November 2010 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Re: [Chimera-users] Display a spider volume data in a specific orientation
by Elaine Meng 08 May '14

08 May '14

Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor… > It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation. I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0 You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used. I'm CC-ing the chimera-users(a)cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer! 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 Apr 7, 2010, at 11:51 AM, Li, Zongli wrote: > Hi Elaine, > I have a spider volume data (or mrc density map) from which I got a > serious 2D projections. I have the Euler angles for each projection. > Is there a way in Chimera that I can use those Euler angles to > display the 3D spider volume data (or mrc density map) in a specific > orientation that corresponding to that 2D projection? > Thank you very much in advance. > Best, > Zongli > > **************************************** > Zongli Li, Ph.D. > > Howard Hughes Medical Institute > Department of Cell Biology > Harvard Medical School > C Building, Room 420B > 240 Longwood Avenue > Boston, MA 02115 > > Tel: 617-432-4095 (Office) > 617-432-4708 (EM Suite) > 617-432-4091 (Computer room) > Fax: 617-432-1144 > Email: zongli_li(a)hms.harvard.edu > *************************************** >

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color surface based on NMR Order parameters
by lalit.deshmukh＠huskymail.uconn.edu 08 Sep '11

08 Sep '11

Hello, I like the 'surface color ' feature in Chimera. I think, right now, the surface can be colored by radius, height, volume data and so on.. Is it also possible to color the surface based upon the NMR order parameters or intensity ratios (it will be an Excel file containing just two columns: residue numbers and the respective parameter values)? Or this can be done in some other way? Thanks in advance, Regards, Lalit Deshmukh, University of Connecticut Storrs, CT 06269

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square of density volume
by 仁田亮 12 May '11

12 May '11

Hi chimera users, I want to calculate the square value for the volume of the electron density because I want to calculate the variance map. Do anyone know whether we can calculate the square value of the volume by chimera? And if we can, could you teach me how to calculate? Thanks for your time and help, Ryo

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how to delete saved state in the "savepos list"
by jinghua 21 Jan '11

21 Jan '11

The savepos is a very useful command to save the state of the graphics. But after a while, the "savepos list" contains a long list. Is there a way to delete some of the states in the list? Thank you in advance, Jinghua

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bond rotation
by Elaine Meng 05 Jan '11

05 Jan '11

On Jun 25, 2010, at 10:20 AM, Watson, Lisa wrote: > Hi Elaine, > I have changed several nucleotide bases in the DNA structure I am working with so that I can model in cytosine methylation. Is there a way that I can rotate the changed bases so that they are aligned to base-pair properly? > Thanks for your help! > -Lisa Hi Lisa, Sure, you can interactively rotate bonds. If you Ctrl-doubleclick a bond it should show a little menu where one of the choices is to rotate that bond. After you activate the rotation, the "adjust torsions" dialog will appear, which includes various ways to rotate the bond. You can have several rotatable bonds at the same time. Here is more about Adjust Torsions: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru…> Also, the tutorial "Structure Comparison and Analysis" includes measuring distances, finding H-bonds and clashes, and rotating bonds: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.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

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Silhouette edges around dashed wire-style bonds
by Dipl.-Ing. Thomas Mitterfellner 05 Jan '11

05 Jan '11

Hello! In some of my structures, I need dashed bonds to indicate hydrogen bonding or metal complexation. As I understand it, in order for bonds to be displayed as dashed, they need to be wire-style. I wondered if silhouette edges could also be extended to these wire-style bonds? Alternatively, could stick-style bonds possibly be displayed in a dashed fashion? Maybe as a series of cylinders, each separated by a certain distance, or eg. as a series of equally spaced small spheres. Thank you, Thomas

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pythonw.exe error
by Hunmin JUNG 01 Dec '10

01 Dec '10

Hi, Whenever I open the chimera after the installation, it gives me an error 'pythonw.exe has stopped working'. It didn't matter the version of the chimera. Please what I need to do to resolve the problem. Thanks, Hunmin (Mike) Jung Department of Chemistry Texas A&M University (979)862-7639

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Closest Waters
by Beale, John 30 Nov '10

30 Nov '10

I am working with a protein in explicit water. Using AMBER tools, I have selected the 100 closest water molecules in and around the protein. Is there a way in Chimera to identify which amino acid residues that the waters are hydrogen bonded to? Or, is there a way to visualize which amino acids the water molecules are closest to? 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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Merging mrc map
by Massimiliano MALETTA 30 Nov '10

30 Nov '10

Hello I would like to know if merging two maps is possible in Chimera. I have two *mrc map files and I would like to figure out how to get a third file containing the two maps, just summed. I tried the option morph volume, but in fact it is always down weighting one of them respect to the other. Thank you for the help. ----------------------------- Post-doc IGBMC/ FRANCE MALETTA Massimiliano Equipe/Service: KLAHOLZ TEL : +33 (0) 3 88 65 57 53 FAX : +33 (0) 3 88 65 32 01

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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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