November 2010 - Chimera-users - RBVI Mailing Lists

loading pdb files
by Beale, John 10 Nov '10

10 Nov '10

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

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

04 Nov '10

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

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Chimera production release candidate
by Elaine Meng 04 Nov '10

04 Nov '10

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

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

03 Nov '10

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

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

03 Nov '10

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

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

03 Nov '10

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

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

03 Nov '10

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

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

01 Nov '10

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

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

01 Nov '10

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

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

01 Nov '10

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

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viewing of trajectory
by atila petrosian 01 Nov '10

01 Nov '10

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

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