From anchorwz at googlemail.com Wed Aug 1 03:57:20 2018 From: anchorwz at googlemail.com (Zhe Wang) Date: Wed, 1 Aug 2018 11:57:20 +0100 Subject: [Chimera-users] Error from running headless Chimera Message-ID: Hi, I am trying to using headless Chimera on RedHat linux server 7.3 to produce some images. But I end up with a segmentation fault. Does anyone have an idea how it comes to this? The headless chimera is from https://www.cgl.ucsf.edu/chimera/download.html (64-bit daily build). The test code was taken without changes from https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html. Any ideas will be appreciated. Best, Zhe PS: OSMesa 11.2.2 has been installed. Executing chimera_surface.py... Processing 6c7m.pdb Opening 6c7m.pdb... #0, chain A: kemp eliminase KE07 6c7m.pdb opened Center of rotation: 0.867528 -1.77985 11.157 /software/chimera_headless/bin/mscalc 1.400000 2.000000 1 MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk Copyright M.F. Sanner (March 2000) Compilation flags Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 2 12 connected surface components Total solvent excluded surface area = 10612 component areas = 10035.4, 126.971, 97.9893, 90.9594, 38.157, 36.4953, 34.1487, 33.7557, 32.681, 30.3253, 29.9037, 25.222 Total solvent accessible surface area = 11324.6 component areas = 11265.5, 25.8506, 19.8737, 10.3135, 0.685134, 0.778238, 0.522429, 0.365982, 0.314644, 0.177358, 0.178001, 0.00214196 Surface 6c7m.pdb, category main has 12 components /software/chimera_headless/bin/mscalc 1.400000 10.000000 1 MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk Copyright M.F. Sanner (March 2000) Compilation flags RESTART FROM TRI: 1 radius of atom 5 goes from 1.880000 to 1.980000 radius of atom 6 goes from 1.880000 to 1.980000 radius of atom 1569 goes from 1.420000 to 1.520000 Partial mode /software/chimera_headless/bin/mscalc 1.400000 10.000000 0 MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk Copyright M.F. Sanner (March 2000) Compilation flags RESTART FROM TRI: 1 radius of atom 5 goes from 1.880000 to 1.980000 radius of atom 6 goes from 1.880000 to 1.980000 radius of atom 1569 goes from 1.420000 to 1.520000 Partial mode Calculation of some surface components failed. A single component of the surface was calculated correctly - the failure occurred for disconnected additional components such as inside bubbles. If the desired surface is already shown, there is no need for concern. However, if it is not shown, see below for possible fixes. Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface. If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed. More details are given at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 10 1 connected surface components Total solvent excluded surface area = 10036.7 Total solvent accessible surface area = 11266.5 Surface 6c7m.pdb, category main has 1 components Rendering high resolution image... Segmentation fault -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Aug 1 11:33:12 2018 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 1 Aug 2018 11:33:12 -0700 Subject: [Chimera-users] Activation buttons (namely "All") Message-ID: Hi all, The activation buttons below the command line have an ?All? button that works much the same way as the ?activate all? button in the Model Panel works: if you check it on, then all models are activated for motion; if you check it off then the previous activation states are restored. It has been suggested that the behavior could instead be that when checked off all models would be deactivated (making it easier in some cases to go from moving all models to moving just one). I?m trying to find out if any users make strong use of the current behavior of that button and wouldn?t want it changed. Conversely, I wouldn?t mind hearing people who would really like to see the behavior switched. Regardless of the outcome of the discussion, the behavior of the corresponding Model Panel button would remain the same for a couple of reasons: 1) when clicked, the text of the button changes to ?restore activities? so there?s less chance of confusion, and 2) there?s a separate ?deactivate? button. I will interpret lack of feedback as ?sure, go ahead?. :-) ?Eric Eric Pettersen UCSF Computer Graphics Lab -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Wed Aug 1 14:56:01 2018 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 1 Aug 2018 14:56:01 -0700 Subject: [Chimera-users] Error from running headless Chimera In-Reply-To: References: Message-ID: <4af07255-02c7-ad83-abef-96fc45819a4a@cgl.ucsf.edu> Works for me :-) I just tried the headless version of Chimera on CentOS 7.5.?? I didn't use a script, but did the following commands: ??? open 6c7m ??? windowsize 512 512 ??? surf ??? copy file test.png ??? stop And it created the image file and exited without a problem. So it is unclear what the problem is.? You'll need to run gdb to find out where the segmentation fault occured.? Create a debugging version of the chimera program script, and change the 'exec $python' at the end to 'gdb $python', run it, and then in gdb, 'run $CHIMERA/share/__main__.py chimera_surface.py'.? When chimera segmentation faults, type 'bt' to get a backtrace and send it to me. FYI, the headless version of Chimera comes with libOSMesa, so you don't need to install it.? But it shouldn't cause problems if you did.? The libOSMesa distributed with chimera is ancient, version 7.6.1. So, if the backtrace shows that the bug is in libOSMesa, there's a good chance that if you replace chimera's libOSMesa.so with the system version, it will work. ??? Good luck, ??? Greg On 08/01/2018 03:57 AM, Zhe Wang wrote: > Hi, > > I am trying to using headless Chimera on RedHat linux server 7.3 to > produce some images. > But I end up with a segmentation fault. Does anyone have an idea how > it comes to this? > The headless chimera is from > https://www.cgl.ucsf.edu/chimera/download.html (64-bit daily build). > The test code was taken without changes from > https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html. > Any ideas will be appreciated. > > Best, > Zhe > > PS: OSMesa 11.2.2 has been installed. > > > Executing chimera_surface.py... > > Processing 6c7m.pdb > > Opening 6c7m.pdb... > > #0, chain A: kemp eliminase KE07 > > > 6c7m.pdb opened > > Center of rotation: 0.867528 -1.77985 11.157 > > /software/chimera_headless/bin/mscalc 1.400000 2.000000 1 > > > MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk > > > Copyright M.F. Sanner (March 2000) > > Compilation flags > > > > Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 2 > > 12 connected surface components > > Total solvent excluded surface area = 10612 > > component areas = 10035.4, 126.971, 97.9893, 90.9594, 38.157, 36.4953, > 34.1487, 33.7557, 32.681, 30.3253, 29.9037, 25.222 > > Total solvent accessible surface area = 11324.6 > > component areas = 11265.5, 25.8506, 19.8737, 10.3135, 0.685134, > 0.778238, 0.522429, 0.365982, 0.314644, 0.177358, 0.178001, 0.00214196 > > > Surface 6c7m.pdb, category main has 12 components > > /software/chimera_headless/bin/mscalc 1.400000 10.000000 1 > > > MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk > > > Copyright M.F. Sanner (March 2000) > > Compilation flags > > RESTART FROM TRI: 1 > > radius of atom 5 goes from 1.880000 to 1.980000 > > radius of atom 6 goes from 1.880000 to 1.980000 > > radius of atom 1569 goes from 1.420000 to 1.520000 > > Partial mode > > > /software/chimera_headless/bin/mscalc 1.400000 10.000000 0 > > > MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk > > > Copyright M.F. Sanner (March 2000) > > Compilation flags > > RESTART FROM TRI: 1 > > radius of atom 5 goes from 1.880000 to 1.980000 > > radius of atom 6 goes from 1.880000 to 1.980000 > > radius of atom 1569 goes from 1.420000 to 1.520000 > > Partial mode > > > Calculation of some surface components failed. > > > A single component of the surface was calculated correctly - the > failure occurred for disconnectedadditional components such as inside > bubbles.If the desired surface is already shown, there is no need for > concern.However, if it is not shown, see below for possible fixes. > > > Surface calculation frequently fails for large, multi-chain > structures. The calculation may be successful if the chains are > treated individually, by using the "split" command before generating a > surface.If splitting is not desired or the structure is already a > single chain, changing molecular surface parameters in the Selection > Inspector or (before surface creation) the New Surfaces category of > Preferences may allow the calculation to succeed. More details are > given at > > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html > > > Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 10 > > 1 connected surface components > > Total solvent excluded surface area = 10036.7 > > Total solvent accessible surface area = 11266.5 > > > Surface 6c7m.pdb, category main has 1 components > > Rendering high resolution image... > > Segmentation fault > > > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From xudongzhuanyong at 163.com Fri Aug 3 00:41:06 2018 From: xudongzhuanyong at 163.com (=?GBK?B?0O22qw==?=) Date: Fri, 3 Aug 2018 15:41:06 +0800 (CST) Subject: [Chimera-users] question Message-ID: <53ff3ff.8442.164febb9eac.Coremail.xudongzhuanyong@163.com> Dear editors: thank you for your excellent work. I had a problem. After i built my protein model, it was shown in software as:but when i tried to save the result, the output was displayed as so could you tell me how to solve this problem? look forward to your reply, thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 350271 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 8633 bytes Desc: not available URL: From anchorwz at googlemail.com Fri Aug 3 03:48:36 2018 From: anchorwz at googlemail.com (Zhe Wang) Date: Fri, 3 Aug 2018 11:48:36 +0100 Subject: [Chimera-users] Error from running headless Chimera In-Reply-To: <4af07255-02c7-ad83-abef-96fc45819a4a@cgl.ucsf.edu> References: <4af07255-02c7-ad83-abef-96fc45819a4a@cgl.ucsf.edu> Message-ID: Hi Tom and Greg, Thank you very much for your help. It works now. I tried out the lines you have shown. It did work. I can produce the image I need. To see what was the problem, I test line by line in this script ( https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html). The problem came from "rc("preset apply publication 1")". Here I post the debugging backtrace information I got. It seems related to the swrast rendering lib. Though my problem solved, it will be good to know the reason of this too. Thank you again for your informative help. Best, Zhe (gdb) bt #0 aa_general_rgba_line (ctx=0x9db160, v0=0x7fffeab809c8, v1=0x7fffeab80bb0) at swrast/s_aalinetemp.h:208 #1 0x00007fffecafd9b9 in _swsetup_edge_render_line_tri (ctx=0x9db160, ef=0x14d4060 '\001' , "@\001", e0=5, e1=6, e2=30, v0=0x7fffeab809c8, v1=0x7fffeab80bb0, v2=0x7fffeab83970) at swrast_setup/ss_triangle.c:80 #2 0x00007fffecaffa7f in _swsetup_render_tri (render=0x7fffecafd8c0 <_swsetup_edge_render_line_tri>, facing=1, e2=30, e1=6, e0=5, ctx=0x9db160) at swrast_setup/ss_triangle.c:165 #3 triangle_twoside_unfilled_rgba (ctx=0x9db160, e0=5, e1=6, e2=30) at swrast_setup/ss_tritmp.h:181 #4 0x00007fffeca82feb in _tnl_render_triangles_elts (ctx=0x9db160, start=0, count=150, flags=) at tnl/t_vb_rendertmp.h:175 #5 0x00007fffeca83f65 in run_render (ctx=0x9db160, stage=) at tnl/t_vb_render.c:320 #6 0x00007fffeca78ccd in _tnl_run_pipeline (ctx=0x9db160) at tnl/t_pipeline.c:158 #7 0x00007fffeca7ae0c in _tnl_draw_prims (ctx=ctx at entry=0x9db160, arrays=arrays at entry=0xa2ab20, prim=prim at entry=0x7fffffffb5d0, nr_prims=nr_prims at entry=1, ib=ib at entry=0x7fffffffb5e0, min_index=, max_index=49) at tnl/t_draw.c:445 #8 0x00007fffeca7b125 in _tnl_vbo_draw_prims (ctx=0x9db160, arrays=0xa2ab20, prim=0x7fffffffb5d0, nr_prims=1, ib=0x7fffffffb5e0, index_bounds_valid=, min_index=0, max_index=49) at tnl/t_draw.c:375 #9 0x00007fffeca6da4e in vbo_validated_drawrangeelements (indices=0x0, type=5125, count=150, end=4294967295, start=4294967295, index_bounds_valid=0 '\000', mode=4, ctx=0x9db160) at vbo/vbo_exec_array.c:661 #10 vbo_exec_DrawElements (mode=4, count=150, type=5125, indices=0x0) at vbo/vbo_exec_array.c:755 #11 0x00007fffeb8221d9 in molecule::ObjectInstances::drawPushMatrix(chimera::LensViewer const*, molecule::ObjectInstances::DrawType) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so #12 0x00007fffeb822253 in molecule::ObjectInstances::drawOpaque(chimera::LensViewer const*) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so #13 0x00007fffeb823f84 in molecule::Shapes::drawOpaque(chimera::LensViewer const*) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so #14 0x00007fffeb84fb76 in molecule::MoleculeLensModel::draw(chimera::LensViewer const*, chimera::LensViewer::DrawPass) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so #15 0x00007fffee09e3f9 in chimera::LensModel::xformDraw(chimera::LensViewer const*, chimera::LensViewer::DrawPass) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so #16 0x00007fffee09a8f4 in chimera::Lens::draw(chimera::LensViewer const*, chimera::LensViewer::DrawPass, int const*) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so #17 0x00007fffee0a6e09 in chimera::LensViewer::drawSilhouette(chimera::Array const&, chimera::LensViewer::DrawPass, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so #18 0x00007fffee0a8b69 in chimera::LensViewer::drawScreenBoxes(chimera::Array const&, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so #19 0x00007fffee0a8e9d in chimera::LensViewer::draw() const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so #20 0x00007fffee0ab551 in chimera::LensViewer::pilImages(int, int, char const*, int, bool) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so #21 0x00007fffee0dc98c in LensViewer_pilImages () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so #22 0x00000000004ad05f in do_call (nk=, na=, pp_stack=0x7fffffffc150, func=) at Python/ceval.c:4571 #23 call_function (oparg=, pp_stack=0x7fffffffc150) at Python/ceval.c:4379 #24 PyEval_EvalFrameEx (f=f at entry=0x296b7d0, throwflag=throwflag at entry=0) at Python/ceval.c:2994 #25 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=, argcount=argcount at entry=1, kws=kws at entry=0x1de02d8, kwcount=10, defs=0x7fffe69c57b8, defcount=19, closure=0x0) at Python/ceval.c:3589 #26 0x00000000004ac4fc in fast_function (nk=, na=1, n=, pp_stack=0x7fffffffc390, func=) at Python/ceval.c:4452 #27 call_function (oparg=, pp_stack=0x7fffffffc390) at Python/ceval.c:4377 #28 PyEval_EvalFrameEx (f=f at entry=0x1de0090, throwflag=throwflag at entry=0) at Python/ceval.c:2994 #29 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=args at entry=0x7ffff7f8a068, argcount=, kws=kws at entry=0x7fffe70e7968, kwcount=kwcount at entry=1, defs=defs at entry=0x7fff975f1458, defcount=defcount at entry=11, closure=0x0) at Python/ceval.c:3589 #30 0x000000000051e205 in function_call (func=0x7fff96df7b90, arg=0x7ffff7f8a050, kw=0x7fffe6d94280) at Objects/funcobject.c:523 #31 0x0000000000425bb3 in PyObject_Call (func=func at entry=0x7fff96df7b90, arg=arg at entry=0x7ffff7f8a050, kw=kw at entry=0x7fffe6d94280) at Objects/abstract.c:2547 #32 0x00000000004a9158 in ext_do_call (nk=, na=, flags=, pp_stack=0x7fffffffc6a0, func=0x7fff96df7b90) at Python/ceval.c:4671 #33 PyEval_EvalFrameEx (f=f at entry=0x1f9acc0, throwflag=throwflag at entry=0) at Python/ceval.c:3033 #34 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=, argcount=argcount at entry=2, kws=kws at entry=0x16dad00, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3589 #35 0x00000000004ac4fc in fast_function (nk=, na=2, n=, pp_stack=0x7fffffffc8d0, func=) at Python/ceval.c:4452 #36 call_function (oparg=, pp_stack=0x7fffffffc8d0) at Python/ceval.c:4377 #37 PyEval_EvalFrameEx (f=f at entry=0x16daae0, throwflag=throwflag at entry=0) at Python/ceval.c:2994 #38 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=args at entry=0x7fffe715bf68, argcount=, kws=kws at entry=0x7ffff7f8a068, kwcount=kwcount at entry=0, defs=defs at entry=0x7fff96dcb2a8, defcount=defcount at entry=1, closure=0x0) at Python/ceval.c:3589 #39 0x000000000051e205 in function_call (func=0x7fff96b5fed8, arg=0x7fffe715bf50, kw=0x7fffe710fb40) at Objects/funcobject.c:523 #40 0x0000000000425bb3 in PyObject_Call (func=func at entry=0x7fff96b5fed8, arg=arg at entry=0x7fffe715bf50, kw=kw at entry=0x7fffe710fb40) at Objects/abstract.c:2547 #41 0x00000000004a9158 in ext_do_call (nk=, na=, flags=, pp_stack=0x7fffffffcbe0, func=0x7fff96b5fed8) at Python/ceval.c:4671 #42 PyEval_EvalFrameEx (f=f at entry=0x7fffe6d58960, throwflag=throwflag at entry=0) at Python/ceval.c:3033 #43 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=, argcount=argcount at entry=1, kws=kws at entry=0x7fffe70a5560, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3589 #44 0x00000000004ac4fc in fast_function (nk=, na=1, n=, pp_stack=0x7fffffffce10, func=) at Python/ceval.c:4452 #45 call_function (oparg=, pp_stack=0x7fffffffce10) at Python/ceval.c:4377 #46 PyEval_EvalFrameEx (f=f at entry=0x7fffe70a53d0, throwflag=throwflag at entry=0) at Python/ceval.c:2994 #47 0x00000000004af3b0 in PyEval_EvalCodeEx (co=co at entry=0x7fffe714d7b0, globals=globals at entry=0x7fffe710f168, locals=locals at entry=0x7fffe710f168, args=args at entry=0x0, argcount=argcount at entry=0, kws=kws at entry=0x0, kwcount=kwcount at entry=0, defs=defs at entry=0x0, defcount=defcount at entry=0, closure=closure at entry=0x0) at Python/ceval.c:3589 #48 0x00000000004af4f2 in PyEval_EvalCode (co=co at entry=0x7fffe714d7b0, globals=globals at entry=0x7fffe710f168, locals=locals at entry=0x7fffe710f168) at Python/ceval.c:669 #49 0x00000000004c41cc in PyImport_ExecCodeModuleEx (name=name at entry=0x7ffff04947fc "chimeraOpenSandbox", co=co at entry=0x7fffe714d7b0, pathname=pathname at entry=0x13a2a40 "test.pyc") at Python/import.c:731 #50 0x00000000004c452e in load_source_module (name=0x7ffff04947fc "chimeraOpenSandbox", pathname=0x13a2a40 "test.pyc", fp=fp at entry=0x1292be0) at Python/import.c:1121 #51 0x00000000004c48d7 in imp_load_source (self=, args=) at Python/import.c:3163 #52 0x00000000004acb39 in call_function (oparg=, pp_stack=0x7fffffffd200) at Python/ceval.c:4357 #53 PyEval_EvalFrameEx (f=f at entry=0x13b0860, throwflag=throwflag at entry=0) at Python/ceval.c:2994 #54 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=args at entry=0x7fff97626668, argcount=, kws=kws at entry=0x7ffff7f8a068, kwcount=kwcount at entry=0, defs=defs at entry=0x7fffee43a1a8, defcount=defcount at entry=1, closure=0x0) at Python/ceval.c:3589 #55 0x000000000051e205 in function_call (func=0x7fffee4469b0, arg=0x7fff97626650, kw=0x7fffe71495c8) at Objects/funcobject.c:523 #56 0x0000000000425bb3 in PyObject_Call (func=func at entry=0x7fffee4469b0, arg=arg at entry=0x7fff97626650, kw=kw at entry=0x7fffe71495c8) at Objects/abstract.c:2547 #57 0x00000000004a9158 in ext_do_call (nk=, na=, flags=, pp_stack=0x7fffffffd510, func=0x7fffee4469b0) at Python/ceval.c:4671 #58 PyEval_EvalFrameEx (f=f at entry=0x139e490, throwflag=throwflag at entry=0) at Python/ceval.c:3033 #59 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=, argcount=argcount at entry=2, kws=kws at entry=0x897058, kwcount=1, defs=0x7fffee436068, defcount=12, closure=0x0) at Python/ceval.c:3589 #60 0x00000000004ac4fc in fast_function (nk=, na=2, n=, pp_stack=0x7fffffffd740, func=) at Python/ceval.c:4452 #61 call_function (oparg=, pp_stack=0x7fffffffd740) at Python/ceval.c:4377 #62 PyEval_EvalFrameEx (f=f at entry=0x896c20, throwflag=throwflag at entry=0) at Python/ceval.c:2994 #63 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=, argcount=argcount at entry=1, kws=kws at entry=0x7ffff7f1fac0, kwcount=0, defs=0x7ffff7ef0f80, defcount=16, closure=0x0) at Python/ceval.c:3589 #64 0x00000000004ac4fc in fast_function (nk=, na=1, n=, pp_stack=0x7fffffffd980, func=) at Python/ceval.c:4452 #65 call_function (oparg=, pp_stack=0x7fffffffd980) at Python/ceval.c:4377 #66 PyEval_EvalFrameEx (f=f at entry=0x7ffff7f1f938, throwflag=throwflag at entry=0) at Python/ceval.c:2994 #67 0x00000000004af3b0 in PyEval_EvalCodeEx (co=co at entry=0x7ffff7f9d230, globals=globals at entry=0x7ffff7f5f168, locals=locals at entry=0x7ffff7f5f168, args=args at entry=0x0, argcount=argcount at entry=0, kws=kws at entry=0x0, kwcount=kwcount at entry=0, defs=defs at entry=0x0, defcount=defcount at entry=0, ---Type to continue, or q to quit--- On Wed, Aug 1, 2018 at 10:56 PM Greg Couch wrote: > Works for me :-) > > I just tried the headless version of Chimera on CentOS 7.5. I didn't use > a script, but did the following commands: > open 6c7m > windowsize 512 512 > surf > copy file test.png > stop > > And it created the image file and exited without a problem. > > So it is unclear what the problem is. You'll need to run gdb to find out > where the segmentation fault occured. Create a debugging version of the > chimera program script, and change the 'exec $python' at the end to 'gdb > $python', run it, and then in gdb, 'run $CHIMERA/share/__main__.py > chimera_surface.py'. When chimera segmentation faults, type 'bt' to get a > backtrace and send it to me. > > FYI, the headless version of Chimera comes with libOSMesa, so you don't > need to install it. But it shouldn't cause problems if you did. The > libOSMesa distributed with chimera is ancient, version 7.6.1. So, if the > backtrace shows that the bug is in libOSMesa, there's a good chance that if > you replace chimera's libOSMesa.so with the system version, it will work. > > Good luck, > > Greg > > On 08/01/2018 03:57 AM, Zhe Wang wrote: > > Hi, > > I am trying to using headless Chimera on RedHat linux server 7.3 to > produce some images. > But I end up with a segmentation fault. Does anyone have an idea how it > comes to this? > The headless chimera is from > https://www.cgl.ucsf.edu/chimera/download.html (64-bit daily build). > The test code was taken without changes from > https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html. > Any ideas will be appreciated. > > Best, > Zhe > > PS: OSMesa 11.2.2 has been installed. > > > Executing chimera_surface.py... > > Processing 6c7m.pdb > > Opening 6c7m.pdb... > > #0, chain A: kemp eliminase KE07 > > > 6c7m.pdb opened > > Center of rotation: 0.867528 -1.77985 11.157 > > /software/chimera_headless/bin/mscalc 1.400000 2.000000 1 > > > MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk > > Copyright M.F. Sanner (March 2000) > > Compilation flags > > > > Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 2 > > 12 connected surface components > > Total solvent excluded surface area = 10612 > > component areas = 10035.4, 126.971, 97.9893, 90.9594, 38.157, > 36.4953, 34.1487, 33.7557, 32.681, 30.3253, 29.9037, 25.222 > > Total solvent accessible surface area = 11324.6 > > component areas = 11265.5, 25.8506, 19.8737, 10.3135, 0.685134, > 0.778238, 0.522429, 0.365982, 0.314644, 0.177358, 0.178001, 0.00214196 > > > Surface 6c7m.pdb, category main has 12 components > > /software/chimera_headless/bin/mscalc 1.400000 10.000000 1 > > > MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk > > Copyright M.F. Sanner (March 2000) > > Compilation flags > > RESTART FROM TRI: 1 > > radius of atom 5 goes from 1.880000 to 1.980000 > > radius of atom 6 goes from 1.880000 to 1.980000 > > radius of atom 1569 goes from 1.420000 to 1.520000 > > Partial mode > > > /software/chimera_headless/bin/mscalc 1.400000 10.000000 0 > > > MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk > > Copyright M.F. Sanner (March 2000) > > Compilation flags > > RESTART FROM TRI: 1 > > radius of atom 5 goes from 1.880000 to 1.980000 > > radius of atom 6 goes from 1.880000 to 1.980000 > > radius of atom 1569 goes from 1.420000 to 1.520000 > > Partial mode > > > Calculation of some surface components failed. > > > A single component of the surface was calculated correctly - the failure > occurred for disconnected additional components such as inside bubbles. If > the desired surface is already shown, there is no need for concern. However, > if it is not shown, see below for possible fixes. > > > Surface calculation frequently fails for large, multi-chain structures. > The calculation may be successful if the chains are treated individually, > by using the "split" command before generating a surface. If splitting > is not desired or the structure is already a single chain, changing > molecular surface parameters in the Selection Inspector or (before surface > creation) the New Surfaces category of Preferences may allow the > calculation to succeed. More details are given at > > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html > > > Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 10 > > 1 connected surface components > > Total solvent excluded surface area = 10036.7 > > Total solvent accessible surface area = 11266.5 > > > Surface 6c7m.pdb, category main has 1 components > > Rendering high resolution image... > > Segmentation fault > > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Fri Aug 3 10:33:09 2018 From: goddard at sonic.net (Tom Goddard) Date: Fri, 3 Aug 2018 10:33:09 -0700 Subject: [Chimera-users] question In-Reply-To: <53ff3ff.8442.164febb9eac.Coremail.xudongzhuanyong@163.com> References: <53ff3ff.8442.164febb9eac.Coremail.xudongzhuanyong@163.com> Message-ID: <7CF134EC-F648-46EA-8AA5-57CD60B0366C@sonic.net> Hi ??, The blank image is because the graphics driver on your computer has problems. Here are ways you can get image save to work. Set the ?supersample? option in the image save dialog from its default 3x3 to 1x1. Supersampling 3x3 using some fancier off-screen rendering and that is where the graphics driver usually fails. Next option is to try to update your graphics driver. The other option is to use another computer which has a working graphics driver. Tom > On Aug 3, 2018, at 12:41 AM, ?? wrote: > > Dear editors: > thank you for your excellent work. I had a problem. After i built my protein model, it was shown in software as:but when i tried to save the result, the output was displayed as > so could you tell me how to solve this problem? look forward to your reply, thank you > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Fri Aug 3 10:41:10 2018 From: goddard at sonic.net (Tom Goddard) Date: Fri, 3 Aug 2018 10:41:10 -0700 Subject: [Chimera-users] Error from running headless Chimera In-Reply-To: References: <4af07255-02c7-ad83-abef-96fc45819a4a@cgl.ucsf.edu> Message-ID: Hi Zhe, This traceback shows the crash is in the OSMesa graphics rendering library. This is a big complex library that we did not develop and I do not know why it is failing. As Greg mentioned, Chimera includes a very old version of OSMesa and a newer version would have a good chance of fixing this. I don?t know how you could swap in a newer version although Greg might know. As to why ?preset apply publication 1? leads to this crash I would bet it is because that preset enables silhouette edges and that the OSMesa bug is hit by the silhouette rendering code. You could try putting in the command ?unset silhouette? after the preset and see if that avoids the crash. Tom > On Aug 3, 2018, at 3:48 AM, Zhe Wang wrote: > > Hi Tom and Greg, > > Thank you very much for your help. > It works now. I tried out the lines you have shown. It did work. I can produce the image I need. > To see what was the problem, I test line by line in this script (https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html ). The problem came from "rc("preset apply publication 1")". > Here I post the debugging backtrace information I got. It seems related to the swrast rendering lib. > Though my problem solved, it will be good to know the reason of this too. > Thank you again for your informative help. > > Best, > Zhe > > (gdb) bt > #0 aa_general_rgba_line (ctx=0x9db160, v0=0x7fffeab809c8, v1=0x7fffeab80bb0) at swrast/s_aalinetemp.h:208 > #1 0x00007fffecafd9b9 in _swsetup_edge_render_line_tri (ctx=0x9db160, ef=0x14d4060 '\001' , "@\001", e0=5, e1=6, e2=30, v0=0x7fffeab809c8, v1=0x7fffeab80bb0, v2=0x7fffeab83970) at swrast_setup/ss_triangle.c:80 > #2 0x00007fffecaffa7f in _swsetup_render_tri (render=0x7fffecafd8c0 <_swsetup_edge_render_line_tri>, facing=1, e2=30, e1=6, e0=5, ctx=0x9db160) at swrast_setup/ss_triangle.c:165 > #3 triangle_twoside_unfilled_rgba (ctx=0x9db160, e0=5, e1=6, e2=30) at swrast_setup/ss_tritmp.h:181 > #4 0x00007fffeca82feb in _tnl_render_triangles_elts (ctx=0x9db160, start=0, count=150, flags=) at tnl/t_vb_rendertmp.h:175 > #5 0x00007fffeca83f65 in run_render (ctx=0x9db160, stage=) at tnl/t_vb_render.c:320 > #6 0x00007fffeca78ccd in _tnl_run_pipeline (ctx=0x9db160) at tnl/t_pipeline.c:158 > #7 0x00007fffeca7ae0c in _tnl_draw_prims (ctx=ctx at entry=0x9db160, arrays=arrays at entry=0xa2ab20, prim=prim at entry=0x7fffffffb5d0, nr_prims=nr_prims at entry=1, ib=ib at entry=0x7fffffffb5e0, min_index=, max_index=49) at tnl/t_draw.c:445 > #8 0x00007fffeca7b125 in _tnl_vbo_draw_prims (ctx=0x9db160, arrays=0xa2ab20, prim=0x7fffffffb5d0, nr_prims=1, ib=0x7fffffffb5e0, index_bounds_valid=, min_index=0, max_index=49) at tnl/t_draw.c:375 > #9 0x00007fffeca6da4e in vbo_validated_drawrangeelements (indices=0x0, type=5125, count=150, end=4294967295, start=4294967295, index_bounds_valid=0 '\000', mode=4, ctx=0x9db160) at vbo/vbo_exec_array.c:661 > #10 vbo_exec_DrawElements (mode=4, count=150, type=5125, indices=0x0) at vbo/vbo_exec_array.c:755 > #11 0x00007fffeb8221d9 in molecule::ObjectInstances::drawPushMatrix(chimera::LensViewer const*, molecule::ObjectInstances::DrawType) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so > #12 0x00007fffeb822253 in molecule::ObjectInstances::drawOpaque(chimera::LensViewer const*) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so > #13 0x00007fffeb823f84 in molecule::Shapes::drawOpaque(chimera::LensViewer const*) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so > #14 0x00007fffeb84fb76 in molecule::MoleculeLensModel::draw(chimera::LensViewer const*, chimera::LensViewer::DrawPass) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_molecule.so > #15 0x00007fffee09e3f9 in chimera::LensModel::xformDraw(chimera::LensViewer const*, chimera::LensViewer::DrawPass) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so > #16 0x00007fffee09a8f4 in chimera::Lens::draw(chimera::LensViewer const*, chimera::LensViewer::DrawPass, int const*) () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so > #17 0x00007fffee0a6e09 in chimera::LensViewer::drawSilhouette(chimera::Array const&, chimera::LensViewer::DrawPass, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so > #18 0x00007fffee0a8b69 in chimera::LensViewer::drawScreenBoxes(chimera::Array const&, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so > #19 0x00007fffee0a8e9d in chimera::LensViewer::draw() const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so > #20 0x00007fffee0ab551 in chimera::LensViewer::pilImages(int, int, char const*, int, bool) const () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so > #21 0x00007fffee0dc98c in LensViewer_pilImages () from /nfs/public/rw/pdbe/httpd-em/software/chimera_headless/lib/_chimera.so > #22 0x00000000004ad05f in do_call (nk=, na=, pp_stack=0x7fffffffc150, func=) at Python/ceval.c:4571 > #23 call_function (oparg=, pp_stack=0x7fffffffc150) at Python/ceval.c:4379 > #24 PyEval_EvalFrameEx (f=f at entry=0x296b7d0, throwflag=throwflag at entry=0) at Python/ceval.c:2994 > #25 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=, argcount=argcount at entry=1, kws=kws at entry=0x1de02d8, kwcount=10, defs=0x7fffe69c57b8, defcount=19, closure=0x0) at Python/ceval.c:3589 > #26 0x00000000004ac4fc in fast_function (nk=, na=1, n=, pp_stack=0x7fffffffc390, func=) at Python/ceval.c:4452 > #27 call_function (oparg=, pp_stack=0x7fffffffc390) at Python/ceval.c:4377 > #28 PyEval_EvalFrameEx (f=f at entry=0x1de0090, throwflag=throwflag at entry=0) at Python/ceval.c:2994 > #29 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=args at entry=0x7ffff7f8a068, argcount=, kws=kws at entry=0x7fffe70e7968, kwcount=kwcount at entry=1, defs=defs at entry=0x7fff975f1458, defcount=defcount at entry=11, closure=0x0) > at Python/ceval.c:3589 > #30 0x000000000051e205 in function_call (func=0x7fff96df7b90, arg=0x7ffff7f8a050, kw=0x7fffe6d94280) at Objects/funcobject.c:523 > #31 0x0000000000425bb3 in PyObject_Call (func=func at entry=0x7fff96df7b90, arg=arg at entry=0x7ffff7f8a050, kw=kw at entry=0x7fffe6d94280) at Objects/abstract.c:2547 > #32 0x00000000004a9158 in ext_do_call (nk=, na=, flags=, pp_stack=0x7fffffffc6a0, func=0x7fff96df7b90) at Python/ceval.c:4671 > #33 PyEval_EvalFrameEx (f=f at entry=0x1f9acc0, throwflag=throwflag at entry=0) at Python/ceval.c:3033 > #34 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=, argcount=argcount at entry=2, kws=kws at entry=0x16dad00, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3589 > #35 0x00000000004ac4fc in fast_function (nk=, na=2, n=, pp_stack=0x7fffffffc8d0, func=) at Python/ceval.c:4452 > #36 call_function (oparg=, pp_stack=0x7fffffffc8d0) at Python/ceval.c:4377 > #37 PyEval_EvalFrameEx (f=f at entry=0x16daae0, throwflag=throwflag at entry=0) at Python/ceval.c:2994 > #38 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=args at entry=0x7fffe715bf68, argcount=, kws=kws at entry=0x7ffff7f8a068, kwcount=kwcount at entry=0, defs=defs at entry=0x7fff96dcb2a8, defcount=defcount at entry=1, closure=0x0) > at Python/ceval.c:3589 > #39 0x000000000051e205 in function_call (func=0x7fff96b5fed8, arg=0x7fffe715bf50, kw=0x7fffe710fb40) at Objects/funcobject.c:523 > #40 0x0000000000425bb3 in PyObject_Call (func=func at entry=0x7fff96b5fed8, arg=arg at entry=0x7fffe715bf50, kw=kw at entry=0x7fffe710fb40) at Objects/abstract.c:2547 > #41 0x00000000004a9158 in ext_do_call (nk=, na=, flags=, pp_stack=0x7fffffffcbe0, func=0x7fff96b5fed8) at Python/ceval.c:4671 > #42 PyEval_EvalFrameEx (f=f at entry=0x7fffe6d58960, throwflag=throwflag at entry=0) at Python/ceval.c:3033 > #43 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=, argcount=argcount at entry=1, kws=kws at entry=0x7fffe70a5560, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3589 > #44 0x00000000004ac4fc in fast_function (nk=, na=1, n=, pp_stack=0x7fffffffce10, func=) at Python/ceval.c:4452 > #45 call_function (oparg=, pp_stack=0x7fffffffce10) at Python/ceval.c:4377 > #46 PyEval_EvalFrameEx (f=f at entry=0x7fffe70a53d0, throwflag=throwflag at entry=0) at Python/ceval.c:2994 > #47 0x00000000004af3b0 in PyEval_EvalCodeEx (co=co at entry=0x7fffe714d7b0, globals=globals at entry=0x7fffe710f168, locals=locals at entry=0x7fffe710f168, args=args at entry=0x0, argcount=argcount at entry=0, kws=kws at entry=0x0, kwcount=kwcount at entry=0, defs=defs at entry=0x0, defcount=defcount at entry=0, > closure=closure at entry=0x0) at Python/ceval.c:3589 > #48 0x00000000004af4f2 in PyEval_EvalCode (co=co at entry=0x7fffe714d7b0, globals=globals at entry=0x7fffe710f168, locals=locals at entry=0x7fffe710f168) at Python/ceval.c:669 > #49 0x00000000004c41cc in PyImport_ExecCodeModuleEx (name=name at entry=0x7ffff04947fc "chimeraOpenSandbox", co=co at entry=0x7fffe714d7b0, pathname=pathname at entry=0x13a2a40 "test.pyc") at Python/import.c:731 > #50 0x00000000004c452e in load_source_module (name=0x7ffff04947fc "chimeraOpenSandbox", pathname=0x13a2a40 "test.pyc", fp=fp at entry=0x1292be0) at Python/import.c:1121 > #51 0x00000000004c48d7 in imp_load_source (self=, args=) at Python/import.c:3163 > #52 0x00000000004acb39 in call_function (oparg=, pp_stack=0x7fffffffd200) at Python/ceval.c:4357 > #53 PyEval_EvalFrameEx (f=f at entry=0x13b0860, throwflag=throwflag at entry=0) at Python/ceval.c:2994 > #54 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=args at entry=0x7fff97626668, argcount=, kws=kws at entry=0x7ffff7f8a068, kwcount=kwcount at entry=0, defs=defs at entry=0x7fffee43a1a8, defcount=defcount at entry=1, closure=0x0) > at Python/ceval.c:3589 > #55 0x000000000051e205 in function_call (func=0x7fffee4469b0, arg=0x7fff97626650, kw=0x7fffe71495c8) at Objects/funcobject.c:523 > #56 0x0000000000425bb3 in PyObject_Call (func=func at entry=0x7fffee4469b0, arg=arg at entry=0x7fff97626650, kw=kw at entry=0x7fffe71495c8) at Objects/abstract.c:2547 > #57 0x00000000004a9158 in ext_do_call (nk=, na=, flags=, pp_stack=0x7fffffffd510, func=0x7fffee4469b0) at Python/ceval.c:4671 > #58 PyEval_EvalFrameEx (f=f at entry=0x139e490, throwflag=throwflag at entry=0) at Python/ceval.c:3033 > #59 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=, argcount=argcount at entry=2, kws=kws at entry=0x897058, kwcount=1, defs=0x7fffee436068, defcount=12, closure=0x0) at Python/ceval.c:3589 > #60 0x00000000004ac4fc in fast_function (nk=, na=2, n=, pp_stack=0x7fffffffd740, func=) at Python/ceval.c:4452 > #61 call_function (oparg=, pp_stack=0x7fffffffd740) at Python/ceval.c:4377 > #62 PyEval_EvalFrameEx (f=f at entry=0x896c20, throwflag=throwflag at entry=0) at Python/ceval.c:2994 > #63 0x00000000004af3b0 in PyEval_EvalCodeEx (co=, globals=, locals=locals at entry=0x0, args=, argcount=argcount at entry=1, kws=kws at entry=0x7ffff7f1fac0, kwcount=0, defs=0x7ffff7ef0f80, defcount=16, closure=0x0) at Python/ceval.c:3589 > #64 0x00000000004ac4fc in fast_function (nk=, na=1, n=, pp_stack=0x7fffffffd980, func=) at Python/ceval.c:4452 > #65 call_function (oparg=, pp_stack=0x7fffffffd980) at Python/ceval.c:4377 > #66 PyEval_EvalFrameEx (f=f at entry=0x7ffff7f1f938, throwflag=throwflag at entry=0) at Python/ceval.c:2994 > #67 0x00000000004af3b0 in PyEval_EvalCodeEx (co=co at entry=0x7ffff7f9d230, globals=globals at entry=0x7ffff7f5f168, locals=locals at entry=0x7ffff7f5f168, args=args at entry=0x0, argcount=argcount at entry=0, kws=kws at entry=0x0, kwcount=kwcount at entry=0, defs=defs at entry=0x0, defcount=defcount at entry=0, > ---Type to continue, or q to quit--- > > > > On Wed, Aug 1, 2018 at 10:56 PM Greg Couch > wrote: > Works for me :-) > > I just tried the headless version of Chimera on CentOS 7.5. I didn't use a script, but did the following commands: > > open 6c7m > windowsize 512 512 > surf > copy file test.png > stop > > And it created the image file and exited without a problem. > > So it is unclear what the problem is. You'll need to run gdb to find out where the segmentation fault occured. Create a debugging version of the chimera program script, and change the 'exec $python' at the end to 'gdb $python', run it, and then in gdb, 'run $CHIMERA/share/__main__.py chimera_surface.py'. When chimera segmentation faults, type 'bt' to get a backtrace and send it to me. > FYI, the headless version of Chimera comes with libOSMesa, so you don't need to install it. But it shouldn't cause problems if you did. The libOSMesa distributed with chimera is ancient, version 7.6.1. So, if the backtrace shows that the bug is in libOSMesa, there's a good chance that if you replace chimera's libOSMesa.so with the system version, it will work. > > Good luck, > > Greg > > On 08/01/2018 03:57 AM, Zhe Wang wrote: >> Hi, >> >> I am trying to using headless Chimera on RedHat linux server 7.3 to produce some images. >> But I end up with a segmentation fault. Does anyone have an idea how it comes to this? >> The headless chimera is from https://www.cgl.ucsf.edu/chimera/download.html (64-bit daily build). >> The test code was taken without changes from https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html . >> Any ideas will be appreciated. >> >> Best, >> Zhe >> >> PS: OSMesa 11.2.2 has been installed. >> >> >> Executing chimera_surface.py... >> Processing 6c7m.pdb >> Opening 6c7m.pdb... >> #0, chain A: kemp eliminase KE07 >> >> 6c7m.pdb opened >> Center of rotation: 0.867528 -1.77985 11.157 >> /software/chimera_headless/bin/mscalc 1.400000 2.000000 1 >> >> MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk >> Copyright M.F. Sanner (March 2000) >> Compilation flags >> >> >> Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 2 >> 12 connected surface components >> Total solvent excluded surface area = 10612 >> component areas = 10035.4, 126.971, 97.9893, 90.9594, 38.157, 36.4953, 34.1487, 33.7557, 32.681, 30.3253, 29.9037, 25.222 >> Total solvent accessible surface area = 11324.6 >> component areas = 11265.5, 25.8506, 19.8737, 10.3135, 0.685134, 0.778238, 0.522429, 0.365982, 0.314644, 0.177358, 0.178001, 0.00214196 >> >> Surface 6c7m.pdb, category main has 12 components >> /software/chimera_headless/bin/mscalc 1.400000 10.000000 1 >> >> MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk >> Copyright M.F. Sanner (March 2000) >> Compilation flags >> RESTART FROM TRI: 1 >> radius of atom 5 goes from 1.880000 to 1.980000 >> radius of atom 6 goes from 1.880000 to 1.980000 >> radius of atom 1569 goes from 1.420000 to 1.520000 >> Partial mode >> >> /software/chimera_headless/bin/mscalc 1.400000 10.000000 0 >> >> MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk >> Copyright M.F. Sanner (March 2000) >> Compilation flags >> RESTART FROM TRI: 1 >> radius of atom 5 goes from 1.880000 to 1.980000 >> radius of atom 6 goes from 1.880000 to 1.980000 >> radius of atom 1569 goes from 1.420000 to 1.520000 >> Partial mode >> >> Calculation of some surface components failed. >> >> A single component of the surface was calculated correctly - the failure occurred for disconnected additional components such as inside bubbles. If the desired surface is already shown, there is no need for concern. However, if it is not shown, see below for possible fixes. >> >> Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface. If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed. More details are given at >> >> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html >> >> Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 10 >> 1 connected surface components >> Total solvent excluded surface area = 10036.7 >> Total solvent accessible surface area = 11266.5 >> >> Surface 6c7m.pdb, category main has 1 components >> Rendering high resolution image... >> Segmentation fault >> >> >> >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sun Aug 5 10:07:07 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sun, 5 Aug 2018 10:07:07 -0700 Subject: [Chimera-users] from govinda - How to save coordinates after rotation and translation fitted in cryo em map In-Reply-To: References: Message-ID: <9F45EA0C-E7BB-444D-8825-5672BFF276A1@cgl.ucsf.edu> Dear Govinda, Please see the User?s Guide page on saving your data, and the links therein: ?including Save PDB ...write command ?saving after fitting It is recommended to send questions to chimera-users at cgl.ucsf.edu (CC?d here). You can also use Chimera menu: Help? Search Documentation. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 4, 2018, at 11:22 AM, Govindasamy, Lakshmanan wrote: > > Dear Dr.Meng, > > How to save the coordinates in chimera after fitting into cryo em map. > i am having difficulty in save the coordinates > Please educate me how to save coordinates. > > thanks > govinda From xudongzhuanyong at 163.com Sat Aug 4 02:46:03 2018 From: xudongzhuanyong at 163.com (=?utf-8?B?6K645Lic?=) Date: Sat, 4 Aug 2018 17:46:03 +0800 (CST) Subject: [Chimera-users] question In-Reply-To: <7CF134EC-F648-46EA-8AA5-57CD60B0366C@sonic.net> References: <53ff3ff.8442.164febb9eac.Coremail.xudongzhuanyong@163.com> <7CF134EC-F648-46EA-8AA5-57CD60B0366C@sonic.net> Message-ID: <3f6beff5.55bf.16504545f7e.Coremail.xudongzhuanyong@163.com> OK. Thank you very much! At 2018-08-04 01:33:09, "Tom Goddard" wrote: Hi ??, The blank image is because the graphics driver on your computer has problems. Here are ways you can get image save to work. Set the ?supersample? option in the image save dialog from its default 3x3 to 1x1. Supersampling 3x3 using some fancier off-screen rendering and that is where the graphics driver usually fails. Next option is to try to update your graphics driver. The other option is to use another computer which has a working graphics driver. Tom On Aug 3, 2018, at 12:41 AM, ?? wrote: Dear editors: thank you for your excellent work. I had a problem. After i built my protein model, it was shown in software as:but when i tried to save the result, the output was displayed as so could you tell me how to solve this problem? look forward to your reply, thank you _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From kesgin-schaefer at chemie.uni-hamburg.de Mon Aug 6 02:50:29 2018 From: kesgin-schaefer at chemie.uni-hamburg.de (kesgin-schaefer at chemie.uni-hamburg.de) Date: Mon, 06 Aug 2018 11:50:29 +0200 Subject: [Chimera-users] problem with electron density map Message-ID: <20180806115029.Horde.1DDtVG7BZNAb98DdQEJk7uN@webmail.chemie.uni-hamburg.de> Dear all, I have a problem with my electron density map: if I load the map in chimera, it will only show a subregion of the map and after "fit to model" the model will not be completely covered (see attachment). Any suggestions about how to solve the problem would be much appreciated. Thanks Steffi -------------- next part -------------- A non-text attachment was scrubbed... Name: chimera.png Type: image/png Size: 52745 bytes Desc: not available URL: From meng at cgl.ucsf.edu Mon Aug 6 09:48:09 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 6 Aug 2018 09:48:09 -0700 Subject: [Chimera-users] problem with electron density map In-Reply-To: <20180806115029.Horde.1DDtVG7BZNAb98DdQEJk7uN@webmail.chemie.uni-hamburg.de> References: <20180806115029.Horde.1DDtVG7BZNAb98DdQEJk7uN@webmail.chemie.uni-hamburg.de> Message-ID: Hi Steffi, If it is only showing a subregion you can use Volume Viewer menu "Features? Subregion selection? to show subregion options in the dialog, and then click the ?Full? button in those options. However, I?m somewhat mystified, because I can?t think of a reason why it would show only a subregion automatically (without your telling it to). There is an option that, when the data is over a specified size, only shows one plane to start with, but your image looks like more than one plane is shown. To set options related to initial display of large data, use Volume Viewer menu ?Features? Data display options? Another related issue is making an X-ray map cover the atomic coordinates as discussed in this recent post, but (at least to me) your image doesn?t look like that kind of situation. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 6, 2018, at 2:50 AM, kesgin-schaefer at chemie.uni-hamburg.de wrote: > > Dear all, > I have a problem with my electron density map: if I load the map in chimera, it will only show a subregion of the map and after "fit to model" the model will not be completely covered (see attachment). > Any suggestions about how to solve the problem would be much appreciated. > Thanks > Steffi From goddard at sonic.net Mon Aug 6 10:16:10 2018 From: goddard at sonic.net (Tom Goddard) Date: Mon, 6 Aug 2018 10:16:10 -0700 Subject: [Chimera-users] problem with electron density map In-Reply-To: References: <20180806115029.Horde.1DDtVG7BZNAb98DdQEJk7uN@webmail.chemie.uni-hamburg.de> Message-ID: <3C808E5F-5058-4AC1-AD2E-1BB88EF6B58A@sonic.net> Hi Steffi, When Chimera opens a map larger than a certain size it only shows one plane. Pressing the ?All? button below the histogram that appears when a single plane is shown will show all the planes. The size threshold for showing one plane is set using menu Volume Viewer / Features / Data Display Options. Tom > On Aug 6, 2018, at 9:48 AM, Elaine Meng wrote: > > Hi Steffi, > If it is only showing a subregion you can use Volume Viewer menu "Features? Subregion selection? to show subregion options in the dialog, and then click the ?Full? button in those options. > > However, I?m somewhat mystified, because I can?t think of a reason why it would show only a subregion automatically (without your telling it to). There is an option that, when the data is over a specified size, only shows one plane to start with, but your image looks like more than one plane is shown. To set options related to initial display of large data, use Volume Viewer menu ?Features? Data display options? > > > Another related issue is making an X-ray map cover the atomic coordinates as discussed in this recent post, but (at least to me) your image doesn?t look like that kind of situation. > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Aug 6, 2018, at 2:50 AM, kesgin-schaefer at chemie.uni-hamburg.de wrote: >> >> Dear all, >> I have a problem with my electron density map: if I load the map in chimera, it will only show a subregion of the map and after "fit to model" the model will not be completely covered (see attachment). >> Any suggestions about how to solve the problem would be much appreciated. >> Thanks >> Steffi > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From nawel.mele at gmail.com Tue Aug 7 02:16:18 2018 From: nawel.mele at gmail.com (Nawel Mele) Date: Tue, 7 Aug 2018 11:16:18 +0200 Subject: [Chimera-users] Problem with FIndHBonds Message-ID: Dear Chimera Users I am using hbond command to determine hydrogen bonds between a receptor and multiple compounds with different conformations from a docking simulation. I used a cmd script to automatise the process however I am facing and error that I am not sure to understand. I just pasted follow the part of the reply log where the problem appeared. The problem here is that when I load the compound with the different docked conformations separatly it is not always the same conformation taht has this error so I don't know what is the real problem. Many thanks for your help. Nawel *Finding intermodel H-bondsFinding intramodel H-bondsConstraints relaxed by 0.4 angstroms and 20 degreesModels used: #0 Representative_confo_site_active_minimum_distance_state001.pdb #1 DB08734_1|LigPrep_output_named|sdf|8330|dock5H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):#0 LYS 73.A NZ #1 UNK 1 O1 no hydrogen 2.924 N/A#0 ASN 76.A ND2 #1 UNK 1 N4 no hydrogen 2.398 N/A2 hydrogen bonds foundDB08734_1|LigPrep_output_named|sdf|8330|dock6 openeddonor: #0 ASN 76.A ND2 acceptor: #1 UNK 1 N4Traceback (most recent call last): File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/chimeraInit.py", line 683, in init chimera.openModels.open(a, prefixableType=1) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/chimera/__init__.py", line 1919, in open models = func(filename, *args, **kw) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/ChimeraExtension.py", line 35, in func processCommandFile(cmdFile) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 108, in processCommandFile _processFile(f, emulateRead, filename) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 143, in _processFile if makeCommand(line): File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/ChimeraExtension.py", line 33, in cmdHBonds specInfo=[("spec", "models", "molecules")]) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 451, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 940, in createHBonds interSubmodel=interSubmodel, cacheDA=cacheDA) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 574, in findHBonds (donorAtom, donorHyds) + args):TypeError: accPhiPsi() takes exactly 8 arguments (9 given)Error while processing chimera_input_step2_bug.cmd:TypeError: accPhiPsi() takes exactly 8 arguments (9 given) File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 574, in findHBonds (donorAtom, donorHyds) + args):See reply log for Python traceback.* -- Dr Nawel Mele, T: +33 (0) 634443794 (Fr) +44 (0) 7704331840 (UK) -------------- next part -------------- An HTML attachment was scrubbed... URL: From kesgin-schaefer at chemie.uni-hamburg.de Tue Aug 7 02:18:11 2018 From: kesgin-schaefer at chemie.uni-hamburg.de (kesgin-schaefer at chemie.uni-hamburg.de) Date: Tue, 07 Aug 2018 11:18:11 +0200 Subject: [Chimera-users] problem with electron density map In-Reply-To: <3C808E5F-5058-4AC1-AD2E-1BB88EF6B58A@sonic.net> References: <20180806115029.Horde.1DDtVG7BZNAb98DdQEJk7uN@webmail.chemie.uni-hamburg.de> <3C808E5F-5058-4AC1-AD2E-1BB88EF6B58A@sonic.net> Message-ID: <20180807111811.Horde.sXoVBfDzz6xWlvBNU8bZeyu@webmail.chemie.uni-hamburg.de> Dear Elaine and Tom, thanks for your comments! Unfortunately, after changing to "all" and playing around with threshold nothing changes. Any further ideas? Thanks Steffi Tom Goddard schrieb/wrote:: > Hi Steffi, > > When Chimera opens a map larger than a certain size it only shows > one plane. Pressing the ?All? button below the histogram that > appears when a single plane is shown will show all the planes. The > size threshold for showing one plane is set using menu Volume Viewer > / Features / Data Display Options. > > Tom > > >> On Aug 6, 2018, at 9:48 AM, Elaine Meng wrote: >> >> Hi Steffi, >> If it is only showing a subregion you can use Volume Viewer menu >> "Features? Subregion selection? to show subregion options in the >> dialog, and then click the ?Full? button in those options. >> >> However, I?m somewhat mystified, because I can?t think of a reason >> why it would show only a subregion automatically (without your >> telling it to). There is an option that, when the data is over a >> specified size, only shows one plane to start with, but your image >> looks like more than one plane is shown. To set options related to >> initial display of large data, use Volume Viewer menu ?Features? >> Data display options? >> >> >> Another related issue is making an X-ray map cover the atomic >> coordinates as discussed in this recent post, but (at least to me) >> your image doesn?t look like that kind of situation. >> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >>> On Aug 6, 2018, at 2:50 AM, kesgin-schaefer at chemie.uni-hamburg.de wrote: >>> >>> Dear all, >>> I have a problem with my electron density map: if I load the map >>> in chimera, it will only show a subregion of the map and after >>> "fit to model" the model will not be completely covered (see >>> attachment). >>> Any suggestions about how to solve the problem would be much appreciated. >>> Thanks >>> Steffi >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> From pett at cgl.ucsf.edu Tue Aug 7 10:34:57 2018 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 7 Aug 2018 10:34:57 -0700 Subject: [Chimera-users] Problem with FIndHBonds In-Reply-To: References: Message-ID: <52F3B0D1-38F4-4D0F-B509-342D9868BE10@cgl.ucsf.edu> Hi Nawel, This typically means that there is some kind of connectivity problem in one of the structures. If you sent me the two structures (Representative_confo_site_active_minimum_distance_state001.pdb and DB08734_1|LigPrep_output_named|sdf|8330|dock5) I might be able to provide a more precise diagnosis of the problem. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Aug 7, 2018, at 2:16 AM, Nawel Mele wrote: > > Dear Chimera Users > > I am using hbond command to determine hydrogen bonds between a receptor and multiple compounds with different conformations from a docking simulation. I used a cmd script to automatise the process however I am facing and error that I am not sure to understand. I just pasted follow the part of the reply log where the problem appeared. The problem here is that when I load the compound with the different docked conformations separatly it is not always the same conformation taht has this error so I don't know what is the real problem. > > Many thanks for your help. > > Nawel > > Finding intermodel H-bonds > Finding intramodel H-bonds > Constraints relaxed by 0.4 angstroms and 20 degrees > Models used: > #0 Representative_confo_site_active_minimum_distance_state001.pdb > #1 DB08734_1|LigPrep_output_named|sdf|8330|dock5 > > H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): > #0 LYS 73.A NZ #1 UNK 1 O1 no hydrogen 2.924 N/A > #0 ASN 76.A ND2 #1 UNK 1 N4 no hydrogen 2.398 N/A > 2 hydrogen bonds found > DB08734_1|LigPrep_output_named|sdf|8330|dock6 opened > donor: #0 ASN 76.A ND2 acceptor: #1 UNK 1 N4 > Traceback (most recent call last): > File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/chimeraInit.py", line 683, in init > chimera.openModels.open(a, prefixableType=1) > File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/chimera/__init__.py", line 1919, in open > models = func(filename, *args, **kw) > File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/ChimeraExtension.py", line 35, in func > processCommandFile(cmdFile) > File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 108, in processCommandFile > _processFile(f, emulateRead, filename) > File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 143, in _processFile > if makeCommand(line): > File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 69, in makeCommand > f(c, args) > File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/ChimeraExtension.py", line 33, in cmdHBonds > specInfo=[("spec", "models", "molecules")]) > File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 451, in doExtensionFunc > extFunc(*tuple(processedArgs), **kw) > File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 940, in createHBonds > interSubmodel=interSubmodel, cacheDA=cacheDA) > File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 574, in findHBonds > (donorAtom, donorHyds) + args): > TypeError: accPhiPsi() takes exactly 8 arguments (9 given) > Error while processing chimera_input_step2_bug.cmd: > TypeError: accPhiPsi() takes exactly 8 arguments (9 given) > > File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 574, in findHBonds > (donorAtom, donorHyds) + args): > > See reply log for Python traceback. > > > > > -- > Dr Nawel Mele, > > T: +33 (0) 634443794 (Fr) > +44 (0) 7704331840 (UK) > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Aug 7 10:48:21 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 7 Aug 2018 10:48:21 -0700 Subject: [Chimera-users] problem with electron density map In-Reply-To: <20180807111811.Horde.sXoVBfDzz6xWlvBNU8bZeyu@webmail.chemie.uni-hamburg.de> References: <20180806115029.Horde.1DDtVG7BZNAb98DdQEJk7uN@webmail.chemie.uni-hamburg.de> <3C808E5F-5058-4AC1-AD2E-1BB88EF6B58A@sonic.net> <20180807111811.Horde.sXoVBfDzz6xWlvBNU8bZeyu@webmail.chemie.uni-hamburg.de> Message-ID: <7D358565-6EA6-495D-A791-0FE2ACE53A83@cgl.ucsf.edu> Hi Steffi, Did you try the other two things I mentioned? (subregion full, or from the discussion in the previous post, ?vop cover?) Secondly, how do you know it is not showing all of your map? If it?s a problem with scale (map shrunken relative to molecule) you can use Volume Viewer menu: Features? Coordinates to adjust voxel size. Without having your exact data we can?t be sure what the issue is. Elaine > On Aug 7, 2018, at 2:18 AM, kesgin-schaefer at chemie.uni-hamburg.de wrote: > > Dear Elaine and Tom, > thanks for your comments! > > Unfortunately, after changing to "all" and playing around with threshold nothing changes. > Any further ideas? > Thanks > Steffi > > Tom Goddard schrieb/wrote:: > >> Hi Steffi, >> >> When Chimera opens a map larger than a certain size it only shows one plane. Pressing the ?All? button below the histogram that appears when a single plane is shown will show all the planes. The size threshold for showing one plane is set using menu Volume Viewer / Features / Data Display Options. >> >> Tom >> >>> On Aug 6, 2018, at 9:48 AM, Elaine Meng wrote: >>> >>> Hi Steffi, >>> If it is only showing a subregion you can use Volume Viewer menu "Features? Subregion selection? to show subregion options in the dialog, and then click the ?Full? button in those options. >>> >>> However, I?m somewhat mystified, because I can?t think of a reason why it would show only a subregion automatically (without your telling it to). There is an option that, when the data is over a specified size, only shows one plane to start with, but your image looks like more than one plane is shown. To set options related to initial display of large data, use Volume Viewer menu ?Features? Data display options? >>> >>> >>> Another related issue is making an X-ray map cover the atomic coordinates as discussed in this recent post, but (at least to me) your image doesn?t look like that kind of situation. >>> >>> >>> I hope this helps, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>>> On Aug 6, 2018, at 2:50 AM, kesgin-schaefer at chemie.uni-hamburg.de wrote: >>>> >>>> Dear all, >>>> I have a problem with my electron density map: if I load the map in chimera, it will only show a subregion of the map and after "fit to model" the model will not be completely covered (see attachment). >>>> Any suggestions about how to solve the problem would be much appreciated. >>>> Thanks >>>> Steffi From sy31802 at 163.com Fri Aug 10 12:35:00 2018 From: sy31802 at 163.com (=?GBK?B?yqbR7w==?=) Date: Sat, 11 Aug 2018 03:35:00 +0800 (CST) Subject: [Chimera-users] Different center when display coordinates with bonds or ribbon Message-ID: <5c18c591.683.1652555bd5e.Coremail.sy31802@163.com> Dear chimera developers and users, Recently, I met a very strange issue about displaying coordinates in chimera. I found the helices were off-centered with the map, when I open a well refined PDB file and the map it was refined against, and keep an eye on the helices which is automatically displayed by Ribbon. But actually they are will aligned in COOT. And if I hide Ribbon and showed Atoms/Bonds, they were well-aligned. The attached files show the same region with different displaying modes. And I have tried several versions of chimera, the results were the same. Actually, I want to use Ribbon to display these helices. Does anyone know how to fix it? Thanks in advance! Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: bonds.png Type: image/png Size: 45606 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ribbon.png Type: image/png Size: 41779 bytes Desc: not available URL: From meng at cgl.ucsf.edu Fri Aug 10 13:53:32 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 10 Aug 2018 13:53:32 -0700 Subject: [Chimera-users] Different center when display coordinates with bonds or ribbon In-Reply-To: <5c18c591.683.1652555bd5e.Coremail.sy31802@163.com> References: <5c18c591.683.1652555bd5e.Coremail.sy31802@163.com> Message-ID: <244E2DFA-CD7A-4C48-A223-129BA7B74270@cgl.ucsf.edu> Hi Yang, The standard ribbon for amino acids centers on CA, and as you can see, the CA atoms (alpha-carbons) are towards the lower side of the contour surface in your image. You can define a ribbon class that uses C (carbonyl carbon) instead of the CA, which will be shifted upward in the orientation shown in your image. Use menu: Tools? Depiction? Ribbon Style Editor, and click on the ?Residue Class? tab. The classes should include ?amino acid? which is the standard one for amino acids, with CA as the guide atom. Then you can change guide atom from CA to C and then click Apply to see if it is good enough for you. I see it makes a helix but narrower than the one using CA, so it might not be good enough. In Ribbon Style Editor, if you might want to use that new class later, you can Save to a new name (since you don?t want to overwrite the regular ?amino acid? one). Then later in the session you can use command ?ribclass? to use that class. Ribbon Style Editor: ?residue classes: ?ribclass command: For example, I started with ?amino acid?, changed guide atom to C, and then saved a new class named ?shifted?. Then later without showing the Ribbon Style Editor again, I can just use the new class with a command like: ribclass shifted #1 ? or change it back to default: ribclass ?amino acid? #1 In the image attached below, the tan ribbon is the default one, the blue one is the one using C as guide atom. Using N shifts in the opposite direction I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 10, 2018, at 12:35 PM, ?? wrote: > > Dear chimera developers and users, > Recently, I met a very strange issue about displaying coordinates in chimera. I found the helices were off-centered with the map, when I open a well refined PDB file and the map it was refined against, and keep an eye on the helices which is automatically displayed by Ribbon. But actually they are will aligned in COOT. And if I hide Ribbon and showed Atoms/Bonds, they were well-aligned. The attached files show the same region with different displaying modes. And I have tried several versions of chimera, the results were the same. > Actually, I want to use Ribbon to display these helices. Does anyone know how to fix it? > Thanks in advance! > Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: shifted-ribbon.png Type: image/png Size: 63003 bytes Desc: not available URL: From nazlidisalex at gmail.com Sat Aug 11 11:45:54 2018 From: nazlidisalex at gmail.com (Alex Nazlidis) Date: Sat, 11 Aug 2018 21:45:54 +0300 Subject: [Chimera-users] Animating peptide bond formation Message-ID: Dear Chimera users and staff, I've been thinking of ways to animate the formation of a peptide bond between two aminoacids but I haven't come up with a solution. Can you help me out here? :) Thanks in advance, Alex Nazlidis -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sat Aug 11 12:02:13 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 11 Aug 2018 12:02:13 -0700 Subject: [Chimera-users] Animating peptide bond formation In-Reply-To: References: Message-ID: <935C9B5F-0FD5-4B30-BDE4-E47B01914F22@cgl.ucsf.edu> Dear Alex, The software isn?t really intended for showing chemical reactions (changes in bonding) so you?d have to do something kind of simple, for example: Say you had 3 models, the two parts not bonded to each other and the third model being the whole structure with the bond. You could move the two parts farther apart initially and save that as one position (see savepos/reset commands) then gradually move them to another previously saved position that is exactly superimposed with the corresponding parts of the bonded structure, but with that third model hidden. Then crossfade to view with the two parts hidden and the third model shown. See ?movie crossfade? command. If you wanted to do something fancier like showing the change in nitrogen hybridization as the bond is formed, that would definitely be more work, and I haven?t figured out how exactly it could be done (or even if it?s feasible with a reasonable amount of work). See movie-related commands list for details on the commands: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 11, 2018, at 11:45 AM, Alex Nazlidis wrote: > > Dear Chimera users and staff, > I've been thinking of ways to animate the formation of a peptide bond between two aminoacids but I haven't come up with a solution. Can you help me out here? :) > Thanks in advance, > Alex Nazlidis From sy31802 at 163.com Sun Aug 12 07:29:39 2018 From: sy31802 at 163.com (Yang Shi) Date: Sun, 12 Aug 2018 15:29:39 +0100 Subject: [Chimera-users] Different center when display coordinates with bonds or ribbon In-Reply-To: <244E2DFA-CD7A-4C48-A223-129BA7B74270@cgl.ucsf.edu> References: <5c18c591.683.1652555bd5e.Coremail.sy31802@163.com> <244E2DFA-CD7A-4C48-A223-129BA7B74270@cgl.ucsf.edu> Message-ID: Dear Elaine, Thanks for your help. Your suggestion is very helpful!! Actually, the CA are in the density map. When I narrowed the ribbon width in ribbon mode and show only CA in atoms/bonds mode, the difference became more clear (attached files). Maybe there are some other algorithms for the ribbon generation, which is not suit for my coordinates and I have not realised. Some helix geometry restrains in ribbon maybe? Changing the guide atom really helps a lot to in terms of display. But it sounds it can also help those who did not refine their pdb well in some cases. For publication, I think, ideally, I should not change the guide atom for ribbon. Eventually, I will use atoms/bonds mode, and display side chains with the chain trace for the backbone. Thank you again! Best wishes, Yang > On 10 Aug 2018, at 21:53, Elaine Meng wrote: > > Hi Yang, > The standard ribbon for amino acids centers on CA, and as you can see, the CA atoms (alpha-carbons) are towards the lower side of the contour surface in your image. > > You can define a ribbon class that uses C (carbonyl carbon) instead of the CA, which will be shifted upward in the orientation shown in your image. Use menu: Tools? Depiction? Ribbon Style Editor, and click on the ?Residue Class? tab. The classes should include ?amino acid? which is the standard one for amino acids, with CA as the guide atom. Then you can change guide atom from CA to C and then click Apply to see if it is good enough for you. I see it makes a helix but narrower than the one using CA, so it might not be good enough. > > In Ribbon Style Editor, if you might want to use that new class later, you can Save to a new name (since you don?t want to overwrite the regular ?amino acid? one). Then later in the session you can use command ?ribclass? to use that class. > > Ribbon Style Editor: > > > ?residue classes: > > > ?ribclass command: > > > > For example, I started with ?amino acid?, changed guide atom to C, and then saved a new class named ?shifted?. Then later without showing the Ribbon Style Editor again, I can just use the new class with a command like: > > ribclass shifted #1 > > ? or change it back to default: > > ribclass ?amino acid? #1 > > In the image attached below, the tan ribbon is the default one, the blue one is the one using C as guide atom. Using N shifts in the opposite direction > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On Aug 10, 2018, at 12:35 PM, ?? > wrote: >> >> Dear chimera developers and users, >> Recently, I met a very strange issue about displaying coordinates in chimera. I found the helices were off-centered with the map, when I open a well refined PDB file and the map it was refined against, and keep an eye on the helices which is automatically displayed by Ribbon. But actually they are will aligned in COOT. And if I hide Ribbon and showed Atoms/Bonds, they were well-aligned. The attached files show the same region with different displaying modes. And I have tried several versions of chimera, the results were the same. >> Actually, I want to use Ribbon to display these helices. Does anyone know how to fix it? >> Thanks in advance! >> Yang > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: CA_trace.png Type: image/png Size: 200431 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: thinner ribbon.png Type: image/png Size: 179565 bytes Desc: not available URL: From ishwor_p_19 at yahoo.com Sun Aug 12 19:51:50 2018 From: ishwor_p_19 at yahoo.com (ISHWOR POUDYAL) Date: Mon, 13 Aug 2018 02:51:50 +0000 (UTC) Subject: [Chimera-users] Bad number format Xplor file format References: <1625210496.6321979.1534128710886.ref@mail.yahoo.com> Message-ID: <1625210496.6321979.1534128710886@mail.yahoo.com> Hello All, I try to convert electron density obtained from iterative phasing in *.xplor file format to view in the chimera. Something went wrong which I could not figure out. The generated density reads as follows for the first few lines.? ########################################################## ??241? ? -120 ? ? 120 ? ? 241? ? -120 ? ? 120 ? ? 241? ? -120 ? ? 120 ?3.26000E+02 3.26000E+02 3.26000E+02 9.00000E+01 9.00000E+01 9.00000E+01 ZYX ?? ? ? 0 ?2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00 ?8.21346E-170 0.00000E+00 5.89700E-171 0.00000E+00 4.23386E-172 0.00000E+00 ############################################################# While I try to view the electron density in chimera it says"SyntaxError:Bad number format in line ?2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00" WOuld you please help me out Many thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From mariana.assmann at gmx.net Mon Aug 13 06:25:07 2018 From: mariana.assmann at gmx.net (Mariana Assmann) Date: Mon, 13 Aug 2018 14:25:07 +0100 Subject: [Chimera-users] AutoVina Dock gives very different results running from GUI/command line tool Message-ID: <603678bf-4230-3232-5c02-a4b7f773333c@gmx.net> Hi everyone, I am trying to do docking using the command line tool in chimera. I found that when I use the GUI opening Tools > Surface/Binding Analysis > AutoDock Vina and following the docking window, I get very similar results for the docking pose and score every time I run the docking. However, if I do the same with the command line tool (with the same parameters, box size, local version of vina, same dock prep), I get very different results: the ligand is never in a good docking position, always on a different side of the pocket, and sometimes even intercepts strands of the protein. The docking scores are also off. I am using using Chimera 1.13 (build 41780), AutoDock Vina 1.1.2 (May 11, 2011), and the following command line for docking: vina docking receptor protein ligand #1.2 output /home/mariana/GTN/docking/keap1/docking_test13 search_center -7,3,-30.32 search_size 19,21,21 backend local location /home/mariana/bin/vina num_modes 9 I also found that the command line does not accept any of the vina receptor or ligand options (e.g. receptor_addh) and gives me error messages when including those ("Keyword 'receptor_addh' doesn't match any known keywords") Does anyone what the problems for those issues could be? Thanks, Mariana -------------- next part -------------- An HTML attachment was scrubbed... URL: From yfli3 at uic.edu Sun Aug 12 20:27:28 2018 From: yfli3 at uic.edu (Yangfeng Li) Date: Sun, 12 Aug 2018 22:27:28 -0500 Subject: [Chimera-users] Chimera for mac issue Message-ID: Hello, I installed the latest version of chimera via your website on my mac (macbook air, 2013, hgih sierra). But it doesn't exist in my "application" file. And every time I need to double click chimera dmg file to launch it, which takss a very long long time verifying chimera. That process is different from Windows. I just wonder whether it's normal. Thanks, Yangfeng -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Aug 13 09:21:52 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 13 Aug 2018 09:21:52 -0700 Subject: [Chimera-users] Chimera for mac issue In-Reply-To: References: Message-ID: <8894BED8-DBAE-4FE9-87BC-D8EB6DDAB8BA@cgl.ucsf.edu> Hi Yangfeng, No, that is not the normal way you would use the program. You didn?t really install the program, you?re just reusing the installer each time. When you click the dmg it is only opening the installer. Then from the installer window, you have to drag the Chimera icon to wherever you want to put the application, like the Applications folder (show new Finder window, go to Applications, and then drag the icon from the installer window to Applications). Then you can just start the application directly instead of reusing the dmg each time, which like you said, is slow. You can also put the Chimera icon on your dock for convenient access. Startup: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 12, 2018, at 8:27 PM, Yangfeng Li wrote: > > Hello, > I installed the latest version of chimera via your website on my mac (macbook air, 2013, hgih sierra). But it doesn't exist in my "application" file. And every time I need to double click chimera dmg file to launch it, which takss a very long long time verifying chimera. That process is different from Windows. > I just wonder whether it's normal. > Thanks, > Yangfeng From meng at cgl.ucsf.edu Mon Aug 13 09:41:18 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 13 Aug 2018 09:41:18 -0700 Subject: [Chimera-users] Bad number format Xplor file format In-Reply-To: <1625210496.6321979.1534128710886@mail.yahoo.com> References: <1625210496.6321979.1534128710886.ref@mail.yahoo.com> <1625210496.6321979.1534128710886@mail.yahoo.com> Message-ID: <06F95620-6CA5-4995-9E29-A6378C56227B@cgl.ucsf.edu> Hello Ishwor, I don?t know what you mean by ?convert? or ?generated? or what you used to do that. Chimera can directly read an xplor "unformatted ASCII density map?, see list of known formats here: ? but maybe your map is not really in that format, so you are just getting errors that the format is wrong. Without example data, this is only a guess. Bests, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 12, 2018, at 7:51 PM, ISHWOR POUDYAL wrote: > > Hello All, > I try to convert electron density obtained from iterative phasing in *.xplor file format to view in the chimera. Something went wrong which I could not figure out. The generated density reads as follows for the first few lines. > > ########################################################## > 241 -120 120 241 -120 120 241 -120 120 > > 3.26000E+02 3.26000E+02 3.26000E+02 9.00000E+01 9.00000E+01 9.00000E+01 > > ZYX > > 0 > > 2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00 > > 8.21346E-170 0.00000E+00 5.89700E-171 0.00000E+00 4.23386E-172 0.00000E+00 > > ############################################################# > > While I try to view the electron density in chimera it says > "SyntaxError:Bad number format in line 2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00" > > WOuld you please help me out > Many thanks From goddard at sonic.net Mon Aug 13 10:09:11 2018 From: goddard at sonic.net (Tom Goddard) Date: Mon, 13 Aug 2018 10:09:11 -0700 Subject: [Chimera-users] Bad number format Xplor file format In-Reply-To: <1625210496.6321979.1534128710886@mail.yahoo.com> References: <1625210496.6321979.1534128710886.ref@mail.yahoo.com> <1625210496.6321979.1534128710886@mail.yahoo.com> Message-ID: HI Ishwor, The XPLOR format requires lines where the first 12 columns holds the first number, the second 12 columns holds the second number, ? 12 columns per number. The example lines you provide do not use 12 columns per number. The software that wrote that file is not writing it in the correct format. My guess is that software fails because of the 3 digit exponents (e.g "E-166?) ? probably the writing software only fails to follow the 12 columns per number rule when you have 3-digit exponents. In single-precision (32-bit floats) you would never get 3 digit exponents and perhaps the error is that the writing program was converted from single precision to double precision. Tom > On Aug 12, 2018, at 7:51 PM, ISHWOR POUDYAL wrote: > > Hello All, > > I try to convert electron density obtained from iterative phasing in *.xplor file format to view in the chimera. Something went wrong which I could not figure out. The generated density reads as follows for the first few lines. > > ########################################################## > 241 -120 120 241 -120 120 241 -120 120 > > 3.26000E+02 3.26000E+02 3.26000E+02 9.00000E+01 9.00000E+01 9.00000E+01 > > ZYX > > 0 > > 2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00 > > 8.21346E-170 0.00000E+00 5.89700E-171 0.00000E+00 4.23386E-172 0.00000E+00 > > ############################################################# > > While I try to view the electron density in chimera it says > "SyntaxError:Bad number format in line 2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00" > > WOuld you please help me out > > Many thanks > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Mon Aug 13 14:13:07 2018 From: goddard at sonic.net (Tom Goddard) Date: Mon, 13 Aug 2018 14:13:07 -0700 Subject: [Chimera-users] Fwd: Bad number format Xplor file format References: <1594560538.6865054.1534194287368@mail.yahoo.com> Message-ID: <803FF66F-557C-4650-9357-D94E7A5570B0@sonic.net> Using single-precision for XPLOR output fixed the problem > > From: ISHWOR POUDYAL > Hello Tom, > > Many thanks! I changed the double precision to single-precision and it works. > > Ishwor > > > On Monday, August 13, 2018, 12:09:15 PM CDT, Tom Goddard wrote: > > > HI Ishwor, > > The XPLOR format requires lines where the first 12 columns holds the first number, the second 12 columns holds the second number, ? 12 columns per number. The example lines you provide do not use 12 columns per number. The software that wrote that file is not writing it in the correct format. My guess is that software fails because of the 3 digit exponents (e.g "E-166?) ? probably the writing software only fails to follow the 12 columns per number rule when you have 3-digit exponents. In single-precision (32-bit floats) you would never get 3 digit exponents and perhaps the error is that the writing program was converted from single precision to double precision. > > Tom > > >> On Aug 12, 2018, at 7:51 PM, ISHWOR POUDYAL > wrote: >> >> Hello All, >> >> I try to convert electron density obtained from iterative phasing in *.xplor file format to view in the chimera. Something went wrong which I could not figure out. The generated density reads as follows for the first few lines. >> >> ########################################################## >> 241 -120 120 241 -120 120 241 -120 120 >> >> 3.26000E+02 3.26000E+02 3.26000E+02 9.00000E+01 9.00000E+01 9.00000E+01 >> >> ZYX >> >> 0 >> >> 2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00 >> >> 8.21346E-170 0.00000E+00 5.89700E-171 0.00000E+00 4.23386E-172 0.00000E+00 >> >> ############################################################# >> >> While I try to view the electron density in chimera it says >> "SyntaxError:Bad number format in line 2.21928E-166 0.00000E+00 1.59337E-167 0.00000E+00 1.14399E-168 0.00000E+00" >> >> WOuld you please help me out >> >> Many thanks >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Aug 14 13:15:46 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 14 Aug 2018 13:15:46 -0700 Subject: [Chimera-users] AutoVina Dock gives very different results running from GUI/command line tool In-Reply-To: <603678bf-4230-3232-5c02-a4b7f773333c@gmx.net> References: <603678bf-4230-3232-5c02-a4b7f773333c@gmx.net> Message-ID: Hi Mariana, Sorry for the difficulties. I can reproduce the problem with prep-script options not being recognized, as well as wrong-looking results (ligand intersecting receptor) from running the vina command. However, I find that results vary regardless of whether I?m running the command-line or GUI, perhaps more evident since I was using low exhaustiveness for testing. I thought that there was some randomization during the search so one wouldn?t necessarily expect identical results from identical input parameters. I.e. re-running with the same inputs and parameters from the GUI does give me different results each time. However, I didn?t see wrong-looking results from GUI runs, so as far as I know the problems are restricted to command-line execution. Anyway, we will have to look into these issues as time permits; thanks for reporting them, and sorry again for the inconvenience. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 13, 2018, at 6:25 AM, Mariana Assmann wrote: > > Hi everyone, > > I am trying to do docking using the command line tool in chimera. I found that when I use the GUI opening Tools > Surface/Binding Analysis > AutoDock Vina and following the docking window, I get very similar results for the docking pose and score every time I run the docking. However, if I do the same with the command line tool (with the same parameters, box size, local version of vina, same dock prep), I get very different results: the ligand is never in a good docking position, always on a different side of the pocket, and sometimes even intercepts strands of the protein. The docking scores are also off. > > I am using using Chimera 1.13 (build 41780), AutoDock Vina 1.1.2 (May 11, 2011), and the following command line for docking: > > vina docking receptor protein ligand #1.2 output /home/mariana/GTN/docking/keap1/docking_test13 search_center -7,3,-30.32 search_size 19,21,21 backend local location /home/mariana/bin/vina num_modes 9 > > I also found that the command line does not accept any of the vina receptor or ligand options (e.g. receptor_addh) and gives me error messages when including those ("Keyword 'receptor_addh' doesn't match any known keywords") > > Does anyone what the problems for those issues could be? > > Thanks, > Mariana From matthias.lauer at roche.com Fri Aug 17 04:52:27 2018 From: matthias.lauer at roche.com (Lauer, Matthias) Date: Fri, 17 Aug 2018 13:52:27 +0200 Subject: [Chimera-users] CHIMERA liscence Message-ID: To whom it may concern. My name is Matthias Lauer. I am working for Pharma Research and Early Development at F. Hoffmann - La Roche Ltd. , in Basel, Switzerland. I would like to use Chimera for visualizing EM structures, as well as for modeling. I am heading a AFM laboratory, and I am closely collaborating with EM groups in academia. I belong to the drug discovery unit, and would need a written licence allowing me to use your software in our company. Your feedback would be highly appreciated, with kind regards from Basel, Matthias Lauer. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guo_f at mercer.edu Fri Aug 17 14:05:36 2018 From: guo_f at mercer.edu (Fengbiao Guo) Date: Fri, 17 Aug 2018 21:05:36 +0000 Subject: [Chimera-users] Chimera download Message-ID: Hello, My name is Fengbiao Guo, I work on Mercer University School of Medicine Savannah campus. I want to download the Chimera software, but I can?t open the page, so I want to ask how could I do can download this? Best regards, Fengbiao Guo -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Aug 17 16:05:19 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 17 Aug 2018 16:05:19 -0700 Subject: [Chimera-users] Chimera download In-Reply-To: References: Message-ID: <364676C1-A98F-4A22-8018-44D64EE4AC50@cgl.ucsf.edu> Hi Fengbiao, The system was down for maintenance but is back up now, so you should be able to download as normal. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 17, 2018, at 2:05 PM, Fengbiao Guo wrote: > > Hello, > My name is Fengbiao Guo, I work on Mercer University School of Medicine Savannah campus. > I want to download the Chimera software, but I can?t open the page, so I want to ask how could I do can download this? > Best regards, > Fengbiao Guo > From yangqi.gu at yale.edu Fri Aug 17 18:53:29 2018 From: yangqi.gu at yale.edu (BuddySphinx) Date: Fri, 17 Aug 2018 21:53:29 -0400 Subject: [Chimera-users] Measure the cross section of an EM map Message-ID: <5b777c1a.1c69fb81.5b01e.ff89@mx.google.com> Dear Chimera users, I am trying to measure the diameter of my filament based on the EM volume. I am wondering which function I can use to measure the cross-section of it? Best, Yangqi Sent from Mail for Windows 10 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Aug 17 19:01:21 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 17 Aug 2018 19:01:21 -0700 Subject: [Chimera-users] Measure the cross section of an EM map In-Reply-To: <5b777c1a.1c69fb81.5b01e.ff89@mx.google.com> References: <5b777c1a.1c69fb81.5b01e.ff89@mx.google.com> Message-ID: Hi Yangqi, You could place markers on opposite sides of the density contour surface, then measure the distance between the markers. For marker creation/placement, see Volume Tracer (in menu under Tools? Volume Data): For distance measurement, markers are treated the same as atoms. One way to do the measurement is to Ctrl-click on one marker to select it, then Shift-Ctrl-doubleclick on the other one to also select it and show context menu with a choice to measure the distance. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 17, 2018, at 6:53 PM, BuddySphinx wrote: > > Dear Chimera users, > I am trying to measure the diameter of my filament based on the EM volume. I am wondering which function I can use to measure the cross-section of it? > Best, > Yangqi > From yangqi.gu at yale.edu Fri Aug 17 19:04:21 2018 From: yangqi.gu at yale.edu (BuddySphinx) Date: Fri, 17 Aug 2018 22:04:21 -0400 Subject: [Chimera-users] Measure the cross section of an EM map In-Reply-To: References: <5b777c1a.1c69fb81.5b01e.ff89@mx.google.com> Message-ID: <5b777ea6.1c69fb81.d6b96.8d65@mx.google.com> Thank you! Best, Yangqi Sent from Mail for Windows 10 From: Elaine Meng Sent: Friday, August 17, 2018 10:01 PM To: BuddySphinx Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Measure the cross section of an EM map Hi Yangqi, You could place markers on opposite sides of the density contour surface, then measure the distance between the markers. For marker creation/placement, see Volume Tracer (in menu under Tools? Volume Data): For distance measurement, markers are treated the same as atoms. One way to do the measurement is to Ctrl-click on one marker to select it, then Shift-Ctrl-doubleclick on the other one to also select it and show context menu with a choice to measure the distance. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 17, 2018, at 6:53 PM, BuddySphinx wrote: > > Dear Chimera users, > I am trying to measure the diameter of my filament based on the EM volume. I am wondering which function I can use to measure the cross-section of it? > Best, > Yangqi > -------------- next part -------------- An HTML attachment was scrubbed... URL: From underoath006 at gmail.com Fri Aug 17 18:50:02 2018 From: underoath006 at gmail.com (Ahmad Khalifa) Date: Fri, 17 Aug 2018 21:50:02 -0400 Subject: [Chimera-users] Changing chain ID for ligands Message-ID: Is there a way to do it in chimera? Regards. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guo_f at mercer.edu Fri Aug 17 19:52:33 2018 From: guo_f at mercer.edu (Fengbiao Guo) Date: Sat, 18 Aug 2018 02:52:33 +0000 Subject: [Chimera-users] Chimera download In-Reply-To: <364676C1-A98F-4A22-8018-44D64EE4AC50@cgl.ucsf.edu> References: <364676C1-A98F-4A22-8018-44D64EE4AC50@cgl.ucsf.edu> Message-ID: <82843BFB-8E01-47C3-A4C8-44EA85E1FB45@mercer.edu> Thank you very much. Fengbiao Guo ?On 8/17/18, 16:05, "Elaine Meng" wrote: Hi Fengbiao, The system was down for maintenance but is back up now, so you should be able to download as normal. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 17, 2018, at 2:05 PM, Fengbiao Guo wrote: > > Hello, > My name is Fengbiao Guo, I work on Mercer University School of Medicine Savannah campus. > I want to download the Chimera software, but I can?t open the page, so I want to ask how could I do can download this? > Best regards, > Fengbiao Guo > From meng at cgl.ucsf.edu Mon Aug 20 11:07:55 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 20 Aug 2018 11:07:55 -0700 Subject: [Chimera-users] Changing chain ID for ligands In-Reply-To: References: Message-ID: <689AE248-BA71-4DD7-8CAF-ECBB8884E246@cgl.ucsf.edu> Hi Ahmad, The Change Chain IDs tool (in menu under Tools? Structure Editing) or ?changechains? command changes the chain ID of all kinds of atoms, including ligand and solvent. For example, if you change the ID of chain A to chain F instead, the ligand and solvent atoms of chain A will become ligand and solvent atoms of chain F. However, if you mean you want to change ONLY the ligand chain ID without changing the ID of other atoms in the same chain (only change the ID of part of a chain), there is no tool do that in Chimera. You could just text-edit the ligand atom lines in the PDB file using your favorite text editor. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 17, 2018, at 6:50 PM, Ahmad Khalifa wrote: > > Is there a way to do it in chimera? > > Regards. From underoath006 at gmail.com Mon Aug 20 11:55:47 2018 From: underoath006 at gmail.com (Ahmad Khalifa) Date: Mon, 20 Aug 2018 14:55:47 -0400 Subject: [Chimera-users] Changing chain ID for ligands In-Reply-To: <689AE248-BA71-4DD7-8CAF-ECBB8884E246@cgl.ucsf.edu> References: <689AE248-BA71-4DD7-8CAF-ECBB8884E246@cgl.ucsf.edu> Message-ID: Thanks, but I have ligands under a certain chain that I want to change to the other chain. In other words, I want to switch ligand chain ID to another chain ID. How can I do that? On Mon, Aug 20, 2018 at 2:07 PM, Elaine Meng wrote: > Hi Ahmad, > The Change Chain IDs tool (in menu under Tools? Structure Editing) or > ?changechains? command changes the chain ID of all kinds of atoms, > including ligand and solvent. For example, if you change the ID of chain A > to chain F instead, the ligand and solvent atoms of chain A will become > ligand and solvent atoms of chain F. > > changechains.html> > > > However, if you mean you want to change ONLY the ligand chain ID without > changing the ID of other atoms in the same chain (only change the ID of > part of a chain), there is no tool do that in Chimera. You could just > text-edit the ligand atom lines in the PDB file using your favorite text > editor. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Aug 17, 2018, at 6:50 PM, Ahmad Khalifa > wrote: > > > > Is there a way to do it in chimera? > > > > Regards. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Aug 20 14:54:13 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 20 Aug 2018 14:54:13 -0700 Subject: [Chimera-users] Changing chain ID for ligands In-Reply-To: References: <689AE248-BA71-4DD7-8CAF-ECBB8884E246@cgl.ucsf.edu> Message-ID: <19002D22-CF04-4DE5-8333-A0E3FBB723CF@cgl.ucsf.edu> If you can?t do it with the Change Chain IDs tool, then you can?t do it in Chimera. As I said before, you could just text-edit the PDB file manually. If you have a large number of PDB files to edit, you could write some kind of script to do it. Elaine > On Aug 20, 2018, at 11:55 AM, Ahmad Khalifa wrote: > > Thanks, but I have ligands under a certain chain that I want to change to the other chain. In other words, I want to switch ligand chain ID to another chain ID. How can I do that? > > On Mon, Aug 20, 2018 at 2:07 PM, Elaine Meng wrote: > Hi Ahmad, > The Change Chain IDs tool (in menu under Tools? Structure Editing) or ?changechains? command changes the chain ID of all kinds of atoms, including ligand and solvent. For example, if you change the ID of chain A to chain F instead, the ligand and solvent atoms of chain A will become ligand and solvent atoms of chain F. > > > > > However, if you mean you want to change ONLY the ligand chain ID without changing the ID of other atoms in the same chain (only change the ID of part of a chain), there is no tool do that in Chimera. You could just text-edit the ligand atom lines in the PDB file using your favorite text editor. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Aug 17, 2018, at 6:50 PM, Ahmad Khalifa wrote: > > > > Is there a way to do it in chimera? > > > > Regards. > From yasser.almeida at gmail.com Wed Aug 22 02:16:33 2018 From: yasser.almeida at gmail.com (=?UTF-8?Q?Yasser_Almeida_Hern=c3=a1ndez?=) Date: Wed, 22 Aug 2018 11:16:33 +0200 Subject: [Chimera-users] Dropdown list of models in groups Message-ID: Hello, I am working with groups of models, and I wonder if there is a way to make a group, with a defined name, and then inspect each models independently without lose the group. Currently, if I make a group, and then ungroup, I lose the definition, notes ans any other action on it. If there is no possibility, I would suggest the developers to consider the option to make groups with dropdown list of models. Best Yasser From al.kupczyk at tlen.pl Wed Aug 22 07:40:54 2018 From: al.kupczyk at tlen.pl (=?UTF-8?Q?al=2Ekupczyk?=) Date: Wed, 22 Aug 2018 16:40:54 +0200 Subject: [Chimera-users] =?utf-8?q?Getting_measure_distance_value?= Message-ID: <3811beebea4e475984611b8c31d81f58@grupawp.pl> Hi,? I'm struggling with getting a value from runCommand in Chimera. I need to measure distance between an atom and a density map and keep it in a variable, so I'm trying to get a value from "measure distance" command in Python, but unfortunately with no results. Is there any way to somehow get it into a variable?? Yours sincerely, Alicja -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Wed Aug 22 10:23:30 2018 From: goddard at sonic.net (Tom Goddard) Date: Wed, 22 Aug 2018 10:23:30 -0700 Subject: [Chimera-users] Getting measure distance value In-Reply-To: <3811beebea4e475984611b8c31d81f58@grupawp.pl> References: <3811beebea4e475984611b8c31d81f58@grupawp.pl> Message-ID: Hi Alicja, runCommand() invokes typed user commands and does not return values and unfortunately the measure distance code in chimera/share/Measure/measure.py (the distance() and report_distance() functions) are not well written for calling directly from Python. Your best approach would be to copy the distance() and report_distance() functions from measure.py and modify them to actually return the distance values you want. Tom > On Aug 22, 2018, at 7:40 AM, al.kupczyk wrote: > > Hi, > I'm struggling with getting a value from runCommand in Chimera. I need to measure distance between an atom and a density map and keep it in a variable, so I'm trying to get a value from "measure distance" command in Python, but unfortunately with no results. Is there any way to somehow get it into a variable? > Yours sincerely, > Alicja > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Wed Aug 22 10:41:21 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 22 Aug 2018 10:41:21 -0700 Subject: [Chimera-users] Dropdown list of models in groups In-Reply-To: References: Message-ID: <8162D35F-C846-4035-AA88-559609B28195@cgl.ucsf.edu> Hi Yasser, This doesn?t solve your problem for a user-defined group, but in ChimeraX, the Models list has disclosure triangles to expand and collapse groups. Opening an NMR ensemble of atomic models (e.g. 1plx) or showing multiple isosurfaces for the same density map automatically makes a group, as in the attached image. However, there isn?t a way for the user to group models manually (at least yet) or add notes to a model or group. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 22, 2018, at 2:16 AM, Yasser Almeida Hern?ndez wrote: > > Hello, > I am working with groups of models, and I wonder if there is a way to make a group, with a defined name, and then inspect each models independently without lose the group. Currently, if I make a group, and then ungroup, I lose the definition, notes ans any other action on it. If there is no possibility, I would suggest the developers to consider the option to make groups with dropdown list of models. > Best > Yasser -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2018-08-22 at 10.39.53 AM.png Type: image/png Size: 26508 bytes Desc: not available URL: From meng at cgl.ucsf.edu Wed Aug 22 11:14:23 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 22 Aug 2018 11:14:23 -0700 Subject: [Chimera-users] Dropdown list of models in groups In-Reply-To: <8162D35F-C846-4035-AA88-559609B28195@cgl.ucsf.edu> References: <8162D35F-C846-4035-AA88-559609B28195@cgl.ucsf.edu> Message-ID: Correction: someone just reminded me that in ChimeraX, users CAN group models by using the ?rename? command to specify new hierarchical model ID numbers. I keep forgetting that this command can change ID numbers, not just model names. > On Aug 22, 2018, at 10:41 AM, Elaine Meng wrote: > > Hi Yasser, > This doesn?t solve your problem for a user-defined group, but in ChimeraX, the Models list has disclosure triangles to expand and collapse groups. Opening an NMR ensemble of atomic models (e.g. 1plx) or showing multiple isosurfaces for the same density map automatically makes a group, as in the attached image. However, there isn?t a way for the user to group models manually (at least yet) or add notes to a model or group. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > >> On Aug 22, 2018, at 2:16 AM, Yasser Almeida Hern?ndez wrote: >> >> Hello, >> I am working with groups of models, and I wonder if there is a way to make a group, with a defined name, and then inspect each models independently without lose the group. Currently, if I make a group, and then ungroup, I lose the definition, notes ans any other action on it. If there is no possibility, I would suggest the developers to consider the option to make groups with dropdown list of models. >> Best >> Yasser From goddard at sonic.net Wed Aug 22 11:16:40 2018 From: goddard at sonic.net (Tom Goddard) Date: Wed, 22 Aug 2018 11:16:40 -0700 Subject: [Chimera-users] Dropdown list of models in groups In-Reply-To: <8162D35F-C846-4035-AA88-559609B28195@cgl.ucsf.edu> References: <8162D35F-C846-4035-AA88-559609B28195@cgl.ucsf.edu> Message-ID: <903FDE21-6E54-4190-8FDC-693BD098BDC5@sonic.net> Hi Yasser, If you want to try ChimeraX you can make the grouping of models and submodels however you like using the ChimeraX ?rename? command to change the model id numbers. For instance to put models #1-10 under a single group #11.1-10 rename #1-10 id #11 You should also be able to rename to id #1 but I got an error doing that which I will fix today. Tom > On Aug 22, 2018, at 10:41 AM, Elaine Meng wrote: > > Hi Yasser, > This doesn?t solve your problem for a user-defined group, but in ChimeraX, the Models list has disclosure triangles to expand and collapse groups. Opening an NMR ensemble of atomic models (e.g. 1plx) or showing multiple isosurfaces for the same density map automatically makes a group, as in the attached image. However, there isn?t a way for the user to group models manually (at least yet) or add notes to a model or group. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > >> On Aug 22, 2018, at 2:16 AM, Yasser Almeida Hern?ndez > wrote: >> >> Hello, >> I am working with groups of models, and I wonder if there is a way to make a group, with a defined name, and then inspect each models independently without lose the group. Currently, if I make a group, and then ungroup, I lose the definition, notes ans any other action on it. If there is no possibility, I would suggest the developers to consider the option to make groups with dropdown list of models. >> Best >> Yasser > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Aug 22 16:22:17 2018 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 22 Aug 2018 16:22:17 -0700 Subject: [Chimera-users] Dropdown list of models in groups In-Reply-To: References: Message-ID: <0A6AD76D-5296-4639-AA50-35DDA4739613@cgl.ucsf.edu> Hi Yasser, Grouping was something that was shoehorned into the Model Panel well after it was originally designed and implemented, and so it doesn?t work quite as naturally as it could otherwise. Others have pointed out that ChimeraX has a more natural grouping mechanism in its Model Panel, though it lack other capabilities (such as adding notes). I guess I don?t understand what you?re saying about ?losing notes?. Groups don?t have notes themselves ? any note you add to a group gets added to all the models in the group instead. If you then ungroup and regroup those models, it will show the same note that you added (unless you then add/edit notes in the individual models). You are correct that you lose which particular models were composing the group though. ?Eric > On Aug 22, 2018, at 2:16 AM, Yasser Almeida Hern?ndez wrote: > > Hello, > > I am working with groups of models, and I wonder if there is a way to make a group, with a defined name, and then inspect each models independently without lose the group. Currently, if I make a group, and then ungroup, I lose the definition, notes ans any other action on it. If there is no possibility, I would suggest the developers to consider the option to make groups with dropdown list of models. > > Best > > Yasser > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From yasser.almeida at gmail.com Thu Aug 23 00:35:16 2018 From: yasser.almeida at gmail.com (=?UTF-8?Q?Yasser_Almeida_Hern=c3=a1ndez?=) Date: Thu, 23 Aug 2018 09:35:16 +0200 Subject: [Chimera-users] Dropdown list of models in groups In-Reply-To: References: <8162D35F-C846-4035-AA88-559609B28195@cgl.ucsf.edu> Message-ID: <0e28341e-9c85-6c6a-9580-749b775d0377@gmail.com> Hello Elaine, Thank you for your answer. I will try ChimeraX and the rename command. In any case, I think many users would appreciate the addition of this functionality to Chimera. I am a big fan of Chimera, and have been using it since 10 years. I have some suggestions for new functionalities. Is this users mailing list proper platform for suggestions? Best regards Yasser On 22.08.2018 20:14, Elaine Meng wrote: > Correction: someone just reminded me that in ChimeraX, users CAN group models by using the ?rename? command to specify new hierarchical model ID numbers. I keep forgetting that this command can change ID numbers, not just model names. > > >> On Aug 22, 2018, at 10:41 AM, Elaine Meng wrote: >> >> Hi Yasser, >> This doesn?t solve your problem for a user-defined group, but in ChimeraX, the Models list has disclosure triangles to expand and collapse groups. Opening an NMR ensemble of atomic models (e.g. 1plx) or showing multiple isosurfaces for the same density map automatically makes a group, as in the attached image. However, there isn?t a way for the user to group models manually (at least yet) or add notes to a model or group. >> Best, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >> >>> On Aug 22, 2018, at 2:16 AM, Yasser Almeida Hern?ndez wrote: >>> >>> Hello, >>> I am working with groups of models, and I wonder if there is a way to make a group, with a defined name, and then inspect each models independently without lose the group. Currently, if I make a group, and then ungroup, I lose the definition, notes ans any other action on it. If there is no possibility, I would suggest the developers to consider the option to make groups with dropdown list of models. >>> Best >>> Yasser > From meng at cgl.ucsf.edu Thu Aug 23 10:24:19 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 23 Aug 2018 10:24:19 -0700 Subject: [Chimera-users] Dropdown list of models in groups In-Reply-To: <0e28341e-9c85-6c6a-9580-749b775d0377@gmail.com> References: <8162D35F-C846-4035-AA88-559609B28195@cgl.ucsf.edu> <0e28341e-9c85-6c6a-9580-749b775d0377@gmail.com> Message-ID: <53482AF8-3999-4205-9D15-8D2E8413C1D9@cgl.ucsf.edu> Hello Yasser, Yes, you can make suggestions for Chimera to this list, and we appreciate your thoughts. However, most effort in our group is now on developing ChimeraX, so it may be more likely for your suggestions to be implemented in ChimeraX than in Chimera. In addition to improvements and completely new features, ChimeraX already has a lot of the same features for working with maps: the ?volume? and ?vop? commands are almost exactly same, ?fitmap? (fitting), ?molmap? (map from atoms), ?vseries? (play volume time series), etc. However, missing currently are segmentation, volume eraser, and many GUI tools (although the same thing may be available in a command). Best regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 23, 2018, at 12:35 AM, Yasser Almeida Hern?ndez wrote: > > Hello Elaine, > > Thank you for your answer. > > I will try ChimeraX and the rename command. In any case, I think many users would appreciate the addition of this functionality to Chimera. > > I am a big fan of Chimera, and have been using it since 10 years. I have some suggestions for new functionalities. Is this users mailing list proper platform for suggestions? > > Best regards > > Yasser From dzhu at niaid.nih.gov Thu Aug 23 09:25:55 2018 From: dzhu at niaid.nih.gov (Zhu, Daming (NIH/NIAID) [E]) Date: Thu, 23 Aug 2018 16:25:55 +0000 Subject: [Chimera-users] some issues with download Chimera Message-ID: Hello, I have some issues with downloading Chimera. I can download and install it onto my computer, but it messed up my screens-I have two computer screens but only one works (with a terrible looking), and the other one cannot be connected. If I want both Chimera and my two computer screens working, what is the basic requirement for a computer? Thank you for your help. Best regards, Daming Zhu Daming Zhu Laboratory of Malaria Immunology and Vaccinology NIAID/NIH Twinbrook I, Room 1118 5640 Fishers Lane Rockville, MD 20852 Phone: 301-761-3993 -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Thu Aug 23 17:16:52 2018 From: goddard at sonic.net (Tom Goddard) Date: Thu, 23 Aug 2018 17:16:52 -0700 Subject: [Chimera-users] some issues with download Chimera In-Reply-To: References: Message-ID: Hi Daming, I guess you mean that Chimera will only display on one of your two displays, and on the display it does work on the appearance is poor? On dual screen computers Chimera usually works correctly on either display and can be dragged between the two displays ? we use this routinely at UCSF where both a display and projector are connected. So the problem has something to do with your exact computer setup, such as the operating system and possibly using 4K displays may be a factor in the poor appearance. If you use menu Help / Report a Bug? in Chimera this will tell us your operating system, Chimera version, and graphics driver. Please also add the display resolutions in the description and a little about what the problem is, e.g. cannot drag Chimera from one screen to the other. After that we will reply to you through the bug tracking system. Tom > On Aug 23, 2018, at 9:25 AM, Zhu, Daming (NIH/NIAID) [E] wrote: > > Hello, > > I have some issues with downloading Chimera. I can download and install it onto my computer, but it messed up my screens?I have two computer screens but only one works (with a terrible looking), and the other one cannot be connected. If I want both Chimera and my two computer screens working, what is the basic requirement for a computer? > > Thank you for your help. > > Best regards, > > Daming Zhu > > Daming Zhu > Laboratory of Malaria Immunology and Vaccinology > NIAID/NIH > Twinbrook I, Room 1118 > 5640 Fishers Lane > Rockville, MD 20852 > Phone: 301-761-3993 > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From babi_abrahim at hotmail.com Fri Aug 24 14:29:43 2018 From: babi_abrahim at hotmail.com (=?utf-8?B?QsOhcmJhcmEgQWJyYWhpbSBWaWVpcmE=?=) Date: Fri, 24 Aug 2018 21:29:43 +0000 Subject: [Chimera-users] Tetramer using Chimera Message-ID: Dear all, We wish apply in our research the Chimera system. Initially, we build our model (monomer) using ab initio and then, we will investigate the active site using docking. However, it is known that the protein is a tetramer. Then, we need to create a tetramer, without any pdb homologous, is it possible? Thanks for your time, ________________________________ B?rbara Abrahim-Vieira Modelagem Molecular ModMolQSAR Faculty of Pharmacy Federal University of Rio de Janeiro -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Aug 24 15:55:27 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 24 Aug 2018 15:55:27 -0700 Subject: [Chimera-users] Tetramer using Chimera In-Reply-To: References: Message-ID: Dear B?rbara, You can place four copies of your structure in any positions, but Chimera will not predict how the tetramer will form (which sides of the protein will form the interfaces). You would have to determine that yourself, and then either place the copies by hand, using activation and deactivation to control which copies can be moved with the mouse ...or specify in the ?sym? command exactly how to create and place the copies. This can be difficult, because even if you know the symmetry group (say C4 or D2), you would also have to give the symmetry center and axis coordinates.. (If you had a structure of the tetramer of a homologous protein, then in Chimera you could match four monomers of your protein onto the four monomers in that tetramer.) There are probably other programs to predict homomultimer structure from monomer structure, but I don?t have any experience with that myself. They might look for multimeric homologous structures, collect homologous sequences and look at sequence conservation and covariation pairs, and/or use protein-protein docking. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 24, 2018, at 2:29 PM, B?rbara Abrahim Vieira wrote: > > Dear all, > We wish apply in our research the Chimera system. > > Initially, we build our model (monomer) using ab initio and then, we will investigate the active site using docking. However, it is known that the protein is a tetramer. > > Then, we need to create a tetramer, without any pdb homologous, is it possible? > Thanks for your time, From meng at cgl.ucsf.edu Sat Aug 25 07:56:08 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 25 Aug 2018 07:56:08 -0700 Subject: [Chimera-users] UCSF Chimera Ribbon Question In-Reply-To: <722601412.2393271.1535161286749@mail.yahoo.com> References: <722601412.2393271.1535161286749.ref@mail.yahoo.com> <722601412.2393271.1535161286749@mail.yahoo.com> Message-ID: Hi Alex, The problem is not the ribbon style (and you don?t need supersmooth, simply smooth will do) but the ?subdivision? graphics quality, which has apparently gotten set to some abnormally low value. Your ion isn?t particularly spherical in the image either, because this parameter also affects atom and bond display. See Tools? Viewing Controls? Effects, ?subdivision? in the lower right area of the dialog. The factory default is 1.5 whereas your image looks something like 0.1. You can also control this value with the ?set? command. This is discussed in the ?Image Tips? under smoothness ?as well as the Effects and ?set? documentation For future reference, we recommend sending questions to chimera-users at cgl.ucsf.edu (CC?d here) to better ensure that you get an answer. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 24, 2018, at 6:41 PM, Alex Yorn wrote: > > Elaine, > I'm having a little difficulty viewing ribbon models. I'm not sure what I did exactly, but I every time I open up Chimera, the default setting is this (see attached photo). This looks like a flat representation of the ribbon, but it's actually the supersmooth representation. I've tried double-checking the Cross Section in the Ribbon Style Editor, but everything looks normal (see attached photo). Can you help me with this? > Sincerely, > Alex Yorn -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2018-08-24 at 6.25.04 PM.png Type: image/png Size: 396779 bytes Desc: not available URL: From meng at cgl.ucsf.edu Sat Aug 25 08:02:02 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 25 Aug 2018 08:02:02 -0700 Subject: [Chimera-users] UCSF Chimera Ribbon Question In-Reply-To: References: <722601412.2393271.1535161286749.ref@mail.yahoo.com> <722601412.2393271.1535161286749@mail.yahoo.com> Message-ID: P.S. Remember to click Save on the Effects dialog after you change the value, so that next time you start Chimera it won?t be crazy again! Elaine > On Aug 25, 2018, at 7:56 AM, Elaine Meng wrote: > > Hi Alex, > The problem is not the ribbon style (and you don?t need supersmooth, simply smooth will do) but the ?subdivision? graphics quality, which has apparently gotten set to some abnormally low value. Your ion isn?t particularly spherical in the image either, because this parameter also affects atom and bond display. See Tools? Viewing Controls? Effects, ?subdivision? in the lower right area of the dialog. The factory default is 1.5 whereas your image looks something like 0.1. You can also control this value with the ?set? command. > > This is discussed in the ?Image Tips? under smoothness > > ?as well as the Effects and ?set? documentation > > > > For future reference, we recommend sending questions to chimera-users at cgl.ucsf.edu (CC?d here) to better ensure that you get an answer. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Aug 24, 2018, at 6:41 PM, Alex Yorn wrote: >> >> Elaine, >> I'm having a little difficulty viewing ribbon models. I'm not sure what I did exactly, but I every time I open up Chimera, the default setting is this (see attached photo). This looks like a flat representation of the ribbon, but it's actually the supersmooth representation. I've tried double-checking the Cross Section in the Ribbon Style Editor, but everything looks normal (see attached photo). Can you help me with this? >> Sincerely, >> Alex Yorn > > From boris.touzeau at gmail.com Mon Aug 27 02:00:52 2018 From: boris.touzeau at gmail.com (Boris TOUZEAU) Date: Mon, 27 Aug 2018 17:00:52 +0800 Subject: [Chimera-users] Chimera: Amber to PDB Message-ID: Hi, I am Boris TOUZEAU, actually a PhD student at the National Taiwanese University (NTU) based in Taipei. I had a question about chimera; Is it possible to output pdb files having amber residues naming convention instead of pdb residues naming convention ? I saw it was possible to do it for the atoms (ligands) but I would be more interested to do it for residues. Best wishes, Boris TOUZEAU -------------- next part -------------- An HTML attachment was scrubbed... URL: From gtzotzos at me.com Mon Aug 27 09:13:22 2018 From: gtzotzos at me.com (George Tzotzos) Date: Mon, 27 Aug 2018 19:13:22 +0300 Subject: [Chimera-users] Depicting entropy and mobility in pdb files Message-ID: <17E69F57-CF53-45C2-AD40-14E249080E13@me.com> Hi everybody, I?ve generated two pdb files which are of identical coordinates. Their only difference is that the b-factor column has been replaced with data indicating residue conservation (structure 1) and residue intrinsic mobility from normal mode analysis (structure 2). Below are indicative atomic coordinates. Structure 1 ATOM 24 NH1 ARG A 5 5.258 -15.260 -22.393 1.00 2.87 N ATOM 25 NH2 ARG A 5 6.717 -16.030 -20.793 1.00 2.87 N ATOM 26 N ARG A 6 3.934 -11.168 -16.245 1.00 2.84 N ATOM 27 CA ARG A 6 5.160 -10.666 -15.652 1.00 2.84 C Structure 2 ATOM 24 NH1 ARG A 5 5.258 -15.260 -22.393 1.00 1.35 N ATOM 25 NH2 ARG A 5 6.717 -16.030 -20.793 1.00 1.35 N ATOM 26 N ARG A 6 3.934 -11.168 -16.245 1.00 1.73 N ATOM 27 CA ARG A 6 5.160 -10.666 -15.652 1.00 1.73 C Is there a way to visualise these differences (e.g. by different thickness of ribbons or any other means e.g. colour of spheres). Thank in advance for any suggestions George From meng at cgl.ucsf.edu Mon Aug 27 10:52:20 2018 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 27 Aug 2018 10:52:20 -0700 Subject: [Chimera-users] Depicting entropy and mobility in pdb files In-Reply-To: <17E69F57-CF53-45C2-AD40-14E249080E13@me.com> References: <17E69F57-CF53-45C2-AD40-14E249080E13@me.com> Message-ID: <234AD253-E0B8-4951-8849-FEC7A023544E@cgl.ucsf.edu> Hi George, Yes, you can can color by B-factor (i.e. whatever values are in the B-factor column) or show ?worms? with thickness scaled by the per-residue average of those values. B-factor is just one example of an ?attribute? or property with values per atom or per residue. Other examples are residue hydrophobicity or conservation in an associated sequence alignment. You can color by any atom or residue attribute value, or ?worm? by any residue attribute value with the Render by Attribute tool (in menu under Tools? Depiction): ... or color by attribute with the ?rangecolor? command: ?for example: rangecolor bfactor min medium blue mid red max yellow (You could also give specific values instead of ?min? ?mid? ?max? and use whatever colors you want. The min/mid/max would include ligand, ion, and solvent values, if any, so you might not see the max color on the ribbon. Render by Attribute GUI is easier for seeing the range of values because it shows a histogram.) There is no command for worms, only the Render by Attribute GUI. In that tool, you can color atoms by by the bfactor attribute of atoms, or change to attributes of residues (instead of atoms) in order to color ribbons and/or show worms. The average bfactor (over the atoms of each residue) is automatically listed as a residue attribute choice when you have a structure with bfactors open. This tutorial has coloring by B-factor of the surface using Render by Attribute, but coloring by atoms is the same, just don?t show surface. It also includes showing a color key. This tutorial includes coloring ribbons and showing worms by the residue attribute of sequence conservation, but you can do it similarly for the residue attribute of average B-factor, which is automatically listed in the Render by Attribute menu of residue attributes: Also, attributes can be loaded in from a separate file, so you don?t have to smush them into the B-factor column, although it?s OK if you want to do it that way. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco 2gbp color and worms by residue average B-factor: > On Aug 27, 2018, at 9:13 AM, George Tzotzos wrote: > > Hi everybody, > > I?ve generated two pdb files which are of identical coordinates. Their only difference is that the b-factor column has been replaced with data indicating residue conservation (structure 1) and residue intrinsic mobility from normal mode analysis (structure 2). > > Below are indicative atomic coordinates. > > Structure 1 > ATOM 24 NH1 ARG A 5 5.258 -15.260 -22.393 1.00 2.87 N > ATOM 25 NH2 ARG A 5 6.717 -16.030 -20.793 1.00 2.87 N > ATOM 26 N ARG A 6 3.934 -11.168 -16.245 1.00 2.84 N > ATOM 27 CA ARG A 6 5.160 -10.666 -15.652 1.00 2.84 C > > Structure 2 > ATOM 24 NH1 ARG A 5 5.258 -15.260 -22.393 1.00 1.35 N > ATOM 25 NH2 ARG A 5 6.717 -16.030 -20.793 1.00 1.35 N > ATOM 26 N ARG A 6 3.934 -11.168 -16.245 1.00 1.73 N > ATOM 27 CA ARG A 6 5.160 -10.666 -15.652 1.00 1.73 C > > Is there a way to visualise these differences (e.g. by different thickness of ribbons or any other means e.g. colour of spheres). > > Thank in advance for any suggestions > > George > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2gbp.png Type: image/png Size: 51189 bytes Desc: not available URL: From gtzotzos at me.com Mon Aug 27 10:55:44 2018 From: gtzotzos at me.com (George Tzotzos) Date: Mon, 27 Aug 2018 20:55:44 +0300 Subject: [Chimera-users] Depicting entropy and mobility in pdb files In-Reply-To: <234AD253-E0B8-4951-8849-FEC7A023544E@cgl.ucsf.edu> References: <17E69F57-CF53-45C2-AD40-14E249080E13@me.com> <234AD253-E0B8-4951-8849-FEC7A023544E@cgl.ucsf.edu> Message-ID: <21DD6BDA-80E5-4109-8238-D061524EFE40@me.com> Grateful to you Elaine. Have a good day George > On 27 Aug 2018, at 20:52, Elaine Meng wrote: > > Hi George, > Yes, you can can color by B-factor (i.e. whatever values are in the B-factor column) or show ?worms? with thickness scaled by the per-residue average of those values. > > B-factor is just one example of an ?attribute? or property with values per atom or per residue. Other examples are residue hydrophobicity or conservation in an associated sequence alignment. > > You can color by any atom or residue attribute value, or ?worm? by any residue attribute value with the Render by Attribute tool (in menu under Tools? Depiction): > > > > ... or color by attribute with the ?rangecolor? command: > > > ?for example: > rangecolor bfactor min medium blue mid red max yellow > > (You could also give specific values instead of ?min? ?mid? ?max? and use whatever colors you want. The min/mid/max would include ligand, ion, and solvent values, if any, so you might not see the max color on the ribbon. Render by Attribute GUI is easier for seeing the range of values because it shows a histogram.) > > There is no command for worms, only the Render by Attribute GUI. In that tool, you can color atoms by by the bfactor attribute of atoms, or change to attributes of residues (instead of atoms) in order to color ribbons and/or show worms. The average bfactor (over the atoms of each residue) is automatically listed as a residue attribute choice when you have a structure with bfactors open. > > This tutorial has coloring by B-factor of the surface using Render by Attribute, but coloring by atoms is the same, just don?t show surface. It also includes showing a color key. > > > > This tutorial includes coloring ribbons and showing worms by the residue attribute of sequence conservation, but you can do it similarly for the residue attribute of average B-factor, which is automatically listed in the Render by Attribute menu of residue attributes: > > > > Also, attributes can be loaded in from a separate file, so you don?t have to smush them into the B-factor column, although it?s OK if you want to do it that way. > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > 2gbp color and worms by residue average B-factor: > <2gbp.png> > >> On Aug 27, 2018, at 9:13 AM, George Tzotzos > wrote: >> >> Hi everybody, >> >> I?ve generated two pdb files which are of identical coordinates. Their only difference is that the b-factor column has been replaced with data indicating residue conservation (structure 1) and residue intrinsic mobility from normal mode analysis (structure 2). >> >> Below are indicative atomic coordinates. >> >> Structure 1 >> ATOM 24 NH1 ARG A 5 5.258 -15.260 -22.393 1.00 2.87 N >> ATOM 25 NH2 ARG A 5 6.717 -16.030 -20.793 1.00 2.87 N >> ATOM 26 N ARG A 6 3.934 -11.168 -16.245 1.00 2.84 N >> ATOM 27 CA ARG A 6 5.160 -10.666 -15.652 1.00 2.84 C >> >> Structure 2 >> ATOM 24 NH1 ARG A 5 5.258 -15.260 -22.393 1.00 1.35 N >> ATOM 25 NH2 ARG A 5 6.717 -16.030 -20.793 1.00 1.35 N >> ATOM 26 N ARG A 6 3.934 -11.168 -16.245 1.00 1.73 N >> ATOM 27 CA ARG A 6 5.160 -10.666 -15.652 1.00 1.73 C >> >> Is there a way to visualise these differences (e.g. by different thickness of ribbons or any other means e.g. colour of spheres). >> >> Thank in advance for any suggestions >> >> George >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Aug 27 13:59:18 2018 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 27 Aug 2018 13:59:18 -0700 Subject: [Chimera-users] Chimera: Amber to PDB In-Reply-To: References: Message-ID: <616D891B-48B4-4235-AD27-0D2F73C1AF9B@cgl.ucsf.edu> Hi Boris, Well, not directly. If you run the AddCharge tool (or ?addcharge? command), which will in turn add hydrogens if any are missing, then the ?Amber name? of the residue is computed and put into the ?amberName? attribute of each residue. So, if you then run the Python script below (simply by opening it with File?Open or the ?open? command), then the regular name of the residue will be overwritten with the amberName attribute and if you then save a PDB file, the residue names will use the Amber convention. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Aug 27, 2018, at 2:00 AM, Boris TOUZEAU wrote: > > Hi, > > I am Boris TOUZEAU, actually a PhD student at the National Taiwanese University (NTU) based in Taipei. > > I had a question about chimera; Is it possible to output pdb files having amber residues naming convention instead of pdb residues naming convention ? I saw it was possible to do it for the atoms (ligands) but I would be more interested to do it for residues. > > Best wishes, > > Boris TOUZEAU > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: amber_res_name.py Type: text/x-python-script Size: 167 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From boris.touzeau at gmail.com Mon Aug 27 17:58:46 2018 From: boris.touzeau at gmail.com (Boris TOUZEAU) Date: Tue, 28 Aug 2018 08:58:46 +0800 Subject: [Chimera-users] Chimera: Amber to PDB In-Reply-To: <616D891B-48B4-4235-AD27-0D2F73C1AF9B@cgl.ucsf.edu> References: <616D891B-48B4-4235-AD27-0D2F73C1AF9B@cgl.ucsf.edu> Message-ID: Hi Eric, Thank you for the quick answer, I tried to use the addcharge command indeed but I think that my HIS residues were still HIS residues for all the histidines and not HID nor HIE. I expected that one could not do it directly and was prepared to write a script but I did not expected you to write it for me. Still I thank you as it is much much shorter than what I envisioned. Best wishes, Boris TOUZEAU Le mar. 28 ao?t 2018 ? 04:59, Eric Pettersen a ?crit : > Hi Boris, > Well, not directly. If you run the AddCharge tool (or ?addcharge? > command), which will in turn add hydrogens if any are missing, then the > ?Amber name? of the residue is computed and put into the ?amberName? > attribute of each residue. So, if you then run the Python script below > (simply by opening it with File?Open or the ?open? command), then the > regular name of the residue will be overwritten with the amberName > attribute and if you then save a PDB file, the residue names will use the > Amber convention. > > ?Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > > On Aug 27, 2018, at 2:00 AM, Boris TOUZEAU > wrote: > > Hi, > > I am Boris TOUZEAU, actually a PhD student at the National Taiwanese > University (NTU) based in Taipei. > > I had a question about chimera; Is it possible to output pdb files having > amber residues naming convention instead of pdb residues naming convention > ? I saw it was possible to do it for the atoms (ligands) but I would be > more interested to do it for residues. > > Best wishes, > > Boris TOUZEAU > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: