- Chimera-users - RBVI Mailing Lists

reset/stereo
by Dougherty, Matthew T 29 Nov '10

29 Nov '10

I had a couple questions about using the reset command. Let's say I have two keyframes (e.g., kf0,kf1) such that the stereo parameters are different between the two. 1) If I do a "savepos kf0" are the stereo parameters saved as part of the keyframe? 2) If I start at kf0 and do a "reset kf1 100", should the stereo parameters be interpolated across the 100 frames? thanks, Matt

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3D dashed lines
by M Sundaramoorthy 29 Nov '10

29 Nov '10

I like to show pseudobonds (H-bonds, metal coordinations and distances) as solid dotted or dashed lines. To draw dashed/dotted line I can choose dashed line style in the Pseduobond attributes panel. But it works only with bond style 'wire' not with 'stick'. It can essentially draws flat lines. How do I show 3D dashed/dotted lines? Some images in the tutorial do have such lines represented as dotted (spheres) lines. Another problem I have is that the Side View panel shows the image but does not show the eye (the small square) and the clipping planes (vertical lines). I am using Chimera 1.5rc in Windows Vista. Thanks Sundar

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Exporting .stl
by Dennis Kolva 25 Nov '10

25 Nov '10

I have been using Chimera to export .stl files of proteins and RNA for 3D printing. The surface models print OK, but sticks or ribbons choke the printer. I looked close at the output meshes, and they have many extra surfaces which should be removed to make "legal" .stl format. Is that portion of the code open source? I'd like to take a closer look and see if it's possible to fix. It would be much easier to rectify the bad surfaces upon creation, rather than trying to remove them by post-processing. Thanks, Dennis Kolva Cornell U.

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PDB with C alpha carbons only
by Sujata 23 Nov '10

23 Nov '10

Hi, I have a PDB file with C-alpha carbons only. I want to know if Chimera can add backbone atoms and sidechains (the PDB has the names of the residues). Thanks, Sujata

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Re: [Chimera-users] Fwd: Re: 3D stereo
by Nadir T. Mrabet 22 Nov '10

22 Nov '10

Hi Greg, Both DepthQ and Christie (made in fact by the same manufacturer. http://www.depthq.com/projector.html; http://www.depthq.com/christie.html) are, as expected, sold in France by a unique firm. They say that DepthQ HDs3D-1 ($2,995) has no capability for 3D for a conference room with 30-50 people, and that my only option is Christie (> $65,000!). Your earlier mail states that DepthQ can go along with a 3-meter size screen, suggesting it could accommodate an audience of 30-50 people. Can you, please, comment on all these issues and eventually let me know if I can go along with DepthQ DLP? Many thanks in advance. Best, Nadir Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabet<at> medecine.uhp-nancy.fr Cell.: +33 (0)6.11.35.69.09 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. On 28/09/2010 12:59, Greg Couch wrote: > > Subject: Re: [Chimera-users] 3D stereo > Date: Tue, 28 Sep 2010 12:59:13 -0700 > From: Greg Couch <gregc(a)cgl.ucsf.edu> > To: Nadir.Mrabet(a)medecine.uhp-nancy.fr > CC: Chimera-users(a)cgl.ucsf.edu > > > > On 07/21/2010 07:24 AM, Nadir T. Mrabet wrote: > > Hi, > > > > This is for teaching purposes so that students can "walk" though 3D structures. Would it be possible to use Chimera via a 3D stereo beamer to project display on a very large screen and watch the selected structure in 3D by means of shutter glasses? If this is so, what kind of equipment would you recommend? > > > > Many thanks, > > > > Nadir > > So there were some developments at SIGGRAPH, but nothing that would > change the previous recommendations made in the chimera-users mailing list. > > To summarize, for a large group of people, you want a setup similar to > what is done for 3D movies in a movie theater, which is to use left-hand > and right-hand circularly polarized light for the left-eye and right-eye > images. There are three parts to the setup: (1) projecting the stereo > images, (2) reflecting the images, (3) receiving the images at the eyes. > > 1. For projecting the stereo images with chimera, you need a > workstation-class graphics card, either an AMD FirePro (or ATI FireGL) > or a NVIDIA Quadro (or Quadro FX, not Quadro NVS), and either (a) two > projectors with passive polarizers, or (b) a single projector with an > active polarizers. The single projector method is much simpler to > maintain because you don't have to keep aligning the two projectors, but > may cost more because the projector has to be able to display at 120Hz > (and there's the cost of the active polarizer). The relative costs of > the two options vary. Active polarizers are available from DepthQ, > http://www.depthq.com/, and RealD, > http://www.reald.com/Content/professional.aspx. DepthQ also sells a 3D > projector that can display 3 meter wide images, and has European > distributers, so that might be the best choice. If you want a larger > image, you'll need a Christie Mirage or a Barco projector. > > 2. To reflect the stereo images, you need a screen that doesn't change > the polarization of the light. There are lots of choices. Google for > "3D projection screen" to see what's available. What screen you want > depends on the layout of the room that the stereo projection will be > in. Narrow rooms can use screens with a smaller viewing cone and higher > gain. I've heard good things about Stewart Filmscreen, but get > recommendations from whoever you buy your projector too. > > 3. Last part of making sure each eye only receives the image it is > supposed to is for the person to wear circularly polarized glasses. > Google for "polarized 3d glasses" to see what's available. I'd avoid > the disposable paper ones. I like the RealD glasses that the movie > theaters use. Perhaps a theater would sell some to you. The glasses > from Zalman displays work too. > > Bon chance, > > Greg >

