- Chimera-users - RBVI Mailing Lists

ViewDock Data Analysis
by felipe vasquez 24 Jul '13

24 Jul '13

Hi, I have been executing a couple of docking processes through Autodock vina module in Chimera. Nevertheless, I am a bit confused about the docking analysis, because although I obtained a score for a certain number of ligand poses, I do not know if this number (-9.2, as an example) is expressed in kcal/mol, kj/mol, or even another units. On the other hand, I could not understand the meaning of RMSD l.b and RMSD u.b. What are they? and what role the play in the docking analysis procedure? Best regards, *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

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Docking with Autodock vina (Chimera)
by felipe vasquez 24 Jul '13

24 Jul '13

Hi, I am trying to perform a docking process via the tool 'autodock vina' embedded into chimera menu. However, once I am baout to run the process, I always obtain the same message: Service 'opal:vina_1.1.2' is unavailable. What can I do in order to overcome this problem? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

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Feature Request
by R.J. Swett 19 Jul '13

19 Jul '13

Hey there, I was wondering if you could enable movie encoding to .wmv in an upcoming build? I know ffmpeg supports that format, so hopefully it'd be an easy update. I usually have to re-encode videos, for some reason my new computer won't play most videos while using presenter-view with HDMI output. It's just a finicky little thing, but it'd make my life a lot easier. I've found a some other people with the same issue with HDMI-output only computers. -- R.J. Swett Wayne State University 357 Chemistry Detroit, MI 48201 Lab Phone 313-577-0552 Cell Phone 906-235-0768

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running chimera 1.8 needs root privilege
by Robert Wohlhueter 16 Jul '13

16 Jul '13

I've been using Chimera 1.5.3 under Linux (Ubuntu 12.04, 64-bit) without problems; that version I had installedas root, andis owned by root. Just now I updated to version 1.8, which, initially, I also installed as root. But trying to run it (as non-root) gave me fairly opaque error messages(copied below). On a hunch that it was a matter of privilege, I tried running with `sudo` -- which works fine. Since it was not obvious where the problem lay, I cleaned out the installation, and installed anew as a normal user (me). Accordingly, the whole installation directory tree is owned by me. But still I cannot run it (same errors) as me, but only with `sudo`. Same user, same start directory, apparently the same Python (2.7) as works with v. 1.5.3. I'm totally flummoxed! Can't imagine where the privilege hang-up is. Any hints where I should look? Thanks, Bob Wohlhueter *****************************C-shell output******************* chimera X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 128 (GLX) Minor opcode of failed request: 198 () Serial number of failed request: 2813 Currentserial number in output stream: 2813

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Fitting multiple atomic structures in a density map
by Anindito Sen 16 Jul '13

16 Jul '13

Dear All, I need to fit atomic structures of two different proteins of different sizes in a density map. The location of both the proteins in the map is well known. While using the fitting tool, I can get the atomic structure of the bigger protein docked very well, the problem arises while fitting the smaller one. The fit option fails and docks the structure into the region of the density map where the atomic structure of the larger protein is docked , an incorrect position. How can I fit both the atomic structures in the density map correctly? The resolution of the density map is ~10Å at FSC cutoff of 0.5 Thanks Andy Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

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molmap and origin index
by Catalin Buiu 15 Jul '13

15 Jul '13

Hello all, I have the following problem: when I use molmap to generate a map from an atomic structure, the result is fine: both align. When I use another (Matlab) program to generate the map, the two, when opened in Chimera do not align anymore. My question is how molmap generates an origin index such that both the map and the structure do align and how Chimera reads (and converts) the xyz origin data from the MRC file? Thank you. Catalin Buiu University of Bucharest, Romania

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Euler angles in "Transform coordinates" tool
by Dan Cohen 15 Jul '13

15 Jul '13

Hello all, I have been wrecking my mind in trying to use the "Transform coordinates" tool to apply a rotation to a PDB file based on Euler angles taken from IMP. I focused my problem to the following : According to IMP, they use the ZXZ notation in the original (lab) coordinate system. According to my understanding of the chimera docs, you use ZXZ in the self (rotating) coordinate system. I have been trying to convert between those two using a python library I found on the net but keep on getting results that either show I'm missing something or a bug in somewhere. (It's called transformations.py by Christoph Gohlke) Are you aware of any issues or similar problems? I saw somewhere that someone mentioned a similar problem that was due to PDB header file with weird axis origin, but i wasn't able to get any more info. Will be thankful for any hint, Dany

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cutting the surface
by Victor Muñoz 15 Jul '13

15 Jul '13

Dear all, I want to make an image using the Surface Cliping option in Chimera. The problem is that I just want to cut the surface and not the molecule when using the Viewer to do that. As an example, I want to so something like this image from the wikipedia (http://en.wikipedia.org/wiki/File:MM_PEF.png ). Thanks for everything in advance. Kind Regards, Victor Muñoz --

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command line for silhouette representation
by Jean Didier Pie Marechal 15 Jul '13

15 Jul '13

Dear all, I am making a movie using a command file. I would like to represent the atom using the same kind of picture than those generated using the Presets option silhouette. Can you tell me how to do so? Cheers, JD Dr. Jean-Didier Maréchal Associate Professor The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es

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Deleting Psubobonds/Connectivity
by Dylan J. Bennett 11 Jul '13

11 Jul '13

Hi, I was wondering if there was a way to delete psudobonds and connectivity in Chimera. I use a protein-protein docking software that does not renumber chains, this results in a structure that has 2 chain As for example. When I go to analyze this in Chimera, it automatically creates a psudobond between the two chains with the same ID. Since it thinks they're connected, I can't rename the chain IDs for just one of them. I know I can hide all the psubobonds, but this doesn't really help as I still need some of them and would like to rename the chain IDs uniquely. Thank you. -- -*Dylan J. Bennett* *Dylan.John.Bennett(a)Gmail.com (914) 621-1149* *Stony Brook University* *dylan.bennett(a)stonybrook.edu* *New York Medical College* *Biochemistry* * BSB Room 102* * dylan_bennett(a)NYMC.edu*

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How Chimera reads a dcd file
by Syeda Hira Batool 10 Jul '13

10 Jul '13

Hello! I have psf and dcd files.I want to read them using my own script(non-commercial/educational purpose).So I want to know how Chimera reads dcd files.Can you please help me out in this regard by providing me some helping material or a script. Thank you Hira Batool Student of BS-Bioinformatics Biosciences Department COMSATS Institute of Information Technology Islamabad, PAKISTAN

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Software Chemistry Linux
by giovanni.ortosecco＠libero.it 09 Jul '13

09 Jul '13

Dear List, kindly would like to know if there is an open-source software for advanced molecular modeling for use with Linux (Ubuntu, CentOS, Debian) along the lines of ChemDraw or ChemSketch. Thanks for Your attention. Best Regards, Giovanni Ortosecco Dr. Giovanni Ortosecco Institute of Biostructures and Bioimaging National Research Council Naples - Italy Posted by: Ubuntu 13.04 Raring Ringtail http://www.ubuntu.com/about/ Use free software!

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Software Chemistry for Linux
by giovanni.ortosecco＠libero.it 09 Jul '13

09 Jul '13

Dear List, kindly would like to know if there is an open-source software for advanced molecular modeling for use with Linux (Ubuntu, CentOS, Debian) along the lines of ChemDraw or ChemSketch. Thanks for your attention. Best Regards, Giovanni Ortosecco Institute of Biostructures and Bioimaging National Research Council Naples - Italy

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color by height
by p.j.depablo 09 Jul '13

09 Jul '13

Hi everybody I am interested in coloring an EM volume by height. In this option you can change the origin and the axis of coloring. Specifically, I rotate t the structure untill a desired orientation. Then, I would like to choose the axis of coloring to be the same as the view axis, but can not find the viewing axis coordinates. Is there possible to find this informaton anywhere? Thank you in adavance. Pedro

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camera horizontal field of view
by Dougherty, Matthew T 09 Jul '13

09 Jul '13

The camera settings allow for a horizontal field of view of 1-179 degrees. Wikipedia states that human horizontal field of view is ~180 degree. using 179 is not anything I normally recognize, looks like star trek enterprise going to warp. In cinematography books, lenses are sometimes referenced at around 20 degrees. For chimera I have found 10-30 gives nominal viewing on LCD. Setting it 1 is effectively orthographic. For DTI in a dome projection (as opposed to dome camera), I frequently will use 80-110, unless I am looking for a orthographic look, then lower values. For the mono & DTI cameras on a flat display, what are the values or the process to determine the values, for the most accurate mapping to normal human vision? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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ergonomics
by Dougherty, Matthew T 08 Jul '13

08 Jul '13

a few suggestions on placement 1) on viewing dialog, change the location of "view all" from the sideview window, relocating it to the bottom next to reset/restore/etc buttons. having additional orthogonal buttons (x,y,z) would be avoid having to do a lot of text commands. 2) on the volume viewer dialog, saving dialog preferences is accessed through its pulldown menu; having it act like other dialogs would be helpful (ie, at the bottom like viewing dialog). 3) the main 3d graphics window when dominant , causes the default pulldown menus to appear such as when chimera starts up. when accessing volume viewing, the overall chimera pulldown menus change. The only way to get the original/main pulldown to return is to put the mouse on the 3d graphics window and doing a left click twice. Since the volume viewing has its own pulldown menus, getting this overall switch of pulldown menus eliminated would help avoid a lot of unneeded mouse movements, particularly for the situation when two displays are used, one dedicated to 3D graphics, and the other having the viz controls. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Creating Average Structure from PSF/DCD --> Include metal ions in final structure
by Peter Murphy 08 Jul '13

08 Jul '13

Hi, I am trying to create an average structure in chimera 1.7 using the built in MDtools (loading a PSF/DCD file to get the trajectory). I am able to create an averaged structure for a select number of frames easily, but it doesn't appear that the metal ions are included when the averaging occurs. Is there someway to force the ions to be included? or alternatively, is there a script to create an average structure that includes selected atoms? Thanks, Peter -- Peter Murphy, Ph.D. Candidate Department of Biochemistry and Molecular Biology Dalhousie University Halifax, NS Canada

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icosehedron enhancement
by Dougherty, Matthew T 08 Jul '13

08 Jul '13

for the mesh adjustment, it would be good to be able to enter the radius of the mesh tubes. currently I have to select the item, go to the inspector to set the radius. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Re: [Chimera-users] [chimera-dev] Trouble with Saving New Atom Attributes
by Elaine Meng 05 Jul '13

