depiction) to slice the volume model. You can position the plane by hand (well, with the mouse) to coincide with the axes, then hide the axes if you want. Click the Help button on the tool dialog for more details of how to use it, or see the same information on our website: 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 > Dear all, > I have a density map of virus-Fab complex. I want to make a central cross > section which pass through the Fab pseudo-symmetry 2-fold axis. I have > measure the angle of Fab relative to the capsid. > Hope someone can help me. > Thank you so much. > Sincerely yours, > Jian From thrabe at sanfordburnham.org Fri Dec 27 15:24:08 2013 From: thrabe at sanfordburnham.org (Thomas Hrabe) Date: Fri, 27 Dec 2013 23:24:08 +0000 Subject: [Chimera-users] Reset surface programatically from python Message-ID: Hi everyone, I have this line of code where I want to load a density and export a negative surface of it: import chimera as ch mod = ch.openModels.open(?./density.em')[0] mod.surface_levels = [-1,0] mod.display = True ch.exports.doExportCommand('WebGL', 'tmp.html?) However, the surface of the density is rendered for positive values. How can I refresh the display after I specify the surface_levels? Thanks, Thomas From matthewd at bcm.edu Fri Dec 27 16:56:56 2013 From: matthewd at bcm.edu (Dougherty, Matthew T) Date: Fri, 27 Dec 2013 18:56:56 -0600 Subject: [Chimera-users] keyboard shortcuts Message-ID: <5A4EB281C1666D43919DEEA432B50533694E726C5D@EXCMSMBX03.ad.bcm.edu> I am writing a bunch of USB-HID keyboard shortcuts for some extensions I am writing. Usually one shortcut per def. Since my decoding of HID is integrally tied to the extension, I would like to simplify all my shortcuts coming from one device to one def. As of now if I have 100 button commands I have to 1) register 100 shortcuts, 2) create 100 defs, 3) do corresponding stuff in my extension. I would prefer to call one def that passes the actual keyboard string to my extension, thereby simplifying my user accelerators to just registration. How do I get the string within my keyboard shortcuts python file? thanks, Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine From gytjyb at 163.com Sat Dec 28 06:27:58 2013 From: gytjyb at 163.com (=?GBK?B?0ruyqA==?=) Date: Sat, 28 Dec 2013 22:27:58 +0800 (CST) Subject: [Chimera-users] Sir, i donot want to recieve antomately letter from chimera, can you remove my email adress from your email list.. Message-ID: <251fb306.18f10.143399abb35.Coremail.gytjyb@163.com> An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sat Dec 28 08:37:55 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 28 Dec 2013 08:37:55 -0800 Subject: [Chimera-users] Sir, i donot want to recieve antomately letter from chimera, can you remove my email adress from your email list.. In-Reply-To: <251fb306.18f10.143399abb35.Coremail.gytjyb@163.com> References: <251fb306.18f10.143399abb35.Coremail.gytjyb@163.com> Message-ID: To unsubscribe, please go to link at the bottom of every chimera-users email: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ... and follow the instructions to unsubscribe. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From ross at cuhk.edu.hk Sun Dec 29 20:36:50 2013 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Mon, 30 Dec 2013 12:36:50 +0800 Subject: [Chimera-users] Failure of energy miminization Message-ID: <000b01cf0518$c17e2f20$447a8d60$@cuhk.edu.hk> In August there was a discussion entitled "Minimization and mystery nonstandard HIS atom name" and that's the exact problem supposed to have been solved last year. What I did is similar to Jason (http://www.cgl.ucsf.edu/pipermail/chimera-users/2013-August/009069.html), and unfortunately I'm unable to resolve the problem, giving that I'm using chimera 1.8.1 on a Win 7 32G RAM computer. I attach two files, one succeeded till completion while the other one failed early. What I did is simply "Structure editing", next, ok, next, .. Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log No MMTK name for atom "HC1" in standard residue "ALA" Any suggestions to fix the problem is highly appreciated because Chimera is so impressive and I've been using it for many good analyses already. A pity to give up and switch to other programs at this very last stage. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ross at cuhk.edu.hk Sun Dec 29 20:37:09 2013 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Mon, 30 Dec 2013 12:37:09 +0800 Subject: [Chimera-users] Failure of energy miminization Message-ID: <001001cf0518$cd3cc6a0$67b653e0$@cuhk.edu.hk> In August there was a discussion entitled "Minimization and mystery nonstandard HIS atom name" and that's the exact problem supposed to have been solved last year. What I did is similar to Jason (http://www.cgl.ucsf.edu/pipermail/chimera-users/2013-August/009069.html), and unfortunately I'm unable to resolve the problem, giving that I'm using chimera 1.8.1 on a Win 7 32G RAM computer. I attach two files, one succeeded till completion while the other one failed early. What I did is simply "Structure editing", next, ok, next, .. Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log No MMTK name for atom "HC1" in standard residue "ALA" Any suggestions to fix the problem is highly appreciated because Chimera is so impressive and I've been using it for many good analyses already. A pity to give up and switch to other programs at this very last stage. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: success_failure.zip Type: application/x-zip-compressed Size: 130085 bytes Desc: not available URL: From pythonchemia at gazeta.pl Thu Dec 26 07:06:55 2013 From: pythonchemia at gazeta.pl (pythonchemia Gazeta.pl) Date: Thu, 26 Dec 2013 16:06:55 +0100 Subject: [Chimera-users] Set and rna commands Message-ID: Hello ! I have winXP and Chimera version 1.8. I wanted to use the commands rna and set. Unfortunately, they do not work. Why? What is it? I tried to repeat the example of the User's Guide for rna command and failed. Please help me or give me examples on the set command and rna Sincerely, Janusz Grabowski -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Mon Dec 30 12:05:04 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 30 Dec 2013 12:05:04 -0800 Subject: [Chimera-users] Reset surface programatically from python In-Reply-To: References: Message-ID: Hi Thomas, You need mod.show() to have the density map recompute its contour surface. You can remove the mod.display = True line. Your code mod.surface_levels = [-1,0] is setting two contour levels one at density value -1 and one at 0. Is that what you intend? If you only wanted a single level you would use mod.surface_levels = [-1] Tom On Dec 27, 2013, at 3:24 PM, Thomas Hrabe wrote: > Hi everyone, > > I have this line of code where I want to load a density and export a negative surface of it: > > import chimera as ch > mod = ch.openModels.open(?./density.em')[0] > mod.surface_levels = [-1,0] > mod.display = True > ch.exports.doExportCommand('WebGL', 'tmp.html?) > > However, the surface of the density is rendered for positive values. > How can I refresh the display after I specify the surface_levels? > > Thanks, > Thomas > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From goddard at sonic.net Mon Dec 30 11:49:22 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 30 Dec 2013 11:49:22 -0800 Subject: [Chimera-users] Movie for various clipping In-Reply-To: References: <97CC6820A5866948B18B7C7B0887B7990102E893E681@EXCH-CCR01.lj.ad.scripps.edu> Message-ID: <5A3777D9-B2FC-45B4-BA54-1D02759C89AC@sonic.net> Hi Hyeong-Tae, I am making a movie now where I show a rectangular indentation in the face of an electron microscopy map, and then the indentation gets gradually deeper tunnelling into the density map. This is for a planetarium movie which has a very wide field of view so I fly the view point into this rectangular tunnel so you can see the data on all sides. Making the rectangular indentation is not easy -- I use 9 copies of the same density map, one for each rectangular face of the indentation (5 faces) and 4 rectangular strips to show a hole in the front face of the original map. Then I move these faces with the volume planes command. I'm not sure if the above example is what you have in mind. Chimera does not have exotic clipping methods -- just planes. You can use box display mode to show 6 faces of a box within a density map using the Orthoplanes feature (volume dialog menu Features / Orthogonal planes). http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#orthogonal Tom On Dec 26, 2013, at 3:10 PM, "Hyeong-Tae Jou" wrote: > Hi, > > I am trying to animate some clipping motion in volume data. > I only find very simple clipping method using plane. > > I'd like to make a movie for clipping motion using prism or 3-D box > (the clipping gear gradually moving deeper into volume data). > > I have tried mask (by inverse masking) using 3-D box, > but it was very inconvenient, and took too much time to make a movie. > Are there any other way to make an animation for some fancy clipping? > > Many thanks, > > Hyeong-Tae > ----------------- > Hyeong-Tae Jou > KIOST > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From