- Chimera-users - RBVI Mailing Lists

Automatic struts for 3D printing?
by Hurt, Darrell (NIH/NIAID) [E] 23 Aug '13

23 Aug '13

Hi everyone, We are assembling an open data portal or "exchange" for producing "ready-to-3D-print" files for biological molecules, EM data, and other imaging data using some automated pipelines. A little bit more on our project can be found here: http://www.hhs.gov/open/initiatives/ignite/3d-printing-exchange.html A few years ago this came up on the "dev" discussion board: http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000800.html In the email thread above, it mentions a script by George Phillips called "struts.py" that was modified for use in RasMol. I am familiar with his version of this script for PyMOL. It works very well and I have been using it for years. However, the VRML from PyMOL is sometimes buggy. I like the exports from Chimera much better, including the X3D2VRML and X3D2STL utilities. If I could get the same functionality of this "struts" script in Chimera, that would be one less thing I need to go to PyMOL for (the list is getting shorter and shorter!). We're looking at doing it here, but I would welcome any contribution from the Chimera community if something already exists. Do you have anything? Is this script something of interest? Anyone interested in contributing to our "exchange" database/web portal? I would love any feedback you might have. Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Minimization and mystery nonstandard HIS atom name
by Jason L Burkhead 22 Aug '13

22 Aug '13

I am trying to minimize a protein structure and run into the following error: 'No MMTK name for atom "HND1" in standard residue "HIS"' My .pdb file specifies this atom as ND1, and if I change it to HND1 it still gives me the same error. Does anyone have any suggestions for a solution? The reply log is below: Thanks Jason No incomplete side chains No SEQRES records for COMMD1_C_terminus_c.2.0.pdb (#0) chain A; guessing terminii instead Chain-initial residues that are actual N terminii: GLY 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: ASN 73.A Chain-final residues that are not actual C terminii: 42 hydrogen bonds Hydrogens added Charge model: AMBER ff99SB Non-standard atom names: HIS HND1 (HIS 17.A HND1, HIS 22.A HND1) Total charge for #0: -4.000 Correct charges are unknown for 1 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms Details in reply log No MMTK name for atom "HND1" in standard residue "HIS"

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Re: [Chimera-users] [chimera-dev] UCSF Chimera Help
by Elaine Meng 22 Aug '13

22 Aug '13

Dear Neil, Chimera does not do docking except for fairly limited single-ligand calculations using an AutoDock Vina web service: you can only dock one ligand at a time and get up to 10 orientations back. You can't search a database of ligands, for example. The interface to the Vina web service is in the menu of Chimera version 1.7 (Jan 2013) and newer: Tools... Surface/Binding Analysis... AutoDock Vina. It is recommended you run other tools first to prepare the receptor before using this tool. See the manual page for details: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> However, Chimera does have a nice "ViewDock" interface for looking at the output from several docking programs that could be run outside of Chimera: DOCK, AutoDock, AutoDock Vina, Glide, GOLD, Mordor. If the fairly simple interface mentioned above does not suffice for what you want to do, you may want to try one or more of those other programs (several are free). The ViewDock man page includes links to their websites; see the "input" section: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.…> There is also a ViewDock tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html> I CC'd the chimera-users list because this is more of a user question than a developer (programming) issue. 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 Aug 21, 2013, at 1:23 AM, Neil Bugeja wrote: > Dear Sir/Madam > > I am a student at the University of Malta and I am currently using your software to carry out homology modelling for my thesis. > > I have a slight problem figuring out how to dock a ligand into a receptor on the program...Is this possible or do I need to install another software? > I tried looking through the available tutorials but cannot find any so far > > Thank you for your help > > Regards

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Re: [Chimera-users] RMSD for two ligands
by Pavithra 22 Aug '13