05 Jul '13

Hi Juliette, PDB format does not include atom-type information, as you have seen. The only sure way to save your atom type changes is to save the Chimera session. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sessions.html> However: Chimera applies chemical perception to try to figure out the atom types when a structure is read in from a file. The Mol2 format does have some atom-type information, but the SYBYL Mol2 types are not related 1-to-1 to the types in Chimera. You could try saving in Mol2 format and reading it back in to see if the information you want is retained. Further, if you have added all hydrogens before writing the file (PDB or Mol2) the chemical perception is more well-determined and it is possible that it will assign the types you intended. If those do not work, however, the session is the way to go. If you just wanted a list of the assignments rather than the assignments per se, you could use "File... Save Attributes" from the menu of Render by Attribute (itself in menu under Tools... Depiction). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html…> This seems more like a "user" question than a developer (programmer) one; it's not necessary to email both lists. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 5, 2013, at 2:34 PM, Juliette Cao wrote: > Hi All, > I was successfully able to change a few atom types using the setattr command. > I checked to see that the atoms I changed were correct (by selecting the atoms and then then clicking the IDATM type option.) > I saved the .pdb file > When I opened up the saved .pdb file and checked the atom types, they had reverted back to their original type. > Is there a specific way to save files after using setattr command? > Regards, > Juliette Cao > University of Houston

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Trouble with Saving New Atom Attributes
by Juliette Cao 05 Jul '13

05 Jul '13

Hi All, I was successfully able to change a few atom types using the setattr command. I checked to see that the atoms I changed were correct (by selecting the atoms and then then clicking the IDATM type option.) I saved the .pdb file When I opened up the saved .pdb file and checked the atom types, they had reverted back to their original type. Is there a specific way to save files after using setattr command? Regards, Juliette Cao University of Houston

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force field for G-quadruplexes
by Gilmar Salgado 05 Jul '13

05 Jul '13

Hello, recently I was looking into the capabilities of Chimera minimization tools to minimize the structure of a DNA G-quadruplex molecule. The problem is that all G-quadruplexes have an ion (K+ or Na+) in-between and stabilizing the tetrads. I wonder if the force field available in chimera are "decent" to water-minimize this kind of structures? ...and which one is more adapted, after all those are non-conventional DNA structures. Thanks in advance for your input Gilmar Salgado Université Segalen Laboratoire ARNA (INSERM U869) Institut Européen de Chimie et Biologie 2 rue Robert Escarpit 33 076 Pessac Cedex FRANCE +33(0) 540 0022 24 +33(0) 557 571 015 (fax)

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Drawing with BILD commands directly from Chimera command line
by Dan Cohen 03 Jul '13

03 Jul '13

Hello all, Is there an option to type in BILD commands directly into the Chimera command line? (I know you can create a file with BILD commands and open it with Chimera but it would be helpful just to open the command line and type them in) Thank you, Dany

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Faraday Discussion on Molecular Simulation and Visualization - call for abstracts deadline 22 July 2013
by baaden＠smplinux.de 30 Jun '13

30 Jun '13

Dear Colleague, You may be interested in the following event: Faraday Discussion #169 - Molecular Simulations and Visualization ** CALL for ABSTRACTS deadline 22.7.2013 ** http://www.rsc.org/ConferencesAndEvents/RSCConferences/FD/FD169/cfp.asp A few more details: Current biology, chemistry and materials science make extensive use of computational methods ranging from applications at the cellular level, e.g. in systems biology, to detailed atomistic simulations of molecular assemblies, materials or small molecules. Faraday Discussion 169 will illustrate and discuss the potential of Human-Computer Interaction and Virtual Reality for computational molecular sciences, focusing on the following themes: * virtual and augmented reality; immersive molecular simulations * advanced visualization and visual analytics * computing power revolution and new algorithms: GP-GPUs, clouds and more * applications and serious games: from docking to protein folding Take part in the excellent scientific programme at this Discussion, in which experts in biology, chemistry and computational science will stimulate discussions and initiate research aimed at deeper involvement, beyond the boundaries of each discipline. Professor Helmut Grubmuller, Max Planck Institute for Biophysical Chemistry, Germany Dr Graham Johnson, University of California, San Francisco, USA Dr David Glowacki, University of Bristol, UK Professor Valerie Daggett, University of Washington, USA Professor Thomas Ertl, University of Stuttgart, Germany Professor Vijay Pande, Stanford University, USA Professor John Stone, University of Illinois at Urbana-Champaign, USA Dr Melanie Stegman, Federation of American Scientists, USA Assistant Professor Jim Zheng, Medical University of South Carolina, USA Professor Frederick Brooks, University of North Carolina at Chapel Hill, USA Professor Thomas DeFanti, University of California, San Diego, USA Virtual Reality represents a formidable communication and learning tool that could significantly speed up understanding of dynamic behaviour of complex biomolecular systems. This meeting is an excellent opportunity to bring the relevant disciplines closer together and benefit from collaborations across diverse fields. Yours sincerely, Marc Baaden -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217

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water display problem
by inhee park 28 Jun '13

28 Jun '13

Is there a xyz coordinate range limit or a residue numbering limit in Chmiera for display? I tried to display all atoms in the PDB file using chimera version 1.8. As shown in the attached figure, not all waters were displayed. If I loaded the same PDB file using other programs such as vmd or maestro, all waters were correctly displayed. FYI, I also attached the PDB file. Thank you for your help. _________ inhee park

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Monitoring hbonds in chimera
by Neha Gandhi 28 Jun '13

28 Jun '13

Dear Users, I am trying to use hbond command in the movie tool of Chimera 1.8. I want to repeat hbond analyses with different criteria simultaneously in a single script these are my commands select :9@O1P,O2P,O3P,N,H :12@N,H findhbond selRestrictboth linewidth 2 color green reveal true (..I want to monitor hydrogen bond between these two residues with default criteria) ~sel select :3@O1P,O2P,O3P :6@O1P,O2P findhbond selRestrict any color black reveal true relax true distSlop 2.7 intraRes false ~sel When I tried these commands in one single script, I could see hydrogen bonds displayed for residue 3 and 6 and not between residues 9 and 12. Hopefully you can correct me. Your help is appreciated -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate

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Re: [Chimera-users] Chimera 1.8rc 64-bit as Default Application
by Antoine Maillard 28 Jun '13

28 Jun '13

Suggestion to Dylan Bennett / Chimera 1.8rc 64-bit as Default Application Hi Dylan, you asked how to get Windows 7 to acknowledge Chimera as the default program to open specific files. In my experience the same problem was solved by running Ccleaner up to 3 times in a row to fix registry keys. After the first run, re-scanning the registry with Ccleaner shows that .pdb entries still need to be fixed. I kept running Ccleaner on my computer's registry until it was deemed as clean and only then was file association successful. Hope this helps, Antoine

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Both chimera (x86) and chimera (x86-64) fail to run on Windows 8
by David Konerding 27 Jun '13

27 Jun '13

Hi, I have a Windows 8 pro machine, 64-bit 8 GB RAM Core i3 and Quadro FX 570. When I start Chimera (x86 and x86-64), I see the splash screen then it says "pythonw.exe has stopped working". When I add --debug: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics I managed to cause windows to try to send an error report, which captured these files: C:\Users\dek\AppData\Local\Temp\WERF405.tmp.appcompat.txt C:\Users\dek\AppData\Local\Temp\WERF464.tmp.mdmp if those are useful for debugging, I can provide them.

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Chimera 1.8rc 64-bit as Default Application
by Dylan J. Bennett 26 Jun '13

26 Jun '13

Hi, I am attempting to associate pdb and mol2 file types with Chimera 1.8rc in Windows 7. I have tried to set it using the right-click>open with... option in Windows as well as through the control panel. I select the chimera executable, but it does not seem to accept it as a valid program, and it returns to the previous screen without adding Chimera to the box for selection. I know this is not a Windows issue, as I can set other programs and it works fine. As well, I can set other programs for the mol2 and pdb file types. Is this a known issue, is there any work around. It's not the biggest deal, but it would make my life a little easier if I could do this. It used to work in the past, but just not with the latest version. Thank you and have a great day! -- -Dylan J. Bennett Dylan.John.Bennett(a)Gmail.com (914) 621-1149 Stony Brook University dylan.bennett(a)stonybrook.edu New York Medical College Biochemistry BSB Room 102 dylan_bennett(a)NYMC.edu

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Leap Motion
by Aurélien Grosdidier 24 Jun '13

24 Jun '13

Hi all, We're planning to try Chimera with the leap motion device (https://www.leapmotion.com/) Has anyone already succeeded to do so ? Best, Aurélien.

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modeling multimers
by Francesco Pietra 24 Jun '13

24 Jun '13

Hello: Modeling a trimer (all three chains present, though missing residues and atoms) with chimera and modeller installed locally. The default is modeling each chain, one at a time. The chains are identical in sequence but the X-ray structure shows different localized conformations. Question: is modeller modeling by taking the other two chains into account? If already answered, beg pardon. thanks francesco pietra

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Re: [Chimera-users] Chimera-users Digest, Vol 122, Issue 25
by Boaz Shaanan 23 Jun '13

23 Jun '13

Hi Francesco, I doubt that modeller knows how to take into account inter-subunit information. I would be surprised if it does. As far as I know, it's a sequence-homology based model building module which also uses fold recognition and probably other pieces of information but not about oligomeric arrangement. When I dealt with a similar problem (modelling a dimer) I modelled the subunit and then superimposed each of the two subunits on top of the corresponding subunit of the known dimer, followed by Chimera's matchmaker. The resulting dimer is still considered a hypothetical structure by me. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Sunday, June 23, 2013 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 122, Issue 25 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. modeling multimers (Francesco Pietra) 2. Fwd: modeling multimers (Francesco Pietra) ---------------------------------------------------------------------- Message: 1 Date: Sun, 23 Jun 2013 07:17:44 +0200 From: Francesco Pietra <chiendarret(a)gmail.com> To: chimera <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] modeling multimers Message-ID: <CAEv0nmt6Sy2MJcs=xk18qMGs2d5h0QOS_i7YXAJ1AEwpdWWsCQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello: Modeling a trimer (all three chains present, though missing residues and atoms) with chimera and modeller installed locally. The default is modeling each chain, one at a time. The chains are identical in sequence but the X-ray structure shows different localized conformations. Question: is modeller modeling by taking the other two chains into account? If already answered, beg pardon. thanks francesco pietra

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Re: [Chimera-users] Antw: Re: atomic models in pdf
by Tom Goddard 20 Jun '13

20 Jun '13

Hi Matthias, I think there are many ways to get Chimera output into 3D PDF if you are willing to drop $600 on commercial software. The trouble is that you have to produce the 3d model in U3D format and then the U3D can be embedded in PDF. Those two conversion steps, going from a Chimera 3d export format such as X3D to U3D and the U3D to PDF I believe can be done by many commercial applications. But I don't know free applications to do it. There may well be free applications but it might take a whole day of digging on the web to find them. If you do find them let us know. It is easier to find a commercial software conversion route. For instance PolyTrans ($395) from Okino Computer Graphics claims to read X3D and export U3D, and Adobe Acrobat Pro X ($200) can put U3D into PDF files. http://www.okino.com/conv/filefrmt_3dexport.htm http://help.adobe.com/en_US/acrobat/X/pro/using/WS58a04a822e3e50102bd615109… I've never tried this and would definitely worry about whether PolyTrans or any other software will faithfully handle Chimera's X3D output. I think the basic problem is U3D and 3D PDF are used by almost noone. The Okino web site gives some idea of the trouble with U3D: "Okino also has a long history involved with the U3D file format. U3D has quite a tainted history in the development community. It was derived from the old Intel IFX 3D gaming toolkit of the 1990's and forced upon developers as the Macromedia 'Shockwave-3D file format' in 2000. The Shockwave-3D format was abandoned in 2002 and then it resurfaced in 2004 when Intel forced it upon Adobe as the 3D file format to use within 3D PDF files (instead of Adobe using the better X3D file format). With the IFX toolkit being so buggy, Okino spent much of 2004 through to 2007 debugging the IFX toolkit and creating the main, defacto implementation of the U3D import/export converters." The AxPyMol plug-in you mention does not produce PDF (and is commercial, $148 academic, or $404 for a lab license, 1 year subscription). It embeds 3d PyMol scenes in PowerPoint -- there is no PDF involved as far as I can tell. It uses an Active X plug-in (only available on Windows). Tom On Jun 20, 2013, at 10:29 AM, Matthias Barone wrote: > Hi Tom and Conrad > Thank you for the fast replies and sorry for not being clear: > Im doing all presentations with the beamer package of latex and hence search an interactive way to show 3D models of x-ray protein structures instead of showing pictures. > What Im therefore searching is a way to make a pdf that provides me a 3D model (incl. mouse gestures like zoom, rotate, clip) with pre-set layout (ribbon, electron density colours and so on set in chimera). > > matthias > > > > > > >>> Conrad Huang <conrad(a)cgl.ucsf.edu> 20.06.13 19.16 Uhr >>> > Collada format is used by Apple's iBooks Author program to embed 3D > graphics. Collada files, with .dae extension, can also be displayed in > Apple's Preview application. > > I don't believe Collada is at all related to PDF, which uses U3D format > for 3D data. MeshLab is supposed to read many data formats, including > Collada, and generate U3D output. Unfortunately, Chimera Collada output > is not read properly by MeshLab; triangle per-vertex colors, specified > as an RGBA data source, seem to be ignored. Worse, saving U3D output > (so at least we get the geometric shape) also fails, producing, from > Chimera's 28MB Collada file, 2 1KB files (no, I don't think it's due to > compression :-) ). > > The bottom line is that I do not have anything new to contribute on the > PDF front. Sorry. > > Conrad > > On 6/19/2013 9:43 PM, Tom Goddard wrote: > > Hi Matthias, > > > > I'm not clear on what your goal is. You talk about embedding > > molecule models in PDF, in Latex and in HTML. > > > > Conrad Huang in our lab added Collada export to Chimera so that > > molecular models could be dropped into some ebook format but I'm not > > sure if that format was PDF or something else. Have to find out from > > him. We are also working on displaying 3d views of molecules in a web > > browser using WebGL and Chimera can export an html file for that. Those > > files tend to be large and you need a web browser that supports WebGL to > > view them. The Collada and HTML export are under Chimera menu entry > > File / Export…. The Collada export is in Chimera daily builds and HTML > > export is in Chimera 1.8. > > > > Tom > > > > > > On Jun 19, 2013, at 5:41 AM, "Matthias Barone" wrote: > > > >> Hi > >> I keep on searching for a solution for embedding atomic models in pdf > >> (by LaTex). In PowerPoint a plugin called AxPyMol does the job nicely, > >> but I want to use chimera. You were already discussing a similar topic > >> in > >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002663.html The > >> question in the topic was whether its possible to incorporate > >> mesh-data (via programs like MeshLab, Photoshop and the movie15 > >> package) into .tex files. > >> But Im searching for latex packages to display and manipulate atomc > >> models. Exporting in html could be a way to desplay everything but > >> electron densities (although html doesnt support mouse gestures) > >> sincerly, matthias > >> _______________________________________________ > >> Chimera-users mailing list > >> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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atomic models in pdf
by Matthias Barone 20 Jun '13

20 Jun '13

Hi I keep on searching for a solution for embedding atomic models in pdf (by LaTex). In PowerPoint a plugin called AxPyMol does the job nicely, but I want to use chimera. You were already discussing a similar topic in http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002663.html The question in the topic was whether its possible to incorporate mesh-data (via programs like MeshLab, Photoshop and the movie15 package) into .tex files. But Im searching for latex packages to display and manipulate atomc models. Exporting in html could be a way to desplay everything but electron densities (although html doesnt support mouse gestures) sincerly, matthias

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Ensemble cluster
by Damien Larivière 20 Jun '13

20 Jun '13

Dear All, As a preamble, it is quite possible that I completely misunderstood the way to use the Ensemble cluster tool. Here is the problem I face: I opened a PDB file containing 8 models. The models have the same number of atoms, the same numbering, the format is Model Endmdl, etc. I launched Ensemble cluster in order to identify clusters. From the image below, one can see visually 2 clusters. Chimera effectively identifies 2 clusters _but _the representatives of each (in red and blue-turquoise) belongs to the same cluster. I expected one representative in each of the two clusters. May you tell me what is wrong with my understanding? Many thanks for your help, Damien ps : Is there a way to cluster according to a previously chosen RMSD?

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Command line history
by Damien Larivière 20 Jun '13

20 Jun '13

Dear All, I just installed the last release for Windows (June 07, 2013). I would like to get back the command line history I had in the previous version. I saved this command line history in a file named/chimera.cmd/. May you tell where to copy/chimera.cmd/ in the program files of my new Chimera? (I've made a search in the Windows explorer for /chimera.cmd/ but nothing was returned) Thanks, Damien

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Hydrophobicity surface
by Anne Simonsen 19 Jun '13

19 Jun '13

Dear Chimera helpers, I'm trying to make a figure showing the hydrophobic surface of one chain (chain A in attached IGA1.pdb file) with a peptide (chain B) shown as ribbon with residues, but I then get a "hole" in the A surface around the peptide (see attached figure). Can you please advice? Thank you! Best wishes, Anne -- Anne Simonsen, PhD, Professor Dept. of Biochemistry, Institute of Basic Medical Sciences University of Oslo, P.B. 1112 Blindern 0317 Oslo, Norway Visiting address: Domus Medica, room 3174 Sognsvannsveien 9 0372 Oslo Phone: +47 22 851110 Fax: +47 22 851058 Mobile: +47 99350960 email: anne.simonsen(a)medisin.uio.no http://www.med.uio.no/imb/english/research/groups/autophagy/

2 1

adding an O in compound 1
by Ibai Gazpio 18 Jun '13

18 Jun '13

Hi all, I'm trying to add an O molecule as compound 1 bound to a Fe of an Hem group. I use a program called GOLD to perform dockings but this doesn't recognize this O atom type, that is a O.3 type.. The output should be a mol2 file. Which atom type should I use? Ibai.

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Chimeras limited capability to visualize correctly molecular structure
by Marek Maly 18 Jun '13

18 Jun '13

Hello all, recently was sent to the Amber mailing list question about how to proceed here with simulation of the piece of graphene. I was just curious about the molecular structure so I tried to visualize attached PDB file in Chimera which was not able to show correct structure so I visualized it using VMD and also Vega ZZ in both cases without any problem. Then I used Vega ZZ to create MOL2 file and tried again to use Chimera for visualizing graphene saved now in MOL2 format but again without success. So maybe there is still some space for improvement of Chimera visualizing capability. Especially in case of MOL2 format I was surprised that Chimera is not able to show correct molecular structure as in this case all the information (including bonds/connectivity info) is included in the input file. All files are attached. (my version of Chimera is: candidate version 1.8 (build 38694)) Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Chimera - ball and stick - 3D printing
by Francois Richard 18 Jun '13

18 Jun '13

Hi everyone, I am trying to print a molecule from its PDB file (ID : 2BEG) using chimera and a 3D printer. I would like to print the ball and stick representation of the molecule, including the hydrogen bond. So far, (using this link : http://www.cgl.ucsf.edu/Outreach/technotes/ModelGallery/index.html) I played with molmap and volume commands and managed to print a volume but it does not include hydrogen bond. Do you have any idea how to improve the output? Thanks a lot, Francois

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protein schematic representaton
by francesco oteri 14 Jun '13

14 Jun '13

Good morning to everybody, someone of you knows whether exist a program that creates schematic representation of a protein like the one in plot b and d of the figure: http://www.nature.com/nature/journal/v427/n6972/fig_tab/nature02165_F3.html Greetings, Francesco

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Missing segment confuses addH
by Sam Egel 13 Jun '13

13 Jun '13

Hi, Basic Problem: I am attempting to use the addH tool on a metal containing active site I have extracted. The problem is that Chimera draws an 11 angstrom pseudo bond representing a missing segment between two residues. This bond seems to be the reason that a terminal carbon is receiving only two hydrogens rather than three. The pseudo bond runs right through the bond axis between two other carbons, both of which are protonated correctly. Can anyone please explain how to actually delete this bond (hiding through ~longbond, closing or hiding through the pseudo bond panel does not work) or provide another method to get this carbon to have three protons? I'm running v 1.6.2 of Chimera locally on Win 7 and the same problem occurs on a remote Red Hat Enterprise Linux machine running v 1.5 of Chimera. More Detail: Getting this carbon protonated in a one-stop-shop by Chimera would save me the world of time for a number of reasons, including that I need to make many files of this active site and every pdb of this enzyme has the same addH/pseudo bond problem between the same residues. The active site was extracted by writing a 10 angstrom zone around the metal to a pdb and then hand selecting the residues I cared about from there and writing them to a pdb. Workarounds: I have tried using command line ~longbond, hiding and closing out the missing segments option in the pseudo bonds panel, and deleting the bond by highlighting it and trying to delete bond under the adjust bond tab in modify structure window. If I write the pdb to an xyz (Molden) and open the xyz in Chimera, addH works just fine. However, I would really like for these files to be real pdbs that have associated residue names at the moment (residue names are, of course, deleted when converted to xyz). Thank you for your time, Sam

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display of glycine atoms
by Levandoski, Mark 11 Jun '13

11 Jun '13

Hello there - I recently got a new office machine and had to reload Chimera. Although I do not recall the number of the version I had used in the past, empirically I can tell that this is some updated version. My problem is that I am trying to display various residues of a protein selectively as space-filling ("sphere") on a ribbon frame. One residue of interest is a glycine. This version of Chimera seems incapable (or I am incapable of discovering how!) of displaying the various atoms belonging to this glycine residue. All other residues seem fine. Is this a glitch? Am I doing something wrong? For comparison, I have every confidence that this should work because with my older version of the program I was able to generate just such a view. Thank you very much in advance for the help, Mark P.S. By selecting the glycine of interest I am able to color the strip of ribbon by preset color, but not by element. Mark M. Levandoski Associate Professor of Chemistry Grinnell College 641-269-4544

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Selecting regions of a PDB structure
by Anindito Sen 11 Jun '13

11 Jun '13

Dear All, I have a pdb file of a large protein complex. I want to select several regions and color them differently to show the various domains. How can I do that. Thanks Andy Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

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Re: [Chimera-users] movie of flying in a density map
by Tom Goddard 11 Jun '13

11 Jun '13

Hi Andy, The way to use saved positions in an animation is to save a session which includes all the saved positions. Then to make the animation you first open that session and then use the "fly" or "reset" command in a script with those named positions. This is a general method for making animations that works quite well. Setup everything in a session (which models are open, where they are placed, colors, lighting, background color, shadows, …), then just use an animation script to modify a few things. If you instead try to do all the setup in a script with no session it is much harder. I don't understand your question about clipping. Normally Chimera does not clip your maps when you zoom in. Only if you turn on clipping or make your view point move right through the map would you see clipping. Tom On Jun 11, 2013, at 1:07 AM, Anindito Sen wrote: > Hi Tom, > > In the Video tutorial about making a movie of flying through the protein complex - how can I have the positions saved (sav pos) and put it in a script. The idea is to modify a script that makes a density map rotate (which I already have) and then fly in through that. I can then alter the script accordingly to show different regions of the map (and will not need to type the whole set of commands). > > Secondly how can modify my script to zoom-in a density map without clipping the region of interest. It is obvious that a major portion of the map will be outside the view but the clipping plane will not move and clip the map (like when we zoom in manually in the Chimera window using the mouse. > > Thanks > > Andy > >> Dr. Anindito Sen (Ph.D) >> Department of Cell Biology & Anatomy >> Graduate School of Medicine >> University of Tokyo

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ligating two models
by Bala subramanian 06 Jun '13

06 Jun '13

Friends, What is the best method in chimera to ligate two models. I have generated a small ligand that has to be attached attached to a protein residue. Thanks in advance, Bala -- C. Balasubramanian

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Maximum volume size
by Tom Goddard 05 Jun '13

05 Jun '13

Hi Svetla, Chimera is correctly handling your 880x880x880 map. But by default Chimera displays only a single plane of very large maps, because the most common case of this is with tomograms where a single plane display is usually what you want. When it does this the Volume Viewer dialog shows a "Planes" slider in the dialog, and below that is a button "All" that will show all planes. If you want Chimera to always show the full map, use Volume Viewer menu entry Features / Data Display Options, and click off "Show plane when data larger than N Mvoxels", and then use Features / Save Default Dialog Settings so it will use that setting in all future uses of Chimera. Tom On Jun 5, 2013, at 9:54 AM, "Stoilova-McPhie, Svetla" wrote: > Dear Tom, > > Are there any limitation for the size of 3D map/volume the Volume viewer can visualize? > > We tried a 880x880x880 voxels map generated with spider and it comes out as a 2D map: 880x880x1. > WE triple checked and the volume file dimensions are indeed 880x880x880 and can be visualized as a 3D volume in the EMAN2 viewer. > > Please advise. > > Best regards, > > > Svetla Stoilova-McPhie, PhD > Assistant Professor, > Department of Neuroscience and Cell Biology > Scientist, Sealy Centre for Structural Biology > and Molecular Biophysics > University of Texas Medical Branch at Galveston > 301 University Boulevard, Galveston, Texas 77555-0620

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sementation
by Jingchuan Sun 05 Jun '13

05 Jun '13

Hello, After segmentation of a 3D map into 16 subunits and assign different colors, the saved .seg map does not save the color. During the preparation of our recent paper, we had to assign the color each time we open the .seg (hundreds of times), which make me very upset, even angry sometime. If the guy writing the program allow us to save the assigned color, that would have saved us many times. Thanks! Jim

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Re: [Chimera-users] Flip handedness of map
by Tom Goddard 05 Jun '13

05 Jun '13

Hi Michael, To flip the hand of map #0 use vop zflip #0 This makes a copy of the map with the z-planes in reverse order. Tom On Jun 4, 2013, at 9:09 PM, Michael Stowell wrote: > Tom, > > There used to be a simple way to change the handedness of a map in Chimera, just use a negative voxel number. However, this no longer works but rather gives an error. Is there a new way to achieve this. This is very helpful when assessing the handedness of EM maps. > > Thanks > > m > > Michael H. B. Stowell > MCD Biology and Mechanical Engineering Departments > University of Colorado > Boulder, CO

1 0

Request for assistance
by Zachary W. Carpenter 04 Jun '13

04 Jun '13

Dear Chimera, I have been a long time user and really love your software. Recently I have used and cited Chimera in 4 high impact publications. One in mBio, two in nature medicine, and a final one in review at Nature Genetics. I have used Chimera to make beautiful images of mutations that we identify in NGS data of tumors. My role has become interpreting the effects of mutations on crystal structure. Thus far this has not been difficult as the effects of the mutations have been obvious. A recent finding however has left me extremely perplexed and I have need for greater accuracy of structural modeling of the mutations. I was wondering if you can put me in the right direction for creating models of mutations that are more reliable then just using Modeller or I-Tasser with the mutant in the sequence to be predicted. I know this is an elaborate question but I'd like to know which Chimera tools I can use to help me along this path. Or if I need to use totally new software/ methods. Thanks for your time, Zach -- Zachary W. Carpenter Department of Pharmacology College of Physicians and Surgeons Columbia University 630 West 168th Street New York, NY 10032 Email: ZWC2101(a)Columbia.edu

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To build ssDNA to base pair with the other strand of DNA
by Wei Shi 04 Jun '13

04 Jun '13

Hi all, I am working on solving the crystal structure of a protein-DNA complex. I could complete one strand of the DNA to fit the electron density using Coot, but for the other strand, the density for several bases at each end of the DNA is not clear and it's missing several bases at each end of the DNA. I am wondering whether in chimera, there is a function I could use to build the missing bases in one strand of the DNA to base pair with the other strand of DNA which is complete. Thank you so much! Best, Wei

2 2

Re: [Chimera-users] Just starting out
by burt.goldberg＠gmail.com 03 Jun '13

03 Jun '13

Dear Elaine, it is very hard for Senior faculty to audit a class. As for the Biochemistry well I have been teaching it for several decades. My interest is to learn how to use Chimera better and I will be working with a post doc experienced in using Chimera. I just want to read so I can ask intelligent questions. I am employing this in an on going research project. Thank you again for you help. ------Original Message------ From: Elaine Meng To: burt.goldberg(a)gmail.com Cc: chimera-users(a)cgl.ucsf.edu List ReplyTo: chimera-users(a)cgl.ucsf.edu List Subject: Re: [Chimera-users] Just starting out Sent: Jun 1, 2013 12:53 PM Hi Burt, This forum is meant for questions about the Chimera program. Proteomics and informatics are vastly broader areas. You might want to look for recent textbooks and journal articles on those topics, and/or audit some classes, and/or attend the group meetings and seminars of academic researchers in those areas. It's not clear whether learning Chimera should be one of your goals at this point. Which tools and programs are needed depend on the research problem at hand, and the types of data that are available for tackling that problem. If you do want to learn how to use Chimera, there are indeed several step-by-step tutorials. Before doing any tutorials you can explore the website just to get a better sense of what the program is for: <http://www.cgl.ucsf.edu/chimera/index.html> The "Quick Links" section on that page includes tutorials. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 1, 2013, at 9:34 AM, burt.goldberg(a)gmail.com wrote: > Dear all, after 40+ years doing wet work I had to leave the bench, medical reasons, and so although my students continue doing work at the bench I have decide to go the route of proteimics and informatic for myself. The informatics is fine. How do I get started on the proteimics? Does the tutorial help? Any thing some one can suggest I read first? Thank, Burt > Sent via BlackBerry from T-Mobile Sent via BlackBerry from T-Mobile

2 1

How to calculate the deviation of two ligands in the same pocket
by felipe vasquez 03 Jun '13

03 Jun '13

Hi, I am working on the modeling of one ligand in a native and mutant receptor. The ligand occupies different positions in the binding cavity, and I am interested in estimate this difference. However, if RMSD is calculated via MatchMaker, the ligand in mutant receptor (non-reference) is moved from its original position to try to minimize the deviation compared to ligand in native receptor (reference). How can I calculate the difference in the ligand position between the two receptors, in an appropriate manner? Best regards, * * *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

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How to force Chimera to properly analyze and visualize in each MD movie frame the ribon representation of the protein structure ?
by Marek Maly 01 Jun '13

01 Jun '13

Dear all, I just found that if one loads several frames from the simulation (Amber prmtop + inpcrd, *.rst files) chimera calculate/set the character of ribons (random colil, beta sheet, alpha helix) just using the first loaded frame and even if structure of the protein is changing in the next frames (e.g. forming beta sheet structure from the originally random coil), the visual ribon representation is not changed. I found this, when I loaded just the isolated frame from the simulation and saw nice forming of the local beta sheet which was nicely highlighted by proper ribon representation (wide arrow) in the palce where was originally (in the initial frame) just random coil. But when I loaded both (initial frame and that after some MD simulation), chimera keep to use random coil representation for both frames. I did also reverse experiment i.e. first loaded later frame from MD simulation and then the initial frame and this time chimera fixed for both frames beta sheet representation in that protein area. Please is there any possibility to prevent such unwanted behavior and to force Chimera that analyses properly protein configuration at each loaded frame and eventually changes properly the ribon representation ? Thank you in advance for any useful advices ! Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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fetching EDS files from the web (python script)
by Laleh 31 May '13

31 May '13

Hello. I'm wondering how I can fetch a bunch of EDS files (from the EDS server) and save them in my local machine in .mrc format. I don't want to do this manually one by one from the user interface... I tried to use open_volume_file with different settings; but it is not working... I'm surprised because this is very starightforward with pdb files. I appreciate your help. Thanks in Advance, Laleh

3 2

castP, Chimera and atom numbers
by Boaz Shaanan 30 May '13

30 May '13

Hi, Apparently Chimera insists on consecutive serial atom numbers (the first column after ATOM in the pdb file) when it reads in castp files. If that's not the case (as most often happens when hydrogens are attached during the refinement run but are not written out to the final pdb) Chimera complains about incompatibility between the mouth file and coordinates and refuses to read in the castp files. This is my first encounter with a program that cares about the atom number column but I learnt it the hard way. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

2 1

Tube representation picture of the eigenvector
by Prasanna Venkatesh 29 May '13

29 May '13

Dear Chimera users and supporters, I would like to generate a tube representation picture similar to one in the article (Figure 5 in "MD Simulations of Papillomavirus DNA-E2 Protein Complexes Hints at a Protein Structural Code for DNA Deformation"). Through Gromacs, I have average.pdb and extreme.pdb of my protein for the MD simulations. Please help me by providing the steps to make the picture. I asked the question earlier but not getting the similar picture with the answer provided. I don't know I asked it right the last time. Thank you in advance. Regards, Prasanna.

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How to deselect a subset of atoms in a non-standard residue
by felipe vasquez 28 May '13

28 May '13

Hi, I am trying to select all hydrogens atoms in a protein structure to achieve an energy minimization process. However, I would like to discard of the selection the hydrogen atoms of a non-standard residue (in my case a cofactor, NADPH). How can I deselect only this subset of hydrogen atoms of the whole hydrogens selection? Best regards, *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

2 2

How to delete range of solvent molecules
by felipe vasquez 22 May '13

22 May '13

Hi, I am trying to prepare a protein structure for docking, and I want to keep just one or a couple of water molecules. How can I do achieve this goal, deleting the rest of solvent molecules? Thanks in advance. Best regards, * * * * *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

2 1

Distance measuring
by T-I 22 May '13

22 May '13

Dear Chimera, I want to know something very simple which is making my life very difficult at the moment. I have an EM map of a virus capsid and I would like to make various distance measurements. I simply want to draw a strait line and measure it or place two points on the map and measure the distance between them. I have read all your help files on this matter and I cannot make any sense out of the instructions Can you help me out ? Thankyou Mr A.I

2 1

Fitmap in batch mode
by ingvar 22 May '13

22 May '13

Hello, I am trying to run fitmap on a set of volumes on a server without a display. I would like to collect the results of the top hits to store in a database – correlation coefficients, inclusion scores, and the transforms. The only way I found to collect the fitting results is to save the session after displaying the listFits dialog. The listFits dialog cannot be displayed when running Chimera in –nogui mode, otherwise this would have been a solution. I tried to use a virtual display, with Xvfb. I have used Xvfb with some java applications in the past. When I use Xvfb with Chimera, it appears that Chimera do not want to start up properly, the process just hangs, i.e. no cpu usage. Is there a way around this, or am I asking for an enhancement, e.g. a “writeListFile toFile” option. I am on RHEL 6.2/6.3 if that matter. Noticed that there is a local correlation option in the pipeline for Chimera 1.8, looking forward to try it out. Kind Regards, Ingvar Typical python script: from chimera import runCommand as rc rc("open emd_5500.map") rc("volume #0 level 1.34 transparency 0.5") rc("open emd_2017.map") rc("volume #1 level 0.58 transparency 0.5") rc("fitmap #1 #0 search 200 metric overlap envelope true inside 0.2 listFits false") #rc("fitmap #1 #0 search 200 metric overlap envelope true inside 0.2") rc("save session5500_2017") rc("stop now") Setup to run with Xvfb (in bash): i=0 while [ -f /tmp/.X$i-lock ] do i=$[$i+1] done Xvfb :$i & pid=$! export DISPLAY=:$i chimera fit5500_2017.py kill $pid

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Pipes and planks representation
by Ernesto Arias Palomo 21 May '13

21 May '13

Dear chimera developers, I have noticed that in the last Chimera releases you have significantly improved the 'pipes and planks' representation. I find it particularly useful because, in my opinion, it makes the structures look simpler and clearer, especially when you are displaying large PDBs. I would like to suggest an improvement. It would be really useful if you could make that representation an attribute of the structure (like the 'ribbons' one) instead of a separate object. That way one could easily show, hide or color different regions of the structure without having to modify the actual PDB file. Thank you very much for your help, and congratulations for your great work. Cheers, Ernesto.

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Re: [Chimera-users] RMSD i.b and RMSD u.b
by Elaine Meng 20 May '13

20 May '13

Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of just my address. The RMSD lb (lower bound) and RMSD ub (upper bound) of a docked ligand are calculated by AutoDock Vina and are described in the manual for that program: <http://vina.scripps.edu/manual.html> (go to that page and search for "RMSD") I believe they just indicate how similar each position is to the best-scoring position found. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 20, 2013, at 6:10 AM, Muhammad ALi <muh.ali741(a)yahoo.com> wrote: > AOA > > sir > when I check my result with ViewDock their are two RMSD values i.e RMSD i.b and RMSD u.b plz tell me about them.....

1 0

3D Printing our protein
by Bart Janssen 20 May '13

20 May '13

Hi My apologies for what are likely to be stupid questions. We are plant developmental biologists and we just obtained our first X-ray crystal structure for a new hormone receptor in plants. We'd really like to make a 3D model of the protein using one of the 3D printers at our institute. I've been trying to use and understand Chimera for the last week and I'm a bit out of my depth :). I can import our protein 4DNP.pdb and display it using solid surface or using the sphere representations of atoms. I can also display it with the "lid" domain hidden and vice versa. My problem has been getting files that our 3D printer can read. The solid surface model of the whole protein can be exported as a scene in .stl format and that can be printed just fine. Although I can't figure out how to adjust resolution or the smoothness of the exported file. But I'd really like to print the two domains of the protein separately. If I use Solid surface model with the lid hidden what I get is an eggshell like model which has no internal detail. If I use atoms shown as spheres instead I get the internal detail I want BUT when I try and export the scene I get a 2 Gb+ file that is unreadable by the printer. If I export .obj format instead the colleague who runs the printer says the file won't load and appears to have errors. I have a horrible feeling I am going about this entirely the wrong way but I can't find a tutorial that describes what I'm trying to achieve. I do realise chimera is not really written for the somewhat trivial use that I am attempting but it really would be helpful if we had a physical model of the protein to look at. Is there a tutorial I should follow or another part of Chimera (or another program) that I should be using instead? Any advice would be much appreciated. Cheers Bart Bart Janssen Scientist Plant Development team Breeding and genomics Plant and Food Research Private Bag 92169 Auckland 1142 New Zealand Ph +64 09 9257179 bart.janssen(a)plantandfood.co.nz The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited.

5 7

showing salt bridges in pdb trajectory movie
by Albert Lyons 18 May '13

18 May '13

Hi all, I am having a problem trying to show salt bridges between selected atoms in a movie of my pdb format trajectory. I am using the following commands in the Per-Frame script, to display H-bonds between the residues but with a less strong distance criterion (to bring the distance of interaction to 6 A) and angle criterion (to make the angle 0deg and so make all angles available): select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 When I apply this script I get a Chimera error saying: Error while sourcing select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 ,line 1: "findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145" Non-alphanumeric character in keyword ':6@2HH2,2HH1,HE,2HH1,1HH1' I have tried tweaking it different ways but just get other error messages, I can't seem to write it in the correct format. Can anyone see a problem with this script and how I might fix it? Cheers Albie

2 1

showing salt bridges in pdb trajectory movie
by Albert Lyons 18 May '13

18 May '13

Hi all, I am having a problem trying to show salt bridges between selected atoms in a movie of my pdb format trajectory. I am using the following commands in the Per-Frame script, to display H-bonds between the residues but with a less strong distance criterion (to bring the distance of interaction to 6 A) and angle criterion (to make the angle 0deg and so make all angles available): select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 When I apply this script I get a Chimera error saying: Error while sourcing select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 ,line 1: "findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145" Non-alphanumeric character in keyword ':6@2HH2,2HH1,HE,2HH1,1HH1' I have tried tweaking it different ways but just get other error messages, I can't seem to write it in the correct format. Can anyone see a problem with this script and how I might fix it? Cheers Albie

1 1

Re: [Chimera-users] Conserved amino acids
by Rebecca Swett 17 May '13

17 May '13

Use match-> align to get a structural superposition and sequence alignment, then set your alignment type to AL2CO. Go to render by attribute and then hit the select by attribute tab. Select the range from 0-whatever your maximum is. Should be around 4 if you've got any conserved tryptophans. That will select all invariant residues. Jean-Paul Boissel <boissel(a)uni-mainz.de> wrote: >Hi, > >By homology modelling, I got putative structures for five closely related >amino acid transporters. Is there any script that will allow the quick >selection and visualisation of the invariant residues on the structures? >Thanks, > >Jean-Paul > > > > > >_______________________________________________ >Chimera-users mailing list >Chimera-users(a)cgl.ucsf.edu >http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

2 1

Conserved amino acids
by Jean-Paul Boissel 17 May '13

17 May '13

Hi, By homology modelling, I got putative structures for five closely related amino acid transporters. Is there any script that will allow the quick selection and visualisation of the invariant residues on the structures? Thanks, Jean-Paul

1 0

Carbon color of 1 chain
by Markus Heller 16 May '13

16 May '13

Hello, I don't seem to be able to figure out how to color a scene by element, but with different carbon colors for different chains. I can't figure out how to get an expression like "color green, chain C C" Or something like that ... How to go about this? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller(a)cdrd.ca<mailto:kessabar@cdrd.ca> | www.cdrd.ca

4 7

Re: [Chimera-users] energy optimization of the modle from homology modeling
by Elaine Meng 16 May '13

16 May '13

Hello, I agree with what Tom Goddard said: "How to make a suitable homology model for docking and what force fields to use are not questions specific to Chimera, they are questions about how to do good quality science, and they depend a great deal on the details of your system. So you aren't likely to get the answers you want on this list." Instead, you have to use your scientific judgement and your knowledge of this protein, how similar it is to the template protein, etc. The procheck statistics are only one thing to consider. One reason is that they are for the whole protein, whereas you mostly care about the binding site. Another is that they focus on stereochemical quality, mainly torsion angles, but not other descriptors such as whether the protein is well packed. You could see what others have done in published papers, and/or ask on the Computational Chemistry List (see <http://ccl.net/cgi-bin/ccl/send_ccl_message>) and the Modeller discussion forum (see <http://salilab.org/modeller/discussion_forum.html>) if it is recommended to minimize homology-modeled structures before docking. In complicated structures like proteins, atoms may "feel" multiple conflicting forces, and minimization will usually relieve some strains (for example, move atoms apart if they are too close together) but increase others (for example, distort the angles of the sidechains containing those atoms). That is why the statistics from procheck got worse. It is important to realize that minimization has very little ability to fix a complicated structure with a rugged energy landscape. It is good for cleaning up small molecules, and sometimes for cleaning up a localized area (leaving the rest of the protein unchanged) where you have made some change such as manually rotating some bonds or mutating a residue. It will not predict any significant conformational change to find the global optimum. If you don't have any specific reason to minimize the structure, it might be better not to minimize it. That is only my guess, and you could probably get more expert opinions by asking your question on the other discussion lists mentioned above. If your docking doesn't take too long, you could try docking to more than conformation of the protein (more than one model). Chimera does not do molecular dynamics, although it can show MD results from other programs. However, Modeller itself does sampling to generate multiple models. Also, you could consider using Modeller to further refine parts of the model(s) from the first Modeller calculation. The Modeller scores should provide some indication of which models and refinements are better. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 14, 2013, at 9:39 AM, Conrad Huang wrote: > Unfortunately, that is getting well beyond my understanding of molecular mechanics. I will have to defer this to our expert when she returns. > > Conrad > > On 5/13/2013 7:56 PM, aixintiankong wrote: >> Dear, >> Thank you for your patience to answer my questions in detail. >> Before /minimizating/ the model, i use the procheck to check the >> quality of the model. the residues in most favoured regions is 95.6% and >> the disallowed regions is 0.0%, the the residues had an averaged 3D-1D >> score>0.2 is 92.02% and the errat is 90.55. >> if i use the chimera to minimizate the model after 200 steps, the >> most favoured regions is 85.5% and the disallowed regions is 0.4%, the >> the residues had an averaged 3D-1D score>0.2 is 99.2% and the errat is >> 95.968. >> if i use the chimera to minimizate the model after 250 using the >> ff99sb! force filed, the most favoured regions is 92.1% and the >> disallowed regions is 0.4%, the the residues had an averaged 3D-1D >> score>0.2 is 96.96% and the errat is 98.000. >> if i use the chimera to minimizate the model after 500ns the most >> favoured regions is 90.8% and the disallowed regions is 0.4%, the the >> residues had an averaged 3D-1D score>0.2 is 96.58% and the errat is 96.047. >> which one model should i select to make docking . >> thank you very much! >> >> At 2013-05-14 00:24:03,"Conrad Huang" <conrad(a)cgl.ucsf.edu> wrote: >>> Unfortunately, our local expert on this is on vacation and will be back >>> at the end of the week, so a more definitive answer should come then. >>> In the mean time, I'll try to answer as best as I can. >>> >>> First, Homology Modeling uses Modeller and that does a bit of >>> optimization already. If the model structure looks reasonable, further >>> energy optimization might be helpful. On the other hand, if the model >>> has extended chains because Modeller does not have appropriate templates >>> or just looks unreasonable because the model is not well packed or has >>> large dangling loops, then energy minimization probably will not help. >>> >>> Second, I do not know the answer, but have you tried using the default >>> paramters? >>> >>> Third, conjugate gradient is much much slower than steepest descent, so >>> it probably pays to use steepest descent to get near the minimum before >>> starting conjugate gradient. You can look at the reported energy values >>> reported to decide whether the minimization is proceeding as expected. >>> Chimera energy minimization is not highly optimized, so it may take a >>> while to run for a large system. If only one portion of the model is >>> "interesting", e.g., an active site, it might be faster to select just >>> the region of interest (plus a buffer around it) and only optimize that >>> part. >>> >>> Hope this helps a bit. Better answers should come later in the week. >>> >>> Conrad >>> >>> On 5/11/2013 6:50 PM, aixintiankong wrote: >>>> Dear, >>>> i am a newer use the chimea, i have some question to consult to you, >>>> please help me. >>>> Frist, after Homology modeling using the chimera modeller, should i >>>> optimizate the modle by energy optimization or Molecular dynamic >>>> simulations? The next step i will use the model to make docking. >>>> Second, i want to use chimera to minimize the structrue of my modle. >>>> i select Tools>Structure Editing>Minimize Structure to perform my >>>> work, but my modle include protein and a organic molecule NAD+, so i >>>> don't know how to select the force fileds for the minimiztion of the >>>> modle. please help me. >>>> Third, if i olny want to use the conjugate gradient to perform the >>>> minimiztion, should i only need to set the steepest descent steps to 0? >>>> in general, how many conjugate gradient s! teps and size should be ? >>>> Thank you very much!

1 0

Error reading PubChem3D SDF Files
by Jon Fuller 15 May '13

15 May '13

I tried to read an SDF file directly downloaded from pubchem into Chimera. However, I ran into the following problem (link to example file used, and reply log below). Is this expected behaviour, or a bug? Additionally I tried to import the pubchem CID 71739 (same compound) from the fetch structure by ID tab, and got the error message: Unexpected end of file (parser state: counts) in MOL/SDF file 'FILEPATH HERE!' Many thanks in advance, Jon http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=2385389770715… You are now running Chimera version 1.8 (build 38642). Your previous version was 1.5 (build 32133). Check the release notes for new features and other info. (To access the release notes, use the Help menu to bring up the User's Guide. Then click the 'Documentation index' link and you will then see a link for the release notes.) Error while processing CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data Error reading CID_3672_e5800000001_conf.sdf: Non-numeric charge (1 -0.65) in PUBCHEM_MMFF94_PARTIAL_CHARGES data Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data

3 4

energy optimization of the modle from homology modeling
by aixintiankong 15 May '13

15 May '13

Dear, i am a newer use the chimea, i have some question to consult to you, please help me. Frist, after Homology modeling using the chimera modeller, should i optimizate the modle by energy optimization or Molecular dynamic simulations? The next step i will use the model to make docking. Second, i want to use chimera to minimize the structrue of my modle. i select Tools>Structure Editing>Minimize Structure to perform my work, but my modle include protein and a organic molecule NAD+, so i don't know how to select the force fileds for the minimiztion of the modle. please help me. Third, if i olny want to use the conjugate gradient to perform the minimiztion, should i only need to set the steepest descent steps to 0? in general, how many conjugate gradient steps and size should be ? Thank you very much!

3 2

desmond in chimera
by lecan 15 May '13

15 May '13

Hi to everybody. Can the newest version of Chimera use the .cms files from desmond by schrodinger to analyse trajectories and make movies? Regrads, Luis L.

3 2

surface
by Gesa Volkers 14 May '13

14 May '13

Hi chimera users/developers, I have a problem with a surface calculation from one monomer of a structure that I want to show. As you can see in this image http://imageshack.us/photo/my-images/801/testss.png/ it looks like the surface calculation failed (?) because the surface is missing in the middle (note the chewed up structure of the surface). Most of the surface is smooth but for whatever reason not this part of the structure. I have played around with probeRadius, vertex density and zone and they all increase quality but do not add the missing surface part (I'm not even sure if zone is applicable to surfaces at all or only to electron density maps). Any suggestions which parameter I am missing? Thanks for suggestions, Gesa

2 2

Contour maps or step-gradient of volume map?
by Bullitt Esther 13 May '13

13 May '13

Hi, Is it possible to choose n levels of gray for a volume map? I'd like to make a known-thickness slice using clip, and then see that slice as a defined number of colors. I can kluge it by displaying the map 4 times at 4 contour levels, but is there a better way? thanks, Esther --- Esther Bullitt, Ph.D. Dept. of Physiology & Biophysics Boston University School of Medicine 700 Albany Street, Room W302 Boston, MA 02118-2526 Email: bullitt(a)bu.edu Telephone: 617-638-5037 Facsimile: 617-638-4041 http://www.bumc.bu.edu/phys-biophys/faculty/bullitt

2 1

mask using volume contour surface
by gongpu zhao 13 May '13

13 May '13

Hi All, I have a question about volume contour surface in chimera. I have a density volume of a shell shape. I plan to use the outer contour surface of the volume to mask out all density encased by the outer surface in a tomogram. But instead, I could only mask out the density within the shell. I am wondering if I can make a surface model only using the outer surface. Thanks a lot. Gongpu

2 1

About Morph Conformations
by 吕柯 13 May '13

13 May '13

Dear Sir./Madam, I am a graduate student in Chinese Academy of Sciences. I have two PDB files: one for virus(4 chains, PDB:3VBS), the other for empty particle(3 chains, PDB:3VBU). I would like to use Morph Conformations to make movie for that. However, it turns out "Can not interpolate models: models have different number of chains". Could you please show me what should I do next? Thanks a lot. Yours, Lyu Ke -- Lyu Ke, Ph.D. student Structural Virology Unit Institut Pasteur of Shanghai Chinese Academy of Sciences No.411 Hefei Road Shanghai, 200025, P.R. China Tel: +86-21-54920652

2 1

Re: [Chimera-users] saving sessions
by Tom Goddard 08 May '13

08 May '13

Hi Thomas, There is no session saving option that copies density map files to the same directory as the session file. All other Chimera models including PDB files are included (not linkied) in the session file. The reason maps are not put into the session file is because they are sometimes very large, Gbytes in size. Some day I intend to add an option to include the maps in the session file so you can have a self-contained session if you want. Copying the files could be another approach but it has problems. What if there is already a map with the same file name in the current directory? Could modify the copied file name I guess. Maybe better put all the map files in a new subdirectory. But are you really going to make copies of all the map files on every session save? If you only do it sometimes it doesn't solve the problem of moving data to a new computer. It will be slow to copy the files and it makes many redundant copies which then can become confusing as to whether two files with the same name really are identical. Hard links could be used to avoid copying the file, but that won't work when a session is on one file system and data on another. I think the way to handle moving data files to a new computer is to keep all your data including sessions under one directory tree so the whole thing can be easily copied. If instead the goal is to occassionally make a self-contained session then copying the map files and session file to a new directory would be a nice option similar to embedding all files in the session. I've noted this in the feature request for embedding the map files. http://plato.cgl.ucsf.edu/trac/chimera/ticket/9763 The sphere/axes display idea is one way to see the axes of a displayed model. The transparent sphere would cause problems in Chimera some of the time because Chimera can only correctly display one transparent model at a time. The current default is to show a single transparent layer, so any transparent model inside the sphere would disappear. This is a longstanding and hard problem to fix. But a mesh could work. Another idea is simply to depict the x,y,z axes. I've made a feature request for this. http://plato.cgl.ucsf.edu/trac/chimera/ticket/12062 Tom On May 8, 2013, at 12:25 AM, "Marlovits,Thomas" wrote: > Hi Tom, > > I do have a question related to saving sessions, which is a great option btw. > Is there a way that one can save the session - let's say in a new folder but then have all models also saved in there. For now, as I understand, it will only save the path/filename of those models. So, whenever we switch computers, hard-drives etc … this can turn out to be a lengthy process to find those models (we often have many models open at the same time). > Ideally, also fetched files from the pdb would be great to be saved locally in this new folder. > > The second question I have is related to turning molecules around specific x/y/z angles. > I'd love to have an option to display a big sphere that encapsulated the other models displayed. Ideally, this sphere would look like a globe with cordinates in there … if this is displayed at semi-transparency, one can easily go to a specific position but get more of an idea to easier naviagte through the 3D space. Sometimes I only would like to get a rough estimate about the angles to turn molecules. Alternatively a mesh-like grid could do the same job (and if one could display the numbers of the lattidude/longitude or so that would be great too). > > Many tx, > -T. > > > ------------------------------------------------------------------------------- > > Thomas C. Marlovits, PhD, M.A.S. > The MarlovitsLab @ IMP/IMBA > http://thomas.marlovits.myresearchlab.org > > Contact/Address/Directions: > http://thomas.marlovits.myresearchlab.org/lab/Contact.html >

2 2

Define centroid issue
by Francesco Pietra 08 May '13

08 May '13

Hello: I was unable to put to work define centroid radius 0.5 color red :ligand_residue_name or define centroid radius 0.5 color red #0&@serialNumber=1972 with a homodimeric protein (I am at CHARMM NAMD/XPLOR, so that the two subunits are only distinguished by either the atom sequential number or the segment name, the latter not being understood by chimera, as far as I know). In the first case, running the movie after the appropriate further steps, the centroid sequence obtained was for the centroid between the two protein ligands, as it was expected. In the second case (as I wanted to refer to the ligand in subunit A only), the command raised the error: AttributeError: 'NoneType' object has no attribute 'openState' File "/opt/UCSF/Chimera64-1.7/share/StructMeasure/Geometry.py", line 293, in _getRefInfo invXForm = lowest.openState.xform Please notice that the line command #0&@serialNumber=1972 correctly selects the ligand on subunit A (a diatomic ligand, where "1972" is the sequential number of one of the two atoms of the ligand. Here "#0" may be redundant, as it deals of a single model. However, using "@serialNumber=1972" raised the same error. I fear I am missing some obvious facet of define centroid, so that I thank you for your patience. francesco pietra

2 2

Question about measuring volume in chimera
by Varun Kumar 07 May '13

07 May '13

Hi, Can we outline a particular area and measure volume in chimera? I wish to measure specifically the purine binding site in the ATP binding pocket of Protein kinase C. Best regards -- Varun Kumar International Graduate Student School of Biomedical Sciences Department of Biological Sciences Kent State University, Kent, Ohio, U.S

2 2

RMSD
by George Tzotzos 04 May '13

04 May '13

Hi everybody, I am trying to measure the RMSD between a docked ligand and the corresponding ligand in an X-ray structure. I've been looking to find a way of doing this in Chimera to no avail. I'd be grateful for any suggestions on how to do this. Best regards George

2 2

save map with the adjusted threshold
by Moumita Dutta 01 May '13

01 May '13

Hello, I'm not sure if I can do this in chimera. Once I open a density map and adjust the threshold and removed dust how can I save the map in this setting so that next time when I open it I don't have to adjust again. Thanks

2 2

Chimera shutsdown when opening sideview
by vamsee 29 Apr '13

29 Apr '13

Hi Elaine, I have recently moved to Linuxmint 14 from Windows 7. I can open virus capsids very easily (much more easier than in Windows 7, which is pretty sweet). But, every time I try to open the Side View option from the menu, Chimera shuts down. I have tried version 1.7 and 1.8rc. Both exhibit the same behavior. The interesting thing is, I can open all the other tabs (Effects, Lighting etc.) on that window from the menu. But when I click on Side View, Chimera crashes immediately with no bug report (Its almost like the process never existed). So, I tried starting chimera from the command line with the Side View option enabled (sudo chimera --start "Side View"). That started the Side View window and that stayed even after I opened my models. I then closed the Side View and re-opened it from the menu bar this time in the same chimera session. That worked again. So, I am kind of at a loss though I seem to have a work around for now. I have used the same features on Windows 7 (I still do using a virtual machine inside Linux) and they work fine. Any reason why this would happen? My computer specifications Processor : Intel® Core™ i7-2630QM CPU @ 2.00GHz × 8 Memory : 8Gb Onboard Video : Intel® Sandybridge Mobile OS : LinuxMint 14 Thank you Vamsee

2 1

morph conformation
by Moumita Dutta 27 Apr '13

27 Apr '13

Hello chimera-users, I'm trying to use the option morph conformations from the command line and cannot specify more than one molecule with the command morph start. How to use the morph start command for more than two molecules ? Thanks for any help. Moumita

2 1

morph map and movie recording
by Moumita Dutta 26 Apr '13

26 Apr '13

Hello, I am trying to morph more than two maps at a time so I am using vop morph instead of Morph map. I am following the mini-video animation example script of vop morph using the recommended chimera 1.7 version 2013. The script actually recorded the movie but in the movie threshold changed from what I set and it turned some maps to x 90 degree not all and it is not showing the morph animation only the superimposed maps. Another problem is though I remove the dust after loading the maps but it came back in the morph and in the movie as well. How can I fix the problems and generate the movie ? Moumita

2 3

Ubuntu 12.10 and Chimera update #2
by Greg Couch 25 Apr '13

25 Apr '13

Found a better solution to Chimera's problems on Ubuntu 12.10 -- just install Ubuntu 13.04! HTH, Greg

1 0

Re: [Chimera-users] movie recording from morph map
by Elaine Meng 25 Apr '13

25 Apr '13

On Apr 25, 2013, at 1:01 PM, "Moumita Dutta" <dutta(a)bio.fsu.edu> wrote: > Hi Elaine, > I am trying to morph more than two maps at a time so I am using vop morph instead of Morph map. I am following the mini-video animation example script of vop morph like below > > Record the movie > # > > movie record supersample 3 > > wait 1 > movie crossfade > vop morph #0,1 frames 200 > wait 200 > > movie encode morphmap.mp4 morphmap.webm morphmap.ogv bitrate 200. > > It starts recording the movie but it does not stop. > Best, > Moumita Hi Moumita, The first thing to check when following a tutorial or examples is your version of Chimera. The top of the mini-examples page <http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html> says that they were made with Chimera version 1.7 from March 2012 or newer. In those versions, movie recording will automatically stop when you use "movie record." In older versions, you have to use the "movie stop" command to stop recording before you do the encoding. (I cc'd chimera-users(a)cgl.ucsf.edu -- please use that address for Chimera questions unless your data are private) I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Seeking guidance on Volume-volume fitting
by ingvar 25 Apr '13

25 Apr '13

Dear Chimera, I am seeking guidance on what would be best practice in doing volume-volume fitting, and what expectations should I have on number of trial conformations. For instance would it be beneficial to resample one of the volumes to the same grid as the other volume. What about volumes with different resolutions, do this require any special handling. In the case below it would probably be more efficient to just align the principal moments of inertia of the envelopes above the contour level and then do a search from there, though this will only work well if the volumes are very similar. In an initial study I used 3 EM volumes from EMDB, (EMD-5500, EMD-5501, and EMD-2017). They are all 30S E. coli ribosomes of similar resolution (12.9, 14.0, 13.5 Å). I thought that this would be a relatively easy starting point, with the intent to then go on to fit 30S subunit in some of the many E. coli 70S EM volumes that are available. The volumes EMD-5500 and EMD-5501 are in similar orientation, while EMD-2017 is in a completely different orientation. The grids are similar but not identical, 125^3 vs 128^3. I adjusted the contour levels from the EMDB recommended values to make the enclosed volumes more similar in size. Contour levels used: EMD-5500 -2.8 -> -2.5 EMD-5501 -2.8 EMD-2017 39 -> 32 I am using scripts like the one shown here: from chimera import runCommand as rc from chimera.tkgui import saveReplyLog rc("open data/EMD-5500.map") rc("volume #0 level -2.5 transparency 0.5") rc("open data/EMD-5501.map") rc("volume #1 level -2.8 transparency 0.5") rc("fitmap #1 #0 search 50000 metric cam envelope true inside 0.2") saveReplyLog(r'/Users/ingvar/chimera/log/fit5500_5501_loc.txt') It seems correlation about mean is the best metric for volume-volume fitting, and that it is best to only use points inside the envelope. The maps EMD-5500, and EMD-5501 have the unusual feature that the density range is shifted downwards so that the average is well below 0. I was concerned about that and moved the density range, but with the fitmap parameters above that did not seem to have any significant impact (with other sets of parameters the density range appears to be an issue). In this case, it is relatively easy to see when you have found the "good" fit, all other fits have clearly worse statistics. What I was surprised about was the number of trial conformations needed to be reasonable certain to find the "good" fit. 5500 in 5501 7 times in 5000 5501 in 5500 2 times in 5000 5500 in 2017 0 times in 5000 5500 in 2017 8 times in 50000 2017 in 5501 0 times in 5000 Many Thanks, Ingvar Lagerstedt

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morph map and molecule together
by Tom Goddard 24 Apr '13

24 Apr '13

Hi Moumita, You can morph both maps and molecules at the same time. You use commands instead of the morphing dialogs in order to get them to play with perfect synchronization. The basic plan is to create the molecule morph and the map morph using the dialogs as usual. Then load a simple command script that starts both playing at the same time and records the movie. I'm sure this works in Chimera 1.7, probably in 1.6, and maybe in 1.5. Here is an example command script morphing a filament map and fit molecule http://www.cgl.ucsf.edu/chimera/data/santa-cruz-aug2012/scripts/movie2.txt and here's the resulting movie http://www.cgl.ucsf.edu/chimera/data/santa-cruz-aug2012/images/morph1.mp4 and here is the web page where I explain how this was done http://www.cgl.ucsf.edu/chimera/data/santa-cruz-aug2012/animate.html This was a demonstration I gave at the Bay Area Cryo EM meeting in Santa Cruz last summer. Tom -------- Original Message -------- Subject: morph map From: Moumita Dutta To: goddard Date: 4/23/13 10:16 PM > Hi Tom, > > I want to morph a set of density maps and the atomic models fitted > into them together and run the two movies concurrently so that I get a > movie that shows how the density and the atomic models change > together. I have been able to make the two different sets of data > morph independently, but thought it more informative if they morphed > together. > > I was wondering whether this can be done using chimera ? If so which > version supports it ? > > Thanks, > Moumita > > >

1 0

Hide bonds
by Masaki Uchida 24 Apr '13

24 Apr '13

Dear Chimera users Is it possible to hide bonds between spheres (atoms/bonds view)? I have a "pdb" file which is a bead model of a protein generated by SAXS analysis. When I open the file and changed a view to "sphere" under "atoms/bonds", bonds between beads are shown. I believe the bonds are meaningless in this case and would like to show just spheres (beads). Thank you in advance for your help -- ********************************************** Masaki Uchida Department of Chemistry&Biochemistry Montana State University **********************************************

2 2

dock
by LW 23 Apr '13

23 Apr '13

Dear all, As attached, I have a structure of Saposin C in the presence of SDS micelle solved using NMR. I took the first model out of its 20-structure ensemble and generated SapC_one_model.pdb. I also have a PDB file(as attached )built to model SDS micelle surrounded by water. Does Chimera allow people to dock these two molecules and generate a combined PDB file for further analysis? While the structure of Saposin C in the presence of SDS micelle, NMR data indicate that the open hydrophobic core is in contact with SDS micelle. Is it possible to use Chimera to determine the relative orientation of the two molecules where (i), they are in intimate contact, (ii), there is no clash, (iii), the shape complementarity is at its optimal? Any clue would be much appreciated. Levi

2 4

batch production of images
by Benjamin SCHWARZ 23 Apr '13

23 Apr '13

Dear list, I am considering to use chimera to render (a tons of) pictures of models that I generated and issued in nice markerSet (.cmm) files. 1. If I understand well, the only way to do that is through the linux headless version, and there is no way to do that under MacOS X for the moment 2. I should then use the "copy" command. Something like : chimera --nogui --script "myscript.py" where myscript.py should contain something like "from chimera import runCommand; runCommand('copy file pipo.png')" 3. All my models were produced in a same cartesian, and I'd like to keep the orientation and "picture frame" similar for all pictures. What I mean here, is that I'd like to be able to set my camera somewhere, looking in a specified direction, which I would probably do under the chimera GUI; and then, shoot all my pictures from that point of view on a batch mode. How shall I do that (set a point of view for the camera and use it on a batchmode) ? Thanks a lot again for your great job, and your constant answers --Ben

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stereo viewing with consumer graphics cards
by Greg Couch 23 Apr '13

23 Apr '13

In the past, Chimera has always needed a workstation-class graphics card (e.g., AMD FirePro or NVIDIA Quadro) to view molecules in 3D stereo and read dialogs at the same time. Now that there are 3D HDTVs, that has changed. I have just confirmed that with a computer running Microsoft Windows 8, with an AMD Radeon HD 7850 graphics card, and a Panasonic 3D HDTV, that 3D stereo worked without fiddling with any display settings. That is awesome -- "without fiddling with any display settings". Windows 8 is a requirement, Windows 7 will not work. I am unaware of any effort to get Linux to work. There is a good chance that Apple Mac OS X will work and we plan to test that soon. Any recent AMD Radeon HD graphics card with HD3D, or NVIDIA GeForce graphics card with 3D Vision support, should work. I hope to test a NVIDIA graphics card soon to confirm that. And supposedly, any 3D HDTV will work. The 3D HDTV in the test was a Panasonic TC-P50GT25, from 2010/2011, and I expect that any 3D HDTV that support a full resolution stereoscopic 3D format will work well. Non-full resolution formats would work for the 3D stereo images, but the associated 2D dialogs would be unreadable. Happy 3D viewing! Greg

1 0

Distance between atoms at the interface
by Mehdi Talebzadeh Farooji 23 Apr '13

23 Apr '13

Dear Chimera Users, I was wondering if there is a way to show distances between two objects (two chains) and filter them; for instance to display all of the distnaces between atomes of two interacting protein chains which are less than 6 A. Any help would be much appreciated, Mehdi

2 1

View Dock plugin
by James Starlight 23 Apr '13

23 Apr '13

Dear Chimera users! I have a question about the View Dock plugin. >From some servers usually I've obtained pdb file of the target protein as well as separate file consisted of all predicted posses which I can visualize in Chimera. So I wounder to know 1- How I could hide hydrogen bonds as well as protein's side chains of the residues which are in contact with the ligands ( on the default both of that two options are turned ON) 2- How I could properly save some poses as the separate pdb models ? E.g when I chose to same target.pdb with the #1_pose from the chimera saving menu I obtain protein and ligand with the surrounded residues as two models in one pdb file ( so I must manually merge it in one model and delete residues from the second model). Does it possible to obtain protein-ligand complex as one model as the output? Thanks for help, James

2 1

multiple volumes' orientation in space
by Yunji Wu 22 Apr '13

22 Apr '13

Dear all -- I am a total newb to Chimera, and I have an issue which I feel like can be easily resolved with your help. I am trying to make a 'structure-based schematic' with the purpose of clarifying the locations of the domains of a complicated crystal structure. There are 12 domains in this structure that I want to represent as 'blobs', and they are oriented in space in a very confusing way, especially if represented as the standard ribbons or cartoons. I used pdb2mrc (in EMAN2) to create 25Å maps from my .pdb files for (with the command e2pdb2mrc.py -R 25 H.pdb K.mrc). These show up fine individually in Chimera, but the separate maps are not oriented properly in space. It looks like the map volume files have no instructions about where to be in space relative to the coordinate files that generated them. If I take a single .pdb file with all 4 chains and generate a single .mrc file, I obviously get something that has the chains correctly oriented. This is less useful and satisfying, since I'd like to make separate chains into separate map volumes so I can color them separately (for example: chains H,K,L,M as H.pdb, K.pdb, L.pdb, M.pdb into H.mrc, K.mrc, L.mrc, M.mrc). When these 4 volumes are plotted in Chimera, they appear to be semi-randomly piled in the middle of the viewing field, with no correlation to the original pdb coordinates (attached screenshot of volumes from 4 chains, calculated from 4 individual pdb files). Is this just a result of a preset in Chimera that I am not aware of that needs to be adjusted? If I plot the original pdb file with the 4 chains from which these volumes were generated, there is no spatial correlation between the structure and the volumes. In trying to solve this, I know that "Fit to Map" will allow the coordinates to be fit into the map volume, but I cannot seem to fit the separately map to the individual chains, which would be a longer way around the issue. Is there some way to do this, or to just create maps that are oriented properly in space relative to each other? Thank you so much for your help, Yunji Wu

2 1

Radius of gyratiion
by George Tzotzos 22 Apr '13

22 Apr '13

Hi everybody, I've search the archive to find a script for measure protein radius of gyration. I came across the following link: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007257.html I'm now trying to find the actual script <radius-of-gyration.py>. Any ideas how to retrieve it? Many thanks in advance George

3 2

euler angle
by Jingchuan Sun 20 Apr '13

20 Apr '13

Hi, After I rotate a volume to a specific orientation, and "save map as" in "volume viewer", the saved volume are still in the original orientation. Could I save it in the new orientation. If I could display the current euler angles, I can rotate it in other software. But how could I display euler angle after rotation? Thanks! Jim

3 4

Doubt
by Víctor J. Gallardo López 19 Apr '13

19 Apr '13

Good Morning Mr./Ms., I have a bit problem with the molecular modeling. I have a dímer (the two chains of this protein are the same sequence) and I want to put 34 residues at the N-terminal in each chain. I load my fasta (with this residues addition) in chimera and I blast a protein structure in the PDB that has the same residues as my protein without this addition. When I modeller (homology) my fasta, the programm only gives me one of the chain with this addition but I need the whole protein (with the two chains and with this residue addition for each chain as well). How can I do it? I hope you resolve my problems. Thanks you for you attention. Sincerely, Víctor J. Gallardo

2 1

Generating trajectory of a user-defined plane
by Lili Peng 18 Apr '13

18 Apr '13

Hi, I am interested in measuring the deviation of an helical segment with respect to the initial structure in a GROMACS trajectory. I have already uploaded my *.tpr and *.trr files into MD Movie and have defined a plane through the helical segment within the initial structure. Is it possible to define another plane through the same helix and track the intersection angle throughout the trajectory? Thank you, Lili

2 1

python script running OUTSIDE chimera possible?
by frederick lee 18 Apr '13

18 Apr '13

hello chimera experts, as far as i know, python scripting for chimera is done within the context of chimera like chimera --nogui myscript.py parameters ... is it possible to run myscript.py without the need of the chimera executable and use import statements of some sort to access the chimera module(s) like python myscript.py parameters best regards, fred

2 1