goddard at sonic.net Mon Dec 30 12:21:52 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 30 Dec 2013 12:21:52 -0800 Subject: [Chimera-users] keyboard shortcuts In-Reply-To: <5A4EB281C1666D43919DEEA432B50533694E726C5D@EXCMSMBX03.ad.bcm.edu> References: <5A4EB281C1666D43919DEEA432B50533694E726C5D@EXCMSMBX03.ad.bcm.edu> Message-ID: Hi Matt, I don't understand your question. Is the idea that you want to register a single keyboard shortcut handler that handles many different shortcuts and takes the two-letter shortcut characters as an argument? You would still need to register that function for every set of shortcut keys it handles. You could do something like from Accelerators import add_accelerator as add add('pq', 'Here is a description of what this shortcut does', lambda: myHandler('pq')) The "lambda" business is Python code that creates a function, in this case taking no arguments. And in this example it calls the funtion myHandler with argument "pq". Tom On Dec 27, 2013, at 4:56 PM, "Dougherty, Matthew T" wrote: > I am writing a bunch of USB-HID keyboard shortcuts for some extensions I am writing. > > Usually one shortcut per def. Since my decoding of HID is integrally tied to the extension, I would like to simplify all my shortcuts coming from one device to one def. > > As of now if I have 100 button commands I have to 1) register 100 shortcuts, 2) create 100 defs, 3) do corresponding stuff in my extension. > I would prefer to call one def that passes the actual keyboard string to my extension, thereby simplifying my user accelerators to just registration. > > How do I get the string within my keyboard shortcuts python file? > > thanks, > > > 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 > From meng at cgl.ucsf.edu Mon Dec 30 12:38:04 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 30 Dec 2013 12:38:04 -0800 Subject: [Chimera-users] [chimera-dev] writing in b-factor field In-Reply-To: <20131229174300.5106428shuf48vf8@inbox.unina.it> References: <20131229174300.5106428shuf48vf8@inbox.unina.it> Message-ID: <48BD4146-1928-4A52-869F-3AC7044D5835@cgl.ucsf.edu> On Dec 29, 2013, at 8:43 AM, MARIA VITTORIA CUBELLIS wrote: > Dear sir/madam, > I have a file that associates to each amino acid of a protein A a given value v. > I would like to transfer this value to the b-factor field of the protein A the value v. I have a single value for each aminoacid N1,N2... I would like to transfer the value to each atom > > let say > > N1 C v1 > N1 CO v1 > N1 N v1 > .... > .... > N2 C v2 > N2 CO v2 > N2 N v2 > > and so on > > is it possible to this withe chimera? > thank you > > mvcubellis Dear M V Cubellis, Yes, you can do it, but another question is why do you want to do it? I'm guessing you want to color by those values. In Chimera you can assign the values to the atoms or residues directly as "attributes" and then do coloring to show those values. The B-factor from an input file is one atom attribute named bfactor, but you can create additional attributes with whatever names you wish, and color by any of them. The main work for you is to create an "attribute assignment file" which is mostly tab-separated columns with the atom (or residue) specifiers and values. The necessary format is described here, and there are also some example files: Probably the trickiest part is how to specify the residues in the file, e.g. could be something like :12.a for residue 12 in chain A. See instructions on atom/residue specification: Once you have created that text file, you can read it in with Define Attribute (in menu under Tools? Structure Analysis) or command defattr. Then Render by Attribute (which may automatically appear when you create the attribute, but also is in menu under Tools? Structure Analysis) can be used to show the values with colors and/or radii: If you really wanted to write a PDB file with values in the B-factor column, you would still need to create an attribute assignment file as described above, but more specifically to assign an atom attribute named bfactor. Then when you use the File menu or write command to output a PDB file, your values will be in the B-factor column. See also the Attributes tutorial for examples of coloring by attribute value. 