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adding density maps
by Anindito Sen 22 Nov '10

22 Nov '10

Dear All I was wondering if there is an option to add multiple density maps of the same box and voxel sizes in Chimera. Thanks Andy Dr. Anindito Sen (Ph.D)

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Measure volume of a cavity encased inside a cryo-EM density
by sudheer molugu 19 Nov '10

19 Nov '10

Hi, I was just wondering if chimera can calculate the volume of a central cavity encased inside the cryo-EM density. Thanjk you, Kumar

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Chimera SASA algorithm
by Devin McBride 17 Nov '10

17 Nov '10

Hello, I have been using UCSF Chimera for a few years. I am currently reviewing the SASA algorithms by various molecular modeling software. I was wondering what the error associated with a given SASA calculation is? The algorithm has an error in the calculated SASA, but I was not able to find out what the error is. Thank you very much for your time and help. -- Devin McBride Ph.D. Candidate Department of Bioengineering Bourns Hall A130 University of California, Riverside Phone: (951) 742-3541 Email: dmcbr001(a)student.ucr.edu

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visualization code optimized using GPU shaders ?
by Mathieu Chavent 16 Nov '10

16 Nov '10

Dear Chimera developers, I try to have a brief overview of molecular programs that can use programmable capabilities of new graphic hardwares (i.e. use of shaders): So, I would like to know if Chimera program have dedicated code that use such shaders to visualize fastly surfaces or to add particular lighting effects.. Thank you in advance. Matthieu Chavent.

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About GPU accelerating on Chimera
by Allan Hou 16 Nov '10

16 Nov '10

Hi Sir, I would like to get help from you to confirm whether Chimera use GPU accelerating function. I have a customer and they are using Chimera: * Customer: Institute of Biophysics of China * Platform: Dell 5500 workstation, Windows VISTA 64bit OS, FX4800 , Quadro driver version : 259.81, * Application: UCSF Chimera 1.5 for protein molecule analysis * Status: Chimera for 64bit OS , the graphic 3D performance would be 5 times fast than Chimera for 32bit OS in VISTA64 * Need to check: Whether Chimera using CUDA/GPU accelerating function Best Regards, Allan Hou(侯宇涛） Enterprise Account Sales Manager Nvidia China 0086-13801005536 ----------------------------------------------------------------------------------- This email message is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. -----------------------------------------------------------------------------------

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Fwd: Trojan alert Chimera 1.5
by Elaine Meng 15 Nov '10

15 Nov '10

Begin forwarded message: From: "Prof. Dirk Volkmer" <dirk.volkmer(a)physik.uni-augsburg.de> Date: November 15, 2010 4:11:32 AM PST To: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: Re: Fwd: [Chimera-users] Trojan alert Chimera 1.5 Thank you for the quick response. I am wondering though, if you could change your code such that the similarity to some kind of Trojan programs might be reduced. The previous Chimera version did not show this problem and I am hesitating to de-activate my virus scanners for the purposed of installing your software, especially since it sends these alerts. With kind regards, dv Am 14.11.2010 18:18, schrieb Elaine Meng: > I didn't know if you already got this (you might not be subscribed to the chimera-users list) so am forwarding. Apologies if you already got the message, > Elaine > > Begin forwarded message: > >> From: Tom Ferrin <tef(a)cgl.ucsf.edu> >> Date: November 13, 2010 6:00:21 PM PST >> To: chimera-users(a)cgl.ucsf.edu >> Subject: Re: [Chimera-users] Trojan alert Chimera 1.5 >> >> It's a false positive, caused by a digital signature match between the >> trojan you cite and an icon within the Chimera executable. We've >> notified the 2 or 3 antivirus s/w vendors who are reporting the warning >> message, and we're looking at other ways to deal with the problem. >> >> >> >> On 11/13/10 4:46 AM, Prof. Dirk Volkmer wrote: >>> To whom it may concern: >>> >>> Dear developers of Chimera. >>> I am facing a problem with the currently distrbuted version (1.5 rc) of >>> Chimera. >>> When I am trying to install the program I receive a warning message from my >>> antivirus program (Avira Antivir with VDF Version: 7.10.13.235) that the >>> chimera.exe >>> windows installer is trying to install the following malware /Trojan >>> software: >>> >>> TR/Crypt.ZPACK.Gen2 >>> TR/Crypt.ZPACK.Gen >>> >>> Could you please be so kind to check if this alert is serious and >>> whether or not >>> your program might be infected ? >>> >>> Many thanks in advance sincerely >>> >>> dv >>> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -- ++++++++++++++++++++++++++++++++++++++++++++ Prof. Dr. Dirk Volkmer Chair of Solid State and Materials Chemistry Institute of Physics Augsburg University Universitaetsstrasse 1 D-86159 Augsburg (Germany) Office Room 4.34 Phone: +49 (0)821 598-3006 Secretary: +49 (0)821 598-3032 FAX: +49 (0)821 598-5955 Mobile-Phone: 0176/24872988 Home-Phone: +49(0)7303/929742 E-mail: dirk.volkmer(a)physik.uni-augsburg.de http://www.physik.uni-augsburg.de/chemie/ under construction http://www.uni-ulm.de/nawi/nawi-anorg2.html ++++++++++++++++++++++++++++++++++++++++++++

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Trojan alert Chimera 1.5
by Prof. Dirk Volkmer 15 Nov '10

15 Nov '10

To whom it may concern: Dear developers of Chimera. I am facing a problem with the currently distrbuted version (1.5 rc) of Chimera. When I am trying to install the program I receive a warning message from my antivirus program (Avira Antivir with VDF Version: 7.10.13.235) that the chimera.exe windows installer is trying to install the following malware /Trojan software: TR/Crypt.ZPACK.Gen2 TR/Crypt.ZPACK.Gen Could you please be so kind to check if this alert is serious and whether or not your program might be infected ? Many thanks in advance sincerely dv -- ++++++++++++++++++++++++++++++++++++++++++++ Prof. Dr. Dirk Volkmer Chair of Solid State and Materials Chemistry Institute of Physics Augsburg University Universitaetsstrasse 1 D-86159 Augsburg (Germany) Office Room 4.34 Phone: +49 (0)821 598-3006 Secretary: +49 (0)821 598-3032 FAX: +49 (0)821 598-5955 Mobile-Phone: 0176/24872988 Home-Phone: +49(0)7303/929742 E-mail: dirk.volkmer(a)physik.uni-augsburg.de http://www.physik.uni-augsburg.de/chemie/ under construction http://www.uni-ulm.de/nawi/nawi-anorg2.html ++++++++++++++++++++++++++++++++++++++++++++

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tuning transparency of VDW spheres
by Boaz Shaanan 15 Nov '10

15 Nov '10

Hi Elaine, Thanks for suggestions. I'll try them and see how it looks. Ribbons won't do here since I want to show a w.t. protein and mutants with substrate analogues in the active site and how they fit (or clash) so I'm only showing a few residues. Thanks again. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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tuning transparency of VDW spheres
by Boaz Shaanan 15 Nov '10

15 Nov '10

Hi, Is it possible to tune the transparency of the VDW spheres (as with surfaces for example) if I choose to render some atoms as spheres and still would like to see the bonds (rendered as sticks)? Just wondering. I'm working with the 1.4 official release. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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Consurf
by Sosnovtsev, Stanislav (NIH/NIAID) [E] 10 Nov '10

10 Nov '10

I wonder if there is a short way to introduce consurf output colors to multiscale models. My virus particle has 60 trimers (three chains of the same protein). Thank you in advance, Stanislav

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loading pdb files
by Beale, John 10 Nov '10

10 Nov '10

I have a series of pdb files that I am loading into Chimera. How can I get each file to load as a backbone structure with a different color for each? I used to be able to do this, but when I loaded a newer version of Chimera it no longer works. I am sure that this must be a preferences issue, but I can't figure it out. Thanks! John John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale(a)stlcop.edu<mailto:jbeale@stlcop.edu>

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Write out frames, but the complete movie
by Leiman Petr 04 Nov '10

04 Nov '10

Hi, A backward question: Is it possible to write out a movie as a set of frames? I would like to show several structures rotating side by side and the simplest way I can think of is to collage frames using imagemagick and create a new video stream with mencoder. Many thanks, Petr

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Chimera production release candidate
by Elaine Meng 04 Nov '10

04 Nov '10

A Chimera production release candidate (version 1.5) is now available: <http://www.cgl.ucsf.edu/chimera/download.html> As described in the release notes, many new features have been added since the previous production release: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.5.html> Please try the candidate release and report any problems (Help... Report a Bug in the Chimera menu). Note Chimera 1.5 will be the last release for the X11 version on Mac. On behalf of the Chimera team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Query regarding solvent accessible surface area of protein
by Aditya Padhi 03 Nov '10

03 Nov '10

Hi all, I have carried out molecular dynamics simulation of my protein of interest using AMBER 10. I need to calculate the "solvent accessible surface area (SASA)" of 6 amino acid residues in wild type and certain mutants. My query is regarding can I use chimera for the same. Is it possible to both visualize and get analytical data for the differences in solvent accessible surface area for wild type and mutants? Another query is, in chimera can I get the SASA for each and every trajectories or I have to generate average PDB (Is it correct)? Kindly help me sir. Any other suggestions will be highly grateful. Thanks and regards Aditya.

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Color sub-region with marker
by Xiaofeng Fu 03 Nov '10

03 Nov '10

Dear Chimera users, I always have problems when I color a sub-region of density map by markers. Rather than a zigzag, boundary, I try to create a smooth curve boundary of sub-region from a whole density 3D volume. In this case, if I just put one marker and select a big coloring radius, the boundary in cross-view will show a circle curve at the boundary, however if I use a very small coloring radius and put more and closer markers on the boundary, the boundary shows a sawtooth in cross-view, even I choose 4 times for subdividing surface. Or is there any other way to do this instead of markers? And I have several other questions: (1) Is that possible to have different coloring radius in one Chimera session? (2) except for ball shape, can we have more options on the coloring object with markers? For example rectangular, ellipse and so on. (3) Is that possible to put markers directly on the clip planes? Thanks in advance, Xiaofeng

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Re: [Chimera-users] Color sub-region with marker
by Xiaofeng Fu 03 Nov '10

03 Nov '10

It seems not as you mentioned, I am sure I have turned off the outline box for both volumes. Xiaofeng ----- Original Message ----- From: "Tom Goddard" <goddard(a)sonic.net> To: "Xiaofeng Fu" <xiaofeng(a)brandeis.edu> Cc: chimera-users(a)cgl.ucsf.edu Sent: Wednesday, November 3, 2010 7:33:46 PM GMT -05:00 US/Canada Eastern Subject: Re: [Chimera-users] Color sub-region with marker Hi Xiaofeng, The Chimera daily build with the outline box fix is not available yet. You can simply turn off the outline box in the volume dialog Data Display Options panel. The Chimera daily builds are made automatically starting at 9 pm Pacific time and then put on the download web page if they succeed, usually after midnight. The builds don't always work, so check the date on the download page for the build you want -- you'll need Nov 4 for the outline box fix. Tom > Hi Tom, > > The second problem was clear to me. > Have you already uploaded tonight's Chimera build? > > Thanks, > Xiaofeng > ----- Original Message ----- > > Hi Xiaofeng, > > I fixed "measure contactarea" so it will ignore outline boxes in > tonight's Chimera builds. > > Tom > >> Hi Xiaofeng, >> >> The measure contactarea command can only handle surfaces consisting >> of a single surface pieces. Surfaces can have more than one selectable >> piece, but molmap makes a single piece surface so I'm puzzled by the >> error you get. I see that if you have an outline box shown for the >> molmap surface then that is considered a second surface piece and will >> generate the error message you see. >> >> For your second problem, I can put markers on the clipping surface >> cap using "place markers on surface" but the trouble is the markers are >> clipped so you don't see them. The near/far clipping planes clip >> everything. You do see half of a spherical marker (clipped in half) if >> you hide the map after placing the marker on the clip surface. I'd >> suggest using Per-Model Clipping (menu Tools / Depiction) to clip just >> the map surface -- that way you will be able to see the markers you >> place on the clip plane. >> >> Tom >> >>> Hi Tom, >>> >>> Thanks for your reply. The questions are: >>> >>> (1) When I follow your procedure until "measure contactarea #0 #1 12 color tan", it promotes "#0 has 2 surface pieces, require1" and stop working. I don't understand what that means(figure attached). >>> >>> (2) The question of number 3 at last time about how to put markers directly on the clipped plane is that, for example, in Side view window, when I move the front bar (normally the front and behind bar just cover the object) into the object to observe inside, I try to put markers on this capped plane inside the object, but it doesn't work even I have chosen "put markers on surface". >>> >>> Xiaofeng >>> ----- Original Message ----- >>> >>> Hi Xiaofeng, >>> >>> The Chimera Color Zone tool has lots of limitations as you've noticed. >>> >>> The jagged edges on the colored region when using color zone happen >>> because the surface is made up of triangles and Chimera can only color >>> each triangle vertex and then linearly interpolates colors across the >>> triangle based on the 3 vertex values. That can look bad. Your >>> solution of using the "subdivide surface" option in the volume dialog >>> surface surface and mesh options panel will help reduce the jaggedness. >>> There is one tricky solution that can produce a smoother edge. It uses >>> a command I just added a month ago called "measure contactarea". The >>> virtue of this approach is that it creates a new surface chopping the >>> triangles at the edge of your zone to make a perfect smooth boundary. >>> But it wasn't intended as a substitute for the color zone dialog. >>> Instead it measures the area on one surface within a given distance of >>> another surface and displays that contact area. The first problem using >>> this is that it doesn't use markers and a surface like color zone -- >>> instead it uses two surfaces. So the first trick is to turn your >>> markers into a surface. If the markers are model #1 use >>> >>> molmap #1 3 >>> >>> to make a 3 Angstrom resolution surfaces for those markers. Now to >>> color a zone around those markers on volume data #0 use >>> >>> measure contactarea #0 #1 12 color tan >>> >>> This will make a new surface matching volume surface #0 within a range >>> of 12 Angstroms from surface #1 (the marker surface created with >>> molmap). It has beautiful smooth edges. See the attached picture. >>> You'll need a Chimera daily build to use "measure contactarea". I >>> suggest tonight's daily build, because I made some changes to "measure >>> contactarea" to make the surface look very smooth. Earlier daily builds >>> had a less smooth edge, and less smooth colored region. If you add >>> "slab 2" as an option it will make the colored patch have thickness 2A >>> (not shown). >>> >>> 1) You can't use different color zone radii on the same surface at >>> the same time. This is item 37 in the Chimera feature request list. >>> >>> http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests >>> >>> You can use the above trick multiple times to create color patches using >>> different radii. >>> >>> 2) Not sure I understand this question. I think you are asking if >>> you can color inside rectangles and ellipses. There's no way to do that >>> now. I'm not sure how you would describe the rectangle or ellipse with >>> a marker since a marker is a sphere and those shapes have non-equivalent >>> axes. You can create such shapes with the Chimera "shape" command but >>> you can't for instance color everything within such a shape. The >>> closest you can do is color near a traced path made with markers and >>> links. This basically lets you color in a cylindrical zone. To enable >>> this you use the bondzone command >>> >>> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bondzone.html >>> >>> 3) Not sure exactly what case you are interested in. If you clip a >>> surface you can place markers exactly of the "cap" surface that covers >>> the hole left by clipping. You would use the Volume Tracer mouse mode >>> with "Place markers on surfaces" enabled. If you wanted to place >>> markers on single data planes of a volume you would enable "Place >>> markers on data planes". >>> >>> Tom >>> >>> >>>> Dear Chimera users, >>>> >>>> I always have problems when I color a sub-region of density map by markers. Rather than a zigzag, boundary, I try to create a smooth curve boundary of sub-region from a whole density 3D volume. In this case, if I just put one marker and select a big coloring radius, the boundary in cross-view will show a circle curve at the boundary, however if I use a very small coloring radius and put more and closer markers on the boundary, the boundary shows a sawtooth in cross-view, even I choose 4 times for subdividing surface. Or is there any other way to do this instead of markers? And I have several other questions: >>>> (1) Is that possible to have different coloring radius in one Chimera session? >>>> (2) except for ball shape, can we have more options on the coloring object with markers? For example rectangular, ellipse and so on. >>>> (3) Is that possible to put markers directly on the clip planes? >>>> >>>> Thanks in advance, >>>> Xiaofeng >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >

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drawing spheres with various radii
by Roni Rayes 03 Nov '10

03 Nov '10

Hello, We are trying to model the FRET data we obtain by drawing spheres from one atom. I know VMD does that, however we are trying to do the same in chimera. How to draw these spheres? I tried to find it in the guide book but did not see anything. Probably missed it. Thank you so much for your help, Roni Roni Rayes (BS, MS) Graduate Research Assistant Institute of Molecular Biophysics Florida State University 91 Chieftan Way Tallahassee, Fl 32306 Phone # (850) 645-1335 Fax # (850)644-7244

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To retrieve intermediate results while using Minimize Structure
by saumyak＠ebi.ac.uk 01 Nov '10

01 Nov '10

Hello, I am using Chimera's Minimize structure for protein minimization. I was hoping if you could suggest me a way to retrieve intermediate PDB files that are generated during the minimization procedure. Many thanks, Saumya

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Trouble with Marker Sets and Movie Recorder in Chimera 1.4.1 build 30365
by Thomas Heuser 01 Nov '10

01 Nov '10

Hi everyone, I am using Chimera 1.4.1 build 30365 on linux2 with windowing x11 and I'm struggling with these two issues: 1.) Opening marker sets: I would like to open a marker set from a previous session, but when I try to open the marker set in the Volume Tracer I get the following reply: Traceback (most recent call last): File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ File "CHIMERA/share/chimera/baseDialog.py", line 328, in command File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK File "CHIMERA/share/OpenSave/__init__.py", line 159, in Apply File "CHIMERA/share/VolumePath/gui.py", line 260, in open_file_dialog_cb AttributeError: 'Volume_Path_Dialog' object has no attribute 'open_marker_set' AttributeError: 'Volume_Path_Dialog' object has no attribute 'open_marker_set' File "CHIMERA/share/VolumePath/gui.py", line 260, in open_file_dialog_cb I've tried opening marker sets which were generated with the same Chimera build and with older builds, but I get the same reply. 2.) Movie Recorder: I can't access the Frame Options or the Movie Options. In earlier builds pressing the triangle symbol next to Frame Options or Movie Options would expand the menu and display your options, but now pressing the triangle does not change anything and nothing expands. Any ideas, suggestions, what I could try? Thanks a lot and big cheers from Boston, Tom -- ************************* Thomas Heuser Nicastro Lab Rosenstiel Center, MS029 Brandeis University 415 South Street Waltham, MA 02454-9110 Phone: (++ 1) 781 736 2608

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Re: [Chimera-users] CCL: trimer from monomer
by Elaine Meng 01 Nov '10

01 Nov '10

Hi Kshatresh, In Chimera there are several ways to get the trimer from the monomer. It depends what information is included in the PDB file. The "biological unit" is supposed to be described in BIOMT records, but many PDB files do not have useful BIOMT records, only an identity matrix. If the PDB file does contain useful BIOMT records (example: 1hxx), you can use the command sym or the "Multiscale Models" tool. For example, if the structure is open as model 0 you can simply use the command: sym #0 A PDB file can also contain various other matrices that describe crystallographic symmetry and the unit cell, which may or may not bear any relationship to the biological unit. These other matrices can also be used by the sym command (it has options), the Multiscale Models tool, and the Unit Cell tool in Chimera. If none of the information in the PDB file makes the trimer, you might also try fetching the predicted biological unit for that PDB entry from the PQS database. That can be done using Fetch by ID in Chimera (see the File menu). Documentation... http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu… http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html 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 Nov 1, 2010, at 2:07 AM, Kshatresh Dutta Dubey kshatresh#,#gmail.com wrote: > Dear all, > I want to model a simulate a protein which is found in trimeric form, but unfortunately i have only monomer of that protein. Can anyone suggest me how to model a trimer from a monomer. Kindly also suggest me modelling software which can do this. I have maestro, chiemera and VMD. > Thanks in advance > Regards > Kshatresh Dutta Dubey

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viewing of trajectory
by atila petrosian 01 Nov '10

01 Nov '10

Hi chimera users I did simulation of protein by gromacs. I want to see my trajectory during simulation by a viewr other than vmd, such as chimera. How and what files is needed for that? -- Atila Petrosian Ph.D. student of BioPhysical Chemistry University of Oulu,Finland

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Fwd: ribbon causes coordinates changing
by Francesco Oteri 30 Oct '10

30 Oct '10

Dear chimera users, I've a problem with ribbon. I've a DNA molecule where the two last base pair is an uncommon T-T pair. When I select these bases to display the ribbon, the coordinateds of the last atoms are changed. Seem that the new position are the end of the ribbon. The chimera version I'm using is 1.5rc1 on a windows7 PC. I attacch the session that represent my problem. The session is saved such to visualize the problem: look at the end of the blue and red ribbons to detect it.

