- Chimera-users - RBVI Mailing Lists

Reading a data set from a text file
by Kyaw Zeyar Myint 29 Jun '07

29 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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rotating items in chimera
by William Jeffrey Triffo 29 Jun '07

29 Jun '07

hello, is there a way to return to a rotational position, without using 'savepos' and 'reset'? For instance, if I don't want to reset translation(s) (which using savepos/reset might do), but just want to return to a 'top down' view, or a specific rotation with respect to the viewer's global axes? I realize that with multiple objects in potentially different rotational orientations, this would require which object to use to calculate the rotation. thanks, -Jeff

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Transformation matrices
by Eduardo Sanz-Garcia 29 Jun '07

29 Jun '07

I am getting the rotation matrices (I am not interested in the translation column) using matrixget command. My naive question: Should I use in this way: x' x y' = [3x3 matrix] y z' z or in this other way? z' z y' = [3x3 matrix'] y x' x Thank you very much.

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IMOD mesh/surface colors
by William Jeffrey Triffo 28 Jun '07

28 Jun '07

hi, is there a way to control the color of surfaces generated from IMOD meshes in Chimera? when I select a surface, and pick a new color in the color editor, I notice that the color of the 'IMOD contours' in the Model Panel changes, but that there is no change in the color of the actual rendered surface. thanks, -- ------------------------------------------------------------- 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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Use of a copyrighted figure for software review note
by Anselm.Horn＠chemie.uni-erlangen.de 27 Jun '07

27 Jun '07

Dear all, sorry, if this is a bit off-topic, but I did not find any e-mail address more suitable on the Chimera website. As I learned from the CCL there is a new Chimera version out. I think this would be a nice opportunity to write a short software review note (approx. 1 column) in the "Nachrichten aus der Chemie", the members journal of the German Chemical Society GDCh, in order to inform a broad public of Chimera. For this I'd like to use the graphic "DNA and Netropsin" from the Chimera Image Gallery, in case there is space enough to have a figure printed as well. The image, however, is marked copyrighted, and thus I'd like to know, whether I may use it for my purpose and what statement/copyright notice should be included in the figure caption. Thanks in advance. Best regards, Anselm

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how to "connect" two proteins
by Damir Perisa 26 Jun '07

26 Jun '07

hi all, maybe this is a little bit too far over the capabilities of chimera, but i hope somebody can help me or give input. i would like to connect two PDB structures into one chain of aminoacids. one PDB is from one globular domain, the other is from another globular domain including linker. i would like to try to put them together and see how (what possible conformations) they fit together. what orientations are possible and how it would look like (visualisation, making movies, convincing non-scientists, ...). i could edit the PDB files in a text editor, but i would not want to calculate the cordinates by hand first - are there no tools to glue together chains? thanx for any input how to do this with chimera or any other programme, best regards, Damir -- Damir Perisa Master Student Biozentrum, University of Basel Department Biochemistry / Focal Area Infection Biology Klingelbergstrasse 50-70 CH-4056 Basel, Switzerland phone: +41 61 267 1492

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Question on Chimera
by Ki Kim 25 Jun '07

25 Jun '07

Hello, I would like to know what is the best way to draw the surface of the binding site of a protein. I would like to add some water molecules to the protein and treat these water as part of the protein. Thank you for your help. Sincerely, Ki Kim

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Re: [Chimera-users] error running Antechamber
by Eric Pettersen 23 Jun '07

23 Jun '07

On Jun 23, 2007, at 11:12 AM, S Datta wrote: > Thanks a lot Eric. You suggest that I modify the input > files by putting the cobalt with residues of their > own. Do you mean as a separate file or in the > methylcobalamin file that i downloaded from the PDB > database ? Also one of the ligands to the > methylcobalamin is a histidine from the protein. Change it in the same file. Change the residue name and number, being careful to keep the rest of the columns in the same place. Also make sure that the new residue number isn't the same as some other residue. The fact that protein histidines are coordinating the metal shouldn't be an issue. Let me know if you run into problems. --Eric

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error running Antechamber
by S Datta 22 Jun '07

22 Jun '07

Hi I am trying to prep a ligand using chimera for docking. When I try to add charges, one error which is always present is "Atom whose IDATM type has no Sybyl type: #-99.-99:1@CO(type: Co). At the end the reply log asks to check the total charge and spin multiplicity. When I manually change the total charge, after the Atom error briefly appears, Chimera either freezes (windows) or runs the program /../antechamber/exe/mopac.sh (in linux) infinitely. Could someone help me decipher what is going wrong ? I tried to change the input format of the ligand file from .pdb to .sy2 but that didnt help. thanks a lot SD ____________________________________________________________________________________ Got a little couch potato? Check out fun summer activities for kids. http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&…

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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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Volume segmentation question
by Toby Starborg 05 Jun '07

05 Jun '07

Dear Chimera users. I am new to using chimera, so this question may seem a bit simplistic. I'm trying to use Chimera to examine EM tomographs of fairly busy data sets. I'd like to be able to divide the data into separate features so that I can better understand which parts are noise and which are structural (segmentation). So far I have found the "Pick Surface Pieces" tool is very useful for colouring the surface of features of interest. I have also found it useful to colour some surfaces with 0 opacity to remove items that are in the way, but I would prefer to do this in a more permanent fashion sot that I can return to a data set and quickly compare structures. I have also tried using "Volume Path Tracker" with "Color Zone" and "Split Map by Color" (after adjusting the voxel size to angstroms rather than nm to give a reasonable volume segmentation). My question is would it be possible to alter "Pick Surface Pieces" so that it colours (or tags in some way) all of the voxels within the chosen mesh, so that it would then be possible to split the map into separate compartments that could be saved and examined separately? This would also offer the ability to use different threshold levels to examine different features. I realise that this is more of a wish list than a trouble shooting question, but I'd also appreciate any input from more experienced Chimera/tomography users. Thank you for your help. Toby S -- Dr T Starborg FLS, University of Manchester Michael Smith Building, Rumford Street, Manchester,M13 9PL. UK tel:+44(0)161 275 1557 fax +44(0)161 275 1505

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(no subject)
by Газизов А.С. 04 Jun '07

04 Jun '07

Hello everybody. Is there Fe2+ ion in Chimera? I'm trying to add charges to hem molecule and it always appears to be Fe3+ (and Add Charge tool reports "There is odd number of electrons..." and fails).Assigning odd overall charge helps (i.e. +1, +3, etc), but I need +2...

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problem with chimera-->followup
by Vinay Kumar 04 Jun '07

04 Jun '07

Hello all, Firstly. Greg, Thank you. Though, i have been using the linux OS for quite sometime, i still have a few doubts about upgrading and these sort of things. I have actually gone to mesa3d, OpenGL, and DRI websites. but they contain terms which i am not acquainted with. I have downloaded, MesaLib 6.4.2 and tried installing it as per their instructions, only to find the installation stopping with some error. ( i shall post the error in the next email.) I would like to know, if the installation went well, would i have upgraded X11?? With regards, Vinay. ps- MesaLib 6.5.3 was available, but 6.4.2 was stated to be a stable release hence opted that.

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problem with chimera
by Vinay Kumar 01 Jun '07

01 Jun '07

Hello all, I have been using chimera and dock6.0 on a RHL9.0 system. More recently if i perform simple processes like coloring a molecule in chimera, the display goes blank and also logs me out of the session. meaning, i come back to the graphical login for my system. I am unable to proceed any further as repeated attempts to do simple tasks simply logs me out. Kindly help with suggestions. With regards, Vinay.

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Volume thresholds in Chimera
by Tom Goddard 01 Jun '07

01 Jun '07

Huang, Ren-Huai wrote: > Hi, > > Thanks for your help before. > > Chimera runs smoothly in my Linux computer. It generates very nice images for > EM reconstruction map. > Could you explain the concepts of thresholds of contour used in Volume > histogram? What is the value mean? > Thanks very much in advance, > > Ren-Huai > Thomas Goddard wrote: > Hi Ren-Huai, > > The map values shown in the Chimera volume viewer dialog are the > values that come from the file. Typically the map files do not have > any meaningful normalization. There is currently no facility for > instead showing values in standard deviation units. Chimera also does > not report the mean. These capabilities are on our requested features > list (entry #88). http://www.cgl.ucsf.edu/chimera/plans.html > > The histogram shows the distribution of map data values. The height > is the logarithm of the number of grid points with values in a small > value range. > > Tom >

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Software tools wiki pages
by Bridget Carragher 01 Jun '07

01 Jun '07

Hi there, In preparation for an announcement to go out about the JSB Software Tools Special Issue I am asking people who have entries on the 3DEM Software Tools wiki pages to update these if possible - eg. can you update the ref from the current "in press" to the right reference and also just check that the entry is otherwise up to date. Thanks, Bridget P.S. The url for these pages is: http://en.wikipedia.org/wiki/ Software_tools_for_molecular_microscopy in case you don't have it handy. ------------------------------------------------------------------------ ---------------------------------------------------------- Bridget Carragher, Associate Professor Automated Molecular Imaging Group, Department of Cell Biology The Scripps Research Institute, MC CB129,10550 North Torrey Pines Road, La Jolla, CA 92037 tel: (858) 784-9070; fax: (858) 784-9090; bcarr(a)scripps.edu; http:// ami.scripps.edu National Resource for Automated Molecular Microscopy: http:// nramm.scripps.edu ------------------------------------------------------------------------ ----------------------------------------------------------

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ESP grid is offset from original PDB coordinates??
by Kenward Vaughan 30 May '07

30 May '07

I was playing with esp results yesterday from Delphi on several structures, and ran a quick calculation on 2ace. To my surprise, the results as visualized as a solid under volume viewer were very obviously offset from the structure itself. They stand alone to one side of the original. I've attached a small jpg of this. I'm using the latest Linux production version (beta version 1 build 2415) on an amd64 box (Debian Sid, kernel 2.6.20). I hope there is a simple explanation... ;-) I am no expert with Delphi, so something may be odd there. I used a couple of the siz/crg files, with the same results in each case, so I suspect something in the original pdb file is messing things up? Cheers! Kenward -- .'^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| 1801 Panorama Drive / ', \ Bakersfield, CA 93305 / o O \ http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) ---========--- ???$$MM$$???

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Python script for reading volume values at atom positions
by Tom Goddard 30 May '07

30 May '07

Hi Terry, Here is a Python script to read a volume map and a PDB file and print the values of the map interpolated at the atom positions. It will work without the Chimera graphical user interface. I tested it in Chimera 1.2415. Tom # ----------------------------------------------------------------------------- # Script that opens PDB and map files and prints the map values interpolated # at each atom position. Can be run without graphical user interface: # # chimera --nogui avalnogui.py # def map_values_at_atoms(pdb_path, map_path): # Open map file. # File name has to have file suffix indicating volume format. from VolumeData import open_file data = open_file(map_path) from VolumeViewer import Data_Region, full_region, Rendering_Options ro = Rendering_Options() map = Data_Region(data, full_region(data.size), '', ro) attribute_name = data.name.split('.')[0] # Open PDB model(s). from chimera import openModels molecules = openModels.open(pdb_path, 'PDB') # Interpolate map values at atom positions. from AtomDensity import set_atom_volume_values for mol in molecules: set_atom_volume_values(mol, map, attribute_name) # Print values. for mol in molecules: for a in mol.atoms: v = getattr(a, attribute_name) print '%-15s %12.4g' % (a.oslIdent(), v) # ----------------------------------------------------------------------------- # map_path = '/usr/local/src/chimera-demos/volume/examples/1a0m.omap' pdb_path = '/usr/local/src/chimera-demos/volume/examples/1a0m.pdb' map_values_at_atoms(pdb_path, map_path)

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Color in Chimera
by Albion Baucom 25 May '07

25 May '07

How do I determine the exact color value of a model from a previous session? I want to open a session, determine the color of a selected chain, and then color another chain that exact color. I can't seem to find an "eye-dropper" or other comparable tool to determine the color value (RGB, hex, etc). Thanks. Albion

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Chimera release candidate
by Elaine Meng 24 May '07

24 May '07

Hello everybody, A new version of Chimera (1.2415) is available for all platforms: http://www.cgl.ucsf.edu/chimera/download.html It is a candidate for a production release we plan to make in about a week. Many new features have been added since our last production release (1.2304, October 2006), as detailed in the release notes: http://www.cgl.ucsf.edu/chimera/1.2415/docs/relnotes/snapshot.html Here are just a few of the changes since last October: - embedded POV-Ray for production of glossy, shadowed images including labels - ability to supersample or to use POV-Ray when recording movies - new input formats: MDL MOL/SDF, Gromacs trajectories - new Fetch by ID types: EDS (fo-fc) electron density difference map, PQS predicted biological unit - Presets menu with display settings for interactive Chimera use or generation of publication images - Side View includes "top view" for interactively adjusting stereo parameters and perspective - expanded morphing capabilities - new Fit Map in Map tool - new windowsize command - updates to handle new naming conventions in the remediated PDB Enjoy! (and do let us know right away via "Report a Bug" or chimera- bugs(a)cgl.ucsf.edu if you find any problems) Thanks, 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] fit map in map
by Thomas Goddard 24 May '07

24 May '07

Hi Gabor, There are no Chimera commands to fit one map into another, but it can be done with a Python script. I've attached a Python script that I made by piecing together code from gui.py and __init__.py from directory chimera/share/FitMap. Tom Gabor Papai wrote: > Hi Tom, > > Can the fit map in map tool be used without the GUI and retreive back > only the transformation matrix? > Bye, > Gabor > # ----------------------------------------------------------------------------- # Example script for fitting one map in another without the graphical user # interface. # # chimera --nogui fitnogui.py # # It can also be run using the graphical Chimera interface using File/Open. # def fit_map_in_map(map1_path, map2_path, initial_map1_transform = None, map1_threshold = None, ijk_step_size_min = 0.01, # Grid index units ijk_step_size_max = 0.5, # Grid index units max_steps = 100, optimize_translation = True, optimize_rotation = True): # Files have to have file suffix indicating volume format. from VolumeData import open_file data1 = open_file(map1_path) data2 = open_file(map2_path) from VolumeViewer import Data_Region, full_region, Rendering_Options ro = Rendering_Options() map1 = Data_Region(data1, full_region(data1.size), '', ro) map2 = Data_Region(data2, full_region(data2.size), '', ro) if initial_map1_transform: from PDBmatrices.matrices import chimera_xform xf = chimera_xform(initial_map1_transform) map1.surface_model().openState.globalXform(xf) use_threshold = (map1_threshold != None) from FitMap import map_points_and_weights, motion_to_maximum points, point_weights = map_points_and_weights(map1, use_threshold) if len(points) == 0: if use_threshold: print 'No grid points above map threshold.' else: print 'Map has no non-zero values.' return move_tf, stats = motion_to_maximum(points, point_weights, map2, max_steps, ijk_step_size_min, ijk_step_size_max, optimize_translation, optimize_rotation) if initial_map1_transform: from PDBmatrices.matrices import multiply_matrices move_tf = multiply_matrices(move_tf, initial_map1_transform) header = ('\nFit map %s in map %s using %d points\n' % (map1.full_name(), map2.full_name(), stats['points']) + ' correlation = %.4g, overlap = %.4g\n' % (stats['correlation'], stats['overlap']) + ' steps = %d, shift = %.3g, angle = %.3g degrees\n' % (stats['steps'], stats['shift'], stats['angle'])) print header from FitMap.gui import transformation_description tfs = transformation_description(move_tf) print tfs # ----------------------------------------------------------------------------- # Example call fitting map into itself. # p1 = p2 = '/usr/local/src/chimera-demos/volume/examples/groel.mrc' fit_map_in_map(p1, p2)

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Electrostatical surface of a virus
by Eduardo Sanz-Garcia 23 May '07

23 May '07

I need to visualize the electrostatic surface of a virus. I don't know how to do it. I was thinking in the following sequence of instructions: 1. Use the DelPhiController to generate the potential map (*.phi) for the asymmetric unit. 2. Use Multiscale Models tool to generate the 60-related units. Is this a logic sequence ? Any hint would be appreciated. Thank you.

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Mac stereo
by Greg Couch 23 May '07

23 May '07

To deal with the issue that the Mac OS X's X11 doesn't work with stereo very well, we have decided to release an Aqua version of chimera concurrent with production releases of the X11 version. The Aqua version will be labeled as a snapshot because we still recommend using the X11 version (the user interface works much better than the Aqua version). But if you need stereo, multisampling (full window antialiasing), or background transparency/opacity, then you need to use the Aqua version. Greg Couch UCSF Computer Graphics Lab

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Re: [Chimera-users] Virus Images for the MSD Database
by Tom Goddard 23 May '07

23 May '07

Hi Jawahar, Unfortunately Chimera is not able to save images without displaying the graphical user interface. The image saving code grabs the image directly from the main window OpenGL graphics buffer, so it also will not work if the main window is covered or iconified. Greg Couch once made a special version of Chimera for Linux using the OSMesa graphics library that could do all the graphics off-screen including saving images. But I don't see that version in the Chimera download archive, and I believe it was made more than a year ago. We recently added raytraced image capture using POVray. Since that does not use the OpenGL graphics it should be able to work in nogui mode but a Chimera bug report indicates that does not work http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=3678&database=chime… and is expected to be difficult to fix. Unfortunately the only option at this time is to have the Chimera window appear to save an image. Tom Jawahar Swaminathan wrote: > Dear Tom, > We are interested in making virus capsid pictures for the MSD Database > atlas pages using chimera. For this purpose, I was recently provided > with a script from Cathy Lawson (RCSB) which makes really pretty > images of viral capsids. I attach the script given by Cathy below. > > However, since we would want to run chimera in an automatic manner > (ideally with the --nogui) option, I've been trying to run the script > with --nogui and this appears to conflict with the module tkgui which > is called in the program. > > So my question: is it possible to make images without necessarily > opening up a GUI ? > > I would be really grateful if you could clear this us.. > > best regards, > > Jawahar Swaminathan > PDB Depositions > Macromolecular Structure Database > EBI

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Problem with DCD not containing periodic box info when I use MD
by Antoine Daina 22 May '07

22 May '07

Hi Eric, I got a "DCD format error 9" returned by MD Movie in Chimera 1.2304 when trying to see the trajectory of a Charmm simulation without periodic box info. Can we easily fix it ? Antoine Daina, PhD, University of Geneva.

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Tips for making density map images.
by Thomas Goddard 21 May '07

21 May '07

Here are some suggestions for making density map images in Chimera 1.2382. White background color. Set with two menu entries Actions/Color/Background and Actions/Color/White. To make white the default use Favorites/Preferences, category Background, set background color button to white and press Preferences dialog Save button. Surface smoothing. Use volume dialog Features/Surface-And-Mesh-Options and click "Surface smoothing..." checkbutton. To make this the default, turn it on then use Features/Save-default-dialog-settings. Close the surface-and-mesh-options panel before saving the settings or it will always be shown taking up alot of space. Image supersampling. Removes saw-tooth edges from saved images that are especially visible with white background. Does this by making a larger image in memory then averaging down to a smaller size. When saving an image you see many small pieces flash by in main window if supersampling is being used. To turn it on use File/Save-image, press the Image Setup button in the save image dialog, then set Supersample to 3x3 in the preferences dialog that appears. Press the Save button in the preferences dialog to make this the default. For Chimera versions after 1.2392 this will look different. Supersample will be an option on the save image dialog. Saving image same size as on screen. To make a saved image the same size in pixels as it appears in the Chimera window press the Get Pixels button in the File/Save-image dialog. In Chimera versions after 1.2392 this will be the default. Silhouette edges. To add black edges around maps that makes it easier to see when part of map is in front of another part use Favorites/Side-view, choose the Effects tab in the viewing dialog that appears, click on silhouette edges. Save raytraced image. Gives glossy appearance and shadows. Use File/Save-image and set "Raytrace with POV-Ray" to True. Make back parts of surface darker. Use Favorites/Side-view and move the right vertical yellow line towards the left. The surface gets dimmer from half way between the yellow lines to the right yellow line. Your eye position in this side view is shown as the square at the left and the red lines indicate how wide your field of view is. If you move the right yellow line (rear clipping plane) it will hide parts of the map -- everything to its right is invisible. Probably want to avoid that. Make recesses in surfaces darker to improve sense of depth. Use Tools/Volume-data/Surface-color. For spherical virus color the surface using "Radius", use 2 colors, Gray pattern, press "Set full range colormap values" to get minimum and maximum surface radius, press Color. You may need to press the Center button if the virus map is not centered at (0,0,0), and also press the "Set full range..." button again in that case. Probably you'll want to modify the minimum and maximum radius to get the best effect, also maybe adjust the two colors. For filaments use "Cylinder radius". Make recesses darker for asymmetric maps. This is a bit trickier than for spherical or cylindrical maps. For ribosomes or other asymmetric maps first create a blurred version of the map using Tools/Volume-data/Gaussian-filter. This tool has to be downloaded separately from the Chimera experimental features web page http://www.cgl.ucsf.edu/chimera/experimental/experimental.html and installed. Choose a gaussian width of about 1/3 the diameter of the surface (in angstroms, maybe 30 for a ribosome) and press Filter. Use the Tools/Volume-data/Surface-color and color the original map using the gaussian smoothed map. High values of the Gaussian smoothed map are in the interior and should be made a dark color. This makes the perception of depth dramatically better. Tom

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