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 From thrabe at sanfordburnham.org Mon Dec 30 12:40:45 2013 From: thrabe at sanfordburnham.org (Thomas Hrabe) Date: Mon, 30 Dec 2013 20:40:45 +0000 Subject: [Chimera-users] Reset surface programatically from python In-Reply-To: References: Message-ID: <8EA65015-AC2B-4E63-950E-31374736CDCB@sanfordburnham.org> Thank you. My script now works on my workstation. On another linux machine where I am running the headless chimera, it is not processed. I start it with chimera ?send tmp.py but all I end up in is the chimera console. Any suggestions? Thanks, Thomas On Dec 30, 2013, at 12:05 PM, Tom Goddard wrote: > Hi Thomas, > > You need > > mod.show() > > to have the density map recompute its contour surface. You can remove the mod.display = True line. Your code > > mod.surface_levels = [-1,0] > > is setting two contour levels one at density value -1 and one at 0. Is that what you intend? If you only wanted a single level you would use > > mod.surface_levels = [-1] > > Tom > > > > > On Dec 27, 2013, at 3:24 PM, Thomas Hrabe wrote: > >> Hi everyone, >> >> I have this line of code where I want to load a density and export a negative surface of it: >> >> import chimera as ch >> mod = ch.openModels.open(?./density.em')[0] >> mod.surface_levels = [-1,0] >> mod.display = True >> ch.exports.doExportCommand('WebGL', 'tmp.html?) >> >> However, the surface of the density is rendered for positive values. >> How can I refresh the display after I specify the surface_levels? >> >> Thanks, >> Thomas >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > From goddard at sonic.net Mon Dec 30 12:48:38 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 30 Dec 2013 12:48:38 -0800 Subject: [Chimera-users] Reset surface programatically from python In-Reply-To: <8EA65015-AC2B-4E63-950E-31374736CDCB@sanfordburnham.org> References: <8EA65015-AC2B-4E63-950E-31374736CDCB@sanfordburnham.org> Message-ID: <57244717-BEED-47F0-89C7-5AA8413B2810@sonic.net> Hi Thomas, I'm not sure why "chimera --send tmp.py" is not working. But I am also confused why you are using the "--send" option? That is intended to send the script to an already running Chimera (or starts a Chimera if it finds none running). If that is not what you are aiming for you can just use "chimera tmp.py" or 'chimera --script "tmp.py 1.5 100"' if your script wants some arguments. If you really are trying to send the script to an already running Chimera, report a bug using Chimera menu Help / Report a Bug? in Chimera (non-headless version) and explain that the problem is with the linux headless version. Tom On Dec 30, 2013, at 12:40 PM, Thomas Hrabe wrote: > Thank you. > > My script now works on my workstation. > On another linux machine where I am running the headless chimera, it is not processed. > > I start it with > > chimera ?send tmp.py > > but all I end up in is the chimera console. > > Any suggestions? > Thanks, > Thomas > > On Dec 30, 2013, at 12:05 PM, Tom Goddard wrote: > >> Hi Thomas, >> >> You need >> >> mod.show() >> >> to have the density map recompute its contour surface. You can remove the mod.display = True line. Your code >> >> mod.surface_levels = [-1,0] >> >> is setting two contour levels one at density value -1 and one at 0. Is that what you intend? If you only wanted a single level you would use >> >> mod.surface_levels = [-1] >> >> Tom >> >> >> >> >> On Dec 27, 2013, at 3:24 PM, Thomas Hrabe wrote: >> >>> Hi everyone, >>> >>> I have this line of code where I want to load a density and export a negative surface of it: >>> >>> import chimera as ch >>> mod = ch.openModels.open(?./density.em')[0] >>> mod.surface_levels = [-1,0] >>> mod.display = True >>> ch.exports.doExportCommand('WebGL', 'tmp.html?) >>> >>> However, the surface of the density is rendered for positive values. >>> How can I refresh the display after I specify the surface_levels? >>> >>> Thanks, >>> Thomas >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > > From goddard at sonic.net Mon Dec 30 12:50:48 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 30 Dec 2013 12:50:48 -0800 Subject: [Chimera-users] Reset surface programatically from python In-Reply-To: <57244717-BEED-47F0-89C7-5AA8413B2810@sonic.net> References: <8EA65015-AC2B-4E63-950E-31374736CDCB@sanfordburnham.org> <57244717-BEED-47F0-89C7-5AA8413B2810@sonic.net> Message-ID: <1E118528-17C7-4A13-BF15-B6C995D9535F@sonic.net> Chimera command-line flags described here http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html Tom On Dec 30, 2013, at 12:48 PM, Tom Goddard wrote: > Hi Thomas, > > I'm not sure why "chimera --send tmp.py" is not working. But I am also confused why you are using the "--send" option? That is intended to send the script to an already running Chimera (or starts a Chimera if it finds none running). If that is not what you are aiming for you can just use "chimera tmp.py" or 'chimera --script "tmp.py 1.5 100"' if your script wants some arguments. If you really are trying to send