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ribbon causes coordinates changing
by Francesco Oteri 30 Oct '10

30 Oct '10

Dear chimera users, I've a problem with ribbon. I've a DNA molecule where the two last base pair is an uncommon T-T pair. When I select these bases to display the ribbon, the coordinateds of the last atoms are changed. Seem that the new position are the end of the ribbon. The chimera version I'm using is 1.5rc1 on a windows7 PC. I attacch the session that represent my problem. The session is saved such to visualize the problem: look at the end of the blue and red ribbons to detect it.

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Re: [Chimera-users] Chimera surfaces
by Tom Goddard 28 Oct '10

28 Oct '10

Hi Vijay, The MSMS molecular surface calculation (Actions / Surface / show) fails on some molecular models. The mailing list describes some tricks that might make surface calculation work: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004713.html An alternative is to use a Gaussian surface instead of the MSMS solvent excluded surface, using the command (Favorites / Command-Line) molmap #0 3 gridSpacing 0.5 to make a 3 Angstrom surface for molecular model #0. Then use the Color Zone dialog (menu Tools / Volume Data / Color Zone) to color the surface to match selected atoms within a specified distance from the atoms. You can select all the atoms with menu Select / Select All or use command "select #0". The Gaussian surface doesn't look much like a solvent excluded surface -- it puts a Gaussian at each atom position to compute a density map. If you prefer the solvent excluded surface then look at the above mailing list message for suggestions. Tom > Hi Tom, Greetings, Hope all is well > > I have a question about generating surfaces. When I load a simple PDB > and try to display surfaces... by selecting a molecule, > > Actions/Surface/Show > > I get the error Surface calculation failed, mscalc returned code 2 > > I could always generate a surface using multiscale models in HIgher > order structure... But how can I can color the surface corresponding > to different region of the protein surface (corresponding to few > residues) in selected colors. > > Many thanks, > > Kind regards > Vijay > > ======================================== > Vijay S. Reddy, Ph.D. > Associate Professor > Department of Molecular Biology, TPC6 > The Scripps Research Institute, > 10550 North Torrey Pines Road, > La Jolla, CA 92037 > > ======================================== > > > > > > > > > > > > > >

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misconfiguration error in just one user account
by Harry Kao 28 Oct '10

28 Oct '10

On a linux workstation, a particular user is receiving the following error message when starting up Chimera: Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions. This error message happened after a previous Chimera session crashed. The user had about 10 models open. The display setting is already at 24bit, and the workstation has the correct Nvidia driver. Here is what we tried: 1. On the same workstation, under a different user account, Chimera starts up fine, no error message. 2. I created a new empty user directory, Chimera starts up fine the first time and the user can re-open models he was working on. However, the error message returns in the next Chimera session. Based on the observation, I am assuming there is a user-specific configuration/preference file that Chimera reads when starting up. Perhaps in that file, some display parameter is being corrupted? If so, where or how can I find and fix or delete such files? Thank you. Harry

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Selecting atoms
by Peter Baker 28 Oct '10

28 Oct '10

Good Morning. I am trying to display the H atoms in the para-position of the all the Phe residues. Could anyone offer me some advice on specific key commands which would help me out. I have tried da: phe@ cz but I was not successful . Thanks Peter.

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help with surfnet results
by saumyak＠ebi.ac.uk 27 Oct '10

27 Oct '10

Hello, Thanks for the reply. I was able to separate all the blobs. I have a new query now. I am trying to retrieve the residues that surround one of the predicted binding pockets by Surfnet. I tried the command #1: za<8.0, but it doesn't work as it needs specification of an atom from which it will calculate the zone. In my case, there is no small molecule that can be used as reference. I want to select and highlight all the residues that surround that predicted pocket. Please suggest how this can be carried out. Thanks, Saumya

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.dx file problem
by Greg Friedland 27 Oct '10

27 Oct '10

Hi, I'm trying to load an electrostatic potential file (.dx) that I created with the online APBS tools. Nothing displays however when I select "color" from the "surface color" dialog. Is this feature working in the current version? I'm using version 1.4.1. The potential file is http://dl.dropbox.com/u/5763765/pot.dx.gz Thanks, Greg

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Raytrace VDW surface with POV-RAY
by #MAZIAR SOLEYMANI ARDEJANI# 26 Oct '10

26 Oct '10

Hi All, Is there a way to have VDW surface in images being ray traced by POV-RAY? Right now, when I ray trace the image using POV-RAY the VDW surface disappears in the generated figure. So much thanks in advance, Maziar

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Waters of hydration in a protein
by Beale, John 26 Oct '10

26 Oct '10

I am conducting molecular dynamics simulations on a protein in explicit water. I would like to be able to determine the positions of waters of hydration of the protein at the beginning and then at various points along the MD trajectory. What I need to do is locate the position of a water molecule that is hydrogen bonded to a given amino acid and somehow tabulate the positional data. Is there a way to do this in Chimera? Thanks! John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale(a)stlcop.edu<mailto:jbeale@stlcop.edu>

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help on virus visualization
by jh 25 Oct '10

25 Oct '10

Dear all, I want to mask area outside certain surface and to visualize the inner capsid of a virus by Chimera. Anyone would be kind to help me with that? C.J.

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Label all atoms except hydrogens
by Michael Day 21 Oct '10

21 Oct '10

How would I label all atoms in a structure without labeling hydrogen atoms? I'm trying to label a small molecule with about 60 non-hydrogen atoms. Cheers, Mike <<< ------------------------------------------------------------------------>>> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday(a)caltech.edu <<< ------------------------------------------------------------------------>>>

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Fwd: Re: GLXBadRenderRequest
by Greg Couch 21 Oct '10

21 Oct '10

(Forgot to reply to list.) -------- Original Message -------- On 10/18/2010 01:56 PM, Gough, Erik S wrote: > > Hello, > > I am receiving the following error when I try and open a structure > running chimera with Mesa 7.0 on Debian 5. > > X Error of failed request: GLXBadRenderRequest > > Major opcode of failed request: 148 (GLX) > > Minor opcode of failed request: 1 (X_GLXRender) > > Serial number of failed request: 5334 > > Current serial number in output stream: 5336 > > I am assuming that this is related to running an older version of the > Mesa driver, but I do not have root on the system and the > administrators are hesitant of upgrading the Mesa package in /usr/lib > to anything beyond the stable release. The servers do not have > access to any hardware based video so doing an updated hardware based > driver install won't help either. I am limited to what I can do and > only have access to my home directory. Would it be possible for me to > compile a newer version of the Mesa driver in my home directory and > then compile chimera to use that version of the driver instead of the > default in /usr/lib? > > Thanks! > If the Debian 5 system is a server, I would remote mount my home directory on my workstation with the hardware graphics driver, and run chimera locally. Or you might be able to copy libGL.so from your workstation to a directory in your home directory on the server and set the LD_LIBRARY_PATH environment variable to that directory. If the Debian 5 system is supposed to be a workstation, I would be very tempted to reboot it with a Ubuntu Live CD and when done, reboot it back to Debian 5, or maybe the administrators would be willing to make it a dual-boot system. Your idea, of compiling a software-only version of Mesa, should work if you set the LD_LIBRARY_PATH environment variable appropriately. In the LD_LIBRARY_PATH cases above you would need to start chimera from the command line after setting up the environment or start chimera after editing the CHIMERA/bin/chimera shell script. Hope this helps, Greg

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Fwd: Re: stereo LCD display
by Greg Couch 21 Oct '10

21 Oct '10

(Forgot to reply to list.) On 10/20/2010 09:02 AM, Wu, Weimin (NIH/NIAMS) [E] wrote: > We are planning to buy a stereo LCD display system. Most of time we will use it to visualize the density map and PDB structure in Chimera. We want a LINUX 64bit system. Has anybody got experience on it? Would you please tell me the specifications of your hardwares? How about Miracube G240? The Miracube is a good product, see our tech note about the Miracube at <http://www.cgl.ucsf.edu/Outreach/technotes/miracube.html>. A Zalman display is an excellent, inexpensive, alternative, and both will work with gaming graphics cards (NVIDIA GeForce and AMD/ATI Radeon). But I would recommend a display where you don't lose half of the vertical resolution, that way the 2D dialogs are readable when you are looking at the 3D stereo image. For that, you will need a workstation graphics card, a NVIDIA Quadro/Quadro FX or a AMD/ATI FirePro/FireGL, and a suitable display: (1) The Planar 3D/Stereoscopic displays use passive glasses, like those that movie theater's use, and will work with both NVIDIA and AMD/ATI workstation graphics cards. (2) 120Hz LCD displays, with active glasses, like what many 3D televisions use, work well too (we have a Samsung 2233RZ that we like). NVIDIA has temporarily cornered this market. For a list of displays, see <http://www.nvidia.com/object/3d-vision-requirements.html>, but for a list of compatible workstation graphics cards, see <http://www.nvidia.com/object/quadro_pro_graphics_boards.html> (and in your case, click on the "Linux customers" link). NVIDIA has just released a "Pro" version of its stereo glasses, and the supported displays are slightly different, see <http://www.nvidia.com/object/3d-vision-pro-requirements.html> for details. I believe that option 2 is currently cheaper, but look at the total cost of the graphics card, glasses, and display for comparison. Planar claims that "flicker from active glasses can cause eye fatigue, headaches and other discomfort", but I have not experienced that, but I have not looked at a stereo display all day either. Hope this helps, Greg

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Chimera on iPad?
by Claire Birone 21 Oct '10

21 Oct '10

Hi all, I'm wondering if anyone has been running Chimera on an iPad. I'm a high school teacher using the software to help students build 3D protein models, and my class has access to iPads. Unfortunately, I haven't had success trying to get Chimera to run on the iPad. Is anyone running it on an iPad? And if so, how do you feel it compares to using it on a computer? Thanks! Claire

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help with Surfnet results
by saumyak＠ebi.ac.uk 20 Oct '10

20 Oct '10

Hello, I am using Chimera to identify binding sites in a protein structure using Surfnet, but I am unable to save the Surfnet results. Is there a way to save the Surfnet results (the density maps). Also please can you suggest a method to generate a list of all the disconnected blobs with their respective volume information that is implemented in Chimera. Many Thanks, Saumya

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Error: no molecule for surface
by Andrea L Edwards 20 Oct '10

20 Oct '10

I am trying the "Write DMS" tool for my molecule, and I get an error that says "no molecule for surface". I followed Actions->Surface->Show then I followed Tools->Structure Editing->Write DMS. -A

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Fusing or bonding two protein chains?!
by #MAZIAR SOLEYMANI ARDEJANI# 20 Oct '10

20 Oct '10

Hello, All! I have created a pdb file by putting two protein structures close to each other through rotation and translation; so that N-terminus of one is close to the C-terminus of the other. I would like to link one protein's C-terminus to the other protein's N-terminus, i.e. to create a peptide bond between two protein chains and then save the fused protein structure as a pdb file with a single chain. Is there a way to do this in chimera? Can Chemira reset atom numbers and the residue and chain names? Thanks in advance and best regards, Maziar S. Ardejani SPMS-CBC-04-37, The Orner Lab Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences 21 Nanyang Link Nanyang Technological University Singapore 637371

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stereo LCD display
by Wu, Weimin (NIH/NIAMS) [E] 20 Oct '10

20 Oct '10

Dear All, We are planning to buy a stereo LCD display system. Most of time we will use it to visualize the density map and PDB structure in Chimera. We want a LINUX 64bit system. Has anybody got experience on it? Would you please tell me the specifications of your hardwares? How about Miracube G240? Thanks, weimin

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Converting EM map to SAXS bead model
by Tom Goddard 19 Oct '10

19 Oct '10

Hi Alexander, I have talked to someone (forgot name, at Grenoble EM fitting workshop a year ago) who was interested in computing SAXS profiles for EM blobs of unknown proteins and your EM2DAM program could make that possible. It might also have utility in analyzing EM maps. I wonder about details like how how far apart are the dummy atoms placed. Is documentation for the program available? About 9 months ago I added to Chimera the ability to compute a SAXS profile from an atomic model which is then plotted against an experimental profile. The idea is that you could test various atomic model conformations to see which is most compatible with SAXS data. Since then YZ in our lab has added new options and made it work using a web service in addition to the option of running a local program. This is in Chimera daily builds but not in the 1 year old Chimera 1.4 production release. We will have a Chimera 1.5 release soon that will have it. It uses FoXS (http://modbase.compbio.ucsf.edu/foxs/about.html) for the profile computation. Here's a description from the Chimera User's Guide of the Chimera user interface. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/saxs/saxs.html Tom > Hi Tom > > First of all, thank you very much for very helpful comments. > Although thanks for such a nice tool as Chimera! > > The reason I was asking all questions about volume viewing and MRC > file format is that I am developing a tool that converts > EM density maps to dummy atom models (EM2DAM). Bead models (PDB format) > can be used by other software to validate EM models for example. > > You can read more here: > http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg17870.html > > I like Chimera a lot. And if you be interested in integrating/using em2dam > (fortran90) in Chimera, let me know. > > Btw, could you comment on SAXS function in Chimera? > > Kind regards from Hamburg > Alexander >

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Problem adding charges to RNA
by Andrea L Edwards 19 Oct '10

19 Oct '10

When I try to add charge to the RNA molecule, I get a message that says "Please specify the net charges for the above residues so that their atomic partial charges can be computed." And above the message it lists every residue in my molecule. What do I do? I cannot find anyway to specify the net charges, and I though that this script was going to assign the charges anyway, so why do I need to specify them before hand? -A

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GLXBadRenderRequest
by Gough, Erik S 18 Oct '10

18 Oct '10

Hello, I am receiving the following error when I try and open a structure running chimera with Mesa 7.0 on Debian 5. X Error of failed request: GLXBadRenderRequest Major opcode of failed request: 148 (GLX) Minor opcode of failed request: 1 (X_GLXRender) Serial number of failed request: 5334 Current serial number in output stream: 5336 I am assuming that this is related to running an older version of the Mesa driver, but I do not have root on the system and the administrators are hesitant of upgrading the Mesa package in /usr/lib to anything beyond the stable release. The servers do not have access to any hardware based video so doing an updated hardware based driver install won't help either. I am limited to what I can do and only have access to my home directory. Would it be possible for me to compile a newer version of the Mesa driver in my home directory and then compile chimera to use that version of the driver instead of the default in /usr/lib? Thanks!

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Molecule fusing
by Brian & Lanie Grech 16 Oct '10

16 Oct '10

Hi Sir/Madam I want to create models which consist of multiple protein molecules, in which the individual protein molecules are fused together to form a single structure. Something like the scanning 3D maps produced by electron microscopes. Is it possible to do this with the Muliscale Models tool or some other tool or method in Chimera? An example of what I want to do appears in the cutaway rotavirus illustration (Fig. 1A) in Chen and colleagues paper, titled, "Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM" (PNAS, vol. 106. no. 26, p. 10644). In this illustration the yellow triangular shaped structure are multiple VP7 molecules fused together. Regards Brian Grech

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Relax H-bond constraints
by Joern Lenz 15 Oct '10

15 Oct '10

Hi, I used the automated H-bond detection of Chimera to detect H-bonds between an target protein and its docked lignds. On your webpages (http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon…) I found the following: "[...] Relax H-bond constraints indicates that tolerances to Relax constraints by should be applied to the precise geometric criteria [...]; empirically, tolerances of 0.4 angstroms and 20.0 degrees work well for most macromolecular structures." Can you lease tell me if there is a literature which discusses this relaxation in more detail and can be referenced Many thanks for a reply. Cheers Joern

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Per-atom RMSD
by Ibrahim Moustafa 08 Oct '10

08 Oct '10

Dear Chimera, I have a question regarding RMSD: I have two structures to superimpose using certain residues; and I am interested to get the RMSD value for each CA-atom in the structure. I wonder if there is a way to do that in Chimera? I think there is no direct way; but I wonder if there is a script that can be used for that. For the developer: It might be useful to have a tool that can directly do that in Chimera Many thanks for help, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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