- Chimera-users - RBVI Mailing Lists

discontinuous ribbon for nuc. structure
by bala 20 Jun '07

20 Jun '07

Hello, While i make the ribbon representation for an RNA duplex, sometimes ribbon is discontinuous in between, what could be the reason for it ? I hve two conformation sof the same duplex taken at 1ns interval from MD trajectory. For one conformation, ribbon is continuous but for the other there is a discontinuity at the middle.. I analysed the structure, it seems ok. thanks in advance, Bala

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Delphi calculation for electrostatic surface potential
by Shunsuke Meshitsuka 18 Jun '07

18 Jun '07

Dear Doctors, I want to calculate surface potential by Delphi type calculation. I have tried from Menu bar, tool --- DelPhi ,but have not obtained the results. Please let me know the way to use them for the calculation of surface potentials from a PDB fie in linux version of chimera-1.2417. Shunsuke Meshitsuka D.Sci., D.Med. Tottori University Graduate School of Medical Science Institute of Regenerative Medicine and Biofunction, Division of Integrative Bioscience 86　Nishimachi Yonago Tottori　683-8503　Japan tel +81-859-38-6422 fax +81-859-38-6423 Email: mesh(a)grape.med.tottori-u.ac.jp

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Help me please with this error
by David Gil Carton 15 Jun '07

15 Jun '07

Hi, I have a HP9400 (AMD Opteronx64bits-Red Hat Linux64bits) with a NVIDIA Quadro FX3500 256MB and I have installed the "chimera-1.2417-linux_x86_64.exe". My problem is that when I run chimera I have this message, %chimera X Error of failed request: GLXUnsupportedPrivateRequest Major opcode of failed request: 129 (GLX) Minor opcode of failed request: 16 (X_GLXVendorPrivate) Serial number of failed request: 1313 Current serial number in output stream: 1314 %glxinfo name of display: :0.0 display: :0 screen: 0 direct rendering: No server glx vendor string: NVIDIA Corporation server glx version string: 1.4 server glx extensions: GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_SGI_video_sync, GLX_SGI_swap_control, GLX_ARB_multisample, GLX_NV_float_buffer, GLX_ARB_fbconfig_float, GLX_NV_swap_group client glx vendor string: SGI client glx version string: 1.4 client glx extensions: GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_MESA_allocate_memory, GLX_MESA_swap_control, GLX_MESA_swap_frame_usage, GLX_OML_swap_method, GLX_OML_sync_control, GLX_SGI_make_current_read, GLX_SGI_swap_control, GLX_SGI_video_sync, GLX_SGIS_multisample, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer, GLX_SGIX_visual_select_group GLX extensions: GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context, GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGI_make_current_read, GLX_SGI_swap_control, GLX_SGI_video_sync, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: Quadro FX 3500/PCI/SSE2 OpenGL version string: 1.2 (2.0.2 NVIDIA 87.62) OpenGL extensions: GL_ARB_depth_texture, GL_ARB_imaging, GL_ARB_multitexture, GL_ARB_point_parameters, GL_ARB_point_sprite, GL_ARB_shadow, GL_ARB_texture_border_clamp, GL_ARB_texture_cube_map, GL_ARB_texture_env_add, GL_ARB_texture_env_combine, GL_ARB_texture_env_dot3, GL_ARB_texture_mirrored_repeat, GL_ARB_texture_non_power_of_two, GL_ARB_transpose_matrix, GL_ARB_window_pos, GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color, GL_EXT_blend_func_separate, GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_draw_range_elements, GL_EXT_fog_coord, GL_EXT_multi_draw_arrays, GL_EXT_packed_pixels, GL_EXT_point_parameters, GL_EXT_rescale_normal, GL_EXT_secondary_color, GL_EXT_separate_specular_color, GL_EXT_shadow_funcs, GL_EXT_stencil_wrap, GL_EXT_texture3D, GL_EXT_texture_edge_clamp, GL_EXT_texture_env_add, GL_EXT_texture_env_combine, GL_EXT_texture_env_dot3, GL_EXT_texture_filter_anisotropic, GL_EXT_texture_lod, GL_EXT_texture_lod_bias, GL_EXT_texture_mirror_clamp, GL_EXT_texture_object, GL_EXT_texture_rectangle, GL_EXT_vertex_array, GL_ATI_texture_float, GL_ATI_texture_mirror_once, GL_IBM_rasterpos_clip, GL_IBM_texture_mirrored_repeat, GL_INGR_blend_func_separate, GL_NV_blend_square, GL_NV_copy_depth_to_color, GL_NV_depth_clamp, GL_NV_fog_distance, GL_NV_light_max_exponent, GL_NV_multisample_filter_hint, GL_NV_texgen_reflection, GL_NV_texture_env_combine4, GL_NV_texture_rectangle, GL_SGIS_generate_mipmap, GL_SGIS_texture_border_clamp, GL_SGIS_texture_edge_clamp, GL_SGIS_texture_lod, GL_SGIX_depth_texture, GL_SGIX_shadow, GL_SUN_multi_draw_arrays, GL_SUN_slice_accum glu version: 1.3 glu extensions: GLU_EXT_nurbs_tessellator, GLU_EXT_object_space_tess What I have to do to resolve my problem? Thanks, David Gil Electron Microscopy Structural Biology Platform CIC bioGUNE Bizkaia Technology Park, Bld 800 48160 Derio-Bizkaia Tel Platf. +34 946 572 516 Fax +34 946 572 502 http://www.cicbiogune.es Este correo electrónico se ha enviado desde CIC bioGUNE. Su contenido, y el de cualquier fichero que le acompañe, son confidenciales y de uso exclusivo de la persona física o jurídica a la que va destinado. Está estrictamente prohibida, y puede ser ilegal, la copia o difusión no autorizada de este correo, o de sus documentos adjuntos, o revelar cualquier información que pudieran contener. Si ha recibido este correo electrónico por error, por favor notifíquelo al remitente o contacte con el teléfono + 34 944 06 13 00 y bórrelo de su sistema informático. Posta elektroniko bidezko mezu hau CIC bioGUNEtik bidali da. Bertako edukia, eta erantsita egon daitekeen edozein fitxategirena, konfidentziala da, mezuaren hartzaile den pertsona fisikoak edo juridikoak bakarrik erabiltzekoa. Erabat debekatuta dago, eta legez kanpokoa ere izan daiteke, mezu hau edo erantsitako fitxategiak baimenik gabe kopiatzea edo zabaltzea, bai eta bertako informazioa besteri jakinaraztea ere. Mezu hau zuretzat ez bada, adieraz iezaiozu bidaltzaileari, edo deitu + 34 944 06 13 00 telefono-zenbakira eta ezabatu zure ordenagailutik. This e-mail is from CIC bioGUNE. The e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised dissemination or copying of this e-mail or its attachments, and any use or disclosure of any information contained in them, is strictly prohibited and may be illegal. If you have received this e-mail in error, please notify or telephone + 34 944 06 13 00 and delete it from your system.

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cavities
by Pablo Emiliano Tomatis 15 Jun '07

15 Jun '07

hello It is possible to find cavities of a protein using chimera? Any hepl??? thanks in advance -- Lic. Pablo E. Tomatis Instituto de Biología Molecular y Celular de Rosario (IBR) Área Biofísica - Departamento de Química Biológica Fac. Cs. Bioq. y Farm. - U.N.Rosario Suipacha 531 - S2002LRK- Rosario- Argentina Phone:+54-341-4350661/4350596 (ext.110) Fax:+54-341-4390465

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to view nmr pdb structures
by Shunsuke Meshitsuka 15 Jun '07

15 Jun '07

Dear researchers, I have used chimera as a viewer of proteins. I have a question how to overlay the 20 structures of NMR pdb data by chimera. When there are 20 structures of structurename01.pdb, structurename02.pdb,,,structurename20.pdb, > chimera structurename**.pdb makes a random location and random orientation of each protein. Please let me know the method. Shunsuke Meshitsuka D.Sci., D.Med. Tottori University Graduate School of Medical Science Institute of Regenerative Medicine and Biofunction, Division of Integrative Bioscience 86　Nishimachi Yonago Tottori　683-8503　Japan tel +81-859-38-6422 fax +81-859-38-6423 Email: mesh(a)grape.med.tottori-u.ac.jp

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release next week
by Elaine Meng 14 Jun '07

14 Jun '07

Dear Chimera users, As you may know, we made a production release earlier this month. Since then, a few bugs have come to our attention that were not revealed by our test suite or by users during the "release candidate" phase. We plan to make another production release late next week with the following fixes: - ensure POV-Ray image view always matches that in Chimera, instead of most of the time 8-) - make Minimize Structure work with metal ions (those in Amber parm94: calcium, magnesium, iron, etc.) - fix saving of sessions when sequences have been added to an alignment in Multalign Viewer (current workaround is to save the modified alignment to an alignment file) There may be additional updates and minor fixes not mentioned here. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Re: [Chimera-users] rotating items in chimera
by William Jeffrey Triffo 14 Jun '07