the script to an already running Chimera, report a bug using Chimera menu Help / Report a Bug? in Chimera (non-headless version) and explain that the problem is with the linux headless version. > > Tom > > > On Dec 30, 2013, at 12:40 PM, Thomas Hrabe wrote: > >> Thank you. >> >> My script now works on my workstation. >> On another linux machine where I am running the headless chimera, it is not processed. >> >> I start it with >> >> chimera ?send tmp.py >> >> but all I end up in is the chimera console. >> >> Any suggestions? >> Thanks, >> Thomas >> >> On Dec 30, 2013, at 12:05 PM, Tom Goddard wrote: >> >>> Hi Thomas, >>> >>> You need >>> >>> mod.show() >>> >>> to have the density map recompute its contour surface. You can remove the mod.display = True line. Your code >>> >>> mod.surface_levels = [-1,0] >>> >>> is setting two contour levels one at density value -1 and one at 0. Is that what you intend? If you only wanted a single level you would use >>> >>> mod.surface_levels = [-1] >>> >>> Tom >>> >>> >>> >>> >>> On Dec 27, 2013, at 3:24 PM, Thomas Hrabe wrote: >>> >>>> Hi everyone, >>>> >>>> I have this line of code where I want to load a density and export a negative surface of it: >>>> >>>> import chimera as ch >>>> mod = ch.openModels.open(?./density.em')[0] >>>> mod.surface_levels = [-1,0] >>>> mod.display = True >>>> ch.exports.doExportCommand('WebGL', 'tmp.html?) >>>> >>>> However, the surface of the density is rendered for positive values. >>>> How can I refresh the display after I specify the surface_levels? >>>> >>>> Thanks, >>>> Thomas >>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users at cgl.ucsf.edu >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >> > From thrabe at sanfordburnham.org Mon Dec 30 13:32:57 2013 From: thrabe at sanfordburnham.org (Thomas Hrabe) Date: Mon, 30 Dec 2013 21:32:57 +0000 Subject: [Chimera-users] Reset surface programatically from python In-Reply-To: <57244717-BEED-47F0-89C7-5AA8413B2810@sonic.net> References: <8EA65015-AC2B-4E63-950E-31374736CDCB@sanfordburnham.org> <57244717-BEED-47F0-89C7-5AA8413B2810@sonic.net> Message-ID: <71BFC674-D815-4167-8383-B30A7763AF00@sanfordburnham.org> Thank you Tom, the script parameter was what I was looking for. My headless chimera now exports those webgl html files. One more question: if I display negative density, how do I programmatically set Surface & Mesh options > Cap high values at box faces? Thanks, Thomas On Dec 30, 2013, at 12:48 PM, Tom Goddard wrote: > Hi Thomas, > > I'm not sure why "chimera --send tmp.py" is not working. But I am also confused why you are using the "--send" option? That is intended to send the script to an already running Chimera (or starts a Chimera if it finds none running). If that is not what you are aiming for you can just use "chimera tmp.py" or 'chimera --script "tmp.py 1.5 100"' if your script wants some arguments. If you really are trying to send the script to an already running Chimera, report a bug using Chimera menu Help / Report a Bug? in Chimera (non-headless version) and explain that the problem is with the linux headless version. > > Tom > > > On Dec 30, 2013, at 12:40 PM, Thomas Hrabe wrote: > >> Thank you. >> >> My script now works on my workstation. >> On another linux machine where I am running the headless chimera, it is not processed. >> >> I start it with >> >> chimera ?send tmp.py >> >> but all I end up in is the chimera console. >> >> Any suggestions? >> Thanks, >> Thomas >> >> On Dec 30, 2013, at 12:05 PM, Tom Goddard wrote: >> >>> Hi Thomas, >>> >>> You need >>> >>> mod.show() >>> >>> to have the density map recompute its contour surface. You can remove the mod.display = True line. Your code >>> >>> mod.surface_levels = [-1,0] >>> >>> is setting two contour levels one at density value -1 and one at 0. Is that what you intend? If you only wanted a single level you would use >>> >>> mod.surface_levels = [-1] >>> >>> Tom >>> >>> >>> >>> >>> On Dec 27, 2013, at 3:24 PM, Thomas Hrabe wrote: >>> >>>> Hi everyone, >>>> >>>> I have this line of code where I want to load a density and export a negative surface of it: >>>> >>>> import chimera as ch >>>> mod = ch.openModels.open(?./density.em')[0] >>>> mod.surface_levels = [-1,0] >>>> mod.display = True >>>> ch.exports.doExportCommand('WebGL', 'tmp.html?) >>>> >>>> However, the surface of the density is rendered for positive values. >>>> How can I refresh the display after I specify the surface_levels? >>>> >>>> Thanks, >>>> Thomas >>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users at cgl.ucsf.edu >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >> > From goddard at sonic.net Mon Dec 30 13:40:33 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 30 Dec 2013 13:40:33 -0800 Subject: [Chimera-users] Reset surface programatically from python In-Reply-To: <71BFC674-D815-4167-8383-B30A7763AF00@sanfordburnham.org> References: <8EA65015-AC2B-4E63-950E-31374736CDCB@sanfordburnham.org> <57244717-BEED-47F0-89C7-5AA8413B2810@sonic.net> <71BFC674-D815-4167-8383-B30A7763AF00@sanfordburnham.org> Message-ID: <1F9B16D8-D2F7-4AE6-AEA3-59ECC1C264B9@sonic.net> Hi Thomas, The best way to set the contour level and also to turn off capping box faces is by calling the set_parameters() method. mod.set_parameters(surface_levels = [-1], cap_faces = False) mod.show() Tom On Dec 30, 2013, at 1:32 PM, Thomas Hrabe wrote: > Thank you Tom, > > the script parameter was what I was looking for. > My headless chimera now exports those webgl html files. > > One more question: if I display negative density, how do I programmatically set > Surface & Mesh options > Cap high values at box faces? > > Thanks, > Thomas > > On Dec 30, 2013, at 12:48 PM, Tom Goddard wrote: > >> Hi Thomas, >> >> I'm not sure why "chimera --send tmp.py" is not working. But I am also confused why you are using the "--send" option? That is intended to send the script to an already running Chimera (or starts a Chimera if it finds none running). If that is not what you are aiming for you can just use "chimera tmp.py" or 'chimera --script "tmp.py 1.5 100"' if your script wants some arguments. If you really are trying to send the script to an already running Chimera, report a bug using Chimera menu Help / Report a Bug? in Chimera (non-headless version) and explain that the problem is with the linux headless version. >> >> Tom >> >> >> On Dec 30, 2013, at 12:40 PM, Thomas Hrabe wrote: >> >>> Thank you. >>> >>> My script now works on my workstation. >>> On another linux machine where I am running the headless chimera, it is not processed. >>> >>> I start it with >>> >>> chimera ?send tmp.py >>> >>> but all I end up in is the chimera console. >>> >>> Any suggestions? >>> Thanks, >>> Thomas >>> >>> On Dec 30, 2013, at 12:05 PM, Tom Goddard wrote: >>> >>>> Hi Thomas, >>>> >>>> You need >>>> >>>> mod.show() >>>> >>>> to have the density map recompute its contour surface. You can remove the mod.display = True line. Your code >>>> >>>> mod.surface_levels = [-1,0] >>>> >>>> is setting two contour levels one at density value -1 and one at 0. Is that what you intend? If you only wanted a single level you would use >>>> >>>> mod.surface_levels = [-1] >>>> >>>> Tom >>>> >>>> >>>> >>>> >>>> On Dec 27, 2013, at 3:24 PM, Thomas Hrabe wrote: >>>> >>>>> Hi everyone, >>>>> >>>>> I have this line of code where I want to load a density and export a negative surface of it: >>>>> >>>>> import chimera as ch >>>>> mod = ch.openModels.open(?./density.em')[0] >>>>> mod.surface_levels = [-1,0] >>>>> mod.display = True >>>>> ch.exports.doExportCommand('WebGL', 'tmp.html?) >>>>> >>>>> However, the surface of the density is rendered for positive values. >>>>> How can I refresh the display after I specify the surface_levels? >>>>> >>>>> Thanks, >>>>> Thomas >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 Dec 30 14:18:23 2013 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 30 Dec 2013 14:18:23 -0800 Subject: [Chimera-users] Failure of energy miminization In-Reply-To: <001001cf0518$cd3cc6a0$67b653e0$@cuhk.edu.hk> References: <001001cf0518$cd3cc6a0$67b653e0$@cuhk.edu.hk> Message-ID: <5343C069-C2E8-489B-962F-1B1D970E2893@cgl.ucsf.edu> Hi Ross, As was the case for the bug report you also submitted for this, both files you included in your zip attachment minimize without error for me. We should continue working on this via the bug report since the readers of the list probably have little interest in the details of this specific problem. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Dec 29, 2013, at 8:37 PM, "Ross KK Leung" wrote: > In August there was a discussion entitled ?Minimization and mystery nonstandard HIS atom name? and that?s the exact problem supposed to have been solved last year. What I did is similar to Jason (http://www.cgl.ucsf.edu/pipermail/chimera-users/2013-August/009069.html), and unfortunately I?m unable to resolve the problem, giving that I?m using chimera 1.8.1 on a Win 7 32G RAM computer. I attach two files, one succeeded till completion while the other one failed early. What I did is simply ?Structure editing?, next, ok, next, ?. > > > Charges of 0.0 were assigned to the unknown atoms > > 1 model(s) had non-integral total charge > Details in reply log > > No MMTK name for atom "HC1" in standard residue "ALA" > > > Any suggestions to fix the problem is highly appreciated because Chimera is so impressive and I?ve been using it for many good analyses already. A pity to give up and switch to other programs at this very last stage. > > > _______________________________________________ > 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 goddard at sonic.net Mon Dec 30 14:44:43 2013 From: goddard at sonic.net (Tom Goddard) Date: Mon, 30 Dec 2013 14:44:43 -0800 Subject: [Chimera-users] Find pseudo 2-fold axes relating heavy and light chain In-Reply-To: <81A69E8B-54BA-48D1-854A-8058BC8D5411@cgl.ucsf.edu> References: <000c01cf031d$e98e8480$bcab8d80$@psu.edu> <000d01cf0333$1d491d20$57db5760$@psu.edu> <81A69E8B-54BA-48D1-854A-8058BC8D5411@cgl.ucsf.edu> Message-ID: <6DB3047E-D901-49C0-8464-539B438EEECC@sonic.net> I improved the Chimera "angle" command so it can report the angle between any two bonds even if they do not share an endpoint. This can replace steps 3 and 4 of the procedure below for measuring the angle between axes. Instead you would select the end-points of the two axes created by "measure rotation" and then use angle sel dihedral false In general, the angle command with the new option "dihedral false" computes the angle between vector 12 an and vector 34 when 4 atoms are specified, for example, angle :47 at CA :52 at CA :121 at CA :115 at CA dihedral false computes the angle between the vector from residue 47 to 52 and vector from residue 121 to 115. Without the "dihedral false" option it reports the dihedral angle. Tom On Dec 27, 2013, at 11:48 AM, Elaine Meng wrote: > Hi Jian, > Most important is to make sure you have superimposed the correct (pseudoequivalent) parts. My earlier answer was for calculating one pseudosymmetry axis. From what you say, and also from this descriptive page I found, you need to calculate two of those, and then measure the angle between them. > > > I was able to do it in Chimera and reproduce the result for the example structure 1bbd in that page. My calculation gave 53 degrees (because the axes in the calculation don't have a direction), whereas the real answer is 180 - 53 = 127 degrees as stated in that page. You can see by just looking at the structure whether it is 53 or 127. > > (1) open two copies, superimpose V-H of one copy onto V-L of the other copy, use "measure rotation" to show that pseudo 2-fold axis. The tricky part is only using the V (variable) parts of the chains instead of the whole H and L chains when superimposing the structures. More detail on that below. > > (2) next superimpose the C-H of one copy onto C-L of the other copy, use "measure rotation" to show that pseudo 2-fold axis. > > (3) now you have two axes, but they are defined as marker sets by the "measure" command and there is no direct way to get the angle between them... so it is necessary to use Define Axes to copy them as axes that can be used in measurements. My Fab copies were models #0,1 and the axes from measure were models #2,3. I selected #2 (for example, command: select #2) and then used define axis for the selected atoms (markers are fake atoms), then selected #3 and used define axis again for the selected atoms, making sure to turn OFF the option to replace the existing define-axis. > > (4) then in the table of Axes/Planes/Centroids, two axes are listed. Use the mouse to choose those two rows in the table, which automatically reports the axes' angle of intersection near the bottom of that dialog. Image of what I had then is attached below. > > OK, now the detail about how to only use parts of the chains in the matches. I opened 1bba two times, so it was models #0 and #1. Each model has chains H (heavy) and L (light). I just used Ctrl-drag in the Chimera window to drag a selection box only around the variable domains. Then in MatchMaker I chose "Chain pairing: Specific chain(s) in reference structure with specific chain(s) in match structure" with reference chain #0 chain L and chain to match #1 chain H, and also checked the box "Further restrict matching to current selection." Thus I could superimpose #0 and #1 using only V-H and V-L. After using "measure rotation" to generate the first axis, I chose from the main Chimera menu "Select... Invert (selected models)" so now only the constant parts are selected, and used Matchmaker again without changing any of the settings in that dialog. Then used "measure rotation" ... etc. The main thing is to draw the first selection box carefully. It doesn't matter if you draw it around variable or constant, because the other one will