22 Aug '13

Dear Ma'am, Thank you so much. its working now. On Thu, Aug 22, 2013 at 2:25 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Dear Pavithra, > Chimera cannot guess which atoms to use when there are different numbers > of atoms in the two groups (#0 and #1). You would have to either > > (A) include all the names of the atoms, in the order you want them > matched, in the rmsd command. It would be something like: rmsd #0:15@c1,c2,c3 > #1:12@c10,c5,c2 (if you wanted to match residue 15 atom C1 with residue > 12 atom C10, residue 15 atom C2 with residue 12 atom C5, etc.). To see the > atom names, show labels, for example command: label #0:15#1:12 > > or > > (B) select all the atoms with the mouse (Shift-Ctrl-click) one by one, > first the atoms you want to match in the first molecule, then the atoms you > want to match in the second molecule in the corresponding order, and then > use "sel" to specify the atoms in the rmsd command > > The "rmsd" manual page can be viewed here (or by using command: help rmsd): > <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/rmsd.html> > > ... and more about how to specify atoms in the command line: > < > http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/atom_spec.html#bas… > > > > 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 Aug 21, 2013, at 1:05 AM, Pavithra wrote: > > > Dear Users, > > I want to calculate the RMSD of two ligand molecules of different atom > counts but have a common scaffold. > > I tried rmsd #0 #1 > > but I'm getting the error: unusual numbers of atoms chosen for > evaluation. > > > > rmsd #0:15-17 #1:15-17 > > atleast one atom must be selected. > > > could somebody help me to find the RMSD between two ligands of different > atom counts. > > -- > > regards, > > Pavithra.K.B. > > -- regards, Pavithra.K.B.

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RMSD for two ligands
by Pavithra 21 Aug '13

21 Aug '13

Dear Users, I want to calculate the RMSD of two ligand molecules of different atom counts but have a common scaffold. I tried rmsd #0 #1 but I'm getting the error: unusual numbers of atoms chosen for evaluation. rmsd #0:15-17 #1:15-17 atleast one atom must be selected. could somebody help me to find the RMSD between two ligands of different atom counts. -- regards, Pavithra.K.B.

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save colored blobs in session
by Zoltan Metlagel 20 Aug '13

20 Aug '13

Hi everyone, I've been trying to color blobs of different sizes in a tomogram by un-hiding them in order of size using the "hide dust" tool and coloring as they become visible. This has been working well and given me some insight into the structure I'm looking for, but I'm unable to restore the session to it's previous state using the "save session"/"restore session" features. The maps open fine, but all the coloring is lost. I've tried this in Chimera 1.7 and 1.8, with the same results. Am I missing something? According to the online manual, colors should be saved in a session. I apologize if this has been asked before, but I haven't been able to find the solution in the archives either. I'm otherwise very happy with Chimera, thanks for all your efforts. Thanks in advance, Zoltan Metlagel, LBNL

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transparencies within transparencies
by Elizabeth Montabana 17 Aug '13

17 Aug '13

Hi All I have a difference map that I'd like to have set to 50% transparent overlaid with the original data map set to 70% transparent. If I do this, I cease to see any off the difference map. Is there anyway to accomplish this in Chimera? thanks Liz Montabana Graduate Student Agard Lab, UCSF

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Hide all ribbons not in specific chain
by Thomas Hrabe 16 Aug '13

16 Aug '13

Hi everyone, I want to display one chain from a structure, only. However, I do not understand how to achieve that. After my PDB file opens, I can do select :*.A #select all residues in chain A that I want to have select invert #select everything else not in chain A ~ribbon hides everything. How can I tell ~ribbon to hide everything not in chain A. Or, how can I select everything not in chain A? I am calling chimera through the socket and do not want to parse out every chain. Thanks in advance, Thomas

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File Operations *veery* slow on Win 7
by Markus Heller 12 Aug '13

12 Aug '13

Hi, I'm running the latest release of Chimera (1.8 build 38824), but I've observed this with the 2 previous releases as well. Computer is a core i7 with 32 GB RAM and an Nvidia Quadro FX 1700 with 512 MB DDR2 memory and latest driver. OS is Windoze 7 64 bit. Pretty much every time I click File --> Save mol2 or Save pdb or Save Session As, I get the blue spinning wheel of death and (not responding) in the window title bar. It's not a deal breaker, but it's pretty annoying. Anybody else seeing this? Also, when I start Chimera, the screen goes black for a second and all window title bars change to standard blue. When I exit Chimera, the process reverses. Are these observations related? And how can I provide more information in addition to my vague description? 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:mheller@cdrd.ca> | www.cdrd.ca [cid:image007.png@01CE950C.D960A9A0] Follow us: [Description: cid:image003.jpg@01CD86A6.39B41A10] <https://twitter.com/C_D_R_D> [Description: cid:image005.jpg@01CD86AE.B197F5D0] <http://www.linkedin.com/groups/CDRD-3186016/about?report%2Esuccess=3NcE4iZo…> [Description: cid:image009.png@01CD86AE.B197F5D0] <https://www.facebook.com/pages/The-Centre-for-Drug-Research-and-Development…> [Description: cid:image010.png@01CD86AE.B197F5D0] <http://www.youtube.com/user/CDRDCVI?view_as=public> This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email.

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Show backbone chain-trace by default
by Thomas Hrabe 09 Aug '13

09 Aug '13

Hi everyone, I was looking for the setting to tell Chimera to open a PDB file in backbone chain-trace mode rather than looking at the ribbon. Is that possible? Thanks in advance, Thomas

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About selection of atom
by Chung Fan LAM 09 Aug '13

09 Aug '13

Hi, I cannot select atoms by using Ctrl+left button/double click left button by using my home PC, but I can do so by using my notebook. I guess the difference between my two computers is the input device. My home PC is using mouse while my notebook is using touch pad. I would like to know if there is any setting I can change, so that I can use the mouse to select atoms. Thanks. Best wishes, Frankie

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Surface calculation failed problem
by Hunter Brown 09 Aug '13

09 Aug '13

Hello, I know this has been a somewhat common problem. When trying to display the molecular surface on a protein (I want to color by hydrophobicity and surface charge) I get the error "Surface calculation failed, mscalc returned code 5." I have tried increasing the VDW radius by 0.5, and lowering probe radius, and turning off 'display disjoint surfaces.' So far I have not been able to display the surface. I have a colleague that has displayed the molecular surface for a viral capsid, so I would think that I should be able to do it for a protein. Is there anything else I can do? It would be really nice to create some hydrophobicity and surface charge images. Thanks in advance! -Hunter Hunter Brown Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major University of New Mexico

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Help with RMSD
by Chee Wezen, Xavier 09 Aug '13

09 Aug '13

Hello, may i know how to i use Chimera to calculate RMSD ? I opened the command line and typed "rmsd #0 #1" but the rmsd that i received from the two molecules above is way too high for something this superimposed. Can someone please suggest what should i do ? Meanwhile, i've also received error warnings for other molecules that i am testing (along the lines of "different number of atoms" found). this should not be the case as the molecules are identical to one another. Any help regarding this is much appreciated ! Thanks !

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ask for help about surface and Label color
by Jian Guan 08 Aug '13

08 Aug '13

Hi, I am Jian, working in Hershey Medical Center, PSU. I am a Chimera User. I have two questions. 1: When I fit protein molecule structure into the density map of Virus particle. Showing the protein molecule in Surface is not allowed by Chimera. An error window popped out said: "surface calculation failed, mscalc returned code 2". I wonder to know how to solve this problem. I want to modify the molecule structure after fitting. 2: When I label the selected residues, they are always with the same color with residues, can I set them separately? Can I edit the label font? Thank you so much. Hope to hear from you soon. Jian

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show middle slice of vol by using command line
by Dieter Blaas 07 Aug '13

07 Aug '13

Hi, I have been trying hard to do the following by using the command line but so far with no avail: select volume #0 and show just the middle slice as solid. Following the way the commands are usually structured I tried something like "vol #0 style solid planes one" but I do get the error "volume invalid planes argument "one" : Value must be x, y ,z, got 'one'''. But when I try ""vol #0 style solid planes x" I get "volume: invalid planes argument 'x'. So what? Thanks a lor for hints, Dieter -- ---------------------------------------------------------------------- Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Constrained movements
by Damien Larivière 07 Aug '13

07 Aug '13

Dear all, The image below shows 2 chains opened separately from 2 PDB files. I would like to move only the cyan chain. For that, I just have to deactivate the white chain. BUT I would also like to keep fixed a specific atom of the cyan chain, for instance the cyan atom in the red circle. This way this atom serves as a pivot point. I know that I can use "Constrained Move". If I understand well, the "origin" is either 0,0,0 or the center of a model bounding box, not a selected atom. Is it possible to manage this? Many thanks for your help Damien

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Shape complementarity
by Hernando J Sosa 07 Aug '13

07 Aug '13

Dear Chimera, Is there a way to evaluate protein-protein interfaces (e.g. using a program like CCP4 Sc) within chimera?. Thanks Hernando

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Re: [Chimera-users] some questions about Chimera
by Elaine Meng 05 Aug '13

05 Aug '13

> From: "Graham Johnson (qb3@UCSF)" <graham(a)grahamj.com> > Subject: Re: [Chimera-users] some questions about Chimera > Date: August 5, 2013 11:59:03 AM PDT > To: Ruijie Chen <spider32123(a)gmail.com> > > Hi Ruijie, > The "missing" colors are in the .dae or .wrl file, however, programs like Maya do not know how to read them (i.e., they only read and display the geometry, not the color-per-vertex colors). For doing this type of work, I recommend installing ePMV to directly manipulate your models in Maya. There are many things that ePMV cannot do where a Chimera–>universalFile–>Maya protocol is still useful, but ePMV will handle most of your goals. > http://epmv.scripps.edu > > Regards, > Graham > > Graham Johnson PhD > qb3@UCSF Fellow > UCSF Lab: http://mesoscope.org > Medical Illustration: http://grahamj.com > > On Aug 5, 2013, at 10:59 AM, Conrad Huang <conrad(a)cgl.ucsf.edu> wrote: >>> Dear Sir / Madam: >>> >>> I am a 3D animation student who recently started to making medical animation videos, and I found Chimera is a very usefull tool for building molecules and proteins. >>> >>> However, there are few things that I don't understand: >>> >>> 1. After I import a .dae file which exported from hemoglobin (PDB: 2hhb), I found that the color I have set for each ribbon is gone, the one I have got inside maya is a hemoglobin molecule with one color. And when I want to select each alpha or beta-globin, I failed to do so because there sometimes have some polygons from other alpha or beta-globin. Is there a way to solve these problems? >>> >>> 2. I have tried to export the scene to a .wrl file and convert it to maya file via wrl2ma, but when I open the finish converted maya file it always give me lots of error messages like this : >>> "Error: file: C:/Users/**/hemo_ribbon.ma line 116: setAttr: Too much data was provided. The last 173 elements were not used. // " >>> and this :"// Error: file: C:/Users/**/hemo_ribbon.ma line 13078: setAttr: Too much data was provided. The last 1193 elements were not used. // " >>> Is this a problem which happen during the export process of Chimera or some other reasons? >>> >>> Looking forward for your reply >>> Thank you >>> -- >>> With kind regards >>> Ruijie Chen

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some questions about Chimera
by Ruijie Chen 03 Aug '13

03 Aug '13

Dear Sir / Madam: I am a 3D animation student who recently started to making medical animation videos, and I found Chimera is a very usefull tool for building molecules and proteins. However, there are few things that I don't understand: 1. After I import a .dae file which exported from hemoglobin (PDB: 2hhb), I found that the color I have set for each ribbon is gone, the one I have got inside maya is a hemoglobin molecule with one color. And when I want to select each alpha or beta-globin, I failed to do so because there sometimes have some polygons from other alpha or beta-globin. Is there a way to solve these problems? 2. I have tried to export the scene to a .wrl file and convert it to mayafile via wrl2ma, but when I open the finish converted maya file it always give me lots of error messages like this : "Error: file: C:/Users/**/hemo_ribbon.ma line 116: setAttr: Too much data was provided. The last 173 elements were not used. // " and this :"// Error: file: C:/Users/**/hemo_ribbon.ma line 13078: setAttr: Too much data was provided. The last 1193 elements were not used. // " Is this a problem which happen during the export process of Chimera or some other reasons? Looking forward for your reply Thank you -- With kind regards Ruijie Chen

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Re: [Chimera-users] Using Surfnet tool in a per-frame python script
by Elaine Meng 01 Aug '13

01 Aug '13

Hi William, Thanks for your kind words! I'd like to suggest an alternative approach: accumulate occupancy for the ligand over the whole trajectory and then show an isosurface for that occupancy map. You'd have to contour at a low level (e.g. 1 for everywhere the ligand has been during at least 1 frame), but in my mind at least, this produces a nice blob showing everywhere the ligand has been. I don't know how successful it would be on this specific data, but it should be relatively easy to try (no scripting involved). It may depend on how flexible everything is and how much it moves around… you can hold steady based on some set of atoms, but there may still be residual "motion blur." See the "Occupancy Analysis" section of the MD Movie man page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#…> You would have to first indicate atoms to "hold steady" (if an appropriate set exists, or maybe your trajectory is already pre-processed to keep the structure in the same place and orientation as possible), select the ligand, and then in the occupancy calculation dialog choose appropriate settings. Sounds like you would turn off (set to false) "limit data collection to within cutoff…" and "collect data separately…", maybe decrease "volume grid spacing" to get a less chunky final result, and adjust anything else as you see fit. As for pruning, you can hide disconnected bits of surface using Hide Dust and/or erase parts of a volume dataset using Volume Eraser (both in menu under Tools… Volume Data). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/hide…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleras…> Just an idea, but maybe worth a try… Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > First, thank you all for such a wonderful program! Also, thanks to the > users' list for such quick, thorough, and always-helpful answers! > > Second, a little background: I have a gromacs MD simulation (well several, > actually) of a small ligand diffusing through a protein. Because the ligand > requires the entire simulation to traverse the protein cavity, I was > thinking of using the Surfnet tool to accumulate or "build-up" the cavity > interface between the ligand and protein using a per-frame python script a > la Eric's suggestion in the Dec 2009 [Chimera-users] Surfnet command line > thread on this mailing list. I was thinking I could then "prune" the > accumulated SurfaceModel using the surfvol.py script available on the > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts download page.

