- Chimera-users - RBVI Mailing Lists

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>

3 4

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

2 2

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

3 6

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

3 4

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.

1 0

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

2 1

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 >

5 6

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)

2 1

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

2 1

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

2 2

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.

2 1

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. -----------------------------------------------------------------------------------

2 1

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 ++++++++++++++++++++++++++++++++++++++++++++

1 0

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 ++++++++++++++++++++++++++++++++++++++++++++

3 2

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

1 0

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

2 1

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

3 6

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>

3 2

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

2 2

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

1 0

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.

2 8

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

2 8

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 >> >

1 0

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

3 6

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

3 2

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

2 1

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

1 0

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

2 1

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.

2 1

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.

1 0

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 > > ======================================== > > > > > > > > > > > > > >

1 0

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

2 1

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.

3 4

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

3 3

.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

2 1

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

2 1

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>

2 1

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.

3 3

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 <<< ------------------------------------------------------------------------>>>

3 5

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

1 0

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

1 0

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

2 1

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

3 2

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

2 1

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

2 4

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

1 0

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 >

5 6

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

2 3

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!

1 0

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

3 3

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

2 2

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

2 2

Compatibility Question
by ayassin＠wadsworth.org 07 Oct '10

07 Oct '10

Hello, I have had some problems using chimera on a PC/Vista laptop with Intel graphis card. Any advice/experience on using chimera with PC/Windows7 laptop and NVIDEA graphics card? Is it better/more compatible/same type of problems? is it the PC or the graphics card? Thank you very much, any feedback will help... Aymen Yassin IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.

2 1

colour residue by value
by Sumitro Harjanto 07 Oct '10

07 Oct '10

Hi Elaine, I am looking into using CHIMERA to create a diagram. Each residue will be coloured according to an assigned value; say if the value is high, the residue will assume a bright red colour; if the value is low, the residue will be coloured light yellow; residue with a medium value will appear somewhat orange. So my question will be: is there a way to specify the colour of a residue by its RGB value? And how does the command look like (as I will be scripting to do it in large scale)? Thanks! =] Cheers, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

2 5

thousands of black rectangles?
by Brandt, Gabriel S. 06 Oct '10

06 Oct '10

Colleagues - Yesterday, I seem to have acquired a case of the Chimera measles. My proteins are being rendered with spots all over them. When I select any atom, all the spots are selected as well. I initially thought it was a problem with that particular PDB file, but formerly fine files all seem to have this problem. The issue seems like it arose spontaneously - I haven't recently updated any software that I'm aware of. I was running 1.2470 under X Windows (Mac OS 10.4.11). I downloaded a new version (1.4.1, Aqua) but the problem persists. Am I being foolish here? Is it simply a setting that I can change? G Malaria Research Institute Johns Hopkins School of Public Health 615 N. Wolfe St. W8704 Baltimore, MD 21205

2 1

Re: [Chimera-users] [chimera-dev] some questions
by Elaine Meng 04 Oct '10

04 Oct '10

On Oct 4, 2010, at 7:44 AM, Gentile, Maria Antonietta wrote: > Hi, > I would have some information about CHIMERA. Is it possible to obtain the topology of a protein structure by using CHIMERA? How? And the second question is about the secondary structure representation of a protein, in my case wiht CHIMERA I am not able to visualize all secondary structure elements, how can I modify the settings for this problem? > Thank you > Hi Maria, I don't understand what you are asking, but I will try to answer. If by topology you mean give you some classification of what fold the protein has, no, Chimera does not do that. You might try using the "Dali server" or "Cathedral server" (google those) or something similar to compare your structure to a set of other proteins and report back which ones are the most similar. For the secondary structure, Chimera just uses the information in the input PDB file on which parts are the alpha-helices and beta-strands, and these are shown in the ribbon representation. If your structure doesn't have HELIX/SHEET information in the input PDB file, Chimera will run the "ksdssp" program to try to identify them. If you are not seeing helix and strand where you expect helix and strand, it might be that they HELIX/SHEET information in the PDB file is that way, or that the geometry is irregular/distorted so that "ksdssp" does not identify what you expect. EIther way, you could either (A) try re-running the secondary structure identification with different parameters (see the "compute SS" function in the Model Panel, which is itself in the Favorites menu, or the command "ksdssp") <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#functions> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html> (B) just manually change secondary structure assignments. Several ways are described in this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2007-April/001514.html> Elaine P.S. for Chimera questions the better address is chimera-users(a)cgl.ucsf.edu (chimera-dev is for chimera-related python programming questions). ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Minimization and dielectric choices
by r charbel maroun 04 Oct '10

04 Oct '10

Hi Conrad, Thanks for your answer. Don't worry, you needn't make a disclaim though. In my opinion, it's not a question of knowing which non-default option is more suitable for use in Chimera, but rather giving the user the choice to use the options that suit him, such as letting him choose the value of the dielectric constant, instead of forcing the value of 1, which would make minimization results useless, i.e. non realistic. It's not either a question of a full-blown MM/MD interface in Chimera, but I feel that the any decent program that does energy minimization should give the user access to steepest-descent *and* conjugate-gradient (CG) methods. Why? Because the 2nd is usually used after the 1st, given that the 1st, as the manual says, is very inefficient if the goal is to find a local minimum of the potential energy. And our purpose is to find energy minima and the conformations that are associated with. To the best of my knowledge, there is no server or free academic program doing energy minimization with these options. Introduction of the choice of dielectric constant and of CG would thus make Chimera rather complete and unique in this sense leading to an increased usage by the community of biocomputational people. Given that MMTK contains CG, what would it take to include the algorithm in Chimera ? Cheers, CM On Wed, Sep 29, 2010 at 8:54 PM, Conrad Huang <conrad(a)cgl.ucsf.edu> wrote: > Before I provide any answers, I have a disclaimer. I only have a > rudimentary familiarity with energy minimization and molecular dynamics. I > understand what force fields are and some of the algorithms used for > minimization and integration, but not much about the details of force field > options. My experience with MMTK is mainly playing with example scripts for > the excellent documentation. So, with that in mind, here are some answers > to your questions. > > The code in MMTKinter uses the Amber 99 forcefield with all default > arguments. THere is an "es_options" parameter that let's you control > electrostatic options, but I'll be the first one to admit that I do not know > which non-default option is more suitable for use in Chimera. The MMTK > documentation ( > http://dirac.cnrs-orleans.fr/Manuals/MMTK_reference/MMTK.ForceFields.Amber.…) > does not explicitly mention dielectric value or functional form for any of > the options. The code that creates the MMTK forcefield instance is in the > MMTKinter_makeUniverse method. (The MMTKinter class is actually designed so > that programmers can pass force field parameters through to MMTK, but > Chimera does not use this capability.) > > As for why only SteepestDescentMinimizer was used, it was mainly for > simplicity. The minimization options that Chimera provides is not very > extensive. Our intent is to provide a tool for simple clean up of small > (regions of) systems. That's why we chose to use default MMTK parameters, > infinite (non-periodic) universe, steepest descent minimizer, etc. The > scope of providing a full-blown MM/MD interface in Chimera is too large for > us to undertake. There are just too many degrees of freedom and we > currently do not have enough resources to do a proper job of it. > > If you are familiar with programming MMTK, there is another way of using > MMTK with Chimera. > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts/MMTK describes an > approach where you can program mostly in MMTK, but display results in > Chimera. Obviously, this is mainly for programmers, but it does let you get > to the full power of MMTK along with visualization from Chimera. > > Conrad > > > On 9/29/2010 8:55 AM, r charbel maroun wrote: > >> Hi everybody, >> >> The value of the dielectric constant used by Chimera is 1, corresponding >> to calculations in vacuo. Is there not an easy way to change this value >> to, say 78 or to include a sigmoid function or the Generalized Born >> approach so as to mime the presence of the solvent ? I looked for it but >> couldn't find it : where in the >> {chimera_install_location}/share/MMMD/MMTKinter.py file can the value of >> the dielectric be changed ? Otherwise, how to mime implicitly the solvent >> ? >> >> Also, it seems that only the Steepest descent, and not the Conjugate >> gradients method, for energy minimization has been implemented in >> Chimera. Why is this so? >> >> It'd be so nice to have these two functionalities added as I don't know >> of any free academic program allowing us to do energy minimization with >> these options without having to parametrize every new ligand (Charmm, >> Namd), a painful task. >> >> Cheers, >> >> Charbel >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > -- R. Charbel MAROUN, PhD, HDR Neurobiologie et Pharmacologie Moléculaire Centre de Psychiatrie et de Neurosciences Broca-Sainte Anne (INSERM U894) 2ter rue d'Alésia 75014 Paris FRANCE Tél. +33 1 40 78 92 77 Fax +33 1 45 80 72 93 e-mail rmaroun(a)gmail.com charbel.maroun(a)inserm.fr

1 0

pseudo bonds in mol2 files
by Francesco Pietra 01 Oct '10

01 Oct '10

I am confused about the meaning of pseudobonds for the aromatic portion of mol2 files. Typical example sustiva.mol2 in the antechamber-sustiva tutorial b4 of amber. I have the same representation for aromatic bonds in modified amino acids. In contrast, normal bonds from pdb files of the same molecules. Thanks for clarifying. francesco pietra

2 2

multiple frames 1topology
by Francesco Oteri 30 Sep '10

30 Sep '10

Dear AMBER users, I've one file with the AMBER topology of my system, but I saved some rappresentative structures as pdb. Since my system is made of a set of circular DNA, I'd manipulate pdb to obtain the correct connectivity. There is a way to load a correct pdb ( or topology file) and exporting this connectivity on the other pdb? For example, should be useful if I load at the beginning the correct pdb and than I'will load the remaining structure whit the same number of atoms of the first but without CONECT and/or TER tag.

2 1

Finding the angle between two aromatic rings
by Miriam Gochin 30 Sep '10

30 Sep '10

Chimera has an Axes / Planes function where you can define the plane through three atoms. If you define two planes, is there a way to get the angle between the planes? Thanks! Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

3 2

ribbon problem
by Francesco Oteri 30 Sep '10

30 Sep '10

Dear all, I'd like to use chimera to do a picture of a circular DNA with ribbon representation. I found the two following problems: 1.If I load the .pdb files, chimera is unable to recognize the topology and shows extra-bond connecting the last base of a strand with the previous of the other strand. 2.If I load the AMBER topology, the connectivity is correctly recognized, but the first base and last are not connected by the ribbon. Is there any solution?

4 14

how to set the transparency of ribbon
by Qinghua Liao 29 Sep '10

29 Sep '10

Dear chimera's users, Could someone tell me how to set the transparency of ribbon of a protein? Thanks very much All the best, Qinghua

2 2

Dielectric ; Steepest descent
by r charbel maroun 29 Sep '10

29 Sep '10

Hi everybody, The value of the dielectric constant used by Chimera is 1, corresponding to calculations in vacuo. Is there not an easy way to change this value to, say 78 or to include a sigmoid function or the Generalized Born approach so as to mime the presence of the solvent ? I looked for it but couldn't find it : where in the {chimera_install_location}/share/MMMD/MMTKinter.py file can the value of the dielectric be changed ? Otherwise, how to mime implicitly the solvent ? Also, it seems that only the Steepest descent, and not the Conjugate gradients method, for energy minimization has been implemented in Chimera. Why is this so? It'd be so nice to have these two functionalities added as I don't know of any free academic program allowing us to do energy minimization with these options without having to parametrize every new ligand (Charmm, Namd), a painful task. Cheers, Charbel

2 1

Re: [Chimera-users] Chimera-users Digest, Vol 89, Issue 30
by vamsi krishna 29 Sep '10

29 Sep '10

Hi all, I am very happy to see modeller interface in chimera latest version.Please help me any one how to use (steps) it for modeling. Thank you Best wishes, vamsi On 29/9/2010 3:00 AM, chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: download of chimera 1.5 (Elaine Meng) > 2. Fwd: Stereo 3D for teaching (Nadir T. Mrabet) > 3. Re: Remove hydrogen (Elaine Meng) > 4. Re: select side chain (Elaine Meng) > 5. Re: Fwd: Stereo 3D for teaching (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 28 Sep 2010 09:22:16 -0700 > From: Elaine Meng<meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] download of chimera 1.5 > To: atila petrosian<atila.petrosian(a)gmail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID:<6FB84799-504C-4FA9-8CFE-4CA7A0E2BB33(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Chimera 1.5 daily build downloads are included in the download page. You have to scroll down to the "Daily Builds" section, or click the "Daily Builds" link at the top to go directly to that section (or just click here): > > <http://www.cgl.ucsf.edu/chimera/download.html#daily> > > "alpha" is whatever is not yet an official release, so yes, right now the "alpha" downloads are version 1.5. > Elaine > > > ------------------------------ > > Message: 2 > Date: Tue, 28 Sep 2010 18:30:34 +0200 > From: "Nadir T. Mrabet"<Nadir.Mrabet(a)medecine.uhp-nancy.fr> > Subject: [Chimera-users] Fwd: Stereo 3D for teaching > To: "chimera-users(a)cgl.ucsf.edu BB"<chimera-users(a)cgl.ucsf.edu> > Message-ID:<4CA2182A.3020902(a)medecine.uhp-nancy.fr> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Elaine, > > Could you please react to my last week's mail, forwarded (again) below? > Thanks, > > Nadir Mrabet > > > -------- Original Message -------- > Subject: [Chimera-users] Stereo 3D for teaching > Date: Fri, 24 Sep 2010 17:23:35 +0200 > From: Nadir T. Mrabet<Nadir.Mrabet(a)medecine.uhp-nancy.fr> > Reply-To: Nadir.Mrabet(a)medecine.uhp-nancy.fr > Organization: Nancy University, School of Medicine > To: chimera-users(a)cgl.ucsf.edu BB<chimera-users(a)cgl.ucsf.edu> > > > > Hi, > > I had addressed previously the question about which equipments would > perform best to display molecular structures in 3D for teaching purposes. > Greg Couch had offered to keep me up on the latest technologies offered > at the last SIGGRAPH conference. > But nothing so far. > Can anyone help me with that? > > Many thanks in advance. > > Nadir >

2 1

clustering of docking results
by Bala subramanian 29 Sep '10

29 Sep '10

Friends, I am using viewdock tool for analysing the docking result obtained from autodock. Is there any way to do some clustering of the docked conformations using the energetically best structure as the reference within chimera ? Thanks in advance, Bala

2 1

Fwd: Stereo 3D for teaching
by Nadir T. Mrabet 28 Sep '10

28 Sep '10

Hi Elaine, Could you please react to my last week's mail, forwarded (again) below? Thanks, Nadir Mrabet -------- Original Message -------- Subject: [Chimera-users] Stereo 3D for teaching Date: Fri, 24 Sep 2010 17:23:35 +0200 From: Nadir T. Mrabet <Nadir.Mrabet(a)medecine.uhp-nancy.fr> Reply-To: Nadir.Mrabet(a)medecine.uhp-nancy.fr Organization: Nancy University, School of Medicine To: chimera-users(a)cgl.ucsf.edu BB <chimera-users(a)cgl.ucsf.edu> Hi, I had addressed previously the question about which equipments would perform best to display molecular structures in 3D for teaching purposes. Greg Couch had offered to keep me up on the latest technologies offered at the last SIGGRAPH conference. But nothing so far. Can anyone help me with that? Many thanks in advance. 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. _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

3 2

3D stereo
by Nadir T. Mrabet 28 Sep '10

28 Sep '10

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 -- 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.

2 2

select side chain
by Enrico Morelli 28 Sep '10

28 Sep '10

Dear all, how can I select the side chain of the residue and to color it using different color from the backbone (possibly the command line)? Thanks -- ------------------------------------------------------------------- (o_ (o_ //\ Coltivate Linux che tanto Windows si pianta da solo. (/)_ V_/_ +------------------------------------------------------------------+ | ENRICO MORELLI | email: morelli(a)CERM.UNIFI.IT | | * * * * | phone: +39 055 4574269 | | University of Florence | fax : +39 055 4574253 | | CERM - via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY | +------------------------------------------------------------------+

2 1

Remove hydrogen
by Enrico Morelli 28 Sep '10

28 Sep '10

Dear, another question. How I can remove or can't display all the protons displayed in chimera? Thanks -- ------------------------------------------------------------------- (o_ (o_ //\ Coltivate Linux che tanto Windows si pianta da solo. (/)_ V_/_ +------------------------------------------------------------------+ | ENRICO MORELLI | email: morelli(a)CERM.UNIFI.IT | | * * * * | phone: +39 055 4574269 | | University of Florence | fax : +39 055 4574253 | | CERM - via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY | +------------------------------------------------------------------+

2 1

download of chimera 1.5
by atila petrosian 28 Sep '10

28 Sep '10

Dear Elaine Meng chimera-alpha<https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=alpha/chimera-alpha-wi…> is the same chimera 1.5. is it true?

2 1

download of chimera 1.5
by atila petrosian 27 Sep '10

27 Sep '10

Dear Elaine Meng thanks for your attention. how to obtain chimera 1.5 ? in website http://www.cgl.ucsf.edu/chimera/, in Download option, there is not chimera 1.5.

1 0

Gorgon EM modeling / visualization software
by Tom Goddard 27 Sep '10

27 Sep '10

Hi Tom, I found in Keren Lasker's book chapter a reference to an EM modeling program called Gorgon from Washington University at St Louis. It was developed in collaboration with NCMI (Wah) and seems to be aimed at modeling high resolution EM maps where protein backbones can be traced. It is embarrassing that I didn't know about this, and also that they didn't leverage Chimera. I guess Chimera code was deemed too complex to reuse so they wrote their own molecule/map display and editor. Ugh. This Gorgon software is a relative of the pipeline for EM modeling that Keren describes in her book chapter, only it is really the NCMI pipeline -- focused on how to model 4 Angstrom EM maps. I think this would be a good case study to investigate why they didn't make use of Chimera extensibility or Chimera code modules. Another recent case of massive reimplementing computer graphics capabilities is a fitting package called UROX from Jorge Navaza's lab. It would be interesting to survey new molecular and EM graphics packages, talk to the authors, and see what we could have done to make Chimera more attractive to them as a development platform or code base. Tom

1 0

change of atom colors
by atila petrosian 27 Sep '10

27 Sep '10

Hi chemera users I am beginner in chemira. I opened a pdb file containing protein by chimera, in my chimera both of carbon and hydrogen atoms have same color (light gray). I want to have carbon as green and hydrogen gray. how can I do that?

2 2

hydrogen bond in proteins
by atila petrosian 27 Sep '10

27 Sep '10

Hi chimera users I used (find Hydrogen bonds) option for my pdb file (containing 2 strands of amino acids), but chimera show HBs that being between O and N atoms, while I want to chimera show HBs that being between O and H atoms (usually, in proteins, HB is formed between O atom of C=O group and H atom of N-H group, consequently; C=O…H-N). Please guide me.

2 1

surface area
by yan zhang 27 Sep '10

27 Sep '10

Hi sir , I used StrucTools server of Area/Volume from Web to calculate the buried surface of ligand . The ligand and protein was docked with glide , and then, i saved the complex into the form of pdb.I calculate the protein, ligand and complex area respectively , but the values of protein and complex were the same . The Surface probe size is 1.5 and Atoms to use is 'atoms+hetatms' . Is there something wrong with the pdb file of the complex or my operation? The three pdb files are in the accessory. Thanks, Sweety

2 1

surface area
by yan zhang 27 Sep '10

27 Sep '10

Hi sir , I used StrucTools server of Area/Volume from Web to calculate the buried surface of ligand . The ligand and protein was docked with glide , and then, i saved the complex into the form of pdb.I calculate the protein, ligand and complex area respectively , but the values of protein and complex were the same . The Surface probe size is 1.5 and Atoms to use is 'atoms+hetatms' . Is there something wrong with the pdb file of the complex or my operation? Thanks, Sweety

1 0

modify structure
by Francesco Pietra 26 Sep '10

26 Sep '10

Hello: New to modify structure. I would like to modify a peptide by changing ARG to VAL. As I wanted to start from the conformer containing ARG, I tried to delete bonds, in the hope to finally change one H to CH3. None worked in my hands. Thanks for suggestions. francesco pietra

3 4

Problem: Electrostatic surface coloring
by Nitesh Sule 24 Sep '10

24 Sep '10

Hi, I am having trouble getting chimera to open .phi files, with the following reply: "Error reading file xyz.phi, format delphi Parameter record size 284 must be 16 or 20 or 36" The .phi file was generated using delphi, and works fine when opened with Grasp2. Can someone please help me with this? On a slightly related note, I am also unable to use the delphi controller in Chimera, with the message: "Delphi exited with status -1073741794". I am not sure if this is a bug. I can provide more details from the log. Chimera version: 1.4.1 (build 29977) Thanks Nitesh.

3 4

Re: [Chimera-users] cover art
by Eric Pettersen 24 Sep '10

24 Sep '10

On Sep 24, 2010, at 3:49 PM, Friedman, Simon H. wrote: > Hey Eric, > Here is a mockup of the cover. I have a question for you: If you > look at the helix, there are some very funky shadows that ended up > very blocky. Other shadows are completely smooth. The helix was > rendered in pov using default everything (from Chimera). Any > insights into the blocky shadows? They are on one strand only! Hi Simon, That's because right now the ribbons are being represented by a bunch of triangles. One of the things on Greg's to-do list is to have them represented by NURBS curves, which POV-ray would be able to shadow smoothly, but that hasn't happened yet. For now, you can mitigate the blockiness by upping the subdivision quality to 5 or higher. Control of the subdivision quality is in the "Effects" tab of the side view. --Eric

1 0

Stereo 3D for teaching
by Nadir T. Mrabet 24 Sep '10

24 Sep '10

Hi, I had addressed previously the question about which equipments would perform best to display molecular structures in 3D for teaching purposes. Greg Couch had offered to keep me up on the latest technologies offered at the last SIGGRAPH conference. But nothing so far. Can anyone help me with that? Many thanks in advance. 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.

1 0

movie command with headless Chimera
by Tom Goddard 23 Sep '10

23 Sep '10

Hi Masako, You want to create a movie by running Chimera in the background (no windows, no console). You are trying the right approach, using "headless" Chimera. I'm afraid the movie command may not work with headless (ie background, no windows) Chimera. Headless Chimera can't create any dialog windows and it may be that the movie command internally relies on the Movie Recorder dialog. I don't know for sure. Your error is caused by the movie command trying to monitor changes in the Chimera graphics window (which does not exist). I can fix that and see if there are subsequent errors. I'll try this today or tomorrow. Image saving works with headless Chimera, but I have not tried background movie recording in the past -- obviously useful though. Tom > Hi, Tom. I hope you had a nice vacation :) > > I was able to run very simple command script with headless chimera, but I > am getting these errors trying to save a simple spinning movie... > > reading final.mrc 2.2 Mb 0% > Done reading final.mrc > final.mrc opened > reading final.mrc 18 Mb 0% > Done reading final.mrc > Traceback (most recent call last): > File "/home/mterada/opt/UCSF/Chimera-headless/share/chimeraInit.py", > line 422, in init > chimera.openModels.open(a, prefixableType=1) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/chimera/__init__.py", > line 1510, in open > models = func(filename, *args, **kw) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/Midas/ChimeraExtension.py", > line 32, in func > processCommandFile(cmdFile) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/Midas/midas_text.py", > line 104, in processCommandFile > _processFile(f, emulateRead, filename) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/Midas/midas_text.py", > line 135, in _processFile > if makeCommand(line): > File > "/home/mterada/opt/UCSF/Chimera-headless/share/Midas/midas_text.py", > line 65, in makeCommand > f(c, args) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/MovieRecorder/ChimeraExtension.py", > line 25, in doMovieCmd > doExtensionFunc(MovieRecorder.processMovieCmd, args) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/Midas/midas_text.py", > line 426, in doExtensionFunc > extFunc(*tuple(processedArgs), **kw) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/MovieRecorder/__init__.py", > line 207, in processMovieCmd > director = getDirector() > File > "/home/mterada/opt/UCSF/Chimera-headless/share/MovieRecorder/__init__.py", > line 342, in getDirector > director = Director.Director() > File > "/home/mterada/opt/UCSF/Chimera-headless/share/MovieRecorder/Director.py", > line 69, in __init__ > top = chimera.tkgui.app.winfo_toplevel() > AttributeError: 'module' object has no attribute 'tkgui' > Error while processing makeimage.cmd: > AttributeError: 'module' object has no attribute 'tkgui' > > File > "/home/mterada/opt/UCSF/Chimera-headless/share/MovieRecorder/Director.py", > line 69, in __init__ > top = chimera.tkgui.app.winfo_toplevel() > > See reply log for Python traceback. > > > This same command script saves spinning movie with no problem, so I am > guessing it's headless chimera not having GUI... Is there a way around > it? > > Thanks, > > Masako >

1 1

Mutagenesis
by r charbel maroun 23 Sep '10

23 Sep '10

Dear Chimera users, Please correct me if I'm wrong, but neither in Chimera nor in the user's list did I find any info on mutating a residue. Is this a missing functionality ? Greetings -- R. Charbel MAROUN, PhD, HDR Neurobiologie et Pharmacologie Moléculaire Centre de Psychiatrie et de Neurosciences Broca-Sainte Anne (INSERM U894) 2ter rue d'Alésia 75014 Paris FRANCE Tél. +33 1 40 78 92 77 Fax +33 1 45 80 72 93 e-mail rmaroun(a)gmail.com charbel.maroun(a)inserm.fr

2 2

Saving new coordinates after superimposing structures
by Sujata 22 Sep '10

22 Sep '10

Hi, After I superimpose two structures using MatchMaker, I would like to save the coordinates of #1 after being superimposed with #0. When I save the PDB with the new coordinates and open #0 and #1 PDBs again, they do not superimpose. Can this be done? What is the best way to achieve this? (Elaine, I have a third fragment I want to bond to the previously bonded one and since the first-second has moved now, I want to do this so that they are on the same axis). Thanks, Sujata

2 1

technical questions about volume viewer in chimera
by Alex Shkumatov 22 Sep '10

22 Sep '10

Hallo Perhaps, this has been on the forum before, but I could not find the answers to my questions: 1. Some EM density maps have a header. I wonder how Chimera recognizes it and calculates map dimensions? 2. Does chimera take default voxel size from header of EM file? Thanks in advance Alex ---------------------------------------------------------------------- Alexander Shkumatov, predoc -- Biological Small Angle Scattering Group EMBL Hamburg Outstation c/o DESY -- Building 25A Notkestraße 85 -- 22603 Hamburg -- Germany tel: +49 40 89902 178 fax: +49 40 89902 149 Email: shkumatau(a)embl-hamburg.de ----------------------------------------------------------------------

3 4

Re: [Chimera-users] Joining fragments in a peptide bond
by Elaine Meng 21 Sep '10

21 Sep '10

Hi Sujata, I'll answer the easy part first: you can specify the axis cylinder radius as an Angstrom value in the Define Axis dialog (opened from the Axes/Planes/Centroids tool) or if you are using the "define" command, with the "radius" keyword, see the general options in that page: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> I see you have a left-handed polyproline helix which also has a superhelical twist, and you wish to extend its length maintaining the same helicity and superhelicity. Then you have assembled three of these into a triple helix. This problem is not really something you want to attack with Build Structure; instead, you need to figure out the symmetry operations to extend this structure, then apply them to additional copies of the identical structure to extend it. One way would be to figure out BIOMT matrices and add those to the PDB file. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html#biomt> However, it can be difficult to figure out the correct values and edit them in using the correct format, so I'll describe a different way that just uses commands. The two fragments you sent are identical (I know you know this, I'm just explaining to the others), and I matched the first half of one copy to the second half of the other copy to try to figure out the symmetry operations. Command: match #1:1-15@ca #0:16-30@ca <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> This match looked pretty good to me, so next I used the measure command to tell me the transformation that had been used to generate this match: measure rotation #0 #1 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> Actually that command will display another axis cylinder, and I don't think you can control the size of that one, but you can just close or hide it with the Model Panel (under Favorites in the menu). The transformation information is given in the Reply Log (also under Favorites in the menu): Position of #1 relative to #0 coordinates: Matrix rotation and translation -0.00777505 -0.89851915 -0.43886545 45.94850252 0.89297961 -0.20375330 0.40133777 -0.02182236 -0.45002996 -0.38877748 0.80394347 -26.28870812 Axis -0.40352597 0.00570191 0.91495042 Axis point 17.07887792 12.85324577 0.00000000 Rotation angle (degrees) 101.75881858 Shift along axis -42.59440324 Then I reset so that the two fragments were again exactly superimposed (since they are identical ), using the command: reset <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html> Then I applied TWICE the reported translation and rotation because the match was of 15 residues, but the whole fragment is 30 and I want to join the ends. I used the axis given in the Reply Log as the axis of movement and the axis point as the center of rotation, and applied twice the rotation angle with the "turn" command and twice the shift with the "move" command: turn -0.40352597,0.00570191,0.91495042 203.5 models #1 coord 0 center 17.07887792,12.85324577,0 move -0.40352597,0.00570191,0.91495042 85.188 models #1 coord 0 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> At this point it looks like they are in a pretty good position to just add the bond and delete the extra atoms at the ends. Since you already have the models in position, don't use Join Models in Build Structure. Instead use "copy/combine" in the Model Panel (or the "combine" command) to merge the two fragments to create another model, and in that model, select the extra atoms that you want to delete (probably all hydrogens on N-term N and one of the oxygens on the C-term carboxyl of the other fragment), use command "del sel" to delete them, then select the two atoms to be bonded, and use command "bond sel". The bond will look a little strained, but this whole approach is going to get you an APPROXIMATE model. You could use command "addh" if you cared about the presence of the amide hydrogen at the join. This approximate model is good enough for a figure, or as a starting point for a simulation in some other package like Amber. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html> Actually, it might have been better to start with the trimeric fragment with all 3 chains, use residues from all 3 chains for the match, etc., and then there would be three bonds to form, rather than repeating only the single strand and then trimerizing. Hard to know without trying. Sorry, it is a rather laborious process. 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 Sep 20, 2010, at 10:31 AM, Sujata wrote: > Hello Elaine, > Thank you for the email below. It was very helpful. > > But, I would like the second fragment to be on the same helical axis as the first one. When I join them this way, by defining the torsion angle, the second one does not stay on the same axis as the first one. So is there a way that I can fix the two peptides to be on the same axis when I fix the bond length and the torsion? > > I am attaching the two individual files and the combined one. > > Also when one defines axis, is there a way to reduce the thickness of the displayed axis. Due to its thickness, the atoms are not visible. > Thank you. > > Regards, > Sujata >

2 1

question
by Domenico Raimondo 17 Sep '10

17 Sep '10

Hi, I have found on the MODELLER web page that Chimera has a Modeller interface in the latest nightly builds. Is it right? and is it possible to use it? Thanks a lot, Domenico. .............................................................................................................. Domenico Raimondo Researcher - Biocomputing group, University of Rome 'La Sapienza' Dep. of Biochemical Sciences, P.le Aldo Moro, 5 - 00185 Rome, Italy. e-mail: domenico.raimondo(a)uniroma1.it domenico.raimondo(a)gmail.com Web page: http://biocomputing.it/index.php/People/raimondo Skype name: domerai3 Tel (work): +39 06 49914297 Tel (mobile): +39 335 6475092 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.

3 4

defining attribute
by Bala subramanian 17 Sep '10

17 Sep '10

Friends, I want to define solvent accessibility as the attribute to create a worm representation. I used the template file 'percentExposed.txt' in the following link to create an attribute file. The sample file i creased is attached (exp.txt) http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/perce… when i give the command: deffattr exp.txt I get the following error. How to resolve the problem. Traceback (most recent call last): File "/usr/local/chimera_15/lib/python2.6/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/local/chimera_15/share/Midas/midas_ui.py", line 260, in processCommand midas_text.makeCommand(text) File "/usr/local/chimera_15/share/Midas/midas_text.py", line 66, in makeCommand f(c, args) File "/usr/local/chimera_15/share/AddAttr/ChimeraExtension.py", line 33, in cmdAddAttr specInfo=[("spec", "models", "molecules")]) File "/usr/local/chimera_15/share/Midas/midas_text.py", line 424, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 77, in addAttributes return _addAttr(attrFile, models, log, raiseTool) File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 239, in _addAttr from ShowAttr import ShowAttrDialog, screenedAttrs ImportError: cannot import name screenedAttrs ImportError: cannot import name screenedAttrs File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 239, in _addAttr from ShowAttr import ShowAttrDialog, screenedAttrs

3 4

Display solvent-accessible surface?
by Hurt, Darrell (NIH/NIAID) [E] 17 Sep '10

17 Sep '10

Hi there, I’ve tried searching the archives and found some interesting information, but nothing specific to this question. Elaine’s response was particularly helpful: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003597.html >From the documentation, it seems that Chimera only displays solvent-excluded surfaces: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/representation.html… I understand that I can map solvent-accessibility to this surface using “Render Attributes”, but I would like to display the actual solvent-accessible surface. I want to do this because it is my understanding that electrostatic potential mapping to a solvent-accessible surface is often more informative than to a solvent-excluded surface: http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrosta… Can it be done? 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 3B62G Bethesda, MD 20892 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) 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.

2 2

Problem with Rainbow and "abnormal" PDB data
by Christian Schudoma 17 Sep '10

17 Sep '10

Dear Chimera-devs and community, I am "abusing" the 3D-rendering capabilities of Chimera to visualise 3D coordinates that do not actually represent molecular data. (Why do I do that? Because I love using Chimera for visualising molecular data and I needed a quick way to display (+ rotate/zoom) 3D data without hassle. I'm sure there are other solutions out there but I found it easier to convert my data to PDB than find a decent tool or code one myself.) I convert my xyz coordinates into PDB-format, using Hydrogen atoms and GLY as residue name (or, alternatively XXX - which wouldn't work either). I use the residue index (resSeq) to identify groups of points that belong together. This of course results in a complete nonsense-"protein" (with GLY-residues consisting of nothing but 100's of hydrogen atoms), which is nevertheless in syntactically correct (I hope) PDB format and both readable as well as displayable by Chimera (as a point cloud using wire-representation). Now to the problem I encountered: I would like to colour my "atoms" by their residue index. I can colour the individual "atoms" manually, using Select-operations or Ctrl-click and then the Color-menu. The Rainbow tool, however, does not work to colour my point cloud. It simply doesn't do anything. My question is, whether Rainbow performs some plausibility checking of the data (and if so, then whether it is necessary to do that? It would seem that Rainbow only needs to access either the residue, chain, or model indices to do what it's supposed to do, i.e. to assign colour)? Of course I am aware that my problem is kinda homemade and Rainbow works fine for normal PDB structures. I am also not saying that Chimera's buggy (although it seems to have a problem processing weird data in some situations (Rainbow) but not in others (manual colouring)). However, I'd like to understand why things don't work as expected ;) Cheers, Christian --- Christian Schudoma, M.Sc. Ph.D. Student Bioinformatics Group Max Planck Institute of Molecular Plant Physiology Am Muehlenberg 1 14476 Potsdam-Golm Germany phone: +49 (331) 567-8624 email: schudoma(a)mpimp-golm.mpg.de http://rloom.mpimp-golm.mpg.de

3 3

find the region around a volume imported from 3V voxelator
by Fabian Glaser 15 Sep '10

15 Sep '10

Daer chimera team, I am interested in finding a channel in a toluene hydrogenase, and extracting all the residues / atoms surrounding this channel. To do that I calculated the channel itself using the 3V voxelator (http://3vee.molmovdb.org) which produces a volume object that can be imported to chimera. See for example the output page http://3vee.molmovdb.org/viewResults.php?jobid=10sep02.ee6, which provides the file channel-004.mrc.gz, which needs to be first unzipped. When uploaded to chimera the volume is very clear and nice. But I want to find the residues/ atoms that form the channel, one the pdb itself 3DHG.pdb.gz, although the select and zone features seem to not work with the volume object. Any idea how to do that? Thanks a lot, Fabian -- ------------------------------------------------------ Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL E-mail: fglaser(a)technion.ac.il Tel: +972-4-8293701 Fax: +972-4-8225153

3 3

transparent background
by Jon N. Rumbley 15 Sep '10

15 Sep '10

I have consistently used the transparent background in chimera in the past. I have upgraded my system to Windows 7 and installed both Chimera 1.4.1 and the daily build from 9/8/2010. When I try to set the transparency to true I get the following: Unable to turn on background transparency. Graphics hardware supports request, but can not switch while maintaining display data. Is there a simple solution for this? Thank you. Dr. Jon N. Rumbley Assistant Professor Dept. of Pharmacy Practice and Pharmaceutical Sciences University of Minnesota-Duluth 127 LSci 1110 Kirby Dr. Duluth, MN 55812 Phone: 218-726-6047 email: jrumbley(a)d.umn.edu

2 1

Walking through a protein
by Daniel Gurnon 14 Sep '10

14 Sep '10

Hi everyone, Coot has an easily implemented way of "walking" through a peptide chain. It works like this: >From the drop down menu, choose "go to atom", pick the first residue. The view zooms to the first residue. Now hit the space bar, and the view smoothly advances to the next residue in the chain. Hold shift-space, and it smoothly moves back. Having an easy way to smoothly transition the view from one residue to the next would would be useful in Chimera. From my perspective it would be great for teaching, but I would think a simple way of walking along the backbone would be generally appreciated. I imagine this feature would be easy to construct with a Python script, maybe using the "fly" or "focus" commands. I'm not sure how to tie this to a keystroke, but an alternative is to give the function a toolbar button. If this capability doesn't already exist, could someone provide some advice on writing the script? I'm only just learning Python. Thanks for the help Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

2 1

Joining fragments in a peptide bond
by Sujata 14 Sep '10

14 Sep '10

Hi All, I have two peptide fragments that I want to join with a peptide bond. So I move the 2nd fragment towards the C terminal of the 1st one and bring the C of 1st and N of 2nd manually closer such that the distance is 1.34 A. I combine the two PDB files into one and I have a peptide I want but in the process of bringing them closer, the angles around the peptide bond CA-C-O and C-O-N are not what they should be? My question is - is there a way to fix these angles while I am fixing the distance? What is the right way to join fragments in a peptide bond? Is there a cleaner way? Thank you. Appreciate your help. Sujata

2 1

MD trajectory hbond analysis
by George Tzotzos 13 Sep '10

13 Sep '10

Hi everybody, I wonder is there's a way that Chimera produces hbond occupancy statistics from amber trajectory files. I can produce hbond information between a ligand and a receptor molecule frame by frame. As the ligand forms hbonds with different amino acid residues in the binding site during the trajectory, I'd like to work out which ones are the most frequently formed. Thanks in advance for your advice Best regards George

3 2

Crash under Ubuntu Linux 10.4
by Mario Dejung 13 Sep '10

13 Sep '10

Hi All, I get a "Segmentation fault" message from Chimera... I tried to use all available version, so the 32bit and 64bit, and also the alpha versions... I can not reproduce the crash, it is not related to any command... Sometimes I can open a map an turn it or filter it a little bit and chimera crashes after 2 minutes... The other time it crashes after 10 seconds... At the moment I try to use the alpha 64bit version, is there a way to get more debug output? I run chimera under Ubuntu 10.4 Regards Mario

2 1

zone command between proteins
by Francesco Pietra 13 Sep '10

13 Sep '10

Hello: How to map the residues at a given distance (<5A) between a protein and its 5-residues peptide ligand? I could only use the zone command for a non-standard residue in the peptide: sel protein & :non-standard_residuename_of_peptide All other peptide residues are standard residues. thanks francesco pietra

3 5

Dielectric constant
by r charbel maroun 10 Sep '10

10 Sep '10

Dear Chimera users, What's the value of the dielectric constant used in the Energy minimize module ? What's the minimization algorithm used, Steepest descent or Conjugate gradients ? Is there any way to modify these values ? Greetings, -- R. Charbel MAROUN, PhD, HDR Neurobiologie et Pharmacologie Moléculaire Centre de Psychiatrie et de Neurosciences Broca-Sainte Anne (INSERM U894) 2ter rue d'Alésia 75014 Paris FRANCE Tél. +33 1 40 78 92 77 Fax +33 1 45 80 72 93 e-mail rmaroun(a)gmail.com charbel.maroun(a)inserm.fr

2 1

Parallel run
by r charbel maroun 10 Sep '10

10 Sep '10

Hi Chimera users, Is there any way to run Chimera functions such as energy minimization in multiple processor machines ? Cheers, -- R. Charbel MAROUN, PhD, HDR Neurobiologie et Pharmacologie Moléculaire Centre de Psychiatrie et de Neurosciences Broca-Sainte Anne (INSERM U894) 2ter rue d'Alésia 75014 Paris FRANCE Tél. +33 1 40 78 92 77 Fax +33 1 45 80 72 93 e-mail rmaroun(a)gmail.com charbel.maroun(a)inserm.fr

2 1

Morphing script
by Rajan Prabu 08 Sep '10

08 Sep '10

Dear Chimera users, I am trying to make a morphing pdb with chimera without opening the interface using --nogui option. It works and calculates the interpolation and then it crashes. If i understood it correctly, it is trying to open the MD Movie GUI. By default morph movie command calls the MD Movie interface. Is it possible to make it work without opening the interface. I am trying to run the script with chimera using the following command chimera --nogui --script chi1.py and my script chi1.py is the following from chimera import runCommand runCommand('open starting.pdb') runCommand('open end.pdb') runCommand('morph start #0') runCommand('morph interpolate #1') runCommand('morph movie') runCommand('stop') Thank you very much for your inputs. Cheers Rajan

2 1

Viewing direction
by Gorelik, Tatiana 07 Sep '10

07 Sep '10

Hi, Can I orient a volume (MRC) in Chimera along a specific direction? - vector given by [x y z] - in principle all floats. Thanks, Tatiana ************************************ Tatiana Gorelik, PhD, Institut für Physikalische Chemie Johannes Gutenberg-Universität Mainz Welderweg 11 55099 Mainz Germany Tel.: 0049 6131 39 22347 Fax: 0049 6131 39 23768 e-mail: gorelik(a)uni-mainz.de ************************************

2 1

Flipping the handedness of a molecule
by Michael Day 02 Sep '10

02 Sep '10

How do you flip the handedness of a molecule? I need to overlap two molecules that are numbered the same but have different handedness. 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 <<< ------------------------------------------------------------------------>>>

2 1

Difference maps
by Katrina Lexa 01 Sep '10

01 Sep '10

Hello, I'm wondering whether it is possible to take the absolute value of a difference map created by the vop subtract command? Otherwise, so far as I can tell, the negative values which should be relevant I can't see because they just show up as a giant box. Thank you for your help, Kat

2 1

PDB opens distorted
by Francesco Pietra 27 Aug '10

27 Aug '10

Hi: I have drawn a slightly modified small peptide (terminal phenylalanine changed to phenylalanine-amide) with an old, efficient package (PCMODEL). I have drawn from from either amino acid templates or atom-per-atom and then saved as pdb. In case of drawing atom-per-atom, I have edited the residue names, changing UNK to the appropriate standard amino acid name, except phenylalanine-amide, named PHA). Opening the pdb file with an editor, the atoms are often scattered, not sequentially grouped together for a given amino acid. Well, both the non-edited and the edited pdb files open correctly with either PCMODEL of VMD, not with CHIMERA. In the latter case, incorrect bonds between the atoms are seen, and the molecule is compressed. Deleting all CONECT generated by PCMODEL was even worse for CHIMERA. With non peptidic molecules I never went into such troubles using the same packages. Thanks for suggestions how to rearrange the pdb for CHIMERA. francesco pietra

2 1

problems loading .mtz files
by rjoshi＠purdue.edu 25 Aug '10

25 Aug '10

Hi, i am having problems loading electron density files from CCP4 and Phenix. The error message reads "Bad MRC grid size (129737328,-319356160,1145110528)". Please advise. Cheers Rakesh Graduate student Dept.of Biochemistry Purdue University

4 3

volume viewer question
by Boaz Shaanan 25 Aug '10

25 Aug '10

Hi William, The way I go about the sigma level contouring in Chimera, though it's somewhat ham-fisted but perhaps less complicated than Tom's suggestion, is to contour the region of interest at the desired sigma level in Coot or O and then play with the contouring in Chimera until both maps look as similar as possible (the maps rarely look identical for technical differences in the contouring techniques, I think). It works. Cheers, 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

2 1

volume viewer question
by William Snee 24 Aug '10

24 Aug '10

Hello, I am trying to make an electron density figure using chimera and need to contour the F0-Fc map to 3 sigma. How can you determine the sigma level displayed with the volume viewer? The levels appear to be different than that observed when using coot or Xtalview. Thank you, William Snee

3 2

Chimera and Sparky
by Hagn, Franz 24 Aug '10

24 Aug '10

Dear all, I am trying to run Chimera connected to Sparky for NMR NOE visualization. I am using the latest Sparky MacOSX distribution (for 10.4) and the last built of Chimera which came out today on a MacOSX 10.6 Intel. When I start Chimera within Sparky, I get a bunch of error messages. Does anybody know which Chimera runs with the latest Sparky? Thanks, Franz -- Franz Hagn, Ph.D. Department of Biological Chemistry & Molecular Pharmacology, Room C1-103 Harvard Medical School 240 Longwood Ave, Boston, MA 02115 Tel: +1(617)432-3211 Fax: +1(617)432-4383 --- Franz Hagn, Ph.D. Department of Biological Chemistry & Molecular Pharmacology, Room C1-103 Harvard Medical School 240 Longwood Ave, Boston, MA 02115 Tel: +1(617)432-3211 Fax: +1(617)432-4383

3 2

ValueError: dimensions too large
by Josh Kacher 24 Aug '10

24 Aug '10

I am trying to use the volume eraser, but whenever I click erase, I get a Chimera Error box come up that says: ValueError: dimensions too large. File "C:\Program Files\Chimera\share\VolumeViewer\volume.py", line 1085, in region_grid m = zeros(shape, d.value_type) Does anyone know how to avoid this? I tried shrinking the volume eraser size. I also tried installing Chimera on a different computer to see if that was the problem, but it still isn't working. Thanks, Josh

3 2

writing MRC maps
by Dougherty, Matthew T 24 Aug '10

24 Aug '10

I have an MRC map that is 800^3. I do a color zone and split the map, generating eight maps, each 800^3. The first of the split maps I throw away, the volume of interest of the other seven maps is 50^3 each. How do I save the seven maps not at 800^3, but reduce their size to 50^3? thanks, Matt

3 2

sausage view
by lalit.deshmukh＠huskymail.uconn.edu 24 Aug '10

24 Aug '10

Hello, Is there anyway to generate a sausage view (see the attached image) by using Chimera? My apologies if I missed something/or this has been discussed before. Thanks in advance, Regards, Lalit

2 1

Ringer: A program to detect molecular motions by systematic X-ray electron-density sampling
by Terry Lang 20 Aug '10

20 Aug '10

The Alber lab at UC Berkeley is pleased to release of the code for Ringer version 1.0 (http://ucxray.berkeley.edu/ringer.htm) which depends on Chimera. Ringer is a program to detect molecular motions by systematic X-ray electron-density sampling. The aim of Ringer is to go beyond static structural snapshots of proteins by uncovering structural ensembles in X-ray electron density. This information can reveal not only which parts of proteins are flexible and which parts are rigid, but it also can define alternate conformations that may be important for function. Alternate conformations of binding sites also may afford additional targets for drug design. The Ringer method is described in Lang et al. /Protein Sci/. 2010 Jul; 19(7):1420-31 <http://www.ncbi.nlm.nih.gov/pubmed/20499387>. An application of Ringer, determining the structural underpinnings of the side chain dynamics critical for the function of the enzyme proline isomerase, was published in Fraser JS et al. /Nature/. 2009 Dec 3;462(7273):669-73 <http://www.ncbi.nlm.nih.gov/pubmed/19956261>. Ringer is freely available to academics. -- PaulaTherese Lang Postdoctoral Scholar Alber Lab, UC Berkeley http://ucxray.berkeley.edu/ringer.htm

1 0

Question regarding Chimera Measurements
by Shahmoradian, Sarah H 19 Aug '10

19 Aug '10

Hello, This is an urgent question and your help would be appreciated. I am trying to find a way to perform measurements in my tomogram volume file (.rec file). I tried using the "Distances" option under Tools --> Structure analysis, but this requires two "atoms." My tomogram does not depict at the atomic resolution and I would like to measure the distance between one area on my tomogram density and another area on the tomogram density. These measurements would be through a 3D section. Could you please let me know how I could do this? Furthermore, I have a question about the scale bar -- when the program generates a default scale bar, how does the program assign the default value to the scale bar size? Does it read the header info from my tomogram file? I am concerned because when I change the label name from Angstrom to nanometers, the scale bar size stays the same-- how then, would I be able to assign an accurate scale bar that would change accordingly with the alterations in scale (Angstrom to nm, etc)? Please let me know if I need to clarify further. Your assistance would be appreciated! Sincerely, Sarah Shahmoradian Molecular Physiology and Biophysics (Baylor College of Medicine) Pre-doctoral fellow, Nanobiology Interdisciplinary Graduate Training Program (Rice University)

2 1

Positioning of water molecules in a protein
by Beale, John 19 Aug '10

19 Aug '10

Is there a way to use Chimera to determine what atoms/groups in a protein are closest to a particular water molecule? I have an x-ray structure that is solvated. I would like to determine the positions of the water molecules in the x-ray structure and compare these to the water molecule positions after molecular dynamics. 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>

4 3

Stereo monitors
by Jeremy Swan 18 Aug '10

18 Aug '10

Hi all, Any recommendations on stereo monitors for chimera on a pc? Thanks! -Jeremy Sent from iPhone

2 1

2D image contour plot using Chimera
by Yao Cong 16 Aug '10

16 Aug '10

Dear Chimera developer, I was wondering that is there any way that I can use Chimera to do a 2D image contour plot? Do I need some extra plug in or tools? Thanks a lot, Yao ------ Yao Cong, Ph.D. Research Associate, National Center for Macromolecular Imaging, Baylor College of Medicine, One Baylor Plaza, Alkek Building N420-BCM125, Houston, TX 77030 Tel:713-798-6989 Fax:713-798-1625 Email: cong(a)bcm.edu

2 2

representing additional residues over ribbons
by Irene Newhouse 16 Aug '10

16 Aug '10

When I try repr sphere :64 or repr stick :64 over the default presentation of my protein in ribbons [the heme group is in sticks, as are automatically selected residues in close proximity], as suggested in today's user mail, it doesn't work. It only seems to work if all atoms of the protein are displayed. I can only reset the display mode of the residues Chimera has chosen to show in addition to ribbons using these commands on the default mostly-ribbon display. How do I get the protein mostly in ribbons with a few residues in stick or ball & stick? While I haven't worked through the entire tutorials referenced in today's mail, the examples of repr shown early on do not do this; they start from a display of all the protein's atoms. Thanks! Irene Newhouse

2 2

displaying specific residues
by Elaine Meng 16 Aug '10

16 Aug '10

On Aug 12, 2010, at 7:04 AM, Reza Heidari wrote: > How can i display just some of residues (in form sphere) on a protein (in form ball & stick), for example: Trp38, Val66, Ala80. Please help me, thanks a lot. Hi Reza, There are many ways to get the same final result. I will give only two examples here. You may want to look at the "Getting Started" tutorial and other tutorials for more information: <http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html> Example 1: Show the command line by choosing from menu: "Favorites... Command Line" If you don't want any ribbon, use command: ~ribbon Show all protein atoms/bonds and hide others with command: show protein (to show ALL atoms/bonds including nonprotein, use command: display) Change style of all atoms/bonds to ball&stick: repr bs Change style of specific residues to sphere: repr sphere :38,66,80 (other commands such as color, display, ... also take these residue lists) Example 2: If you don't want any ribbon, use menu: Actions... Ribbon... hide Show all atoms/bonds with menu: Actions... Atoms/Bonds... show ( If there is water and you want to hide it, menu: Select... Structure... solvent menu: Actions... Atoms/Bonds... hide menu: Select... Clear Selection ) Change style of all atoms/bonds with menu: Actions... Atoms/Bonds... ball & stick Display sequence window with menu: Favorites... Sequence Click on Sequence window top bar, then inside that window, use mouse to choose residue 38; then it will be selected in the main window Change selected residue to sphere with menu: Actions... Atoms/Bonds... sphere Go back to Sequence window, choose next residue, etc. For the future: general questions should go to chimera-users(a)cgl.ucsf.edu (chimera-dev is for programming questions) and include a brief description in the Subject line of the mail. Thanks, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

OpenGL misconfiguration & Nvidia
by Hernando Sosa 14 Aug '10

14 Aug '10

Hi I recently installed the proprietary Nvidia driver in a Linux box (OpenSuse 11.3 64bits) and now every time that chimera start there is a warning dialogue saying that there is an OpenGL misconfiguration detected. If I ignore the warning (press YES to continue) chimera seems to run fine. So my question is how can I either fix the problem or get rid of the warning dialogue? At the terminal the following message is displayed when starting chimera >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Error: API mismatch: the NVIDIA kernel module has version 256.44, but this NVIDIA driver component has version 256.35. Please make sure that the kernel module and all NVIDIA driver components have the same version. <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< I am not sure which one is "this NVIDIA driver component" that I need to fix and why it was not updated when installing the proprietary driver. Thanks System details: Chimera version: production release 1.4.1. (for 64 bit Linux) Card: Nvidia geforce GT 230 Processor: AMD Phenom X6 1090T OS: 64bit Linux OpenSuse 11.3 -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa(a)einstein.yu.edu -----------------------------------

2 1

Re: [Chimera-users] surfnet - separating clefts from cavities
by Elaine Meng 12 Aug '10

12 Aug '10

Hi Irene, Unfortunately surface models aren't directly saved in sessions. Molecular surfaces and volume isosurfaces are effectively saved in that they are regenerated from the underlying atomic or volume data when the session is restored. Some other surface-generating tools are also integrated with sessions, but not Surfnet. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sessions.html#whatsaved> I should mention that limitation in the docs. Experiments also reveal that "Surfnet Selection" is ignoring my atom specification of "protein" -- it seems to be using all atoms. However, I can get the desired result by using "Surfnet Interface" instead and specifying "protein" as both the ligand and receptor. This problem with Surfnet Selection is in both the release 1.4.1 and the current daily build, and I will be reporting it as a bug. If the volume method (alternative (B) in my chimera-users message earlier today) had been used, that surface would be restored along with the saved session. There is still the drawback that it "forgets" it has been split and partially hidden. Upon session restore it is regenerated anew and shown in its multiblobbed entirety. Drats, foiled again! Sorry about that, 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 12, 2010, at 4:05 PM, Irene Newhouse wrote: > Thanks for your response! I've gone on ahead, manually deleting the clefts. > Also, is there a way to save the computation? When I did a 'save session' > & brought it back, the surfnet calculation wasn't there. The calculation itself > is quick, it's the hiding the bits you don't want to show that's a pain to regenerate...

2 2

surfnet - separating clefts from cavities
by Irene Newhouse 12 Aug '10

12 Aug '10

I've been random-walking my way with surfnet, starting from the stand-alone version. I haven't been able to get the output file I need for displaying via RasMol, & while I was googling for cures to that, I discovered the surfnet plugin to Chimera, hurray. I have a protein with several internal cavities, plus many more surface clefts. Has someone worked out an efficient way to display only the internal cavities? From my previous mucking about with the stand-alone, I already had a 'cavity atoms' pdb-format file which I loaded as model 1 & used that. However, generating the cavity atoms file involved considerable work by hand. At the moment, I can picture splitting the surfaces [using directions in the chimera user archive] & deleting all the surface ones. This is also a fair amount of manual labor - 50 blobs are generated & only 9 are internal. I have other proteins in this family to analyze, & they're probably similar. Thanks for any advice! Irene Newhouse

2 2

Re: [Chimera-users] unsubscribe
by Elaine Meng 12 Aug '10

12 Aug '10

Hi Arne et al., Today there is a glut of messages that had been held up in our system over the last several days. Apologies, and now that we know the problem, it should not recur. Those who wish to unsubscribe can do so at <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Chimera on Linux
by Jay Brown 12 Aug '10

12 Aug '10

Dear Chimera: I successfully installed Chimera on a Linux machine, and it worked as expected for about an hour. Then it began shutting down any time I tried to rotate a volume image (e.g. emd_1015.map). Nothing comparable happens with the version I have running on a PC. Is there something about Linux I need to know? Thanks. -Jay Brown Jay C. Brown Department of Microbiology University of Virginia School of Medicine 1300 Jefferson Park Ave. Charlottesville, VA 22908 Email: Jcb2g(a)virginia.edu Phone: 434-924-1814 http://people.virginia.edu/~jcb2g/index.htm

3 2

3d chimera viewing with nvidia vision and geforce 220
by William Tieu 12 Aug '10

12 Aug '10

Dear chimera users I am having problems with getting the sequential stereo view on chimera 1.4.1 windows 32bit. The error i'm getting is: Unable to turn on stereo viewing Unable to find hardware stereo support (couldn't choose stereo pixel format Couldn't figure togl widget) I recently obtained a samsung 2233RZ monitor, 3d nvidia vision and using a nvidia geforce 220. My question is, whether the problem is because of using a geforce over a quadro? and whether there is a way to resolve this problem with a geforce card. Or is there another reason for the error message. Thank You William Tieu Department of Chemistry and Physics Adelaide University

2 1

how is the threshold calculated?
by Mitul Saha 12 Aug '10

12 Aug '10

Hi! In Chimera's Volume viewer, how is the default density threshold computed for a given loaded 3D density map? Thanks, MS

2 1

Chimera List posting
by Hagn, Franz 12 Aug '10

12 Aug '10

Franz_Hagn(a)hms.harvard.edu

1 0

Chimera startup options
by Beale, John 12 Aug '10

12 Aug '10

I have a new installation of Chimera on a Linux box. I am working with a protein/nucleic acid complex. When I start the program with "chimera file.pdb" the ribbon representation of the structure is shown. Also, a plank representation of the nucleic acid is shown. I have to hide the ribbon and select "Actions -> Atoms/Bonds -> Show" to see the atoms. Can someone tell me how to change the startup options so that the ribbon and planks are not automatically generated and that the atoms/bonds are shown by default? 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>

4 3

64-bit Windows version of chimera available
by Greg Couch 11 Aug '10

11 Aug '10

For users with larger datasets, we now have a 64-bit Windows version of chimera available in the daily builds section on the chimera download page, <http://www.cgl.ucsf.edu/chimera/download.html#daily>. While we believe it is bug-for-bug compatible with the other daily builds, please try it out and let us know if you have any problems. - Greg

1 0

Fwd: Re: Question about selection...
by Yasser Almeida Hernández 11 Aug '10

11 Aug '10

It works!!! Thanks a lot, ;) -------- Original Message -------- Subject: Re: [Chimera-users] Question about selection... Date: Tue, 10 Aug 2010 13:49:55 -0500 From: Elaine Meng <meng(a)cgl.ucsf.edu> Reply-To: Chimera BB <chimera-users(a)cgl.ucsf.edu> To: Yasser Almeida Hernandez <almeida(a)cim.sld.cu> CC: Chimera BB <chimera-users(a)cgl.ucsf.edu> Hi Yasser, if you want to generally select all singleton atoms (atoms not bonded to other atoms), you could use this command: sel @/!bonds this is an example of specification by attribute, described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descri…> 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 10, 2010, at 7:49 AM, Yasser Almeida Hernández wrote: > Hi... > The problem is that I have hundreds of pdb files with this format: > four models (or less), where each one is an aminoacid and a single > atom. Mostly, the single atom is an heteroatom and i select it with > :/isHet, but sometimes this atom is a protein atom with the ATOM > field and then, the :/isHet selection doesn't work... > There is some tricky way to select this single atom types (ATOM), > according to the structure of the pdb file...??? > Thanks . ----- Terminar mensaje reenviado ----- -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI -------- Original Message -------- Subject: Re: [Chimera-users] Question about selection... Date: Tue, 10 Aug 2010 13:49:55 -0500 From: Elaine Meng <meng(a)cgl.ucsf.edu> Reply-To: Chimera BB <chimera-users(a)cgl.ucsf.edu> To: Yasser Almeida Hernandez <almeida(a)cim.sld.cu> CC: Chimera BB <chimera-users(a)cgl.ucsf.edu> Hi Yasser, if you want to generally select all singleton atoms (atoms not bonded to other atoms), you could use this command: sel @/!bonds this is an example of specification by attribute, described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descri…> 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 10, 2010, at 7:49 AM, Yasser Almeida Hernández wrote: > Hi... > The problem is that I have hundreds of pdb files with this format: four models (or less), where each one is an aminoacid and a single atom. Mostly, the single atom is an heteroatom and i select it with :/isHet, but sometimes this atom is a protein atom with the ATOM field and then, the :/isHet selection doesn't work... > There is some tricky way to select this single atom types (ATOM), according to the structure of the pdb file...??? > Thanks .

1 0

64-bit Windows version of chimera available
by Greg Couch 10 Aug '10

10 Aug '10

For users with larger datasets, we now have a 64-bit Windows version of chimera available in the daily builds section on the chimera download page, <http://www.cgl.ucsf.edu/chimera/download.html#daily>. While we believe it is bug-for-bug compatible with the other daily builds, please try it out and let us know if you have any problems. - Greg

1 0

64-bit Windows version of chimera available
by Greg Couch 10 Aug '10

10 Aug '10

For users with larger datasets, we now have a 64-bit Windows version of chimera available in the daily builds section on the chimera download page, <http://www.cgl.ucsf.edu/chimera/download.html#daily>. While we believe it is bug-for-bug compatible with the other daily builds, please try it out and let us know if you have any problems. - Greg

1 0

Question about selection...
by Yasser Almeida Hernández 10 Aug '10

10 Aug '10

Hi chimerians... I have this pdb file with some models... MODEL ATOM 1 N ARG 2 75 3.566 -4.680 2.408 1.00 27.73 N ATOM 2 CA ARG 2 75 3.319 -3.762 1.307 1.00 27.44 C ATOM 3 C ARG 2 75 4.363 -2.641 1.381 1.00 27.43 C ATOM 4 O ARG 2 75 4.900 -2.249 2.434 1.00 26.54 O ATOM 5 CB ARG 2 75 1.901 -3.115 1.361 1.00 29.76 C ATOM 6 CG ARG 2 75 0.685 -4.005 1.574 1.00 30.19 C ATOM 7 CD ARG 2 75 1.021 -5.453 1.347 1.00 32.01 C ATOM 8 NE ARG 2 75 1.567 -5.689 0.064 1.00 35.22 N ATOM 9 CZ ARG 2 75 2.123 -6.788 -0.467 1.00 37.99 C ATOM 10 NH1 ARG 2 75 2.301 -7.901 0.253 1.00 37.85 N ATOM 11 NH2 ARG 2 75 2.343 -6.799 -1.796 1.00 37.02 N TER ATOM 1 OE1 GLU 3 561 2.565 -3.602 -1.919 1.00 35.57 O TER ENDMDL MODEL ATOM 1 N ARG B 75 3.153 -4.497 2.431 1.00 25.72 N ATOM 2 CA ARG B 75 2.895 -3.593 1.311 1.00 26.52 C ATOM 3 C ARG B 75 3.980 -2.519 1.148 1.00 26.28 C ATOM 4 O ARG B 75 4.530 -2.055 2.176 1.00 26.18 O ATOM 5 CB ARG B 75 1.566 -2.890 1.541 1.00 30.04 C ATOM 6 CG ARG B 75 0.249 -3.353 1.047 1.00 33.78 C ATOM 7 CD ARG B 75 -0.666 -3.815 2.137 1.00 37.95 C ATOM 8 NE ARG B 75 -0.707 -5.248 2.257 1.00 42.21 N ATOM 9 CZ ARG B 75 -0.886 -6.067 3.286 1.00 44.76 C ATOM 10 NH1 ARG B 75 -1.060 -5.717 4.569 1.00 44.33 N ATOM 11 NH2 ARG B 75 -0.888 -7.403 3.027 1.00 45.78 N TER ATOM 1 OE1 GLU 3 561 2.565 -3.602 -1.919 1.00 35.57 O TER ENDMDL MODEL ATOM 1 N ARG H 75 2.710 -4.027 1.931 1.00 41.50 N ATOM 2 CA ARG H 75 2.475 -2.983 0.948 1.00 38.30 C ATOM 3 C ARG H 75 3.422 -1.785 1.027 1.00 39.34 C ATOM 4 O ARG H 75 3.907 -1.419 2.105 1.00 38.57 O ATOM 5 CB ARG H 75 1.022 -2.521 1.055 1.00 41.90 C ATOM 6 CG ARG H 75 0.718 -1.195 0.370 1.00 48.73 C ATOM 7 CD ARG H 75 -0.639 -0.637 0.779 1.00 50.05 C ATOM 8 NE ARG H 75 -1.742 -1.354 0.145 1.00 56.64 N ATOM 9 CZ ARG H 75 -2.422 -2.353 0.705 1.00 57.10 C ATOM 10 NH1 ARG H 75 -2.121 -2.773 1.928 0.00 56.09 N ATOM 11 NH2 ARG H 75 -3.413 -2.931 0.040 0.00 56.09 N TER ATOM 1 OE1 GLU 3 561 2.565 -3.602 -1.919 1.00 35.57 O TER ENDMDL MODEL ATOM 1 N ARG K 75 2.718 -3.987 1.949 1.00 40.34 N ATOM 2 CA ARG K 75 2.510 -2.935 0.974 1.00 40.91 C ATOM 3 C ARG K 75 3.439 -1.730 1.052 1.00 41.44 C ATOM 4 O ARG K 75 3.779 -1.257 2.143 1.00 44.22 O ATOM 5 CB ARG K 75 1.045 -2.492 0.991 1.00 46.88 C ATOM 6 CG ARG K 75 0.759 -1.285 0.109 1.00 57.01 C ATOM 7 CD ARG K 75 -0.722 -0.981 -0.005 1.00 64.03 C ATOM 8 NE ARG K 75 -0.939 0.301 -0.673 1.00 70.73 N ATOM 9 CZ ARG K 75 -0.576 1.482 -0.173 1.00 75.39 C ATOM 10 NH1 ARG K 75 0.025 1.563 1.009 1.00 75.51 N ATOM 11 NH2 ARG K 75 -0.798 2.594 -0.862 1.00 77.70 N TER ATOM 1 OE1 GLU 3 561 2.565 -3.602 -1.919 1.00 35.57 O TER ENDMDL How can i select the 1 OE1 GLU atom in each the model? Any hint... Thanks... ;) -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI

2 3

64-bit Windows version of chimera available
by Greg Couch 10 Aug '10

10 Aug '10

For users with larger datasets, we now have a 64-bit Windows version of chimera available in the daily builds section on the chimera download page, <http://www.cgl.ucsf.edu/chimera/download.html#daily>. While we believe it is bug-for-bug compatible with the other daily builds, please try it out and let us know if you have any problems. - Greg

1 0

Re: [Chimera-users] Ramachandran Plots
by Conrad Huang 10 Aug '10

10 Aug '10

Actually, you can now bring up a Ramachandran plot via the user interface in the Chimera daily build (http://www.cgl.ucsf.edu/chimera/download.html#daily) If you pop up the Model Panel (Favorites -> Model Panel), there should be a "Ramachandran plot..." button that displays a plot for each selected model. This is still an early implementation, so please send us bug reports and suggestions. Conrad On 8/9/2010 5:53 PM, Daniel Gurnon wrote: > Conrad, This script isn't working for me- I get the following error: > > Traceback (most recent call last): > File "C:\ProgramData\Chimera\ram3.py.txt", line 2, in <module> > from Plotdialog import PlotDialog > ImportError: No module named Plotdialog > > > Can you tell me how to make it work? > Thanks > Dan > > > On Mon, Jun 7, 2010 at 1:55 PM, Conrad Huang <conrad(a)cgl.ucsf.edu > <mailto:conrad@cgl.ucsf.edu>> wrote: > > It's been on our list for a while now. In the mean time, try out > this script. It generates a Ramachandran chart for the first open > molecule. > > Conrad > > > On 6/3/10 8:55 AM, James Nettles wrote: > > Does Chimera do Ramachandran Plots and I'm missing something > obvious? > > I like doing just about everything else in Chimera :-) > > Thanks, > > Jim _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > -- > ____________________________ > > Daniel Gurnon, Ph. D. > Assistant Professor of Chemistry > DePauw University > Greencastle, IN 46135 > > p: 765-658-6279 > e: danielgurnon(a)depauw.edu <mailto:danielgurnon@depauw.edu>

1 0

Fitting with constrained motion
by Tom Goddard 06 Aug '10

06 Aug '10

Hi Julio The Chimera fitting code does a full 3-degree-of-freedom rotational search. It cannot search fewer rotational degrees of freedom. It would be nice to adapt the code to be able to consider only rotations about an axis. The needed changes would be in the FitMap Chimera module not the fitnogui.py script. Optimizing using only two rotational degrees of freedom that are Euler angles seems like a bizarre case and we are not likely to ever handle that. Please post future questions to the chimera-users mailing list so others can answer and read the answers. Tom > Hi Tom, > > Sorry to bother you again. Is there a way fix one of the Euler angles > for the fitting? Since we have a small theta, we would like to fix > psi=0, and optimize on phi and theta only, plus the translations. I'm > using the fitnogui script. > > Many thanks, > Julio > > > On Jul 28, 2010, at 5:13 PM, Tom Goddard wrote: > >> >> Hi Julio, >> >> I guess you are using the fitnogui.py script. >> >> >> http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/fitnogui.py >> >> The parameters are right near the top -- ijk_step_size_min is the one >> you're interested in. >> >> The initial contour level is set as described in the documentation: >> >> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum… >> >> The "volume" command can set the contour level: >> >> volume #0 level 27.6 >> >> Tom >> >>> Hi Tom, >>> >>> Thanks again. Editing the line of code would be perfect for us, >>> since we are calling Chimera from our program with the "nogui" >>> option. Could you point me the place where I need to change that 0.01? >>> >>> What happens with the contour level when I'm calling Chimera in that >>> way (nogui)? Can I similarly set it somewhere in the code? Or with >>> an option in the command line? >>> >>> Best, >>> Julio >>> >>> >>>

1 0

UCSF Chimera Visual Identity
by Jessen Vernon Bredeson 06 Aug '10

06 Aug '10

To whom this may concern, I downloaded the UCSF Chimera 1.4.1 update for Mac OS X and noticed that the Chimera symbol had a grey outline around it, likely due to multiple alpha channels in rendering the image into .ICNS format, so I recomposed the image in higher quality and it is attached below. Also below is an accompanying symbol for MS Windows format (.ICO). These icons are free of charge, keep up the good work. Jessen Bredeson Fourth-Year Genetics, Genomics & Development Molecular and Cellular Biology University of California, Berkeley

2 2

model panel: add/edit note
by Dougherty, Matthew T 03 Aug '10

03 Aug '10

Is there a command to be able to modify notes on the model panel? If not, it would a useful addition when creating a command file to load in & color datasets.

3 3

Small molecules and antechamber
by Jon Rumbley 02 Aug '10

02 Aug '10

I have several small organic molecules constructed in ChemDraw and converted in Chem3D to .mol2 files. I can open them in Chimera but cannot seem to add charges to. I was simply using the add charge menu commands and AM1-BCC and assuming the structures would be read as nonstandard but antechamber reports an error with residue ****. The error log has no real indication of what the trouble might be. Are there additional steps I must take before assigning charges? The structures already have hydrogens added. An example .mol2 file is below: @<TRIPOS>MOLECULE **** 44 45 1 0 0 SMALL USER_CHARGES @<TRIPOS>ATOM 1 C -2.8306 2.5311 -0.9622 C.2 1 **** 0.0000 2 C -2.8728 1.1718 -1.0363 C.2 1 **** 0.0000 3 C -4.0552 0.3840 -0.9622 C.1 1 **** 0.0000 4 C -1.6082 0.4134 -1.1450 C.2 1 **** 0.0000 5 N -5.0052 -0.2769 -0.8917 N.1 1 **** 0.0000 6 O -1.8883 -0.9222 -1.2800 O.3 1 **** 0.0000 7 O -0.4722 0.8459 -1.1451 O.2 1 **** 0.0000 8 C -0.8034 -1.8901 -1.1282 C.3 1 **** 0.0000 9 C -0.3965 -1.8485 0.3585 C.2 1 **** 0.0000 10 C -1.4383 -3.2075 -1.5077 C.3 1 **** 0.0000 11 N 0.6925 -2.6041 0.6991 N.am 1 **** 0.0000 12 O -1.0062 -1.1536 1.1745 O.2 1 **** 0.0000 13 C 1.2426 -2.6055 2.0833 C.3 1 **** 0.0000 14 C 2.4273 -3.5343 2.1380 C.ar 1 **** 0.0000 15 C -3.9592 3.4353 -0.8741 C.ar 1 **** 0.0000 16 C -3.7802 4.6664 -0.1923 C.ar 1 **** 0.0000 17 C -4.8234 5.5702 -0.0757 C.ar 1 **** 0.0000 18 C -6.0611 5.2454 -0.6673 C.ar 1 **** 0.0000 19 C -6.2633 4.0447 -1.3692 C.ar 1 **** 0.0000 20 C -5.2063 3.1490 -1.4690 C.ar 1 **** 0.0000 21 O -7.0408 6.1768 -0.5154 O.3 1 **** 0.0000 22 C 3.5525 -3.2801 1.3388 C.ar 1 **** 0.0000 23 C 4.6333 -4.1642 1.3545 C.ar 1 **** 0.0000 24 C 4.6017 -5.2952 2.1768 C.ar 1 **** 0.0000 25 C 3.4888 -5.5395 2.9865 C.ar 1 **** 0.0000 26 C 2.3994 -4.6635 2.9668 C.ar 1 **** 0.0000 27 H -1.8332 3.0176 -0.9495 H 1 **** 0.0000 28 H 0.0351 -1.5845 -1.7993 H 1 **** 0.0000 29 H -0.6942 -4.0150 -1.5686 H 1 **** 0.0000 30 H -1.9272 -3.1457 -2.4932 H 1 **** 0.0000 31 H -2.2150 -3.5214 -0.7935 H 1 **** 0.0000 32 H 1.1669 -3.2048 0.0167 H 1 **** 0.0000 33 H 1.5395 -1.5662 2.3712 H 1 **** 0.0000 34 H 0.4439 -2.9024 2.8058 H 1 **** 0.0000 35 H -2.8085 4.9012 0.2576 H 1 **** 0.0000 36 H -4.7042 6.5169 0.4530 H 1 **** 0.0000 37 H -7.2285 3.8279 -1.8322 H 1 **** 0.0000 38 H -5.3406 2.2282 -2.0442 H 1 **** 0.0000 39 H -7.9024 5.8992 -0.9622 H 1 **** 0.0000 40 H 3.5844 -2.3950 0.7014 H 1 **** 0.0000 41 H 5.5045 -3.9710 0.7250 H 1 **** 0.0000 42 H 5.4465 -5.9867 2.1870 H 1 **** 0.0000 43 H 3.4659 -6.4183 3.6333 H 1 **** 0.0000 44 H 1.5299 -4.8643 3.5946 H 1 **** 0.0000 @<TRIPOS>BOND 1 1 2 2 2 1 15 1 3 1 27 1 4 2 3 1 5 2 4 1 6 3 5 3 7 4 6 1 8 4 7 2 9 6 8 1 10 8 9 1 11 8 10 1 12 8 28 1 13 9 11 1 14 9 12 2 15 10 29 1 16 10 30 1 17 10 31 1 18 11 13 1 19 11 32 1 20 13 14 1 21 13 33 1 22 13 34 1 23 14 22 2 24 14 26 1 25 15 16 2 26 15 20 1 27 16 17 1 28 16 35 1 29 17 18 2 30 17 36 1 31 18 19 1 32 18 21 1 33 19 20 2 34 19 37 1 35 20 38 1 36 21 39 1 37 22 23 1 38 22 40 1 39 23 24 2 40 23 41 1 41 24 25 1 42 24 42 1 43 25 26 2 44 25 43 1 45 26 44 1 Thanks for any help you can provide. Dr. Jon N. Rumbley Assistant Professor Dept. of Pharmacy Practice and Pharmaceutical Sciences University of Minnesota-Duluth 127 LSci 1110 Kirby Dr. Duluth, MN 55812 Phone: 218-726-6047 email: jrumbley(a)d.umn.edu

2 1

model panel: color patch
by Dougherty, Matthew T 31 Jul '10

31 Jul '10

using a command or python file, how do I set the color patch on the model panel?

2 1

Fwd: Visualizing inertia axes as arrows
by Eric Pettersen 31 Jul '10

31 Jul '10

Hi Miguel, Thanks for the corrections! I just fired that one off without testing it. I thought there might be an error or two. I'm glad you find it useful after fixing it. --Eric Begin forwarded message: > From: Miguel Ortiz Lombardía <miguel.ortiz-lombardia(a)afmb.univ-mrs.fr> > Date: July 31, 2010 1:39:33 AM PDT > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Visualizing inertia axes as arrows > > Hi Eric, > > Thanks for this useful script! > > I think I found two errors though: >> >> from chimera.selection import currentAtoms, numpyArrayFromAtoms > > should be: > > from chimera.selection import currentAtoms > from chimera import numpyArrayFromAtoms > > and: > >> for val, vec in zip(vals, vecs): >> bildString += ".arrow %g %g %g %g %g %g .1 .2 .9\n" % ( >> centroid[0], centroid[1], centroid[2], >> centroid[0] + val[0] * vec[0], >> centroid[1] + val[1] * vec[1], >> centroid[2] + val[2] * vec[2]) > > has to be: > > for val, vec in zip(vals, vecs): > bildString += ".arrow %g %g %g %g %g %g .5 1. .9\n" % (centroid[0], > centroid[1], centroid[2], centroid[0] + val * scale * vec[0], > centroid[1] + val * scale * vec[1], centroid[2] + val * scale * > vec[2]) > > (you can ignore the scale thing, that's simply a 50/max(vals) > correction > so the longest axis is 50 A) > > Best, > > > -- > Miguel > > Architecture et Fonction des Macromolécules Biologiques (UMR6098) > CNRS, Universités d'Aix-Marseille I & II > Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France > Tel: +33(0) 491 82 55 93 > Fax: +33(0) 491 26 67 20 > e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. >

1 0

Visualizing inertia axes as arrows
by Jozef Lewandowski 30 Jul '10

30 Jul '10

Hi everybody, Lately, I have been using "measure inertia" command a lot. For my purposes I needed to visualize the inertia axes as arrows instead of the default ellipsoid. I used the vectors from the reply log to write BILD files defining the arrows for the inertia axes. Is there an easy way to script just that? Or differently, is there an easy way to visualize as arrows inertia axes for peptide planes in a protein? Any tips would be appreciated. Thanks, Józef

2 1

Re: [Chimera-users] about transformation matrix
by Tom Goddard 28 Jul '10

28 Jul '10

Hi Julio, I guess you are using the fitnogui.py script. http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/fitnogui.py The parameters are right near the top -- ijk_step_size_min is the one you're interested in. The initial contour level is set as described in the documentation: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum… The "volume" command can set the contour level: volume #0 level 27.6 Tom > Hi Tom, > > Thanks again. Editing the line of code would be perfect for us, since we are calling Chimera from our program with the "nogui" option. Could you point me the place where I need to change that 0.01? > > What happens with the contour level when I'm calling Chimera in that way (nogui)? Can I similarly set it somewhere in the code? Or with an option in the command line? > > Best, > Julio > > > > Hi Julio, > > The details of the fitting algorithm are given in the User's Guide. > > > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht… > > You should definitely read that if you want the best understanding. But > the brief answers to your questions are that the convergence criteria > looks for optimization steps of less than 0.01 grid index to decide > convergence. The user interface does not allow you to change the 0.01 > grid index criteria -- it could be done by editing a line of Python. > The default settings do mask using the contour level of the fit map as > an outer boundary. So that level is important. > > Tom > > >

2 1

Camera parameters
by Tom Goddard 27 Jul '10

27 Jul '10

Hi Matt, The Chimera camera always points along the negative z-axis. The positions of the models are moved/rotated to get different view-points. Do you mean you want camera location (x,y,z) and horizontal angular field of view to the edges of the window (for perspective projection)? I know how to get at these using Python code, but I'm not sure if any Chimera commands report those values. Also I don't know if that info makes its way into X3D or VRML exported from Chimera. Greg Couch would know these answers. He is at SIGGRAPH this week. A quite gruesome way to get the parameters is to find them in the Chimera session file. grep formattedPositions mysession.py formattedPositions = {'p2': (0.3954088241213373, 18.749999499320985, (14.059999585151672, 7.399999618530273, 8.628906249999993), (36.02048479676247, -18.762672296762467), 8.62890625, {(0, 0): ((13.338430482851305, 2.7738552720503122, 6.309792459458727), (0.3889244976446376, 0.8937166155966246, 0.22362545950400858, 33.757570197325826))}, {(0, 0, 'Volume'): (False, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, False, 5.0)}, 4, (29.312384727061698, 10.919780805124898, 8.628906249999993), False), 'p1': (1.0, 18.749999499320985, (14.059999585151672, 7.399999618530273, 8.62890625), (36.02048479676247, -18.762672296762467), 8.62890625, {(0, 0): ((-1.913954659058722, -0.7459259145443079, 6.309792459458727), (0.3889244976446376, 0.8937166155966246, 0.22362545950400858, 33.757570197325826))}, {(0, 0, 'Volume'): (False, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, False, 5.0)}, 4, (14.059999585151669, 7.399999618530277, 8.628906249999993), False)} This is pretty messy and the values depend on which Chimera version saved the file. The values are defined by Python code chimera/share/Midas/__init__.py in the _savePosition() routine: return ( viewer.scaleFactor, viewer.viewSize, cam.center, cam.nearFar, cam.focal, xforms, clips, om.cofrMethod, cofr, viewer.clipping ) If you want a Python script to simply dump the camera positions for all savepos positions I can provide that. Tom > Hi Tom, > > I am creating a workaround for my graphics problem. What I have done in the past is to create a VRML file from Chimera export, extract the openGL camera parameters using a text editor, start up Amira, using TCL I would recreate the same camera view within Amira. At this point I could splice animation clips made by Chimera& Amira using Final Cut Pro. > > It has been a while since I have done this. I am now looking at the exported VRML files and they are lacking the camera info. > > Is there a command I can use to get the camera parameters for the savepos keyframes? > > thanks, Matt > >

2 2

coordinate transformation
by Dougherty, Matthew T 27 Jul '10

27 Jul '10

I was trying to locate details on maxtrix, coordinate transformations & scenegraph, relative to camera transformations.

2 1

about transformation matrix
by Kovacs, Julio A 27 Jul '10

27 Jul '10

Hi, I am doing fitting of two maps and am getting different values of the transformation parameters: the ones given in the window where I specify the options (these seem to be correct), and those given by using the command "matrixget" --- these give a very large translation vector, and moreover, I don't see any relation between that vector and the correct translation. Also, could you tell me what is the order used in Chimera: rotation, then translation? or translation, then rotation? Thank you very much. Julio Kovacs

2 2

Problem
by Reza Heidari 27 Jul '10

27 Jul '10

2 1

Nvidia 3D Vision
by "Christoph Höglinger" 27 Jul '10

27 Jul '10

Dear Chimera developers, I just bought the Nvidia 3D Vision Kit, because i was interested in the 3D Visualisation of it. First I tried it with the latest drivers from Nvidia's Homepage. (Quadro Driver Version: 258.49 & 3Dvision 258.49 ). I changed the Settings in the NV Control Panel (for Stereo output). Sequential Stereo worked fine in an other 3D Application. But when i change the view settings in chimera (sequential Stereo) i get that error: (After The Error MSG ist Quits and displays the Exit Code 3) Runtime Error! Program: C:\Program Files\Chimera\bin\pythonw.exe This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. Then i was looking for hints to solve that problem i found following article. http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005173.html There you mentioned that its probably a problem with the "new" drivers (197.XX). So I installed the driver that had been recommended by you. (Quadro Drv. 191.87 + 3D Vision 191.00). The Problem was that this 3D Vision driver won't support my LCD, its an Acer GD245HQ). I have installing it "manually" it won't activate the shutter glasses when Sequential Stereo is switched "on" in chimera (Shutter doesnt even work in games or any other Application) That means that the 3D-Vision driver is to blame. 197.03 Will recognize my LCD, but that won't work with chimera. Tried also QDRO 191.87 & 3DVision 258.49 (but theres no way to run the 3DVision Setup) Have you got an idea on how to fix that Problem? That would be really great! This is my System Configuration: Intel Pentium E5200 @ 3.5GHz PNY Quadro FX 570 4GB Ram Windows 7 64 Bit Acer GD245HQ Thank you so much for your help! Best regards, Christoph -- GMX.at - Österreichs FreeMail-Dienst mit über 2 Mio Mitgliedern E-Mail, SMS & mehr! Kostenlos: http://portal.gmx.net/de/go/atfreemail

3 4

Directly representing ellipsoids
by Thomas Ouldridge 26 Jul '10

26 Jul '10

Hi, I'm afraid I'm not a crystallographer/protein simulator, and so this question might seem quite naive. I run coarse-grained simulations, and I would like to represent the objects as ellipses in chimera. I have the position (which I am able to use) and the orientation that I would like my ellipses to take, encoded as a matrix relative to (x,y,z) cartesian coordinates. This matrix gives me the principal axes and radii of the ellipse. As I understand, Chimera is designed to display a "Thermal ellipsoid" - I would like this ellipsoid to have the axes and radii given by my matrix. However, it seems that the input (via pdb format files) is interpreted as an "anisotropic temperature factor", and I can't find a way to convert my matrix into the anisotropic temperature factor (I tried some papers online but they seemed to be talking in terms of transformations between lab frame and crystallographic frames, but I cannot see how that applies - what is my crystallographic frame?). In short, is there a way to convert my matrix into the "anisotropic temperature factor" representation so that Chimera can read it and convert it back? I did try just plugging in the matrix elements to the PDB file but got some weird ellipsoids out. Any help would be gratefully appreciated, Tom

2 1

Transparency doesn't look right
by Tom Goddard 26 Jul '10

26 Jul '10

Hi Mitalee This is a Chimera limitation. Two or transparent models will not be shown correctly. Transparency works correctly only when at most one model is transparent. You have the volume data displayed in "solid" style which is a kind of transparent rendering, and you have a surface model which is transparent. How defective the transparency looks depends on the order the models were opened in Chimera (or maybe it depends on which has higher model id number, don't recall). In any case, both orders look seriously wrong. If you reverse the order of opening your two models I think your surface will remain totally invisible until it becomes 0% transparent when it will suddenly appear. This limitation is a rather fundamental design problem in Chimera. Chimera draws the models one at a time. A model that is drawn after another model can only appear in front of the first model. Chimera first draws all opaque models, then draws all transparent models. If you look at the termite gut video I made http://www.cgl.ucsf.edu/chimera/animations/movies/termitegut.mov where surfaces fade in you'll see at the start of the fade in, a black blob suddenly appears representing the object. This is the same bad behavior you see in your case, but your surface is white (the background color) and is in front of the volume data making it look especially bad. This problem has arisen many times in, especially in movie making where transparency is used to fade objects in and out. I have an idea for a solution although it is not yet implemented. But we just hired Daren Weber to work on animation improvements in Chimera and perhaps he can try this. The idea is to enhance the movie command to add a "crossfade" option. You would display the volume, then use a command like "movie crossfade 25" then show the opaque surface. The command would take the image right before the command was issued and the next image and linearly blend them over 25 frames. This would be useful for many fade scenarios. It is limited in that it won't be able to have models moving and a fade occurring at the same time since that is not simply a linearly blending of two images. I'll see if Darren is interested in trying to add this if you are interested. If you do not want to wait for this, another option is to record your movie without the fade -- just have the surface suddenly appear. Then drop the movie into an video editing program like Final Cut and add the crossfade with that software. Tom > Hi Tom, > > I was using the surft command, trying to make a segment appear inside of a > cmap file. Basically, I have a cmap file open and visible, and I want to > show the segmented cell appear slowly. My problem is that when I set the > transparency of the segmented cell to 100 (i.e. surft 100 #0), it doesn't > exactly become transparent, or what I thought would be transparent. When I > enter this command, it makes the entire image transparent at that point > (so the shape of the segmented cell is preserved and matches the > background. I've attached an image of what I got as a result. Is there a > way to make preserve the cmap image and just make the segmented cell > overlay onto it without completely "removing" the section where the > segmented cell will appear? > > Thanks, > Mitalee

1 1

Question about match
by Ibrahim Moustafa 26 Jul '10

26 Jul '10

Dear Chimera developers, I have a question related to the ³match² command. I wanted to align 4 related proteins and I used the default in the match menu. The alignment is fine; but I have a question about the output in the reply log. In the log it says: ³evaluating superpositions across all 439 fully populated columns in the final alignment² Then the pair-wise RMSD between the different pairs (range from 0.7 1.6 A) are given. What is meant by 439 fully populated columns? Does it mean 439 C-alpha atoms for those amino acids in the fully occupied aligned columns? I¹m asking because I want to report these values of RMSD and I want to be more specific and state the number of atoms over which the RMSD value is being reported. P.S. The proteins vary in their length (461,462,460 and 470). Thanks for your reply in advance, Ibrahim

2 2

protonated carboxyl group
by Elaine Meng 26 Jul '10

26 Jul '10

> right now I'm getting stuck on things like adding hydrogens (e.g. I would like a -COOH and not -COO group) Hi, We may make some changes to make this easier in the future, but for now here is the procedure: (a) change the atom type of the oxygen to be protonated to O3. This could be done by Ctrl-clicking to select that oxygen and then using the command: setattr a idatmType O3 sel (b) add hydrogens with command "addh" or the AddH tool (c) if this is in a "standard residue" (amino acid ASP or GLU) and you are also going to assign charges in Chimera, you will also need to adjust the names of the atoms so they will receive the correct Amber partial charge values. If the residue is ASP, you will need to make sure that the sidechain oxygen without the hydrogen is named OD1, the one with the hydrogen is named OD2, and the hydrogen itself is named HD2. If GLU, it is analogous except the names contain E instead of D. Show atom labels for that residue to see the current names (e.g. to show atom labels for residue 9 in chain A, use command: lab :9.a). To rename an atom, you could select it and use a command something like: setattr a name OD1 sel Once the names are correct, charge assignment will give you the correct Amber values for residue ASH (protonated ASP) or GLH (protonated GLU). I hope this helps, ELaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

map normalization; ccp4 file saving
by Jean-Paul Armache 26 Jul '10

26 Jul '10

hello, i would like to pose two questions: 1. is there a way of adjusting one map so that it's adjusting to the levels of another map? i believe it should be achievable with "vop" command, but i am not sure whether the vop scale is the appropriate thing to use. 2. would it be possible to save the output map as a ccp4 map? currently you're permitting mrc saving, which is not that very much different from ccp4, so i was wondering if it was possible to add this feature. the difference is large enough so that coot does not allow for map loading of mrc files. best regards, jean-paul

2 1

Problem
by Reza Heidari 25 Jul '10

25 Jul '10

1 0

More on extracting data from the reply log
by Jean Didier Pie Marechal 21 Jul '10

21 Jul '10

Hi everyone, I want to write only a part of the reply log in a file. I was trying to use the script you gave to katrina months ago but I have a problem in parsing the reply log text output. If I understand correctly the reply log text is a raw text. I'd like to parse it in "lines" and then only write in the output file a intersting bit, like for example lines that contains "RMSD". I thought it would be enough to split text using the '\n' return character but that does not work. Could you give me a hand please? Best JD def save_reply_log(path): from chimera import dialogs r = dialogs.find('reply') text = r.text.get('1.0', 'end') f= open(path, 'w') i=text.split("\n") f.close() save_reply_log("d:/tmplog.txt") Dr. Jean-Didier Maréchal Lecturer 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 ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Divendres, Juliol 16, 2010 7:33 pm Assumpte: Chimera-users Digest, Vol 87, Issue 13 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: alignment + missing residues (Gesa Volkers) > 2. Re: alignment + missing residues (Gesa Volkers) > 3. Re: alignment + missing residues (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 16 Jul 2010 11:58:48 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402D58.7090906(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Eric, > > thanks for your suggestions. Unfortunately removing the SEQRES > record > did not help. I also downloaded and installed the new chimera- > version > today. The false numbering in the alignment still occurs. Also when > I > remove the SEQRES record and try with the new chimera version the > false > numbering appears. Quite annoying... The pdb-file is not in the > protein > data bank yet. > > Any more suggestions? Could I add "dummy atoms" in the structure? > > Thanks, > Gesa > > > > Eric Pettersen schrieb: > > On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > > > >> Dear All, > >> > >> I observed an issue with the alignment function of Chimera. > >> I loaded a crystal structure where in between a loop is not > modelled > >> due to low electron density- so these residues are missing in > the > >> structure and the numbering also has this gap. When I align this > >> structure with others, the missing residues are not recognized > and > >> chimera just overrides the numbering so after this loop all the > >> numbers in the alignment do not fit anymore to the residues they > >> should belong to although the structure and numberings are shown > in > >> the right way in the graphics window. How can I overcome this > issue? > >> Should I change the pdb-file? In which way? > >> > >> Thanks for all responses! > > > > Hi Gesa, > > I had a similar problem reported with 1JFF 12 days ago and > haven't yet > > worked on fixing it. It seems to only happen for a small subset > of > > structures. 1JFF has a missing loop and also exactly one missing > > residue at the N terminus. Is your structure like that? Is it a > > standard PDB entry (if so, what's the ID code)? I'll add you to > the > > recipient list for the ticket we have open in our bug database > for > > this (#8585) so you will be notified when it gets fixed. It'll > > probably be fairly soon. > > Until then the only workaround that occurs to me is for you to > remove > > the SEQRES records from the PDB file before you open it. Then > the > > Sequence viewer will depict only the residues physically present > in > > the structure -- no gaps (incorrect or otherwise) will be depicted. > > > > --Eric > > > > Eric Pettersen > > > > UCSF Computer Graphics Lab > > > > http://www.cgl.ucsf.edu > > > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 2 > Date: Fri, 16 Jul 2010 12:06:56 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402F40.2010604(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Additionally I downloaded 1JFF and did an alignment with another > tubulin-structure. And still the numbering does not recognize this > gap > between 34 and 61. > > Gesa Volkers schrieb: > > Dear Eric, > > > > thanks for your suggestions. Unfortunately removing the SEQRES > record > > did not help. I also downloaded and installed the new chimera- > version > > today. The false numbering in the alignment still occurs. Also > when I > > remove the SEQRES record and try with the new chimera version the > > false numbering appears. Quite annoying... The pdb-file is not in > the > > protein data bank yet. > > > > Any more suggestions? Could I add "dummy atoms" in the structure? > > > > Thanks, > > Gesa > > > > > > > > Eric Pettersen schrieb: > >> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >> > >>> Dear All, > >>> > >>> I observed an issue with the alignment function of Chimera. > >>> I loaded a crystal structure where in between a loop is not > modelled > >>> due to low electron density- so these residues are missing in > the > >>> structure and the numbering also has this gap. When I align > this > >>> structure with others, the missing residues are not recognized > and > >>> chimera just overrides the numbering so after this loop all the > >>> numbers in the alignment do not fit anymore to the residues > they > >>> should belong to although the structure and numberings are > shown in > >>> the right way in the graphics window. How can I overcome this > issue? > >>> Should I change the pdb-file? In which way? > >>> > >>> Thanks for all responses! > >> > >> Hi Gesa, > >> I had a similar problem reported with 1JFF 12 days ago and > haven't > >> yet worked on fixing it. It seems to only happen for a small > subset > >> of structures. 1JFF has a missing loop and also exactly one > missing > >> residue at the N terminus. Is your structure like that? Is it > a > >> standard PDB entry (if so, what's the ID code)? I'll add you to > the > >> recipient list for the ticket we have open in our bug database > for > >> this (#8585) so you will be notified when it gets fixed. It'll > >> probably be fairly soon. > >> Until then the only workaround that occurs to me is for you to > remove > >> the SEQRES records from the PDB file before you open it. Then > the > >> Sequence viewer will depict only the residues physically present > in > >> the structure -- no gaps (incorrect or otherwise) will be depicted. > >> > >> --Eric > >> > >> Eric Pettersen > >> > >> UCSF Computer Graphics Lab > >> > >> http://www.cgl.ucsf.edu > >> > >> > >> > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 3 > Date: Fri, 16 Jul 2010 10:32:39 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] alignment + missing residues > To: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <CF134751-B951-403B-B9E3-E441DB44644D(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Gesa, > I suspect you are using a Mac, since the daily builds failed last > night for the Mac platforms. You need to get a daily build dated > July > 16 or later. I tried opening the sequence view for 1JFF in one of > the > successful daily builds and it was correct, e.g.: > > > > You can see that the interior gap is correctly recognized now. > Hopefully the daily builds on the Mac platforms will work tonight. > > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > > Ah, the "remove SEQRES records" hack will only work for the single- > sequence viewer, not an alignment. I tested that in the 1.4.1 > release > and it indeed worked as I expected: > > > > The whole sequence is smushed together with no gaps, but the > correspondences are correct. You could then align additional > sequences to the smushed sequence and the correspondences would > remain > correct. Nonetheless it's probably simply better to wait for a > daily > build to succeed than to use the hack now. So make sure you check > the > date in the download table. If you still have problems with a > release > later than July 16, let me know. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Jul 16, 2010, at 3:06 AM, Gesa Volkers wrote: > > > Additionally I downloaded 1JFF and did an alignment with another > > tubulin-structure. And still the numbering does not recognize > this > > gap between 34 and 61. > > > > Gesa Volkers schrieb: > >> Dear Eric, > >> > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > >> > >> Any more suggestions? Could I add "dummy atoms" in the structure? > >> > >> Thanks, > >> Gesa > >> > >> > >> > >> Eric Pettersen schrieb: > >>> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >>> > >>>> Dear All, > >>>> > >>>> I observed an issue with the alignment function of Chimera. > >>>> I loaded a crystal structure where in between a loop is not > >>>> modelled due to low electron density- so these residues are > >>>> missing in the structure and the numbering also has this gap. > >>>> When I align this structure with others, the missing residues > are > >>>> not recognized and chimera just overrides the numbering so > after > >>>> this loop all the numbers in the alignment do not fit anymore > to > >>>> the residues they should belong to although the structure and > >>>> numberings are shown in the right way in the graphics window. > How > >>>> can I overcome this issue? Should I change the pdb-file? In > which > >>>> way? > >>>> > >>>> Thanks for all responses! > >>> > >>> Hi Gesa, > >>> I had a similar problem reported with 1JFF 12 days ago and > haven't > >>> yet worked on fixing it. It seems to only happen for a small > >>> subset of structures. 1JFF has a missing loop and also exactly > > >>> one missing residue at the N terminus. Is your structure like > >>> that? Is it a standard PDB entry (if so, what's the ID code)? > >>> I'll add you to the recipient list for the ticket we have open > in > >>> our bug database for this (#8585) so you will be notified when > it > >>> gets fixed. It'll probably be fairly soon. > >>> Until then the only workaround that occurs to me is for you to > >>> remove the SEQRES records from the PDB file before you open it. > > >>> Then the Sequence viewer will depict only the residues > physically > >>> present in the structure -- no gaps (incorrect or otherwise) > will > >>> be depicted. > >>> > >>> --Eric > >>> > >>> Eric Pettersen > >>> > >>> UCSF Computer Graphics Lab > >>> > >>> http://www.cgl.ucsf.edu > >>> > >>> > >>> > >> > >> > > > > > > -- > > Gesa Volkers > > Institut f?r Biochemie, Molekulare Strukturbiologie > > Felix-Hausdorff-Stra?e 4 > > 17489 Greifswald > > Germany > > +49 (3834)-864392 > > > > > > > > >

2 1

Re: [Chimera-users] save density map relative to...
by Tom Goddard 20 Jul '10

20 Jul '10

Hi Jie, You want to save a map that has been rotated relative to another map so that when you open both maps later they align. The difficulty is that the common map file formats like MRC and Spider don't have any place in the file header to specify a rotation. There are two ways to work around this limitation. One is that Chimera does some special trickery and puts the rotation information into a "label" in MRC map files so that when it later reads the file it can restore it in the right position. The trouble is that no other software will recognize that rotated position -- only Chimera. Another difficulty is that Chimera won't record the rotated position when you fit one map in another. The reason for that is because Chimera saves the rotation of the map grid relative to the maps local coordinate system. But fitting doesn't change the orientation of the grid -- instead it moves the local coordinate system (the map coordinate axes move instead of the data moving). Each map has its own set of coordinate axes. I think it would be pretty easy to add a "save relative to" option to the Same Map As... dialog that would take account of both types of rotation. But again, the orientation would only be restored by Chimera. The second method is to resample the rotated map on the grid of the map you fit into and save that resampled map. This will allow other software to open the maps and show the correct alignment. The drawback here is that the resampled map may have degraded quality since it interpolated the original map (trilinear interpolation). The Chimera command to do that looks like vop resample #3 onGrid #2 Here #3 is the id number (shown in Favorites / Model Panel or the volume dialog) of the rotated map that was fit into map #2. This will make a new map that you can save and it will align with map #2 when opened in another session or with other software since they share identical grids. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample Tom > Hi Tom, > > Hope this email finds you well. This is Jie from Joachim Frank's lab. > We met at the UCSF molecular animation workshop. > > I am writing about the "save map as" function in Chimera. Is there a > way to save map relative to another map (like the option available in > "save PDB")? The fitting algorithm ("fit in map" function) in Chimera > is very good, and I sometimes use it to align two density maps. > However, I couldn't save the density map after it was shifted. If > there's no such option, is it possible to add it? > > Best regards, > > > -Jie >

1 0

Re: [Chimera-users] Chimera-users Digest, Vol 87, Issue 13
by Jean Didier Pie Marechal 20 Jul '10

20 Jul '10

Hi again, I'd like to do a mmaker for a region of space leading to something like this: mmaker #(ref-model and part of the selection) #(flex-model and part of the selection) So far I haven't found the correct syntax to do so but I am pretty sure we can do that. any help? Cheers JD Dr. Jean-Didier Maréchal Lecturer 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 ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Divendres, Juliol 16, 2010 7:33 pm Assumpte: Chimera-users Digest, Vol 87, Issue 13 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: alignment + missing residues (Gesa Volkers) > 2. Re: alignment + missing residues (Gesa Volkers) > 3. Re: alignment + missing residues (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 16 Jul 2010 11:58:48 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402D58.7090906(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Eric, > > thanks for your suggestions. Unfortunately removing the SEQRES > record > did not help. I also downloaded and installed the new chimera- > version > today. The false numbering in the alignment still occurs. Also when > I > remove the SEQRES record and try with the new chimera version the > false > numbering appears. Quite annoying... The pdb-file is not in the > protein > data bank yet. > > Any more suggestions? Could I add "dummy atoms" in the structure? > > Thanks, > Gesa > > > > Eric Pettersen schrieb: > > On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > > > >> Dear All, > >> > >> I observed an issue with the alignment function of Chimera. > >> I loaded a crystal structure where in between a loop is not > modelled > >> due to low electron density- so these residues are missing in > the > >> structure and the numbering also has this gap. When I align this > >> structure with others, the missing residues are not recognized > and > >> chimera just overrides the numbering so after this loop all the > >> numbers in the alignment do not fit anymore to the residues they > >> should belong to although the structure and numberings are shown > in > >> the right way in the graphics window. How can I overcome this > issue? > >> Should I change the pdb-file? In which way? > >> > >> Thanks for all responses! > > > > Hi Gesa, > > I had a similar problem reported with 1JFF 12 days ago and > haven't yet > > worked on fixing it. It seems to only happen for a small subset > of > > structures. 1JFF has a missing loop and also exactly one missing > > residue at the N terminus. Is your structure like that? Is it a > > standard PDB entry (if so, what's the ID code)? I'll add you to > the > > recipient list for the ticket we have open in our bug database > for > > this (#8585) so you will be notified when it gets fixed. It'll > > probably be fairly soon. > > Until then the only workaround that occurs to me is for you to > remove > > the SEQRES records from the PDB file before you open it. Then > the > > Sequence viewer will depict only the residues physically present > in > > the structure -- no gaps (incorrect or otherwise) will be depicted. > > > > --Eric > > > > Eric Pettersen > > > > UCSF Computer Graphics Lab > > > > http://www.cgl.ucsf.edu > > > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 2 > Date: Fri, 16 Jul 2010 12:06:56 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402F40.2010604(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Additionally I downloaded 1JFF and did an alignment with another > tubulin-structure. And still the numbering does not recognize this > gap > between 34 and 61. > > Gesa Volkers schrieb: > > Dear Eric, > > > > thanks for your suggestions. Unfortunately removing the SEQRES > record > > did not help. I also downloaded and installed the new chimera- > version > > today. The false numbering in the alignment still occurs. Also > when I > > remove the SEQRES record and try with the new chimera version the > > false numbering appears. Quite annoying... The pdb-file is not in > the > > protein data bank yet. > > > > Any more suggestions? Could I add "dummy atoms" in the structure? > > > > Thanks, > > Gesa > > > > > > > > Eric Pettersen schrieb: > >> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >> > >>> Dear All, > >>> > >>> I observed an issue with the alignment function of Chimera. > >>> I loaded a crystal structure where in between a loop is not > modelled > >>> due to low electron density- so these residues are missing in > the > >>> structure and the numbering also has this gap. When I align > this > >>> structure with others, the missing residues are not recognized > and > >>> chimera just overrides the numbering so after this loop all the > >>> numbers in the alignment do not fit anymore to the residues > they > >>> should belong to although the structure and numberings are > shown in > >>> the right way in the graphics window. How can I overcome this > issue? > >>> Should I change the pdb-file? In which way? > >>> > >>> Thanks for all responses! > >> > >> Hi Gesa, > >> I had a similar problem reported with 1JFF 12 days ago and > haven't > >> yet worked on fixing it. It seems to only happen for a small > subset > >> of structures. 1JFF has a missing loop and also exactly one > missing > >> residue at the N terminus. Is your structure like that? Is it > a > >> standard PDB entry (if so, what's the ID code)? I'll add you to > the > >> recipient list for the ticket we have open in our bug database > for > >> this (#8585) so you will be notified when it gets fixed. It'll > >> probably be fairly soon. > >> Until then the only workaround that occurs to me is for you to > remove > >> the SEQRES records from the PDB file before you open it. Then > the > >> Sequence viewer will depict only the residues physically present > in > >> the structure -- no gaps (incorrect or otherwise) will be depicted. > >> > >> --Eric > >> > >> Eric Pettersen > >> > >> UCSF Computer Graphics Lab > >> > >> http://www.cgl.ucsf.edu > >> > >> > >> > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 3 > Date: Fri, 16 Jul 2010 10:32:39 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] alignment + missing residues > To: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <CF134751-B951-403B-B9E3-E441DB44644D(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Gesa, > I suspect you are using a Mac, since the daily builds failed last > night for the Mac platforms. You need to get a daily build dated > July > 16 or later. I tried opening the sequence view for 1JFF in one of > the > successful daily builds and it was correct, e.g.: > > > > You can see that the interior gap is correctly recognized now. > Hopefully the daily builds on the Mac platforms will work tonight. > > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > > Ah, the "remove SEQRES records" hack will only work for the single- > sequence viewer, not an alignment. I tested that in the 1.4.1 > release > and it indeed worked as I expected: > > > > The whole sequence is smushed together with no gaps, but the > correspondences are correct. You could then align additional > sequences to the smushed sequence and the correspondences would > remain > correct. Nonetheless it's probably simply better to wait for a > daily > build to succeed than to use the hack now. So make sure you check > the > date in the download table. If you still have problems with a > release > later than July 16, let me know. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Jul 16, 2010, at 3:06 AM, Gesa Volkers wrote: > > > Additionally I downloaded 1JFF and did an alignment with another > > tubulin-structure. And still the numbering does not recognize > this > > gap between 34 and 61. > > > > Gesa Volkers schrieb: > >> Dear Eric, > >> > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > >> > >> Any more suggestions? Could I add "dummy atoms" in the structure? > >> > >> Thanks, > >> Gesa > >> > >> > >> > >> Eric Pettersen schrieb: > >>> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >>> > >>>> Dear All, > >>>> > >>>> I observed an issue with the alignment function of Chimera. > >>>> I loaded a crystal structure where in between a loop is not > >>>> modelled due to low electron density- so these residues are > >>>> missing in the structure and the numbering also has this gap. > >>>> When I align this structure with others, the missing residues > are > >>>> not recognized and chimera just overrides the numbering so > after > >>>> this loop all the numbers in the alignment do not fit anymore > to > >>>> the residues they should belong to although the structure and > >>>> numberings are shown in the right way in the graphics window. > How > >>>> can I overcome this issue? Should I change the pdb-file? In > which > >>>> way? > >>>> > >>>> Thanks for all responses! > >>> > >>> Hi Gesa, > >>> I had a similar problem reported with 1JFF 12 days ago and > haven't > >>> yet worked on fixing it. It seems to only happen for a small > >>> subset of structures. 1JFF has a missing loop and also exactly > > >>> one missing residue at the N terminus. Is your structure like > >>> that? Is it a standard PDB entry (if so, what's the ID code)? > >>> I'll add you to the recipient list for the ticket we have open > in > >>> our bug database for this (#8585) so you will be notified when > it > >>> gets fixed. It'll probably be fairly soon. > >>> Until then the only workaround that occurs to me is for you to > >>> remove the SEQRES records from the PDB file before you open it. > > >>> Then the Sequence viewer will depict only the residues > physically > >>> present in the structure -- no gaps (incorrect or otherwise) > will > >>> be depicted. > >>> > >>> --Eric > >>> > >>> Eric Pettersen > >>> > >>> UCSF Computer Graphics Lab > >>> > >>> http://www.cgl.ucsf.edu > >>> > >>> > >>> > >> > >> > > > > > > -- > > Gesa Volkers > > Institut f?r Biochemie, Molekulare Strukturbiologie > > Felix-Hausdorff-Stra?e 4 > > 17489 Greifswald > > Germany > > +49 (3834)-864392 > > > > > > > > >

3 2

alignment + missing residues
by Gesa Volkers 20 Jul '10

20 Jul '10

Dear All, I observed an issue with the alignment function of Chimera. I loaded a crystal structure where in between a loop is not modelled due to low electron density- so these residues are missing in the structure and the numbering also has this gap. When I align this structure with others, the missing residues are not recognized and chimera just overrides the numbering so after this loop all the numbers in the alignment do not fit anymore to the residues they should belong to although the structure and numberings are shown in the right way in the graphics window. How can I overcome this issue? Should I change the pdb-file? In which way? Thanks for all responses! -- Gesa Volkers Institut für Biochemie, Molekulare Strukturbiologie Felix-Hausdorff-Straße 4 17489 Greifswald Germany +49 (3834)-864392

2 5

Positions Available in Electron Crystallography of Membrane Proteins
by Iban Ubarretxena 14 Jul '10

14 Jul '10

Positions Available: Electron Crystallography of Membrane Proteins A number of different positions are available with the Transcontinental Electron Microscopy Initiative for Membrane Protein Structure (TEMIMPS;http://temimps.nysbc.org) TEMIMPS is a new center funded by the NIH Protein Structure Initiative and is composed of five research groups with combined expertise in membrane protein production, 2D crystallization, electron microscopy, image processing, and structure determination. Our center will focus on the development and implementation of high-throughput and high-resolution approaches to structure determination of membrane proteins using cryo-electron microscopy and 2D crystals. We are seeking highly motivated individuals with good communication skills and ability to interact with an interdisciplinary group ranging from biochemists to mathematicians. Individual positions will be available in New York, Cleveland, Seattle and Houston, working in the laboratories of Drs. David Stokes, Iban Ubarretxena, Andreas Engel, Tamir Gonen and Pawel Penczek. These positions include a project manager, postdoctoral associates, software engineers and technical staff; up-to-date descriptions of the individual positions can be obtained at http://temimps.nysbc.org/jobs . Further questions or applications should be sent to temimps(a)nysbc.org. Applications should include a cover letter, a curriculum vitae and contact information for three referees. Applications will be reviewed as they are received and will continue until the positions are filled. Iban Ubarretxena-Belandia, PhD Assistant Professor Dept. Structural and Chemical Biology Mount Sinai School of Medicine Icahn Medical Institute Bldg., Room 16-70E 1425 Madison Avenue, Box 1677 New York, NY 10029 Office: 212-659-5593 Fax: 212-849-2456 Email: iban.ubarretxena(a)mssm.edu WWW: http://www.mssm.edu/physbio/ This e-mail is confidential and may well also be legally privileged. If you have received it in error, you are on notice of its status. Please notify us immediately by reply e-mail and then delete this message from your system. Please do not copy it or use it for any purposes, or disclose its contents to any other person: to do so could be a breach of confidence. Thank you for your co-operation

1 0

volume and area measurements
by Chinthaka Silva 13 Jul '10

13 Jul '10

Hi, Could you please tell me what is the difference between the values we get from the following two options? Volume Viewer: Tools --> Measure Volume and Area Tools --> Volume Mean, SD, RMS Is SD means standard deviation? What is RMS? In the 2nd option, we get 'Surface V and A'. What does 'Surface' mean in here? Thanks, Chinthaka.

2 2

SAXS Profile
by yann sterckx 13 Jul '10

13 Jul '10

Dear all, I'm trying to run the SAXS Profile Option in Chimera, but it doesn't seem to work properly. Every time I try to run the option, I get the following error message. Error processing trigger "check for changes": HTTPError: HTTP Error 504: Gateway Time-out File "/Applications/Chimera.app/Contents/Resources/lib/python2.6/urllib2.py", line 516, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) See reply log for Python traceback. I work in Snow Leopard. Can anybody help me out? Thanks, Yann

2 2

Fwd: request for stick and ball size in Atoms/Bonds menu
by Bala subramanian 12 Jul '10

12 Jul '10

Friends, I apologize that i sent the following mail wrongly to chimera-bugs. So i am fwdg it to the users list once again. ---------- Forwarded message ---------- From: Bala subramanian <bala.biophysics(a)gmail.com> Date: Mon, Jul 12, 2010 at 7:18 AM Subject: request for stick and ball size in Atoms/Bonds menu To: chimera-bugs(a)cgl.ucsf.edu Dear developers, Greetings. I downloaded a recent daily builds (July 8th) and I am quite happy to see the new additions on the Atoms/Bonds menu. I thank you all for your effort. I would like to request you for the addition the Stick and Ball size settings in the Atoms/Bonds menu. Because when i change the stick/Ball size from preference-New molecules option. I am not able to see the change for the molecule presently loaded in Chimera. It would be of great help to have this option in Atoms/Bonds menu itself. Regards, Bala

2 1

Structural alignment of a protein-ligand complex with other ligands only
by N.R. Jena 09 Jul '10

09 Jul '10

Hi, We are new to Chimera. Can you please let us know, if we have to superpose a protein-ligand complex with other ligands or a DNA-protein complex with few nucleotide-peptide complex, what is the better way to do in Chimera. I guess MatchMaker option is meant for superposition of one DNA or Protein on another DNA or Protein, right?

2 1

Best density map contour level
by Thomas Goddard 08 Jul '10

08 Jul '10

Hi Maria, Unfortunately I don't think your procedure for setting the contour level will work very well. The problem is that the isosurface is not just the outside surface of the capsid. Usually the virus genome has lower density then the protein capsid so there contour surface may show the virus as hollow, or maybe layers of RNA/DNA will appear. So the expected volume is not going to be the volume of a solid ball. There are no well accepted standards for how to set the contour level when showing EM maps. On the other hand there probably is no "right" answer. A good level for looking at the protein capsid will be different from a good level for looking at the genome packing. If a capsid feature of an icosahedral virus does not appear at all 60-fold symmetric locations then symmetry averaged maps will show lower density and you will need a lower contour level to see such features. In practice I believe people analyzing map primarily choose the contour level by eye that best suits their analysis. Tom > Hi Tom, > > Thank you very much for your help. > I'll measure the radius of my 2 d images afterwards I'll use the radius to calculate the volume of my virus and finally > set the contour level so that this volume is enclosed. > > Thanks a lot, > Maria > > >> Hi Maria, >> >> Chimera shows the volume data as an "isosurface" meaning all points >> on the surface are at a specific map value. That map value is called >> "level" in the volume viewer dialog. The values in a map (volume data >> file) determined by electron microscopy are often not normalized in any >> way -- useful values could be 10000 or 0.1 depending on the map. For >> x-ray maps it is common to normalize so that standard deviation over the >> unit cell is 1.0. In EM there no unit cell so the standard deviation >> would depend on how big a box surrounded the virus density -- so this is >> not as useful a normalization. There is no standard accepted EM map >> normalization that I know of. If you knew the expected volume occupied >> by the structure you could set a contour level so that the surface >> encloses that volume. Here's an explanation of how to do that in Chimera >> >> >> http://www.cgl.ucsf.edu/chimera/tutorials/eman07/chimera-eman-2007.html#par… >> >> More often you just visually choose a level that you believe gives a >> surface matching the envelope of the proteins in the structure. The map >> mean, standard deviation and root mean square value can be calculated >> with menu entry >> >> Tools / Volume Data / Volume Mean, SD, RMS >> >> Tom >> >> >> >>> Dear Chimera users, >>> >>> I'm using Chimera to inspect my calculated density maps of viruses. In >>> order to compare different tree d reconstructions I would like to know >>> what the 'Level' value in Volume Viewer dialog means. At present I'm using >>> the level value 1 but I'm not sure if this is correct. >>> >>> Could you please give me some advice how to define the right contouring >>> threshold to present my data in order to inspect it? >>> >>> Thank you for your help, >>> >>> Maria L. >>> >>

1 0

Alternative to the model panel
by Varela, Lawrence Rocco 07 Jul '10

07 Jul '10

Chimera seems to be consistently crashing or slows down drastically when I open the model panel when I have a lot of molecules loaded (200 or more). I'm often times looking at hundreds of small molecules and there relative conformations which requires me to load such big data sets. Is there an alternative to using the model panel? Like for example writing to file all the info that displays in the model panel including most importantly the model ids? Thanks in advanced, --Rocco

2 1

structural alignment
by Bala subramanian 07 Jul '10

07 Jul '10

Friends, I have 10 conformations of the same RNA molecule obtained from 5 separate MD simulations. Now to compare the conformations, I want to make a structural alignment of these conformations and make an alignment map ( something like multiple seq. alignment for protein ) so as to show residues (or residue positions) that higher flexibility among these ten conformations. What is the best way to do it in Chimera. Thanks, Bala

2 4

Parameters choice for match->align and quality assessment
by compchem compchems 06 Jul '10

06 Jul '10

Dear Chimera developers, great thanks to you for possibility to work with your very useful program. I am new in structural alignment studies and have some questions about parameters in match->align. My set cosists of few closely related proteins with same function and conservative spatial structure, but with some divergence in aminoacid sequences except of conservative functional residues. First, what "Residue aligned in column if within cutoff of" influences on and what preferable choice may be in my case. Second, "Superimpose full column" - how can i decide what to select for my set or what play can help me. Third, how can i evaluate quality or correctness of obtained alignment (may be, common procedure). I am sorry for long letter and thanks for your attention to my problem. D. Yegorov.

2 3

(no subject)
by Maria Ingrid Liebl 06 Jul '10

06 Jul '10

Dear Chimera users, I'm using Chimera to inspect my calculated density maps of viruses. In order to compare different tree d reconstructions I would like to know what the 'Level' value in Volume Viewer dialog means. At present I'm using the level value 1 but I'm not sure if this is correct. Could you please give me some advice how to define the right contouring threshold to present my data in order to inspect it? Thank you for your help, Maria L.

2 1

movie panel
by Susan Tsutakawa 02 Jul '10

02 Jul '10

Dear Users List, I apologize for these novice questions. I looked in the archives and could not find it. How do I get a MD molecular movement panel if I accidentally close it or I start a new session? I made a morph and I can see it on the model panel. Another very novice question is how do I delete a pdb in my model panel. Thank you in advance. Sincerely, Susan

2 2

Chimera Installation - NOVELL SUSE Enterprise Linux Desktop 11 (64bit)
by Madhumita Pattanayak 01 Jul '10

01 Jul '10

Request you let me know, whether the following specification will support the installation of Chimera: Operating System Novell SUSE Enterprise Linux 11 (64 bit) Processor Intel® Core?2 Duo Processor E8400 Chipset Intel® Q43 Express Memory (RAM) 4 GB PC-3-10600 (1333 MHz) DDR3 SDRAM Memory Graphics ATI Radeon HD 3470 256MB Appreciate an early reply in this regard. Many thanks for your help. Regards, Madhumita Senior Research Fellow CCMB, Hyderabad India "The person addressed in the email is the sole authorized recipient. Should you receive it in error, immediately notify the sender of the error and delete the e-mail. Any unauthorized dissemination or copying of this e-mail (or any attachment to this e-mail) or the wrongful disclosure of the information herein contained is prohibited. Also note that this form of communication is not secure, it can be intercepted, and may not necessarily be free of errors and viruses in spite of reasonable efforts to secure this medium."

2 1

renumber model IDs
by Dougherty, Matthew T 24 Jun '10

24 Jun '10

There are a number of times I would like to change the model ID numbers. Sometimes it is because a researcher gives me a session file that has sequences like monomer-b, monomer-d, monomer-a, monomer-c; or sometimes when I got an easy sequence to memorize (monomer-a, monomer-b, monomer-c, monomer-d), I do a colorzone split map that causes sequence names to comeback in a different order (monomer-b, monomer-d, monomer-a, monomer-c). Is there a way using commands to maintain better ID order?

1 0

Re: [Chimera-users] structure based sequence alignment
by Eric Pettersen 24 Jun '10

24 Jun '10

Hi Sonya, On Jun 24, 2010, at 7:39 AM, Sona Vasudevan wrote: > Hello Eric, > > Thanks for all the great features you have added in the last couple > of years since I was last in touch with you. This is a fantastic tool! Thanks! Glad you like it. > I need some help with the alignment editor. > > I am trying to import an alignment in fasta format (fasta aligned) > (see attached). The alignment as you can see has three structures. I > use Load structures from the sequence > window and it brings in all the chains corresponding to teh > structures. It does, but there's a subtlety here that I should point out. The first two sequences in the alignment are for 1XVA, chain A and chain B. Chimera opens two copies of 1XVA and associates one copy with each sequence, but it associates chain A in both, since the sequences of the two chains are identical. It doesn't really look at the sequence name to try to figure out which chain to associate, just how well the sequences match and in this case they both match perfectly. By hovering the mouse over the sequence name you can see which structure/ chain it is associated with. To change the association of the second sequence to use chain B, you need to go to the alignment's Structure menu and choose "Associations...". Thus will bring up a panel showing the association of each structure to a sequence. Change the association of "1xva (#1)" from "chain A" to "chain B" and then click OK. > I then use Matchmaker to align them. I have a few questions: > > 1. Does the match maker use the info from the imported alignment > since the structures are already aligned? In other words is the > structural alignment I am seeing the saem as that was imported. No. MatchMaker is its own tool and doesn't use any open alignments. After all, you could have several alignments involving those structures open. If you want to superimpose the structures based on your alignment, use the alignment's own "Structure->Match" menu item. That brings up a dialog offering a variety of options as to how to carry out the match. I like using the "Iterate" option, but it's totally up to you. > 2. Is there a way to just output the superposed co-ordinates without > the chains that are not being used? There are probably several ways. One that comes to mind is to click on one of the alignment's "Consensus" letters to select all the residues in that column. Then click into the graphics window and hit the up-arrow key to expand the selection to the entire chain. Then either choose Select->Invert or hit right-arrow to invert the selection -- now the unused chains are selected. Actions->Atoms/Bonds- >delete will delete them. You can then write out what's left. Keep in mind that if you want to get model 2's coordinates as superimposed with model 0's original coordinates (for instance) then make sure to use the "relative 0" option in the "write" command or check the "Save relative to" option in the Write PDB dialog and choose model 0. Or you could just write out all models current coordinates. They will all differ from their originals, but they will be superimposed. > 3. Looks like I can add sequences to the alignement. Can I add a > fasta file with many sequences? No. It is on my to-do list but I haven't gotten to it yet. I'll open a feature-request ticket in our Trac database with you on the recipient list so you'll know when it gets implemented. Sorry! > Thanks so much! I have alignment files for 100 families which are > high-qualityas they were manually aligned with Cn3d and I would like > to import them into chimera for further analysis. > > Thanks so much for your time! You're welcome! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Paint a pseudobond....
by Yasser Almeida Hernández 24 Jun '10

24 Jun '10

Hi... I want to connect two atoms that belongs to different models with a pseudobond. It's that possible with Chimera? If it does, how would be the Python API code? Thanks ;) -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI

2 1

Question about attribute assignment file
by Peng Ni 24 Jun '10

24 Jun '10

Hi, I am trying to use the define attribute function. However, the attribute assignment sheet I generated cannot be read. It reports: "Line 1 of file is either not 'name: value' or is missing initial tab". I cannot spot anything wrong in my txt file, which is also attached in the e-mail. I'd greatly appreciate it if you could help me fix this problem. Regards Peng

2 1

Lost hydrogens when saving mol2 file
by Varela, Lawrence Rocco 23 Jun '10

23 Jun '10

I'm encountering a problem where I'm loosing hydrogens from my small molecules after saving them in Chimera. Here is the situation: the original mol2 file I open has a number of small molecules listed under separate MOLECULE tag identifiers. Using the GUI menu I select "save Mol2", select all the models to save, and select the Save multiple models in "a single file [combined @MOLECULE section] option. When I open the newly saved Mol2 file with the combined MOLECULE section it's obvious that the hydrogens have been removed. How do a save multiple models in a combined MOLECULE section without loosing any hydrogen atoms? Thanks :-) Rocco

2 3

PDB
by Dougherty, Matthew T 23 Jun '10

23 Jun '10

Hi, When PDF files are read by Chimera and the session is written, the PDB data becomes part and parcel with the session files. That is, Chimera does not go back to the PDB files when it reloads the session, it uses the PDB data within the session file instead; as contrasted to density volume files, which are referenced by the session file, and the density volume files reloaded when the session file is read by Chimera. Is there a way to force the session file not to save the PDB internally to the session file, and instead reference and interact with it similar to the way volume files are managed? Matthew

2 4

Grouping Molecules
by Varela, Lawrence Rocco 23 Jun '10

23 Jun '10

Is there a way of grouping molecules in Chimera? Here is my situation. I have 4 molecules A, B, C, and D and I want to group A with B and C with D so that A and B has one center of rotation and C and D has another center of rotation. Rocco

2 1

Fwd: Chimera 3-D viewing
by Eric Pettersen 21 Jun '10

21 Jun '10

Forwarding Ed Pate's question (below) to this list, in the hope that someone who actually knows the answer can chime in! --Eric Begin forwarded message: > From: Edward Pate <edpate(a)hotmail.com> > Date: June 19, 2010 2:39:09 PM PDT > To: <pett(a)cgl.ucsf.edu> > Subject: Chimera 3-D viewing > > Hi Eric: > > I am looking into getting a new workstation for Chimera. In the > past, we have gotten CRT displays in order to do 3-D visualization. > Could you recommend other display options that are available now and > that users have been happy with? Is a CRT still the best option? > > Thanks for the help. > > Ed

3 2

vop binning
by Katrina Lexa 21 Jun '10

21 Jun '10

Hello - Is the volume data (vop) code available somewhere? Particulary the code for binning electron densities? I'm interested in looking at how chimera handles xplor files since I want to find the density of solvent at the edges of my grid. I would love to try to play with the volume code in order see if it can be done through chimera. Thank you, Katrina

2 3

Re: [Chimera-users] Chimera -RMSD
by Eric Pettersen 21 Jun '10

21 Jun '10

On Jun 21, 2010, at 6:25 AM, S. Shunmugasundararaj wrote: > Dear Eric, > > I am using Chimera v1.4. When aligning 2 or more structures, it > gives the > RMSD as a bar graph. Is it possible to get the RMSD value for each > residue? > > Thanks > Raj Hi Raj, I'm guessing the "RMSD as a bar graph" is the RMSD header at the top of the Multalign Viewer tool. You can save the header values to a file with the "Headers->Save..." menu entry at the top of the tool. This will save the RMSD value for each alignment position to a file. This may or may not be useful for you since the residues associated with each alignment position aren't indicated in the file. Alternatively, each residue involved in the Multalign Viewer RMSD header calculation gets a "mavRMSD" attribute assigned to it. You can save these attributes to a file by using the "File->Save Attributes..." menu of the Render By Attribute tool (available in the Depiction and Structure Analysis tools menus). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Error running chimera
by Christian Hesketh 21 Jun '10

21 Jun '10

Hi there, I have been able to use Chimera many times in the past, but now when I try to run it, a dialog box pops up and I get get any further. In fact, it seems to be spawned infinitely and I cannot close it. Here is the message: "Class DBPuppet.AC_KEY_ERROR'> Can't open web info file for reading". I don't know what has changed on my system to cause this, it was working fine a week ago. Does anyone have any ideas? I am using the most stable production version right now. My operating system is Windows Vista. Thanks in advance, Christian

2 1

total sum of a map
by Mario Dejung 21 Jun '10

21 Jun '10

Hi all, I try to multiply two maps in chimera. At the moment my workflow is the following: *open my two maps in chimera and try to fit map into map... *then I use "vop resample #1 inGrid #2" to set the same orientation *after this step, I convert the mrc files to Imagic and do a total-sum *what I get is one volume. Isn't there a way to do this in chimera? Thanks to all for any suggestions. Kind regards Mario

2 1

Rendering solid objects and POVRAY
by Mario J. Borgnia 16 Jun '10

16 Jun '10

Hi, I am trying to render an image that includes a difference map density displayed as a solid object. When I try to get the image directly from the screen it shows patterns of pixelation. I then tried POVRAY and the solid object data does not show up. Is there anything that I am missing? Thanks -- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia(a)nih.gov | +---------------------------------+

4 3

Open dialog box
by Rocco Varela 15 Jun '10

15 Jun '10

Is there a way to change the look-and-feel of the GUI open dialog box? Every time I try to open a file using the File>Open option in the GUI menu I'm faced with the problem of not being able to see the entire file names in the file navigator window. Enlarging the size of the open dialog box doesn't seem to resolve the issue. -Rocco

2 1

Re: [Chimera-users] dock prep multiple models
by Eric Pettersen 14 Jun '10

14 Jun '10

On Jun 14, 2010, at 1:22 PM, Francesco Pietra wrote: > Eric: > Thanks. Headache adding hydrogen atoms (just as you mentioned addH) > with my present system. Neither CHIMERA nor REDUCE were able to treat > ASH/ASP HIP/HIE etc as I know from experiments, and software for pKa > simulation also dropped. But it may be my fault. As per the AddH documentation you should be able to get the protonation states you want if you specifically know those states beforehand: Protonation States AddH aims to generate protonation states reasonable at physiological pH. For example, hydrogens are not added to the phosphodiester moieties of DNA and RNA. By default, aspartic acid and glutamic acid sidechains are assumed to be negatively charged, while arginine and lysine sidechains are assumed to be positively charged (although other states can be attained). Two chemical moieties are treated as ambiguous at biological pH: imidazoles such as histidine sidechains; histidine protonation states can be specified by the user or guessed by the method terminal phosphates (the third ionization); if one P–O bond is at least 0.05 Å longer than the others around that same phosphorus atom, that oxygen will be protonated Potentially ambiguous or rare (shifted-pKa) protonation states, especially in binding sites and nonstandard residues, should be verified and corrected as needed. For example, extra hydrogens can be deleted, and atom types can be edited (before hydrogen addition) with setattr or Build Structure. That last part could probably use an example. Let's say you know that the asparagine which is residue 39 in chain A should have atom OD1 protonated. Changing the atom type to O3 (from O2-) [before AddH] would accomplish that: setattr a idatmType O3 :39.a@od1 If you don't know specifically which oxygen should be protonated, this may not be a big help. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu > > As to the dockprep with either multiple pdb file, or single files > followed by "cat", it seems to me now that the latter is advantageous, > One can combine single-molecule mol2 files at will, and modify one or > more mol2 files without repeating the whole calculation. > > francesco > > On Mon, Jun 14, 2010 at 8:29 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> > wrote: >> On Jun 14, 2010, at 10:48 AM, Francesco Pietra wrote: >> >> With the combined pdb file, does dockprep operate on single >> molecules >> one after the other, so that it will not encounter obstacles even for >> many (more complex) ligands? >> >> I think this will be okay. Chimera ignores sibling submodels (e.g. >> #0.2 is >> a "sibling" of #0.1) when adding hydrogens so you will be okay if >> all your >> ligands come from one file. >> --Eric >> >> Eric Pettersen >> >> UCSF Computer Graphics Lab >> >> http://www.cgl.ucsf.edu >> >> >

1 0

dock prep multiple models
by Francesco Pietra 14 Jun '10

14 Jun '10

Hi: I always docked different molecules to the same receptor molecule per molecule, by using dockprep in chimera. Is it possible with dockprep to provide DOCK6.4 a single file containing mol2-type data for a number of different molecules to dock to the same receptor? That is, circumventing submission to the ZINC database server. I tried to get mol2 from a small list of molecules, methane and ethane, getting wrong charge (-1) for methane. If adjusted to zero, antechamber fails. The file was ATOM 1 C MTH 1 -0.370 -0.262 0.000 1.00 0.00 ATOM 2 H MTH 1 0.743 -0.262 0.000 1.00 0.00 ATOM 3 H MTH 1 -0.741 -0.787 0.909 1.00 0.00 ATOM 4 H MTH 1 -0.741 -0.787 -0.909 1.00 0.00 ATOM 5 H MTH 1 -0.742 0.787 0.000 1.00 0.00 MODEL ATOM 1 C ETH 1 -0.757 -0.113 -0.004 1.00 0.00 ATOM 2 C ETH 1 0.757 0.113 0.004 1.00 0.00 ATOM 3 H ETH 1 -0.998 -1.202 -0.006 1.00 0.00 ATOM 4 H ETH 1 -1.234 0.342 0.895 1.00 0.00 ATOM 5 H ETH 1 -1.225 0.343 -0.907 1.00 0.00 ATOM 6 H ETH 1 1.225 -0.343 0.907 1.00 0.00 ATOM 7 H ETH 1 1.234 -0.341 -0.895 1.00 0.00 ATOM 8 H ETH 1 0.998 1.202 0.006 1.00 0.00 ENDMDL Thanks francesco pietra

3 5

Adding Partial Charges
by Nancy 14 Jun '10

14 Jun '10

Hi All, I am trying to add charges to nicotinamide adenine dinucleotide (NAD+) using UCSF Chimera; the total charge on this molecule should be -1 (assuming the ionization of NAD+ at pH ~7.0, see attached figure). When I add Gasteiger charges, the total charge sums up incorrectly to 0, even though the net charge specified in the drop-down box is -1. However, using the "AM1-BCC" method, the net charge correctly sums up to -1. The charge model used is "Amber ff99SB". I have also noticed that the partial charges on individual atoms assigned when using the "AM1-BCC" method are generally of greater magnitude compared to charges assigned using the Gasteiger method. I am wondering why the Gasteiger method assigns an incorrect net charge in the case of NAD+. The mol2 structure code (with incorrect Gasteiger charges) is written below (and attached as NAD.mol2 with corresponding PNG structure image). Thanks in advance, Nancy ============================================================================ @<TRIPOS>MOLECULE NAD.mol2 70 74 1 0 0 SMALL USER_CHARGES @<TRIPOS>ATOM 1 C1 -1.4117 5.8700 -3.4377 C.2 1 LIG1 -0.0471 2 C2 -0.2808 5.1989 -2.9922 C.2 1 LIG1 -0.0472 3 C3 0.0698 5.2540 -1.6463 C.2 1 LIG1 -0.0021 4 N1 -0.7125 5.8930 -0.7233 N.2 1 LIG1 -0.2845 5 C4 -1.7621 6.6431 -1.1880 C.2 1 LIG1 0.0105 6 C5 -2.1590 6.6215 -2.5315 C.2 1 LIG1 0.0510 7 C6 -3.3433 7.3892 -2.9991 C.2 1 LIG1 0.2416 8 O1 -3.7255 7.3875 -4.2002 O.2 1 LIG1 -0.2721 9 N2 -4.0978 8.1475 -2.0847 N.3 1 LIG1 -0.3250 10 O2 0.0324 4.4339 0.9916 O.3 1 LIG1 -0.3484 11 C7 -1.0355 3.6965 1.6402 C.3 1 LIG1 0.1165 12 C8 -1.4243 2.4599 0.8071 C.3 1 LIG1 0.1276 13 O3 -0.4100 1.4351 0.9207 O.3 1 LIG1 -0.1602 14 P1 0.8613 1.4216 -0.0633 P.3 1 LIG1 0.5624 15 O4 2.0180 2.1020 0.5580 O.2 1 LIG1 -0.3429 16 O5 0.5634 2.0116 -1.3891 O.3 1 LIG1 -0.3429 17 O6 1.1223 -0.1529 -0.1877 O.3 1 LIG1 0.0575 18 P2 0.0541 -1.2893 -0.5527 P.3 1 LIG1 0.5624 19 O7 -1.1823 -1.2052 0.2607 O.3 1 LIG1 -0.3429 20 O8 0.6340 -2.6390 -0.3765 O.2 1 LIG1 -0.3429 21 O9 -0.2208 -1.0077 -2.1109 O.3 1 LIG1 -0.1602 22 O10 -2.0844 -2.0838 -4.0533 O.3 1 LIG1 -0.3483 23 C9 -1.7580 -0.6726 -3.9721 C.3 1 LIG1 0.1165 24 C10 -1.4291 -0.3206 -2.5098 C.3 1 LIG1 0.1276 25 N3 -5.5165 -1.9977 -1.1853 N.2 1 LIG1 -0.2341 26 C11 -5.3009 -1.7637 -2.4944 C.2 1 LIG1 0.0912 27 N4 -4.1259 -2.3733 -2.8716 N.3 1 LIG1 -0.2445 28 C12 -3.5825 -3.0679 -1.8327 C.2 1 LIG1 0.1583 29 C13 -4.4622 -2.7976 -0.7674 C.2 1 LIG1 0.1418 30 N5 -2.5159 -3.8010 -1.6563 N.2 1 LIG1 -0.2186 31 C14 -2.2518 -4.3018 -0.4707 C.2 1 LIG1 0.1192 32 N6 -3.0604 -4.0697 0.5431 N.2 1 LIG1 -0.2228 33 C15 -4.1365 -3.3442 0.4336 C.2 1 LIG1 0.1340 34 N7 -4.8438 -3.2010 1.5627 N.3 1 LIG1 -0.2849 35 C16 -2.1891 4.7099 1.7524 C.3 1 LIG1 0.1128 36 C17 -1.4568 6.0605 1.7533 C.3 1 LIG1 0.1256 37 C18 -0.3444 5.8071 0.7094 C.3 1 LIG1 0.1560 38 C19 -3.0362 0.0509 -4.4501 C.3 1 LIG1 0.1128 39 C20 -3.9053 -1.0632 -5.0633 C.3 1 LIG1 0.1257 40 C21 -3.5098 -2.2874 -4.2107 C.3 1 LIG1 0.1588 41 O11 -2.9991 4.5200 2.9209 O.3 1 LIG1 -0.3874 42 O12 -0.8413 6.3227 3.0256 O.3 1 LIG1 -0.3858 43 O13 -3.5425 -1.3145 -6.4282 O.3 1 LIG1 -0.3858 44 O14 -2.7472 1.1126 -5.3700 O.3 1 LIG1 -0.3874 45 H1 -1.6809 5.8357 -4.4909 H 1 LIG1 0.0632 46 H2 0.3396 4.6461 -3.6934 H 1 LIG1 0.0636 47 H3 0.9656 4.7572 -1.2733 H 1 LIG1 0.0793 48 H4 -2.2796 7.2615 -0.4632 H 1 LIG1 0.0801 49 H5 -4.8503 8.7190 -2.4374 H 1 LIG1 0.1458 50 H6 -3.7587 8.2854 -1.1465 H 1 LIG1 0.1458 51 H7 -0.6981 3.4004 2.6380 H 1 LIG1 0.0660 52 H8 -1.5845 2.7299 -0.2407 H 1 LIG1 0.0645 53 H9 -2.3510 2.0430 1.2095 H 1 LIG1 0.0645 54 H10 -0.9095 -0.4615 -4.6296 H 1 LIG1 0.0660 55 H11 -1.2870 0.7565 -2.4090 H 1 LIG1 0.0645 56 H12 -2.2603 -0.6329 -1.8739 H 1 LIG1 0.0645 57 H13 -5.9324 -1.1833 -3.1491 H 1 LIG1 0.1018 58 H14 -1.3609 -4.8928 -0.3242 H 1 LIG1 0.1064 59 H15 -4.6910 -3.8437 2.3366 H 1 LIG1 0.1259 60 H16 -5.8375 -2.9879 1.5154 H 1 LIG1 0.1259 61 H17 -2.8150 4.6581 0.8568 H 1 LIG1 0.0659 62 H18 -2.1232 6.8857 1.5028 H 1 LIG1 0.0675 63 H19 0.5295 6.4594 0.8618 H 1 LIG1 0.0853 64 H20 -3.5627 0.4623 -3.5840 H 1 LIG1 0.0659 65 H21 -4.9700 -0.8302 -5.0011 H 1 LIG1 0.0675 66 H22 -3.6913 -3.2429 -4.7274 H 1 LIG1 0.0854 67 H23 -3.4491 3.6578 2.8683 H 1 LIG1 0.2107 68 H24 -0.3142 7.1392 2.9619 H 1 LIG1 0.2108 69 H25 -3.3167 -0.4612 -6.8446 H 1 LIG1 0.2108 70 H26 -3.5789 1.5634 -5.6077 H 1 LIG1 0.2107 @<TRIPOS>BOND 1 1 45 1 2 1 2 ar 3 1 6 ar 4 2 46 1 5 2 3 ar 6 3 47 1 7 3 4 ar 8 4 5 ar 9 5 48 1 10 5 6 ar 11 6 7 1 12 7 9 am 13 7 8 2 14 9 50 1 15 9 49 1 16 10 11 1 17 10 37 1 18 11 35 1 19 11 51 1 20 11 12 1 21 12 53 1 22 12 52 1 23 12 13 1 24 13 14 1 25 14 17 1 26 14 16 1 27 14 15 1 28 17 18 1 29 18 21 1 30 18 20 1 31 18 19 1 32 22 40 1 33 22 23 1 34 23 24 1 35 23 54 1 36 23 38 1 37 24 21 1 38 24 56 1 39 24 55 1 40 25 29 ar 41 25 26 ar 42 26 57 1 43 26 27 ar 44 27 28 ar 45 28 30 ar 46 29 33 ar 47 29 28 ar 48 30 31 ar 49 31 58 1 50 31 32 ar 51 32 33 ar 52 33 34 1 53 34 60 1 54 34 59 1 55 35 36 1 56 35 61 1 57 35 41 1 58 36 37 1 59 36 62 1 60 36 42 1 61 37 4 1 62 37 63 1 63 38 64 1 64 38 44 1 65 38 39 1 66 39 65 1 67 39 43 1 68 39 40 1 69 40 27 1 70 40 66 1 71 41 67 1 72 42 68 1 73 43 69 1 74 44 70 1 @<TRIPOS>SUBSTRUCTURE 1 LIG1 1 GROUP 1 LIG 1 ============================================================================

2 1

Re: [Chimera-users] Hydrophobicity surface]
by Elaine Meng 12 Jun '10

12 Jun '10

Michael Wise brings up an excellent point: several different amino acid hydrophobicity scales have been developed, and although the Kyte-Doolittle scale is one of the earliest and most-used, be aware that the ordering of residue types may be surprising if considered on purely physicochemical grounds. The "hydrophobicity surface" is for qualitative visual interpretation, so we are not highly concerned about the precise values, but users performing detailed or quantitative analyses may want to consider using alternative scales. Below I describe how other scales can be defined in Chimera, and mention that data for two alternative scales are already included with Chimera and merely need to be read in to be used in your own analyses. > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html> Elaine Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: June 11, 2010 9:45:28 AM PDT > > On Jun 10, 2010, at 6:48 PM, Michael Wise wrote: > >> Dear Elaine >> Have you ever considered using an alternative hydrophobicity scale >> rather than K&D? I'm attaching a PPT slide from one of my bioinformatics lectures which compares the two scales. You'll note some real oddities in the KD scale. Most notable is Proline (hydrophilic, despite being a cyclised aromatic), but also see W, Y, G, H (which is usually thought of as only slightly basic at physiological pH). KD is by now very well established so I guess you can simply change to an alternative, but it would be a good idea to give users the option. >> Just a thought >> Cheers >> MichaelW > > Hi Michael, > It seemed like the "classical" choice, out of dozens (hundreds?) of published hydrophobicity scales, each with their own strengths and weaknesses. > > However, it is very easy (really!) to use whatever scale you like in Chimera. You would just create an attribute definition file and read it in with command "defattr" or the tool Define Attribute. It's a simple text format, and we include examples that define additional hydrophobicity scales, Wimley-White (as published in Nat Struct Biol 1996) and Hessa-von Heijne (as published in Nature 2005). The files look something like this: > > attribute: wwHydrophobicity > recipient: residues > :asp -1.23 > :glu -2.02 > :asn -0.42 > [ ... etc. ...] > > The three scales are shown in this table: > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html> > > Attribute file format: > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin…> > > and the complete definition files are linked to both those pages. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco >

1 0

animating "HIDE DUST"
by Dougherty, Matthew T 11 Jun '10

11 Jun '10

Hi, I was trying to generate an animation transition using the HIDE DUST feature. Any suggestions on how to do it (e.g., chimera command, python, etc)? thanks, Matt

4 3

redirecting runCommands output
by Bala subramanian 10 Jun '10

10 Jun '10

Friends, I wrote a small script to calculate the distance between two atoms in a list of pdb files. I would like to know how i can redirect the message that appears in replyobj to a text file. Some chimera commands like findhbon has option to save the result in file. But distance command dosent have the same. import glob from chimera import runCommand as rc filenames=[ fn for fn in glob.glob('*.pdb.*')] for fn in filenames: rc("open " + fn) * rc("distance :1@CA :166@CA") # I have to write this distance to a file.* rc("close all") Thank you, Bala

2 1

User defined h bonds
by snoze pa 10 Jun '10

10 Jun '10

Dear Chimera Users, Manually How can I show hbonds in chimera. Suppose I want to h bonds between residue 65 NH and 80 O. and show them using red or blue color. Is it possible to read this information from a file so that I can read all hbonds information in one run. Thank you S

2 1

Problems for mol2 with H atoms added with REDUCE
by Francesco Pietra 10 Jun '10

10 Jun '10

Hi: With CHIMERA alpha version 1.5 (build 30471 linux 64bit) and protein with H atoms added with program REDUCE: Tools -> Structure editing -> Dock prep (choice: If alternate locations keep only the highest occupancy; Add charges; write mol2) whereby I was asked to confirm residue CL- charge -1 and choose charge method AM1-BCC. getting warning: current charges are unknown for 1 non-standard atom names in otherwise standard residues. Charge 0.0 assigned to unkknown atoms. The log files reports: Charge model: AMBER ff99SB Assigning partial charges to residue CL- (net charge -1) with am1-bcc method Non-standard atom names: CYS H (CYS 55.A H, CYS 134.A H, CYS 141.A H + 39 others) Total charge for #0: -106.4198 The following residues had non-integral charges: CYS 55.A -1.2719 CYS 134.A -1.2719 CYS 141.A -1.2719 CYS 156.A -1.2719 CYS 252.A -1.2719 CYS 272.A -1.2719 CYS 276.A -1.2719 CYS 285.A -1.2719 CYS 287.A -1.2719 CYS 299.A -1.2719 CYS 307.A -1.2719 CYS 323.A -1.2719 CYS 325.A -1.2719 CYS 329.A -1.2719 CYS 55.B -1.2719 CYS 134.B -1.2719 CYS 141.B -1.2719 CYS 156.B -1.2719 CYS 252.B -1.2719 CYS 272.B -1.2719 CYS 276.B -1.2719 CYS 285.B -1.2719 CYS 287.B -1.2719 CYS 299.B -1.2719 CYS 307.B -1.2719 CYS 323.B -1.2719 CYS 325.B -1.2719 CYS 329.B -1.2719 CYS 55.C -1.2719 CYS 134.C -1.2719 CYS 141.C -1.2719 CYS 156.C -1.2719 CYS 252.C -1.2719 CYS 272.C -1.2719 CYS 276.C -1.2719 CYS 285.C -1.2719 CYS 287.C -1.2719 CYS 299.C -1.2719 CYS 307.C -1.2719 CYS 323.C -1.2719 CYS 325.C -1.2719 CYS 329.C -1.2719 As an example, the mol2 file reads for CYS 55: 877 N -27.8300 7.7310 -8.8380 N.am 55 CYS -0.4157 878 CA -28.5410 7.2460 -9.9870 C.3 55 CYS -0.0351 879 CB -27.9030 5.9690 -10.5570 C.3 55 CYS -0.2413 880 SG -26.2400 6.2310 -11.2140 S.3 55 CYS -0.8844 881 C -29.8950 6.7930 -9.5500 C.2 55 CYS 0.5973 882 O -30.0670 6.3000 -8.4370 O.2 55 CYS -0.5679 883 H -27.9010 7.1340 -8.0390 H 55 CYS 0.0000 884 HA -28.5450 8.0610 -10.7260 H 55 CYS 0.0508 885 HB2 -27.8610 5.2050 -9.7670 H 55 CYS 0.1122 886 HB3 -28.5460 5.5710 -11.3560 H 55 CYS 0.1122 ***************************** In the past I encounterd a similar problem, solving it by adding atoms with CHIMERA. This time, however, the complexity of the system suggests to use REDUCE. Thanks for suggestions. francesco pietra

2 1

Console window in Chimera
by Varela, Lawrence Rocco 10 Jun '10

10 Jun '10

Is there a console window option available in Chimera similar to that of the single command-line tool? Rocco

2 1

Write Amber/GAFF atom types
by Francesco Pietra 10 Jun '10

10 Jun '10

Hi: With CHIMERA alpha version 1.5 (build 30471 linux 64bit) and protein with H atoms added with program REDUCE: Tools -> Structure editing -> Dock prep (choice: If alternate locations keep only the highest occupancy; Add charges; write mol2) whereby I was asked to confirm residue CL- charge -1 and choose charge method AM1-BCC. getting warning: current charges are unknown for 1 non-standard atom names in otherwise standard residues. Charge 0.0 assigned to unkknown atoms. The log files reports: Charge model: AMBER ff99SB Assigning partial charges to residue CL- (net charge -1) with am1-bcc method Non-standard atom names: CYS H (CYS 55.A H, CYS 134.A H, CYS 141.A H + 39 others) Total charge for #0: -106.4198 The following residues had non-integral charges: CYS 55.A -1.2719 CYS 134.A -1.2719 CYS 141.A -1.2719 CYS 156.A -1.2719 CYS 252.A -1.2719 CYS 272.A -1.2719 CYS 276.A -1.2719 CYS 285.A -1.2719 CYS 287.A -1.2719 CYS 299.A -1.2719 CYS 307.A -1.2719 CYS 323.A -1.2719 CYS 325.A -1.2719 CYS 329.A -1.2719 CYS 55.B -1.2719 CYS 134.B -1.2719 CYS 141.B -1.2719 CYS 156.B -1.2719 CYS 252.B -1.2719 CYS 272.B -1.2719 CYS 276.B -1.2719 CYS 285.B -1.2719 CYS 287.B -1.2719 CYS 299.B -1.2719 CYS 307.B -1.2719 CYS 323.B -1.2719 CYS 325.B -1.2719 CYS 329.B -1.2719 CYS 55.C -1.2719 CYS 134.C -1.2719 CYS 141.C -1.2719 CYS 156.C -1.2719 CYS 252.C -1.2719 CYS 272.C -1.2719 CYS 276.C -1.2719 CYS 285.C -1.2719 CYS 287.C -1.2719 CYS 299.C -1.2719 CYS 307.C -1.2719 CYS 323.C -1.2719 CYS 325.C -1.2719 CYS 329.C -1.2719 As an example, the mol2 file reads for CYS 55: 877 N -27.8300 7.7310 -8.8380 N.am 55 CYS -0.4157 878 CA -28.5410 7.2460 -9.9870 C.3 55 CYS -0.0351 879 CB -27.9030 5.9690 -10.5570 C.3 55 CYS -0.2413 880 SG -26.2400 6.2310 -11.2140 S.3 55 CYS -0.8844 881 C -29.8950 6.7930 -9.5500 C.2 55 CYS 0.5973 882 O -30.0670 6.3000 -8.4370 O.2 55 CYS -0.5679 883 H -27.9010 7.1340 -8.0390 H 55 CYS 0.0000 884 HA -28.5450 8.0610 -10.7260 H 55 CYS 0.0508 885 HB2 -27.8610 5.2050 -9.7670 H 55 CYS 0.1122 886 HB3 -28.5460 5.5710 -11.3560 H 55 CYS 0.1122 ***************************** In the past I encounterd a similar problem, solving it by adding atoms with CHIMERA. This time, however, the complexity of the system suggests to use REDUCE. Thanks for suggestions. francesco pietra

1 0

Hydrophobicity surface
by Beale, John 10 Jun '10

10 Jun '10

I am creating a hydrophobicity surface for a protein using the "Presets -> Hydrophobicity surface" commands. I would like to know what the colors on the surface are telling me. I see a couple of shades of blue, white, and pink to orange. What do these colors mean? Thanks! John M. Beale, Jr., Ph,D. Professor of Medicinal Chemistry and Pharmacognosy St. Louis College of Pharmacy 4588 Parkview Place St. Louis, Missouri 63110 (314)-446-8461 Cell: (314)-315-0409 FAX (314) 446-8460 jbeale(a)stlcop.edu

2 1

Chimera - Surface calculation
by Braker, Jay 09 Jun '10

09 Jun '10

I wanted to contact you about the surface representation of a protein. I used to be able to show the surface of our protein and lately I can't show the surface on most multiple subunit proteins because the calculation fails. However, I noticed that on some previously edited structures (the same one as before, except I deleted some of the subunits/ligands) that the surface calculation would work. So, I started deleting lines in the PDB file to see if I could get the surface to start working. Sure enough, when I got to only 1 subunit left, it worked. So after more investigation, I found that if I insert "End" between each of the subunits/ligands in the PDB file then the surface calculation works for the whole structure. I have seen in the release notes of Chimera that some protein surface calculations fail, so having found a way to get mine to work, I thought I would pass it on in case it could shed some light on this surface calculation issue. Or if you have another idea how to "fix" this issue I am having, I would be glad to hear about it. Finally, I wanted to let you know that I thoroughly enjoy using Chimera, it is a great tool. Thanks. Jay

2 1

superimposing two vrml files ?
by Boaz Shaanan 09 Jun '10

09 Jun '10

Hi, Here is a question raised by a colleague on the ccp4 bulletin board. Since Chimera was mentioned in his post I thought you guys might have an answer to his question (positive or negative), hence I'm posting his message here. Cheers, Boaz Hello, I am working on a protein whose EM model has been built long time ago. The crystal structure has been solved recently and I want to know the difference between the crystal structure and EM model. Unfortunately there is no data in the EM data base, so I can not use Chimera or Phaser to fit the crystal structure into the EM electron density directly. My friend downloaded the VRML file of the EM model ,which can be viewed using Cosmo player. And I can make VRML file from my crystal structure using Pymol or Chimera. My questions is: can I superpose two VRML files which come from EM and crystal models? If so, how can I do that? Thanks in advance! Best wishes leo 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

2 1

DCD to PDB file Residue number
by snoze pa 09 Jun '10

09 Jun '10

Dear Chimera Users, I have a simple query related to the residue numbers in chimera. If I will save pdb file in chimera then the residue numbers are not changing but if I will save a pdb file from DCD trajectory file then it set the first residue number to 1 and so on. How to save it to original PDB residue number, which is not starting from residue number 1. Thank you for your help. S

2 2

hbond analysis
by George Tzotzos 09 Jun '10

09 Jun '10

Hi everybody, Is there a way in CHIMERA allowing to detect hbond between ligand and receptor from AMBER trajectory files? Best regards George

2 1

Get xpos and ypos of selected residues automatically
by wei li 07 Jun '10

07 Jun '10

Dear all, Here is my problem: I need to write a cmd script to use 2dlables automatically assign some annotations to some selected residues for many different proteins. However, I did not know the xpos and ypos for these residues and for different proteins there will be different residues which need to be assigned. So, is there any method to get the xpos and ypos via some commands when I only know the residue identifiers? Thanks Wei Li 2010-6-3

3 3

Ramachandran Plots
by James Nettles 07 Jun '10

07 Jun '10

Does Chimera do Ramachandran Plots and I'm missing something obvious? I like doing just about everything else in Chimera :-) Thanks, Jim

2 1

byte order? mac.
by Raymond Wightman 03 Jun '10

03 Jun '10

Hi, I'm trying to open several files that were prepared on imod on a unix system - an imod .rec file, tif stacks and an .mrc file. When I open any of these file formats on my mac the histogram seems to be inverted. Inverting the LUT on the tifs using imagej does not work and using the mrcx command of imod to toggle between big- and little-endian of the .mrc file has no effect - Chimera still displays the same inverted histogram. Is there a way that I can invert everything using Chimera? The mac is intel. Much appreciated, Ray.

2 1