be calculated after you invert selection. > > I don't have any ideas about what to do if the angle is near zero, but if you really superimposed the structures correctly, my guess is it should not be near zero. > > Well, now I've learned a lot (too much?) about Fab structures! > Elaine > > > > On Dec 27, 2013, at 10:40 AM, Jian Guan wrote: > >> Hi Elaine, >> Thank you so much for your reply. >> I did what you said in the letter. However the return is "Rotation angle is >> near zero". Then no axis came out. >> What I want to do is to get the elbow angle of the Fab. The elbow angle is >> the angle between pseudo 2-fold axes relating heavy and light chains in the >> variable domain and heavy and light chains in the constant domain. So I have >> to make two axes for variable and constant domain respectively. Then measure >> the angles. >> Looking forward to your reply. >> Thanks, >> Jian > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Mon Dec 30 15:51:50 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 30 Dec 2013 15:51:50 -0800 Subject: [Chimera-users] Set and rna commands In-Reply-To: References: Message-ID: <98BAB00A-9C03-4657-88AA-E7D1DFF82F93@cgl.ucsf.edu> Hello Janusz Grabowski, It is impossible to tell what was wrong with your commands given so little information. You would need to say exactly what commands you tried (including all keywords). The commands I tried worked. Notice that several of the "rna" sub-commands and examples in the manual page specify data that must already exist (sequence text file in FASTA format, markers in Chimera tracing out the desired 3D path, etc.), or require the results from some earlier modeling step (minimizing requires you to have already built something). So of course if you copy the example exactly but you don't have the sequence file or the markers or anything to minimize, it wouldn't work. Although it is possible to make short sequences with "rna" without using pre-existing data files, for example: rna model AACCAAAAAAGGUU pairs 1,14,4 ?the "rna" command is mainly for making *approximate* models, especially for very long sequences. How to use the various options is given along with descriptions of the algorithms in the manual page: If you want to make a more precise model, a different approach may be preferred: (a) if you want to make a regular helical conformation and the sequence is not too long to type, you may prefer to use the Build Structure graphical interface (in menu under Tools? Structure Editing). The "Start Structure" section of Build Structure has a "helical DNA/RNA" option. (b) if you want to build a larger RNA with complicated secondary structure, there is a nice plugin "Assemble2" available separately from Chimera: The set command is pretty simple. It is described here (or use command "help set" to see the same thing): Examples: set shadows ~set shadows set bgColor gray 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 Dec 26, 2013, at 7:06 AM, "pythonchemia Gazeta.pl" wrote: > Hello ! > I have winXP and Chimera version 1.8. I wanted to use the commands rna and set. > Unfortunately, they do not work. Why? What is it? > I tried to repeat the example of the User's Guide for rna command and failed. Please help me or give me examples on the set command and rna > Sincerely, Janusz Grabowski From meng at cgl.ucsf.edu Mon Dec 30 16:01:42 2013 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 30 Dec 2013 16:01:42 -0800 Subject: [Chimera-users] Set and rna commands In-Reply-To: <98BAB00A-9C03-4657-88AA-E7D1DFF82F93@cgl.ucsf.edu> References: <98BAB00A-9C03-4657-88AA-E7D1DFF82F93@cgl.ucsf.edu> Message-ID: I forgot to mention that the graphical interface to building helical nucleic acids in Build Structure is newer than the 1.8 release, so you would need to get a daily build to try it. Elaine On Dec 30, 2013, at 3:51 PM, Elaine Meng wrote: > (a) if you want to make a regular helical conformation and the sequence is not too long to type, you may prefer to use the Build Structure graphical interface (in menu under Tools? Structure Editing). The "Start Structure" section of Build Structure has a "helical DNA/RNA" option. > what's new since the 1.8 release: From haiderabbasphy at gmail.com Tue Dec 31 21:21:05 2013 From: haiderabbasphy at gmail.com (Haider Abbas) Date: Wed, 1 Jan 2014 10:51:05 +0530 Subject: [Chimera-users] rate of a reaction Message-ID: Dear all user, Could you please let me know how to calculate reaction rate of a barrierless chemical reaction in gas phase by chimera. with regards Haider Abbas -------------- next part -------------- An HTML attachment was scrubbed... URL: