- 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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Re: [Chimera-users] [chimera-dev] Protein to ligand shortest distances?
by Elaine Meng 21 May '07

21 May '07

Hi Kate, The Find Clashes/Contacts tool will report all atoms near your ligand and the corresponding distances. However, it does not work with a single strict cutoff, but instead uses the atoms' VDW radii. For example, if you used a cutoff of 0.0 overlap, that would find all atoms with VDW surfaces either intersecting or just touching. It finds all the atoms meeting your specified cutoff criteria, so you would still need to look at the list of results to see which atom is the closest from each residue. There are two cutoff parameters, the amount of VDW overlap and the extra closeness allowed for H-bonding pairs. As mentioned in the manual page, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/ findclash.html the suggested values for these two parameters are: 0.4-1.0 and 0.2-0.6, respectively, if you only want to detect "clashes" (unfavorably close contacts) -0.4-1.0 (negative values) and 0.0, respectively, to detect contacts in general It sounds like you want the latter. Select your ligand (for example by Ctrl-click on one atom and then hitting the keyboard up arrow), open the tool (Tools... Structure Analysis... Find Clashes/Contacts), click "Designate" to specify you want to find contacts of the selected atoms (the ligand) versus all other atoms. Set the parameters to -0.5 and 0.0. In the bottom section check "Write information to reply log" and uncheck the other options. Open the reply log (it's in the Favorites menu). Click Apply and the list of results will be written in the Reply Log window. You could play around with the VDW overlap parameter and when you think you have what you want, you could use the "Write information to file" instead of the reply log. As I mentioned above, you would still have to look through the results to see the closest atom from each residue. The more negative the parameter, the more atoms will be found (including those which are further away from the ligand). There is also a command version of this tool, http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html If you really care that you include all residues with any atom within 5 angstroms, you could do an additional step first: select the ligand, then Select... Zone using 5 angstroms, then use Actions... Write List to save the names of the "selected residues" to a file. You can compare this list to the more detailed results from Find Clashes/Contacts to find the closest atom from each of the residues. I hope this helps, Elaine p.s. I'm sending this to chimera-users too because that is more for user questions, while chimera-dev is more for developer/programmer questions ----- 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 May 20, 2007, at 10:12 PM, khar6039(a)mail.usyd.edu.au wrote: > Hi all, > I'm new to chimera and would like a simple way to zone 5 Angstroms > around a > ligand and then have chimera tell me what the shortest distances are > between these residues and the ligand. Is this possible? > Cheers, > Kate

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Multiple stucture comparision
by Pankaj Barah 19 May '07

19 May '07

Dear all, I have been using UCSF Chimera for structural superpositions for last few days. But while trying to do multiple superimposition for a set of proteins, i am unable to perform it. can anybody give me any suggestion? Regards Pankaj Barah Junior Research Fellow, Phone:+91-9922346120(M) Bioinformatics Centre, +91-20-25692039(O) University of Pune, Pune 411 007,Maharashtra, India. Pankaj Borah MSc Bioinformatics Univ of Madras(HCAS) Mobile number: 09884270481(Chennai)/ 09844514157(B'lore) Home number:(03752)259201 Alt. Mail id: pankajborah(a)gmail.com Group homepage: http://groups.yahoo.com/group/bioinformatrix/ --------------------------------- Office firewalls, cyber cafes, college labs, don't allow you to download CHAT? Here's a solution!

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Pub3D database URL
by Elaine Meng 18 May '07

18 May '07

Hi everybody, In a previous message I mentioned Pub3D as a useful source of 3D coordinates (SDF files) for many PubChem entries. The URL for that server is now http://www.chembiogrid.org/cheminfo/p3d Enjoy! 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: > From: Rajarshi Guha <rguha(a)indiana.edu> > Date: May 17, 2007 4:44:53 PM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: Pub3D SDFs > >> I noticed that your Pub3D site has not been reachable for a while. >> ( http://rguha.ath.cx/~rguha/p3d/ ) > > Aah! My Apache redirect failed again :( > > Actually, we have a new URL for it which should be constant (and is > independent of my machine) > > http://www.chembiogrid.org/cheminfo/p3d > > ------------------------------------------------------------------- > Rajarshi Guha <rguha(a)indiana.edu> > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > -------------------------------------------------------------------

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mac stereo
by Dougherty, Matthew T. 14 May '07

14 May '07

what is the status of mac quadro fx4500 stereographics on chimera? thanks, matt Matthew Dougherty *** 713-433-3849 *** National Center for Macromolecular Imaging***

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benchmark
by Dougherty, Matthew T. 14 May '07

14 May '07

nvidia quadro fx 4500 macpro Dual-Core Intel Xeon clock 2.66 GHz macos 10.4.9 pci express date 5/11/7 chimera 2382 graphics memory 512 MB main memory 2GB unknown apple graphics driver Molecule (Atoms): Null Wire Stick BStick Ribbon Sphere Ops 1GCN (246): 4439.0 4263.0 827.0 828.0 4344.0 1201.0 11755.0 1YTI (798): 4285.0 4034.0 307.0 307.0 4119.0 475.0 3562.0 2GBP (2575): 3384.0 3217.0 103.0 102.0 3139.0 166.0 1063.0 1GOT (6449): 1833.0 1602.0 41.0 41.0 1702.0 67.0 395.0 2HMG (12189): 461.0 478.0 22.0 21.0 489.0 35.0 143.0 2PDA (18894): 271.0 293.0 14.0 14.0 297.0 22.0 76.0 1YNJ (24369): 211.0 230.0 11.0 11.0 232.0 18.0 56.0 1F4H (33805): 154.0 166.0 8.0 8.0 169.0 13.0 38.0 Matthew Dougherty *** 713-433-3849 *** National Center for Macromolecular Imaging***

2 1

Normal Modes, arrows and more...
by Jean-Didier Marechal 14 May '07

14 May '07

Dear All, I am trying to use chimera to draw arrows of the Normal Modes vectors I previously calculated with charmm. I see different possibilities to provide chimera with the vectors, but how can I draw the arrows? I found a request on the list from Mingfeng Yang that Petter answered in october 2004 regarding a similar problem. Unfortunately the link indicated for VRML does not work anymore. What are the actual features of chimera that would allow me to do something like this ? All the best, JD -- Dr. Jean-Didier Maréchal Professor Assistant Physical-Chemistry Unit Department of Chemistry University Autonomous of Barcelona 08193 Bellaterra, Spain Tel: (+34).93.581.49.36 Fax: (+34).93.581.29.20 e-mail: jeandidier.marechal(a)uab.es

2 1

Re: [Chimera-users] imod model viewing
by Tom Goddard 11 May '07

11 May '07

Hi David, The Chimera IMOD model file reader only handles the meshes in the file. My guess is that the file you made does not contain meshes. Maybe it only has contour lines for the spheres. Or maybe the file format can contain geometric primitives like spheres without contour lines or meshes being specified. I don't know enough about IMOD to be sure. Tom David G. Morgan wrote: > Tom, > > I was trying to use the new IMOD file reader and must be doing something > foolish. I downloaded the newest chimera snapshot release (1.2392) and > the imod.zip file and made a new installation. I can load my IMOD > volume into chimera without any trouble. I then "opened" the IMOD model > file (it opened as an "IMOD segmentation" type). That works without > trouble, but I don't ever see the model. Even trying to use "focus" to > bring it into the field of view gives me a blank field. > > It's possible that my model is the wrong type - I'm playing with chimera > in preparation for needing to do something fancy, so I simply created a > set of spheres of different colors and different radii in IMOD, saved > that model and tried to read it into chimera. I thought I'd simply be > able to read this into chimera and see a couple of spheres, but I don't. > I'm sure I'm doing something silly, but figured I'd bother you while I > play around with it. > > David Gene Morgan > University of California at Davis >

3 6

Question about background transparency
by Vanacore, Roberto M 09 May '07

09 May '07

What are the system requirements to run -bgopacity option in a windows machine? I've tried adding to option (--bgopacity) to the startup command but I can not get a transparent background I'm using Chimera 2.2199 Thanks! Roberto Roberto Vanacore, PhD B-3101 Medical Center North Vanderbilt University Medical Center 1161 Twenty-first Ave South Nashville, TN 37232-2372 Phone: 615-322-7306 Fax: 615-322-7381

2 1

contour levels in Morph Map
by Gabor Papai 09 May '07

09 May '07

Dear all, Is it possible with the Morph Map tool to set the contour levels of the two maps differently? For e.g. if I would like to morph between a map, which is obtained from single particle analysis and has the right contour level of 0.2 - and a second map, which is obtained from tomography and has the right contour level of 2.2, it gives weird result. Other question: does somebody consider to make chimera able to read Imagic files? Thanks for the help! Regards, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748 Fax +33-3-88653201 E-mail: papai(a)igbmc.u-strasbg.fr

2 1

chain selection in a multi-conformatin pdb file.
by Hong Liang 09 May '07

09 May '07

Hi Chimera fans, 1. If a pdb file contains more then one struture, how can I select and keep just one and get rid of the rest. Such as 1X95. It is a big mess after Chimera load the the DNA pdb structure. How can I leave just one double helix? 2. Can Chimera do the extension of DNA. Such as 1X95 has the hexamer with the sequence of ATGCAT, can Chimera double it to a dodecamer with a sequence ATGCATATGCAT? It Chimera can not do that, do you know which software has such a function. I tried PyMol but did not get what I wanted. Thanks a lot. Hong

2 1

Defining a zone around a point defined by x, y, z coordinates
by Jean-Didier Marechal 08 May '07

08 May '07

Dear all, We are having difficulties in defining a certain type of selection zones in chimera. Our problem is that we don't want to centre the zone on an atom selection but on one point of the space defined by its 3D coordinates. Typically we want to give chimera the x,y,z coordinates and select all the atoms included in a sphere of 25 angstroms around this point. How can we do so? Thanks a lot JD -- Dr. Jean-Didier Maréchal Professor Assistant Physical-Chemistry Unit Department of Chemistry University Autonomous of Barcelona 08193 Bellaterra, Spain Tel: (+34).93.581.49.36 Fax: (+34).93.581.29.20 e-mail: jeandidier.marechal(a)uab.es

3 2

Find Hbonds in batch
by Stefan Bienert 08 May '07

08 May '07

Hello Chimera fans! Is there a way to use chimera for finding hydrogen bonds for tons of molecules? I'm thinking of something like a command line script, which loads a pdb file, fetches the hbonds and writes them to a file. I got around 1000 pdb files and therefore doing everything manually is not an option ;-) greetings, Stefan -- Stefan Bienert Zentrum fuer Bioinformatik Universitaet Hamburg Bundesstrasse 43 20146 Hamburg Germany Email: bienert(a)zbh.uni-hamburg.de Phone: +49 (40) 42838 7345 Fax: +49 (40) 42838 7332

2 3

importing sdf files from PubChem
by Mark Andrake 07 May '07

07 May '07

Hey Folks, It is a relatively new feature to be able to read SDF compound structure files in Chimera. (I have release 2350 for Windows - I will be upgrading to the new snapshot that I just saw while looking around the site) Anyway - I tried with a compound sdf file that I got from PubChem (enclosed) - but seemed to have problems. At first it gave an error shown in the first lines below - and then seemed to say that it opened the files - but no atoms were displayed and no new model ID was generated and put into the Model Panel . Opening C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf Error reading C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf: Unexpected end of file (parser state: post header 1) in MOL/SDF file 'C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf' Done opening C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf Opening C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf Error reading C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf: Unexpected end of file (parser state: post header 1) in MOL/SDF file 'C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf' Done opening C:\Documents and Settings\andrake\My Documents\WORK f\PDBs\Cy3_CID_16048627.sdf I tried various atom selections and displaying all - but it seems obvious that it has not read in atoms and bonds. I have browsed around the documentation and only found a link to the sdf file formats. (I checked this out and tried editing out two of the header lines - ) It seems the error is unexpected end of file past the header. When checking the sdf file format information it seems that the $$$$ should be the only end of file mark - and there is only one at the end of my file. I also tried the whole procedure with a different sdf file from PubChem. Can anyone recognize what is causing the error in the enclosed file? Beyond that - are there other instructions on sdf file use in chimera that I did not see in searching the documentation? Thanks in advance, Mark -- Mark Andrake, Ph.D. Research Associate Fox Chase Cancer Center ICR428 7701 Burholme Ave. Philadelphia, PA 19111 215-728-3654 mark.andrake(a)fccc.edu 16048627 -OEChem-05040716572D 113118 0 0 0 0 0 0 0999 V2000 3.4030 4.5407 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 11.7288 -2.2663 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 2.5369 5.0407 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9030 5.4067 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9030 3.6746 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.7288 -3.2663 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 10.7288 -2.2663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.7288 -2.2663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1864 -3.2991 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 17.1265 4.0641 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8972 -2.1423 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 16.7693 2.3693 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.6424 -5.4263 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0223 -3.0754 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 18.7407 5.5226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 18.0148 2.0782 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9473 2.7359 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 11.5196 1.7056 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.5185 -4.0434 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 18.1050 3.8579 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.9473 4.3454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.1258 0.9008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5309 3.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.5309 1.8086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0010 4.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.8628 0.2337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0010 3.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.7288 0.7337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7573 4.9318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6399 5.2970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2579 1.7854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4553 0.1588 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.2129 1.3091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1874 2.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5309 3.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0309 2.6746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1350 4.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.8628 -0.7663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5901 1.0411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.1659 2.2436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1350 2.5407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.5948 0.2337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0309 2.6746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2690 4.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.7288 -1.2663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2690 3.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9007 0.0906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.5948 -0.7663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8338 2.9879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2329 -0.6537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.8123 2.7817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5436 -1.6042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.4801 3.5260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8757 -2.3485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.4586 3.3198 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7281 -5.0211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5238 -3.9406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.8470 4.5283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.5133 2.9450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8630 -5.5226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1187 -4.8548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 19.7139 4.0298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 19.5076 3.0513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1208 4.4296 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2595 5.2953 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3937 5.4340 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2299 5.4876 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4493 5.8870 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0499 5.1064 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8048 2.0774 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6405 1.2975 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9953 0.5745 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0397 -0.3012 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9154 -0.2568 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.4661 1.8751 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6470 1.5623 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9598 0.7432 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 11.6611 2.7775 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 12.4187 3.0251 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8409 4.0776 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3409 3.2116 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1350 5.1607 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3258 -1.0763 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0432 0.7491 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2075 1.5290 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 12.9347 1.6684 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 13.6923 1.9160 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1350 1.9207 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 13.1318 0.5437 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7209 2.1377 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7321 2.7307 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2833 -0.3973 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4477 0.3826 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 13.1318 -1.0763 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 14.0650 3.5632 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 13.3074 3.3156 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6860 -0.9457 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8503 -0.1658 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 15.3386 2.4541 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 14.5810 2.2065 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9261 -2.0921 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0905 -1.3122 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 15.7114 4.1013 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 14.9538 3.8537 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 4.7307 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4029 -5.9383 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2283 -6.0236 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5812 -4.5457 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7551 -5.3570 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 19.9651 4.5966 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 20.3038 3.8392 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 20.1244 2.9876 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 19.5087 2.4313 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 0 0 0 1 4 2 0 0 0 0 1 5 2 0 0 0 0 1 44 1 0 0 0 0 2 6 1 0 0 0 0 2 7 2 0 0 0 0 2 8 2 0 0 0 0 2 45 1 0 0 0 0 3105 1 0 0 0 0 9 19 1 0 0 0 0 9 54 1 0 0 0 0 10 20 1 0 0 0 0 10 55 1 0 0 0 0 11 54 2 0 0 0 0 12 55 2 0 0 0 0 13 56 2 0 0 0 0 14 57 2 0 0 0 0 15 58 2 0 0 0 0 16 59 2 0 0 0 0 17 23 2 0 0 0 0 17 27 1 0 0 0 0 17 31 1 0 0 0 0 18 24 1 0 0 0 0 18 28 1 0 0 0 0 18 34 1 0 0 0 0 19 56 1 0 0 0 0 19 57 1 0 0 0 0 20 58 1 0 0 0 0 20 59 1 0 0 0 0 21 23 1 0 0 0 0 21 25 1 0 0 0 0 21 29 1 0 0 0 0 21 30 1 0 0 0 0 22 24 1 0 0 0 0 22 26 1 0 0 0 0 22 32 1 0 0 0 0 22 33 1 0 0 0 0 23 35 1 0 0 0 0 24 36 2 0 0 0 0 25 27 2 0 0 0 0 25 37 1 0 0 0 0 26 28 2 0 0 0 0 26 38 1 0 0 0 0 27 41 1 0 0 0 0 28 42 1 0 0 0 0 29 64 1 0 0 0 0 29 65 1 0 0 0 0 29 66 1 0 0 0 0 30 67 1 0 0 0 0 30 68 1 0 0 0 0 30 69 1 0 0 0 0 31 39 1 0 0 0 0 31 70 1 0 0 0 0 31 71 1 0 0 0 0 32 72 1 0 0 0 0 32 73 1 0 0 0 0 32 74 1 0 0 0 0 33 75 1 0 0 0 0 33 76 1 0 0 0 0 33 77 1 0 0 0 0 34 40 1 0 0 0 0 34 78 1 0 0 0 0 34 79 1 0 0 0 0 35 43 2 0 0 0 0 35 80 1 0 0 0 0 36 43 1 0 0 0 0 36 81 1 0 0 0 0 37 44 2 0 0 0 0 37 82 1 0 0 0 0 38 45 2 0 0 0 0 38 83 1 0 0 0 0 39 47 1 0 0 0 0 39 84 1 0 0 0 0 39 85 1 0 0 0 0 40 49 1 0 0 0 0 40 86 1 0 0 0 0 40 87 1 0 0 0 0 41 46 2 0 0 0 0 41 88 1 0 0 0 0 42 48 2 0 0 0 0 42 89 1 0 0 0 0 43 90 1 0 0 0 0 44 46 1 0 0 0 0 45 48 1 0 0 0 0 46 91 1 0 0 0 0 47 50 1 0 0 0 0 47 92 1 0 0 0 0 47 93 1 0 0 0 0 48 94 1 0 0 0 0 49 51 1 0 0 0 0 49 95 1 0 0 0 0 49 96 1 0 0 0 0 50 52 1 0 0 0 0 50 97 1 0 0 0 0 50 98 1 0 0 0 0 51 53 1 0 0 0 0 51 99 1 0 0 0 0 51100 1 0 0 0 0 52 54 1 0 0 0 0 52101 1 0 0 0 0 52102 1 0 0 0 0 53 55 1 0 0 0 0 53103 1 0 0 0 0 53104 1 0 0 0 0 56 60 1 0 0 0 0 57 61 1 0 0 0 0 58 62 1 0 0 0 0 59 63 1 0 0 0 0 60 61 1 0 0 0 0 60106 1 0 0 0 0 60107 1 0 0 0 0 61108 1 0 0 0 0 61109 1 0 0 0 0 62 63 1 0 0 0 0 62110 1 0 0 0 0 62111 1 0 0 0 0 63112 1 0 0 0 0 63113 1 0 0 0 0 M CHG 2 6 -1 17 1 M END > <PUBCHEM_COMPOUND_CID> 16048627 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR> 15 > <PUBCHEM_CACTVS_HBOND_DONOR> 1 > <PUBCHEM_CACTVS_ROTATABLE_BOND> 19 > <PUBCHEM_CACTVS_SUBSKEYS> AAADcfB/vABgAAAAAAAAAAAAAAAAAWLFiAAwYAAAAAAAAFgBQAAAHgQECAAADgjB2AQyyYMQAIKoAyXyXHDCAEAhAgAoiBk4ZJgIIDLAkZGEIAhkhCDIyAedyMAPgAQAgAACAAAACAEAAAQAAAAAAAAAAA== > <PUBCHEM_IUPAC_OPENEYE_NAME> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indoline-5-sulfonate > <PUBCHEM_IUPAC_CAS_NAME> (2E)-1-[5-[(2,5-dioxopyrrolidin-1-yl)oxy-oxo-methyl]pentyl]-2-[(E)-3-[1-[5-[(2,5-dioxopyrrolidin-1-yl)oxy-oxo-methyl]pentyl]-3,3-dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indoline-5-sulfonate > <PUBCHEM_IUPAC_NAME> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indole-5-sulfonate > <PUBCHEM_IUPAC_SYSTEMATIC_NAME> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indole-5-sulfonate > <PUBCHEM_IUPAC_TRADITIONAL_NAME> (2E)-1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-2-[(E)-3-[1-[5-(2,5-dioxopyrrolidin-1-yl)oxycarbonylpentyl]-3,3-dimethyl-5-sulfo-indol-2-yl]prop-2-enylidene]-3,3-dimethyl-indoline-5-sulfonate > <PUBCHEM_NIST_INCHI> InChI=1/C43H50N4O14S2/c1-42(2)30-26-28(62(54,55)56)16-18-32(30)44(24-9-5-7-14-40(52)60-46-36(48)20-21-37(46)49)34(42)12-11-13-35-43(3,4)31-27-29(63(57,58)59)17-19-33(31)45(35)25-10-6-8-15-41(53)61-47-38(50)22-23-39(47)51/h11-13,16-19,26-27H,5-10,14-15,20-25H2,1-4H3,(H-,54,55,56,57,58,59)/f/h54H > <PUBCHEM_CACTVS_EXACT_MASS> 910.276 > <PUBCHEM_OPENEYE_MF> C43H50N4O14S2 > <PUBCHEM_OPENEYE_MW> 911.008 > <PUBCHEM_OPENEYE_CAN_SMILES> CC1(C2=C(C=CC(=C2)S(=O)(=O)O)[N+](=C1C=CC=C3C(C4=C(N3CCCCCC(=O)ON5C(=O)CCC5=O)C=CC(=C4)S(=O)(=O)[O-])(C)C)CCCCCC(=O)ON6C(=O)CCC6=O)C > <PUBCHEM_OPENEYE_ISO_SMILES> CC1(C2=C(C=CC(=C2)S(=O)(=O)O)[N+](=C1\C=C\C=C\3/C(C4=C(N3CCCCCC(=O)ON5C(=O)CCC5=O)C=CC(=C4)S(=O)(=O)[O-])(C)C)CCCCCC(=O)ON6C(=O)CCC6=O)C > <PUBCHEM_CACTVS_TPSA> 245 > <PUBCHEM_OPENEYE_MONOISOTOPICWT> 910.276 > <PUBCHEM_TOTAL_CHARGE> 0 > <PUBCHEM_HEAVY_ATOM_COUNT> 63 > <PUBCHEM_ATOM_DEF_STEREO_COUNT> 0 > <PUBCHEM_ATOM_UDEF_STEREO_COUNT> 0 > <PUBCHEM_BOND_DEF_STEREO_COUNT> 2 > <PUBCHEM_BOND_UDEF_STEREO_COUNT> 0 > <PUBCHEM_ISOTOPIC_ATOM_COUNT> 0 > <PUBCHEM_COMPONENT_COUNT> 1 > <PUBCHEM_CACTVS_TAUTO_COUNT> 9 > <PUBCHEM_BONDANNOTATIONS> 25 27 8 25 37 8 26 28 8 26 38 8 27 41 8 28 42 8 37 44 8 38 45 8 41 46 8 42 48 8 44 46 8 45 48 8 $$$$

3 2

Suggestion for Metal Geometry Feature
by Walter Fast 07 May '07

07 May '07

Hi Elaine (I think!), I know there is a measure angle feature in Chimera. I have been using this to define metal ligand geometries in our protein structures (for example, distinguishing between square pyramidal and trigonal bypramidal geometries). Maybe if there is enough interest, this could be an automated feature in the future where a metal ion is selected and then all of the ligands and angles are automatically displayed along with an assigned geometry. We've been using the following reference for assigning them. Just a suggestion! Many thanks, Walt -- Walter Fast, Ph.D. Assistant Professor The University of Texas at Austin College of Pharmacy The Division of Medicinal Chemistry Phone: (512) 232-4000 Fax: (512) 232-2606 Lab: (512) 471-5839 Email: WaltFast(a)mail.utexas.edu http://www.utexas.edu/pharmacy/divisions/medicinalchem/faculty/fast.html

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Re: [Chimera-users] importing sdf files from PubChem
by Elaine Meng 05 May '07

05 May '07

Hi Mark, You're welcome! I tried getting an SDF directly from PubChem, and that caused the same error you sent, again fixed by cutting and pasting the contents into another SDF file. Cutting/pasting (or otherwise getting rid of bad invisible characters) is the way to go for SDFs from PubChem, at least for now. We may take a look at those files (although I doubt there is a high demand for viewing 2D structures in Chimera!). 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 On May 5, 2007, at 7:32 AM, Mark Andrake wrote: > Elaine, > > Thanks so much for your fast reply. > I can see from the users group that you guys do such a great job in > responding to user questions and concerns. > > After a quick gaze and trying on my laptop chimera at home - > it looks like there must be a hidden character issue. > I also had tried MS Word and saved it as a txt file > (in case there was some problem in the browser creating the file) > but maybe MS Word does not flatten out the file with just ASCI > characters. > > Next time I will try cutting and pasting through something like > WordPad first. > > In any case your test.sdf opened fine in my laptop chimera. > Thanks so much - have a great weekend! > > Mark > > Mark Andrake, Ph.D. > Research Associate > > Fox Chase Cancer Center > ICR428 > 7701 Burholme Ave. > Philadelphia, PA 19111 > 215-728-3654 > mark.andrake(a)fccc.edu > > > Elaine Meng wrote:Hi Mark, >> I've attached the test.sdf file mentioned in my previous message. >> 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 >> >> >>

1 0

selecting a unique ligand structure from multiple copy
by Jean-Didier Marechal 03 May '07

03 May '07

Hi everyone, I am working with different protein structures that have at least two copies of the ligand in their binding site. How could I select only one of them? (I'd like a selection specification that does not require the atom numbers if possible). Cheers JD -- Dr. Jean-Didier Maréchal Professor Assistant Physical-Chemistry Unit Department of Chemistry University Autonomous of Barcelona 08193 Bellaterra, Spain Tel: (+34).93.581.49.36 Fax: (+34).93.581.29.20 e-mail: jeandidier.marechal(a)uab.es

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wwPDB Announcement: Release of Remediated PDB Data
by Cathy Lawson 03 May '07

03 May '07

***wwPDB Announcement: Release of Remediated PDB Data*** The wwPDB has collaborated on a project to remediate the PDB archive and create a new set of corrected files. The entire archive has been reviewed and remediated with the objectives of improving the detailed chemical description of non- polymer and monomer chemical components; standardizing atom nomenclature; updating sequence database references and taxonomies; resolving any remaining differences between chemical and macromolecular sequences; improving the representation of viruses; and verifying primary citation assignments. In addition, the atom nomenclature for amino acids and nucleotides now conforms with IUPAC standards. A new FTP server containing the remediated data has been set up for testing. The access details for this site are provided at http:// www.wwpdb.org/remediation-downloads.html. The new ftp site will be updated weekly in concert with the current production site at ftp:// ftp.rcsb.org. Both sites share the same directory structure. Starting May 1, the remediated data will be served using gzip compression. Your input is very important to us. PDB users are encouraged to test the remediated data files between now and July 2007. The details of the final transition will be announced on the wwPDB website (http:// www.wwpdb.org) Detailed information about the wwPDB remediation project can be found at http://remediation.wwpdb.org. Comments about the files should be sent to info(a)wwpdb.org. Major announcements will be made at the wwPDB website (http:// www.wwpdb.org) as well as on the individual member websites.

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Ligand structure minimization
by Jean-Didier Marechal 02 May '07

02 May '07

Dear all, I don't know whether my problem falls in "bug" or "user request" category, pcorry if I use the wrong list. I am preparing a course where students will perform some protein-ligand dockings. I was thinking in minimizing the ligand in chimera using the "minimize structure" tool. I have installed the 1.2356 (that's what I thought but the message in the "About UCSF Chimera" pop up window says 1.2376 actually) version of chimera on ubuntu 6.10 and when I try to minimize my ligand (a HIV protease inhibitor), I am stopped at the PARMCHK run. Chimera seems to have compatibility problems with numpy. I join here the message given in the reply log file: .... Charges for residue U0E determined Total charge for #0: 1.0000 Running PARMCHK for U0E1.pdb command: /usr/local/chimera/bin/antechamber/exe/parmchk -i /tmp/tmpc6R8F8/parmchk.in.0 -f mol2 -o /tmp/tmpc6R8F8/frcmod.0 -p /usr/local/chimera/share/MMMD/parm/gaff.dat Finished PARMCHK for U0E1.pdbThis version of Chimera uses numpy for calculations. Numeric is only available in Chimera 1.2318 and earlier. Is there an easy way to move around this problem or should I install a earlier version of chimera for the moment? cheers, JD

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How does chimera invoke msms?
by aladdin 30 Apr '07

30 Apr '07

I need to know the solvent accessible surface of a protein, that means the info of solvent accessibility of residues or atoms . If I directly run "msms" with "-af" option, I can get an .area file in which stored such information. But in chimera's surface model, I cannot find what I need. How can I get the solvent accessible info in chimera? Thanks. liren --------------------------------------------

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Re: [Chimera-users] mutating amino acid side chain_deleting single atom
by Gary Laco 24 Apr '07

24 Apr '07

Hi, How can I mutate an amino acid side chain in a protein to another residue using Chimera? Also, how do I delete a single atom on an amino acid (for example a hydrogen). I looked through all the tools and did not find a way to do it. Thanks, Gary Gary S. Laco, Ph.D. Assistant Professor of Biochemistry Lake Erie College of Osteopathic Medicine-Bradenton 5000 Lakewood Ranch Blvd. Bradenton, FL 34211 Office: 941-782-5666 Fax: 941-782-5729 E-mail: <mailto:glaco@lecom.edu> glaco(a)lecom.edu

2 1

movie and 'side view'
by jean-francois menetret 23 Apr '07

23 Apr '07

Is it possible to include the 'side view' during movie recording ? 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

2 1

Secondary Structure Editing
by anat＠chem.ch.huji.ac.il 23 Apr '07

23 Apr '07

Hi, I would like to know if it's possible to edit (manually) the secondary structure attribute of single amino acid in the computed sequence given by Chimera (e.g. from strand to helix). Thank you for your help, Anat, the Hebrew university of Jerusalem. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Re: [Chimera-users] Chimera-users Digest, Vol 48, Issue 17
by Puey Ounjai 21 Apr '07

21 Apr '07

Dear all; I am wondering can we manually assign secondary structure to each residues in the PDB file in chimera? Thanks Puey

2 1

Chimera crash
by hsosa＠aecom.yu.edu 20 Apr '07

20 Apr '07

Hi, I'm having problems later with chimera. Sometimes when rotating molecules or volumes the whole computer freezes for a while. Sometimes recover and will freeze again after a few more molecule movements. Sometimes the whole system crash with blue screen and reboot. It seems like a new problem as I've bee using chimera for a while and it didn't' happen before. As far as I know everything is the same in the computer. I'm running the latest snapshot release of chimera but that doesn't seem to be the problem. I deinstalled this version and installed the latest production release and got the same problem. Any ideas what the problem may be ?. Thanks Hernando System details UCSF chimera version 1.2382 (or 1.2304) OS: Windows XP service pack-2 Computer: Dell Precision 530 with Dual Xeon 1.4 GHZ processors and 1 GB RAM Graphic Card: NVDIA Quadro 900 XGL Video BIOS version 4.25.00.27.05 ForceWare version 91.36 -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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Transform Molecule Coordinates
by rkhayat＠scripps.edu 19 Apr '07

19 Apr '07

Hi, I was wondering if there is a stand alone version of the "Transform Molecule Coordinates" Chimera extension available. Alternatively, how will I be able to use this feature outside of Chimera? Thanks. Reza

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Re: [Chimera-users] rotating maps in chimera
by Tom Goddard 19 Apr '07

19 Apr '07

Hi Preethi, Here's what caused the misalignment when you opened "subtracted map 2", let's call that one map 3, into Chimera where the original map 2 and reoriented map 1 were already opened. When you open map 3 Chimera needed to give it an initial transformation. Maps 1 and 2 had different transforms. Chimera chooses the transform of the map with the lowest id number (shown in Model Panel, menu entry Favorites / Model Panel). Map 1 must have had the lowest id number, so it got the transform of map 1 instead of the transform of map 2. Chimera had no way of knowing that map 3 was just a modified version of map 2. When you open data in Chimera it assigns an id number to it (shown in Model Panel). The id number is 0 for the first opened data set, then 1 for the next, .... In general it assigns the lowest available id number when a new data set is opened. When restoring Chimera sessions maps get their original model id numbers in Chimera versions 1.2354 and later, but are assigned new model id numbers in older versions. Since the data sets with lowest id number determines the transform of all newly opened models it is best to think of that data set as defining the reference frame. You can use the Model Panel / Transform As... button to correct the transform of a newly opened model. In the case you described you would need to transform map 3 as map 2 to fix the misalignment. This is probably easier than editing a session file. Tom preethi(a)bu.edu wrote: > Hi Tom, > > Chris I think had already discussed with you about how we transform > the PDB files that were originally fit into a brix map so that it now > fits into an MRC file in chimera. > > I am just repeating that here because I came across a problem when I > did this. > > I saved a session in chimera where I had rotated a MRC map say map 1 > w.r.t another MRC map 2 and then used the "fit map into map" feature > to align map 1 into map 2.So I saved the session(which would save the > transformation matrix) and then used the matrix to move certain PDB > files(using "transform as"). > > Now I did some zoning and volume erasing on map 2(the unrotated map) > and then saved the resulting map and then with another program outside > chimera subtracted the zoned out volume from the whole volume of map 2. > > SO when I read in the subtracted file into chimera it is now rotated > w.r.t the map 2 instead of being read with the original matrix that > was used for map2. I fixed this problem by going into chimera session > file and maunally changing the rotation and translation values for > this map to match that of map2. > > Also, if I opened chimera afresh and didnt restore the session where I > had done all the transformations but just opened map 2 and the > subtracted map then it reads them correctly without displacing one map > w.r.t the other. > > So I was just wondering why chimera automatically rotates the > subsequent MRC files that are read into a session where a > transformation was applied to some files only ? > > -Preethi > > > > > >

1 0

rotating 2 models side-by-side
by jean-francois menetret 19 Apr '07

19 Apr '07

How can I make two models rotate side-by-side around their respective centers using chimera ? 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

2 1

Re: [Chimera-users] Proper display of oligosaccharide
by Greg Couch 18 Apr '07

18 Apr '07

To followup, I just tried the first Human milk saccarides example on the Sweet webside, 2'-Fucosyllactose, and the PDB file it generates doesn't display at all because of the non-standard data in columns 67-72. We have decided that we're being too strict in this case and will change chimera. In the iterim, if you're on a UNIX system (Linux, Mac OS X, etc.), you can truncate the lines with the following: awk '{if (/^ATOM/) print substr($0, 1, 67); else print $0}' < original > fixed with appropriate filename replacements for original and fixed. Greg Couch UCSF Computer Graphics Lab

1 0

Proper display of oligosaccharide
by R. Andrew Byrd 18 Apr '07

18 Apr '07

We study protein:carbohydrate interactions, and we use chimera for protein displays. We have a model built for an oligosaccharide using the SWEET server at http://www.dkfz-heidelberg.de/spec/sweet2/doc/index.php The file is in pdb format, but it has neither amino acid residue names nor nucleotide names. Hence, the molecule is invisible in Chimera. How could we make this a recognizable molecule so that we can examine various visualizations and modeling efforts using Chimera? Thanks! Andy P.S. I can send the file if you want.

3 2

using different scale for 2 models
by jean-francois menetret 17 Apr '07

17 Apr '07

Is it possible to vary the scale of one model in respect to another during a movie ? 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

2 1

Re: [Chimera-users] Rotate or rock commands for making movie?
by Elaine Meng 17 Apr '07

17 Apr '07

On Apr 17, 2007, at 2:14 PM, Walter wrote: > Hi Elaine, > > I would like to make a movie using CHIMERA, but can only figure out > how to > rotate the molecule by hand and it ends up looking sloppy. Are there > command line entries for smoothly rotating or rocking a molecule? > > Thanks for your help! > > Walt Hi Walter, Sounds like you are looking for the "roll" command. http://www.cgl.ucsf.edu/chimera/1.2376/docs/UsersGuide/midas/roll.html This page lists commands especially useful for scripting movies, and links to a few example command files: http://www.cgl.ucsf.edu/chimera/1.2376/docs/UsersGuide/movies.html 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

1 0

Help with installing DMS and Chimera
by Ben Keshet 17 Apr '07

17 Apr '07

Hello everybody, I am a very inexperienced new user of Linux / cygwin and having problems in installing DMS and Chimera: 1. I am trying to install DMS but having problems with specifying correctly the pathway to the appropriate locations of the BINDIR and LIBDIR directories in the GNUmakefile. I am getting a message: "Cannot create directory. not such file or directory". I have tried it both on Linux enterprise 4 and on Windows using cygwin. My pathway includes spaces, i.e: /cygdrive/c/Documents and Settings/User Name/Desktop/dms/bin Can anyone please tell me how exactly I should enter the pathway (I think the spaces cause the problem but not sure)? 2. I am having problems running the chimera-installer.exe. file of Chimera on Linux. When I double-clicked on it, it tells me that I cannot execute the file, so as suggested in the instructions (http://www.cgl.ucsf.edu/chimera/1.2304/linux.html) I typed chmod +x 'filename' . When I checked the properties of the file after chmod, the box of 'execute' was checked (so I believe that I really changed the file's permissions). However, I am still getting the same error message when I double-click it. Does anyone know what am I doing wrong? Please consider my lack of experience in UNIX terminology if you try to answer one of my questions, Thanks a lot, Ben

2 1

switching object on/off at the command line
by jean-francois menetret 16 Apr '07

16 Apr '07

Is it possible to switch a model on/off from the command line ? "objdisplay #model / ~objdisplay #model" sound promissing but it doesn't work ... 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

2 2

gromacs trajectory - only atoms, no bonds
by Moo Cow 16 Apr '07

16 Apr '07

I believe one has to have a very recent chimera in order to be able to read gromacs trajectories. I have "beta version 1 build 2376 2007/04/11 It is terrific that chimera can read the trajectories (without problem), but it then does not seem to join the atoms with bonds (it certainly does so for normal pdb files). My trajectory is displayed as a set of lonely unbonded atoms. I believe I checked for obvious mistakes on my part. I went to the tutorial, found the lines repr stick and so on. They gave no error message, but did not help. Many thanks for any advice. = Search for products and services at: http://search.mail.com

2 1

Re: [Chimera-users] Ribosomal RNA depiction
by Tom Goddard 13 Apr '07

13 Apr '07

Hi Dave, The RNA display using surfaces for each base could be done easily in a Python script, but not with Chimera commands since those are not available for multiscale. The result could be exported to POV-ray, or since Chimera now includes POV-ray the raytraced image can be directly produced in Chimera. I still think that a fat tubular ribbon with a single base atom shown as sphere gives a cleaner coarse view of RNA that indicates base orientations. Here's a ribbon and sphere image, also a ribbon with surface bases, also an image with bases with NDB colors. http://www.cgl.ucsf.edu/home/goddard/temp/1s72-rna/1s72.html Tom David Konerding wrote: > > > On 4/12/07, *Thomas Goddard* <goddard(a)cgl.ucsf.edu > <mailto:goddard@cgl.ucsf.edu>> wrote: > > Hi Jean-Francois, > > Here are some tips for showing coarse RNA depictions. > > I too had lots of different colors for the ribosome rna bases using > the nucleic acid blobs tool but I changed them. Here was my > procedure. > > 1. open 1s72 > 2. select chain 0 (menu Select / Chain / 0) > 3. invert selection to select all proteins (menu Select / Invert) > 4. delete all the proteins (menu Actions / Atoms+Bonds / Delete > 5. open reschains.py > 6. open multiscale (menu Tools / Higher-order Structure / > Multiscale Models) > 7. select multiscale multimer type None and press Make models. > 8. press multiscale select All button, change resolution to 2, press > Resurface > 9. ctrl-click on backbone to select it > 10. invert selection (menu Select / Invert) > 11. click multiscale color button and set color of all bases > > > Tom- > > This looks nice. I don't have a lot of time to look into the > implementation right now, > but can steps 6-11 be done programmatically easily? > > Will the resulting images export to povray? > > Dave > >

1 2

questions using chimera
by Xiaoyun Chen 12 Apr '07

12 Apr '07

I have two questions: 1) Is there a way for chimera to display the x-y-z axes? For example, for a pdb file, all the x/y/z coordinates are referenced to the molecular coordinate system. In the chimera screen, we can rotate the molecules. I want to know the orientation of the molecular coordinate system in the laboratory/chimera coordinate system, but cannot find a way for the x/y/z to show up on the screen. Many other protein visualization software (VMD, Molw, etc) have this feature. 2) by default, the z coordinate point out from the screen. often i would like to see the protein with its z direction in the plane of the screen and pointing up. tools-viewing controls-side view allow me to get what i want, but the image is only the protein projected onto the y-z plane. but it would be nice if there are two side view panels, one with an image in the y-z plane, one with an image in the x-z plane. Thank you! Xiaoyun Chen

3 2

Ribosomal RNA depiction
by Thomas Goddard 12 Apr '07

12 Apr '07

Hi Jean-Francois, Here are some tips for showing coarse RNA depictions. I too had lots of different colors for the ribosome rna bases using the nucleic acid blobs tool but I changed them. Here was my procedure. 1. open 1s72 2. select chain 0 (menu Select / Chain / 0) 3. invert selection to select all proteins (menu Select / Invert) 4. delete all the proteins (menu Actions / Atoms+Bonds / Delete 5. open reschains.py 6. open multiscale (menu Tools / Higher-order Structure / Multiscale Models) 7. select multiscale multimer type None and press Make models. 8. press multiscale select All button, change resolution to 2, press Resurface 9. ctrl-click on backbone to select it 10. invert selection (menu Select / Invert) 11. click multiscale color button and set color of all bases http://www.cgl.ucsf.edu/home/goddard/temp/1s72-rna.png Nicer simplified depictions can be made using ribbons with a single side chain atom as a sphere. The ribbon style editor (Tools / Depictions / Ribbon Style Editor) can fatten up the ribbon. Or for fancier bases shown as slabs use the Nucleotides tool (Tools / Depiction / Nucleotides), for example, http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/stmvrna/1a34.png Tom jean-francois menetret wrote: > > Hi Tom, > > the new reschains.py works well; but how did you specify the color > scheme in 1s72_rna.png using "multiscalemodel" option ? I am getting so > many different colours (see attached jpeg) > > Jean-François Ménétret, PhD > Boston University School of Medicine

1 1

exporting ".pov" session
by Tom Goddard 12 Apr '07

12 Apr '07

Jean-Francois asks about what is exported to POV-ray. jean-francois menetret wrote: > > Hi Thomas, > > I have a question about saving ".pov" session > > Items of the chimera window that are not shown at the time of the > export command are saved in the povray scene. > Is that normal ? How can I save one object at a time ? > > Jean-Francois

3 3

Suggestion on biological assembly load
by Miguel Ortiz-Lombardia 11 Apr '07

11 Apr '07

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, I have small suggestion to make that I would find helpful if implemented in chimera: I think it would be great if the "biological assembly" could be fetched by ID from the File menu, just as it goes now for the pdb coordinates file from the RCSB site. Such assemblies are kept at the PQS database at the EBI (Cambridge). The links there follow this syntax: http://pqs.ebi.ac.uk/pqs-doc/macmol/<ID>.mmol where <ID> is obviously that of the PDB structure. Despite the extension, it is a plain PDB file. The CRYST1 record (for crystallographic structures) of such coordinates files has been modified to space group P1, since the crystallographic operations of the original structure don't hold. A potential problem if these files is that they don't seem to care about having duplicated atom numbers... These assemblies are most often correct and validated by experiments. However, you might want to add a caveat or, even better, an intermediate window with a link to the place where the PQS explains how that particular oligomer was generated and why it is considered biologically relevant: http://pqs.ebi.ac.uk/pqs-bin/macmol.pl?filename=<ID> Best regards, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork(a)yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFGGL+gF6oOrDvhbQIRAtQ2AKCi9oIpIJffYwshk1PgB2aiG4e9rgCghjzZ Uz0yTug1VXEHXNP2MG2HsmI= =EGzy -----END PGP SIGNATURE-----

4 3

exporting a mineral structure as VRML
by Janet Iwasa 11 Apr '07

11 Apr '07

Hello, I'm trying to use Chimera to export a mineral file ( http://virtual-museum.soils.wisc.edu/soil_smectite/soil_smectite.pdb) as a ball and stick VRML structure, but I'm running into a bit of difficulty since some of the bonds don't get made into sticks -- rather, they appear as purple dotted lines in the viewer. Any suggestions on how to get these bonds to be made into geometry? thanks! Janet Iwasa

4 3

Extra Chimera marker attributes
by Tom Goddard 10 Apr '07

10 Apr '07

Hi Jeff, The Chimera path tracer markers accommodate extra attributes that are read and written to the XML marker files. There is no user interface to define new marker attributes in Chimera. A user interface to define new marker attributes does not seem hard. You could specify an attribute name and value in a command or dialog that assigns that attribute for all selected markers. For these new attributes to be of any use within Chimera more capabilities would be needed. For example some command or dialog that would allow you to select all markers with a certain attribute and value (e.g. is_filament = true). These kinds of capabilities already exist for attributes of atoms of molecules. For example, see the "setattr" and "defattr" commands, and "Render/Select by Attribute" tool, and atom specifiers that can test for specific attribute values. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/defattr.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descri… These will work with path tracer markers since markers are implemented as atoms. But there are problems. For example "defattr" uses names of atoms and the names of the path tracer atoms are not meaningful. Probably "setattr" is more useful and you can set an attribute for all currently selected atoms. The main weakness is that these atom attributes will not be saved in marker XML files. That is probably easy to fix but I would need to investigate how atom attributes are implemented. For markers the attributes are kept in a Python dictionary marker.extra_attributes. I do not know if atom attributes on markers will be saved in Chimera session files. Would have to test that. Tom Jeff wrote: > Tom, > > how hard would it be to add other attribute(s) to the markers > generated with the volume path tracer tool, aside from > marker-to-marker connectivity? Such as the ability to enumerate > individual filaments/objects within a single marker set, or a flag > that would tell whether a set/group is composed of filaments, or > surfaces, or just a point cloud? Either of of these (enumeration, or > object type) could be stored as an integer. > > -Jeff

1 2

transparency factor
by jean-francois menetret 09 Apr '07

09 Apr '07

Is it possible to change the transparency factor of a volume at the command line ? 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

3 3

Fetch EMDB map by id
by Thomas Goddard 09 Apr '07

09 Apr '07

Hi Cathy, It is a good idea to allow fetching EMDB maps by id in the current File / Fetch by ID dialog. Their are two issues related to the large size of some maps that I would like to solve to make that work well. First I would like Chimera not to freeze while the fetching is done. That is what currently happens when fetching files. Instead it could show a progress dialog with a cancel button (like a web browser) and open the map when it finally arrives. Second I would like the map to be saved on your local machine so that you don't have to fetch the same large file more than once. Perhaps the way that would work is the the first time you fetch any file it asks you where to save this and future fetched files, and there will be an option not to save them. This would be remembered in your Chimera preferences file. When you subsequently used the fetch dialog it could first look in the directory where you save fetched files and use the copy there if available. Thanks for the suggestion. It is on my requested features list. Tom

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Re: [Chimera-users] hkcage command
by Thomas Goddard 09 Apr '07

09 Apr '07

Hi Padma, The code for the hkcage command had to be changed for Chimera version 1.2348 and newer because we switched from using the Numeric Python array package to its not completely compatible successor called NumPy. The new code for the hkcage command is on the experimental features web page http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Use that new code with Chimera 1.2363. I have not had time to try flattening an icosahedral map. I made a small step toward another request of yours, plotting radial density. I tried a Python 2-d plotting library called matplotlib that could be used for making radial density plots. It is a pretty big package so we have not decided whether to include it in Chimera. Tom

1 0

GIF animations in Chimera
by Tom Goddard 09 Apr '07

09 Apr '07

Anyone interested in GIF animation output from Chimera? Their main appeal is that they play directly in most web browsers (like banner ads). It was easy to add to the Chimera movie recorder using ffmpeg which is included in the Chimera distribution. But ffmpeg uses a fixed color palette causing severe color banding and does not offer LZW compression resulting in large file sizes. That option looks unusable. I tried another approach using a separate program called "gifsicle". That gave decent coloring and compression but it would require adding gifsicle to the Chimera distribution. I am reluctant to do that (entails future maintenance) unless there is strong interest in making GIF animations. Tom

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[Fwd: Re: GIF animations in Chimera]
by Thomas Goddard 09 Apr '07

09 Apr '07

Miguel uses ImageMagick to make GIF animations from Chimera movie frames. Tom -------- Original Message -------- Subject: Re: [Chimera-users] GIF animations in Chimera Date: Sat, 07 Apr 2007 09:09:43 +0200 From: Miguel Ortiz-Lombardia To: Tom Goddard Hi Tom, I make animated GIFs with Chimera by simply saving the frames and using convert (from ImageMagick). I run an extremely simple script to do so and the results are up to my needs. Cheers, Miguel En/na Tom Goddard ha escrit: > Anyone interested in GIF animation output from Chimera? Their main > appeal is that they play directly in most web browsers (like banner ads). > > It was easy to add to the Chimera movie recorder using ffmpeg which is > included in the Chimera distribution. But ffmpeg uses a fixed color > palette causing severe color banding and does not offer LZW compression > resulting in large file sizes. That option looks unusable. I tried > another approach using a separate program called "gifsicle". That gave > decent coloring and compression but it would require adding gifsicle to > the Chimera distribution. I am reluctant to do that (entails future > maintenance) unless there is strong interest in making GIF animations. > > Tom > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Re: [Chimera-users] [chimera-dev] Building a multimer model
by Elaine Meng 07 Apr '07

07 Apr '07

Hi Benjamin, There is probably more than one way to do this in Chimera, but I'd open the protein of interest six times and match it to the six monomers of the related protein. Let's call your protein "A" and the similar protein "B" (for which a hexamer is available or can be easily constructed from matrices in the PDB file). Since you didn't mention the specifics, I didn't try the whole process outlined below (not having a good example to work with), but have used the tools in other contexts. This is kind of a brute force approach. Someone else may know of a more elegant way... Making the hexamer of B: If the PDB file doesn't already have a hexamer, it should have matrix information that allows it to be constructed. If BIOMT, use Multiscale Models (under Tools... Higher-Order Structure). Initially, this doesn't copy all the atoms but just makes surfaces for computational expediency. Since you will need copies of all the atoms for matching, using the Multiscale Models GUI: select "All" chains, change their style to anything other than surface (e.g. Show... Ribbons). You can see the model IDs of the copies of B in the Model Panel (under Favorites). If SMTRY, CRYST1, or MTRIX you could use the Unit Cell tool (under Tools... Higher-Order Structure) instead of Multiscale Models. Relevant manual pages: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/ framemulti.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/ unitcell.html Matching the 6 copies of A to the monomers of B: Options for matching are the "match" command or MatchMaker (GUI under Tools... Structure Comparison, also implemented as a command, "matchmaker"). If you wanted to name specific atoms to use for fitting, you'd use the "match" command. That can be tedious, and I'd try MatchMaker first - if there is some sequence similarity, even fairly low, it usually works quite well. By default, it iterates the fit so that only residues that match well in space are ultimately used to superimpose the proteins. That means the parts that are different should not interfere with a good fit of the parts that are the same. You can adjust several parameters, but for example if B is model 0, chains A-F and copies of A are models 1-6, these commands would use the matchmaker defaults: matchmaker #0:.a #1 pair ss matchmaker #0:.b #2 pair ss matchmaker #0:.c #3 pair ss matchmaker #0:.d #4 pair ss matchmaker #0:.e #5 pair ss matchmaker #0:.f #6 pair ss (pair ss just means to use the specified chains rather than trying all chain combinations between the models) You could specify other parameters with various keywords, for example the stringency to use when iterating the fit, how much weight secondary structure should have vs. the residue types in the sequence, etc. Relevant manual pages: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/ matchmaker.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html 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 Apr 5, 2007, at 12:10 AM, Benjamin G.S. Horsman wrote: > Hello, > > My name is Benjamin Horsman and I am a student at the University of > Toronto. I have what should be a basic (possibly naive) question > regarding protein modelling that I was hoping you might be able to > answer for me or point my in the right direction. I have been > studying the structure of a bacterial protein complex, trying to > understand how it interacts with several known binding partners. The > complex is known to be a hexameric homomultimer. Recently the > structure of the subunit protein was solved. However, only the > monomeric form of the protein was determined, and the corresponding > PDB file does not contain coordinates for the multimer (i.e., no > BIOMT1, BIOMT2, BIOMT3 matrix values). I would like to assemble a > model of the hexameric complex for visual inspection and for some > docking studies. What would be the best way to accomplish this? > > There are several structures in the PDB of hexameric protein complexes > composed of subunits with very close structural alignment to my > protein of interest, differing in two regions of the protein that are > outside of the multimer binding regions. I believe that my protein > complex posses very similar or nearly identical geometry to these > known complexes. Is there any way to basically insert my protein into > this geometry? Can this be done in Chimera? If not, is there any > program or web server that allows this to be done? Or are you aware > of a better way to get this done? > > Thank you for your time. Any help is greatly appreciated. > > > Benjamin Horsman > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Re: [Chimera-users] viewing & comparison of multiple overlay structures
by Roberta King 04 Apr '07

04 Apr '07

Thank you Eric for your very detailed answers to my several questions. It will take me a few days to work through the suggestions. If I have any more troubles, I will contact you next week. Thanks very much, Roberta King ******************************** Roberta S. King, Ph.D. Department of Biomedical and Pharmaceutical Sciences College of Pharmacy University of Rhode Island http://www.uri.edu/pharmacy/faculty/king _____ From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Tuesday, April 03, 2007 7:57 PM To: Roberta King Cc: Chimera BB Subject: Re: [Chimera-users] viewing & comparison of multiple overlay structures On Apr 3, 2007, at 1:47 PM, Roberta King wrote: First, After overlaying multiple protein (pdb) structures with ligands using MultiAlign based on alignment, how does one easily view only the overlaid ligands? [Note: I have up to 36 structures overlaid, each with 0-2 ligands.] Hi Roberta, Using the command line (Favorites->Command Line), typing "~disp; show ligand" will hide all structures and then show only the ligands. If every structure had a ligand you would only need "show ligand" since the show command hides parts of structures that aren't to be shown, but if no part of a structure matches the show criteria, the structure isn't changed -- so you need the "~disp" also to guarantee that ligand-less structures get hidden. This is also doable with the menus by Select->Structure->ligand followed by Select->Invert Selection (or shift-right-arrow instead to invert the selection in all models) and then Actions->Atoms/Bonds->hide. From there, you will probably want to select the ligand clump by control dragging the mouse across the clump (there will be a green box outline as you drag the mouse) and then use Actions->Focus to zoom in on the clump and make it the center of rotation. Secondly, can chimera then calculate a solvent-accessible closed surface for the protein cavity surrounding each ligand? Alternatively, I could calculate the cavity first, then overlay based on alignment. The goal is to view the overlaid cavities for visual comparison. It depends. If the cavity is actually completely enclosed then Chimera won't depict it. If there is some channel to the binding pocket, then it should be depicted. I say "should" because the surfacing library we are currently using (MSMS) is known to have problems when there are narrow channels in a surface. We are working on a replacement library that should solve both these problems, but it's not ready yet. Providing that MSMS doesn't fail, your pockets should be depicted. It is also sometimes possible to work around the MSMS problem by adding hydrogens to a structure or by slightly changing VDW radii (with the vdwdefine command) -- but you have to do this before any surfaces fail because after a failure surfacing won't work again until you restart Chimera. You create a surface with Actions->Surface->show or the "surf" command. If with experience you know that surfacing certain models is problematic, you can restrict the surfacing to particular models by selecting them before using the menus or providing the model numbers as arguments to the surf command (e.g. "surf #0,3-7,9"). Thirdly, can chimera calculate electrostatic charge on amino acids surrounding a binding cavity and reflect that charge onto the closed cavity surface? Can this surface be included in overlay view? You can use the Add Charge tool (in the Structure Editing category) to add partial charges to all atoms. You can then use the Render By Attribute tool (Structure Analysis category) to color the surface and/or atoms based on the partial charges. For more precise electrostatics, you can use an external tool such as APBS or Delphi to generate an electrostatic grid, and open that in Chimera and then use the Electrostatic Surface Coloring tool (Surface/Binding Analysis category) to color the surface with the grid data. You can certainly show the surface(s) with the ligands overlaid. You would probably only want to show a few surfaces at most simultaneously for understandability (see next answer). Given the number of structures, I would much appreciate any advice on how to make this manageable. If Chimera cannot do the calculations, can it import multiple structures saved by another capable software, then overlay them using MultiAlign (including the surfaces)? Depending on the speed of your computer, its amount of memory and its graphics card, working with 36 structures and their surfaces at once may or may not be satisfactory (and unless you have a real high-end machine my guess would be not). You will want to use the Model Panel (under Favorites) to control which surfaces/structures are being shown -- particularly which surfaces since I imagine that looking at more than a few would be incredibly confusing. Another thing that will help is to delete parts of structures that you aren't interested in. One trick here is to use MultAlign Viewer to select one residue in each structure (create a region by mouse dragging that covers one column in the alignment -- those residues will be selected), then select the corresponding chains by clicking into the main window and hitting the up-arrow key, then right-arrow to invert the selection, and finally Actions->Atoms/Bonds->delete to delete all atoms that are not part of chains in the alignment. Hopefully your ligands will have the same chain ID as the chain in the alignment and therefore will not be deleted. You might want to look at your ligands after you've inverted the selection and make sure none are selected for the following deletion. If some are selected, deselect them with "~select ligand". As a quasi-extreme measure you could prune away parts of the structure more than a certain distance from the ligands. Select the ligand clump and use Select->Zone... to select residues further than a certain distance from the clump and then delete the selected residues. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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render several models by attribute on an absolute scale
by E. Merkley 03 Apr '07

03 Apr '07

Hello Chimera users, I am using the "Define Attribute" and "Render by Attribute" features to color structures by number of native contacts observed during a molecular dynamics simulation. I would like to compare several simulations at once, applying a single color scale to several (~6) models at once. It seems that this can't be done using a separate attribute file for each model: The "render by attribute" dialog doesn't let you change the limits past the min and max of the data in the attribute file, but each simulation (and hence each attribute file) has a different range. Any suggestions? Thanks, Eric

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viewing & comparison of multiple overlay structures
by Roberta King 03 Apr '07

03 Apr '07

Hello, I am relatively new to Chimera (and the user group), but am using it to compare ligand binding pockets for multiple (36) structures of related proteins. My proteins overlay nicely based on alignment, but I am having difficulty with the comparisons of multiple structures at once. First, After overlaying multiple protein (pdb) structures with ligands using MultiAlign based on alignment, how does one easily view only the overlaid ligands? [Note: I have up to 36 structures overlaid, each with 0-2 ligands.] Secondly, can chimera then calculate a solvent-accessible closed surface for the protein cavity surrounding each ligand? Alternatively, I could calculate the cavity first, then overlay based on alignment. The goal is to view the overlaid cavities for visual comparison. Thirdly, can chimera calculate electrostatic charge on amino acids surrounding a binding cavity and reflect that charge onto the closed cavity surface? Can this surface be included in overlay view? Given the number of structures, I would much appreciate any advice on how to make this manageable. If Chimera cannot do the calculations, can it import multiple structures saved by another capable software, then overlay them using MultiAlign (including the surfaces)? I appreciate any help provided. Roberta ******************************** Roberta S. King, Ph.D. Assistant Professor Department of Biomedical and Pharmaceutical Sciences College of Pharmacy University of Rhode Island

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