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Using Surfnet tool in a per-frame python script
by William McDonald 01 Aug '13

01 Aug '13

Dear Chimera Developers, First, thank you all for such a wonderful program! Also, thanks to the users' list for such quick, thorough, and always-helpful answers! Second, a little background: I have a gromacs MD simulation (well several, actually) of a small ligand diffusing through a protein. Because the ligand requires the entire simulation to traverse the protein cavity, I was thinking of using the Surfnet tool to accumulate or "build-up" the cavity interface between the ligand and protein using a per-frame python script a la Eric's suggestion in the Dec 2009 [Chimera-users] Surfnet command line thread on this mailing list. I was thinking I could then "prune" the accumulated SurfaceModel using the surfvol.py script available on the http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts download page. Now, I can generate a Surfnet surface easily (as Eric points out) for each MD frame using the python commands from Surfnet import interface_surfnet interface_surfnet("LigandAtoms","ProteinAtoms") But how, if possible, can I combine all the individual SurfaceModels into one surface? Also, and not secondarily, does this seem like a reasonable approach to obtain the ligand-protein cavity surface? Thanks again for all your generous support. -- William J. McDonald Postdoctoral Scholar Department of Chemistry and Biochemistry University of California, Santa Cruz

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Hello
by A Amiri 30 Jul '13

30 Jul '13

Hello. I have a problem with chimera! I want to combine two different pdb file by chimera , which will be merge into a single model. I used the "join models" section from chimera but the "apply" button was inactive and i don't know how i can activate it! please help me. thank you for your useful software.

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Amino acid scanning
by Alper Yilmaz 30 Jul '13

30 Jul '13

Hi, We are conducting a study to figure out the best amino acid mutation for increased affinity for a particular metal ion. I'm pretty novice in this field so I wanted to get suggestions as to my approach makes sense or not. I'll write a demo script (more probably python script) to substitute certain amino acids with all standard amino acids and then minimize the structure. As far as I know, Chimera can not calculate free energy, so I will save the PDB files and then use another program to calculate the free energy. My first question is, whether the commands below are appropriate for my purpose or not? The sample below is a snippet from an exhaustive list. I preferred to save the information regarding clashes before the minimization just to keep record. swapaa ala :22.a findclash :22.a log true saveFile clash_report_22ala minimize nogui true write #0 test_22ala swapaa val :22.a findclash :22.a log true saveFile clash_report_22val minimize nogui true write #0 test_22val swapaa ile :22.a findclash :22.a log true saveFile clash_report_22ile minimize nogui true write #0 test_22ile ... My second question is, when I have many PDB files, which software is suitable for calculating the free energy for each. Thanks, Assist.Prof.Dr. Alper YILMAZ Department of Bioengineering Faculty of Chemical and Metallurgical Engineering Yildiz Technical University Esenler, Istanbul/TURKEY 34210 Phone: +90.212.383-4657 (office) Fax: +90.212.383-4625

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Using Chimera in a non-graphics environment
by Devan Bicher 24 Jul '13

24 Jul '13

To Whom it may concern, Hi, my name is Devan Bicher and I am a researcher at Lehigh University. I am working on computational studies of proteins and Chimera's findHBond function is extremely useful! I have been using chimera a lot recently, however since I am working with a number of different protein/substrate combinations it would be great for me to use findHbond in a batch sort of way in which I can supply numerous inputs and allow chimera to run on all of them. Does chimera have any sort of built in batch processing option like this? -- -Devan Bicher Bioengineer, Computer Science minor Lehigh University

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volume viewer window
by jparmache＠lmb.uni-muenchen.de 24 Jul '13

24 Jul '13

Hello, I would like to ask, whether there could be a possibility to define how many density levels one is able to see at the same time in the Volume Viewer window? Currently, there are max 3, however, with larger monitors, this could be for some beneficiary if one could define the max amount. What do you think, would that be possible ? Best regards, Jean-Paul Armache

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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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