14 Jun '07

hi Elaine, I just loaded a pdb, selected an off-center atom, typed 'cofr' at commandline, and the cofr does not appear to change (rotation looks the same in the chimera window). I submitted a bug report, -Jeff Elaine Meng wrote: > > > On Jun 14, 2007, at 11:56 AM, William Jeffrey Triffo wrote: > >> thanks, >> >> I have actually had some weird instances where 'cofr' didn't seem to >> reset the center, if I can reproduce I'll let you know. >> >> -Jeff > > Yes, do (and send to the chimera-bugs address)! > E > -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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Re: [Chimera-users] export scene to maya, obj, iges, stl, dwg-dxp?
by Greg Couch 14 Jun '07

14 Jun '07

Just to follow up, the Maya VRML2 importer is actually a conversion program in Maya's bin directory. On Windows the program is called wrl2ma.exe and on Linux and Mac OS X it is called wrl2ma. See the Maya documentation for details. - Greg

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export scene to maya, obj, iges, stl, dwg-dxp?
by Damir Perisa 14 Jun '07

14 Jun '07

dear all, is it possible, to export a scene from chimera to mayaBinary, obj, iges, stl or dwg-dxp formats? i have checked and chimera can export to a X3D format (vrml) as well as PovRay. i didn't find any info about transforming one of these to some other format. has anybody successfully exported chimera scenes (ribbon+surface+single_residue_atoms mix structures, not just a pdb file as atoms alone) to a file-format used by designers? thanx in advance for any help, damir -- .·´¯`·.¸.·´¯`·.¸¸.·´¯`·.¸.·´¯`·.¸.·´¯`·.¸.·´¯`·.¸¸.·´ ° ° ° ° ° ° ><((((º> ° ° ° ° ° <º)))>< <º)))><

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Reading a data set from a text file
by Elaine Meng 14 Jun '07

14 Jun '07

Hi Kyaw, The only ways I can think of are: - create a VRML file describing a surface with those points, read into Chimera - write a Python script to be opened in Chimera that reads in the numbers and generates a Chimera surface model However, I do not know the details about how to do either of these things. Others, feel free to chime in! Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html Begin forwarded message: > Hi Dr. Meng, > > I am sorry for my vague question. > > I have a table of numbers in a text file and I'd like to read in > those numbers and convert them into cartesian coordinates so that > they can be displayed as a surface in Chimera. > > If you could give me some suggestions on how to do it, I'd really > appreciate it. > > Thank you, > Kyaw _______________________________________________ Chimera-dev mailing list Chimera-dev(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Chimera: Reading a data set from a text file
by Kyaw Zeyar Myint 14 Jun '07

14 Jun '07

Hi, I am Kyaw Myint, a summer intern at NIAMS branch of NIH. I am working under the supervision of Dr. Bernard Heymann from the Lab of Structural Biology research. The project I am working on currently is to improve the 3D reconstruction of viruses' structures from 2D electron micrographs. The programs I am using include Chimera and Bsoft. For the project, I want to read in a data set from a text file and display the 3D surfaces based on that data set. I'd like to use Chimera for that purpose and I'd really appreciate any suggestion or comment on how I should do that. Thank you very much for your help in advance. Looking forward to hearing from you soon, Kyaw

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Problems with DMS installation
by 63668＠unimo.it 14 Jun '07

14 Jun '07

DMS is the only program requested to generate DOCK input files I was not able to install. I read something similar in this same mailing list. The first problem I encountered was an error message referred to "radii" directory. Thus I created the radii directory and I put radii.proto file into it. Now the error message is "Unknown atom type N", and by eliminating N atoms from my input file the new error message is "Unknown atom type CA", and so on. It seems that the program is not able to recognize atoms with their atomic radii, thus I think that the problem is still in this file. Any suggestion? Thank you, Valeria ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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toolbar
by Eric Pettersen 13 Jun '07

13 Jun '07

On Jun 13, 2007, at 12:21 AM, Graham Palmer wrote: > Eric: Another thing. In Favorites/Preferences/ Category Tools I > checked putting the Command Line on the Toolbar. But it never > appears there by default. I must always select the Command Line > in Favorites. I would prefer having it on the Toolbar by default. Hi Graham, You need to click the "Save" button on the preferences panel to make your changes permanent. --Eric

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new feature: conversion of atomic coordinates to electron density map
by Thomas C Marlovits 13 Jun '07

13 Jun '07

Hi, I am not quite sure, whether this is possible with Chimera ... but it would be great if there is a feature that would allow to convert a .pdb structure (atomic coordinates) into a map usually obtained by electron microscopy (sections) - for example into mrc/ccp4 format. Even filtering this map then to different resolutions (including storing entire maps) would be an interesting feature. Thanks, -Thomas __________________________________________ Thomas C Marlovits, PhD, M.A.S IMP - Institute of Molecular Pathology IMBA - Institute of Molecular Biotechnology, Austrian Academy of Sciences Dr. Bohr-Gasse 3 A-1030 Vienna AUSTRIA marlovits(a)imp.univie.ac.at Tel (+ 43) 1 79044 4630

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Looking for a Ramachandran plot display
by Oren Shalev 12 Jun '07

12 Jun '07

Hi all, I'm looking for a tool or an extension that displays the Ramachandran plot of a protein model, similar to the DeepView (SPDBViewer) tool. I'm not interested in the interactive features, just the display of residues as dots on the phi/psi plane, with dots colored, for example, by their C-Alphas' color. Do you know if such a tool was written for Chimera? With regards, Oren

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atoms/residues within a certain distance of another structure
by Terry Nelson 12 Jun '07

12 Jun '07

Hi, 1. I was wondering if Chimera has the option of finding for instance : "residues within 5 Angstrom of a bound protein inhibitor" or "residues within 3Ang. of solvent molecules", etc. I use a similar command in VMD that specifies the residues. 2. Does Chimera archive mails have a search engine that I missed? Cheers, Terry

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atoms/residues within a certain distance of protein
by Terry Nelson 11 Jun '07

11 Jun '07

Hi, 1. I was wondering if Chimera has the option of finding for instance : "residues within 5 Angstrom of a bound protein inhibitor" or "residues within 3Ang. of solvent molecules", etc. I use a similar command in VMD that specifies the residues. 2. Does Chimera archive mails have a search engine that I missed? Cheers, Terry

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Re: [Chimera-users] dock prep in batch mode?
by Eric Pettersen 11 Jun '07

11 Jun '07

On Jun 9, 2007, at 7:52 AM, figo wrote: > I have seen your solution to the dock > prep in batch mode (http://blur.compbio.ucsf.edu/pipermail/dock- > fans/2007-May/001043.html ) , but when I run the command : > chimera --nogui pdb:1gcn dockprep.py , the chimera want to Fetch > protein 1gcn from web site www.rcsb.org, I have download the > entire PDB, so how can I specify the PDB path to the chimera? Thanks. If you have the PDB files laid out the same way that the RCSB distributes them (e.g. entry 1GCN is in gc/pdb1gcn.ent) then Chimera will automatically look in /mol/pdb and /usr/mol/pdb for them. To have it look elsewhere you need to edit the file <your Chimera installation>/share/chimera/pdbDir and follow the reasonably simple instructions contained in that file. The drawback is that you will need to do that edit every time you install a new Chimera. Putting a better mechanism in place is on our to-do list. Other alternatives include putting the full path to the PDB file in your command, or putting all the files you need into one directory and using the PDB preferences (Favorites...Preferences...[change to PDB category]) to get Chimera to look in that directory. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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rmsd and display queries
by bala 09 Jun '07

09 Jun '07

Hello, 1) Basically i hav three conformations (only 3 pdb) of the same molecule picked up from three different regions of a simulated trajectory. I hv to calculte rmsd and superimpose structure. I tried the emsemble match but it seems that it can work on only two conformation. Kindly suggest me how i can overcome this. 2) Is it possible to create a substructure (subset) of a molecule and do rmsd calcutn and superimposing only on the substructures for the conformations i have.

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New to the board
by Campbell, Patrick 08 Jun '07

08 Jun '07

Hello, I am a grad student and have only been recently been introduced to Chimera. I have a quick question which I hope, someone will be able to assist me with. I am looking at a pdb protein, 2NEF which is composed of 40 NMR structures. I was able to isolate one of the chains and was wondering if a. It is possible to change part of the sequence on the chain (from AAAA to EEEE for instance). b. Is it possible to then use the changed sequence (B) to morph it against the original 3d sequence (A) c. Is it possible to align the changed fragment of B with the original A d. Could the changed sequence (B) be saved for future use or does one have to go through the process of creating it each time it is used on CHIMERA? thanks much pat

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Re: [Chimera-users] rmsd and display queries
by Elaine Meng 08 Jun '07

08 Jun '07

On Jun 8, 2007, at 12:06 AM, bala wrote: > Hi Elaine, > Thank you for your inputs. I think i didnt mention my second query > reg. substructure creation clearly, > I hve a 20 mer duplex RNA, i want to visualize only a few base > pairs at the middle. Is there any way that i can select, display > and do actions only the portion of interest and undisplay other > portion > Bala Hi Bala, Of course. The general procedure is to (1) select what you are interested in (2) invert the selection so now it contains only what you are *not* interested in (3) hide or delete the selection (if you're confident you won't want the other parts, deleting will make later steps simpler) (4) if you only hid rather than deleting, now select the parts of interest again, and use the Actions menu to work with those parts There are many different ways to do each step, too many to describe in this mail. Below, I'll just give an example using commands, but be aware that selection can also be done with Ctrl-click and arrow key operations, or with the Select menu, or using the Sequence tool: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/seqpanel.html Commands example: open 6bna sel :4-8.a,5-9.b sel invert delete sel Then carry on with what is left, using commands or the menu as you prefer. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Re: [Chimera-users] IMOD mesh/surface colors
by Elaine Meng 07 Jun '07

07 Jun '07

Hi Jeff, There are two general reasons why the *displayed* marker radius and link radius might not equal the values shown in Volume Path Tracer. In the following explanation, atom = marker and bond = link. (1) The atom or marker is in the "ball" representation rather than "sphere." displayed ball radius = (ball scale)(atom radius) where the default ball scale is 0.25. You could - change the atom to the "sphere" representation, which uses the full radius. "Actions... Atoms/Bonds... sphere" or the command "repr sphere sel" will change the selected atoms to the sphere representation. or - stay in the "ball" representation but change the "ball scale" factor to 1.0 (I'll describe how to get to this parameter below) (2) Similar to the markers, displayed bond or link radius = (stick scale)(bond radius) You could make sure that the "stick scale" factor is 1.0. It probably already is, since that's the default. Of course, the bond or link should also be the stick representation, not wire. Volume Path Tracer automatically makes them sticks when the radius is >0, however. In the Model Panel, if you click the IMOD contours model (or any molecule model) on the left and "attributes..." on the right (or just double-click the model on the left), that opens the molecule model attributes panel. In there you can see and change the ball scale and stick scale values. In your example file trial2.mod, I selected a few markers and links and set all their radii to 20. After I changed the marker to sphere, it did match up in size with the connected link. The more I zoomed in, the better it looked. It may be a level of detail issue if they don't look matched up when zoomed out. You can increase the number of subdivisions used to draw the spheres/cylinders with subdivision quality in Effects (under Tools... Viewing Controls). The parallel links did not quite touch, however, but since you said the contours were approximately 40 A apart, I think it is working correctly! If you still have trouble, though, let me know. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 7, 2007, at 12:12 PM, William Jeffrey Triffo wrote: > thanks Elaine, > > another thing I noticed, when I change the marker (atom?) radius in > Volume Path Tracer, it does not appear to change quite right. For > instance, if I set the 'Link' radius to something like '20', and > likewise the Marker radius to '20', they will not be the same size. > > In general when making marker sets, this is not the case, and the > radius acts the same between the two settings. For these markers, > the contours were place approx. 40 A apart, so a marker (or link) > radius of '20' should make the contours 'kiss' when viewed as a > marker set, correct? > > thanks for your prompt response, it would make sense that I would > miss the color setting instructions on the actual page for the tool... > > -Jeff

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Saving images with the povray option
by jean-francois menetret 07 Jun '07

07 Jun '07

I am trying to save images with the povray option using chimera2416, but the camera viewpoint is lower than the center of the scene, so that I just see the bottom of the scene. Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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IMOD scaling and alignment
by Tom Goddard 05 Jun '07

05 Jun '07

Points placed in IMOD may not have proper scale and alignment when opened in Chimera together with the original MRC map. There are some IMOD settings that can fix this. Jeff wrote: > great, > > I don't know if I replied earlier or not, but if the issue comes up > with anyone else, setting the magnitude of the IMOD model (which a > user would typically do in the IMOD tool 3dmod) to be equal in > magnitude to the pixel size listed in the MRC header of the > desired/corresponding volume map is enough to ensure the proper > scaling; the default for units in 3dmod appears to be nm, while in MRC > files it is generally Angstroms. Applying a translation equal to the > origin offset that chimera uses in the MRC header is then sufficient > to co-register the two. > > -J

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Little help to write a python script
by Eduardo Sanz Garcia 05 Jun '07

05 Jun '07

I have previously written command scripts for chimera. Now, I need to do something more complicated that, I believe, is not possible to do from the command line. This is the task: I have a list of 100 electron density maps. 1- I want to display each map, one by one. 2- Change the default threshold. 3- Save an image of the current volume. 4- Close the current volume and open the next model. Has anyone done this before? An example of a python script that can do this or something similar could help me a lot. Thanks in advance.

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