May 2008 - Chimera-users - RBVI Mailing Lists

povray problem
by Fabian Gmail 27 May '08

27 May '08

Dear chimera team, I have a recurrent problem with the povray facility for saving high quality figures, in many cases I get a black-white figures like the attached. Is there a way to avoid that ? Thanks a lot in advance, 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 Web: http://bku.technion.ac.il Email: fglaser(a)tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396

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Replacing lysine with alanine
by Tom Goddard 23 May '08

23 May '08

Hi Neville, You can replace all lysine residues in a molecule with alanines using the Chimera command swapaa ALA #0:LYS The #0 refers to the molecule id number shown in model panel. Here is further documentation on swapaa. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html Tom yimnai forlemu wrote: > Hi Tom > I have a quick question about chimera. > Can you perform multi amino acid residue mutation > using chimera. For example lets say you have a protein > of 340 amino acids with about 100 lysine, and you want > all the lysines to become say ALaninis. Is that > possible > Thanks > Neville >

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map 3d pdf
by Tom Goddard 23 May '08

23 May '08

Richard Newman wrote: > Hi Tom > > Does CHIMERA have the ability to export a map format which can be used > by 3D PDF? > > We would like to make the EMDB maps available in this format. > > All the best > Richard Hi Richard, Chimera can export map surfaces in several 3-D file formats Wavefront OBJ, POV-Ray, RenderMan, VRML, or X3D using menu entry File / Export Scene.... The format for objects embedded in 3D PDF is called U3D which Chimera does not export. I used a program called MeshLab to read OBJ format produced by Chimera and write U3D format, then used another program to convert LaTeX to PDF (pdflatex). Here's an example showing EMDB map 1356. It requires Adobe Acrobat Reader 8.0. It will not display on Mac OS 10.4 Preview. http://www.cgl.ucsf.edu/home/goddard/temp/emd_1356.pdf Producing the file was painful and Chimera can't export the surface coloring in OBJ format. I think it would be more interesting for the EM Databank to show 3D models in the web browser like JMol shows PDB models. I don't know if a java applet has been written to do that. Perhaps JMol could do it. Tom

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rotate a helix
by Maurice Ho 23 May '08

23 May '08

Hi there, I would like to rotate a helix at a particular angle. How could I accomplish the following? 1. How to define the central axis of the helix in chimera? 2. How to set a particular angle to rotate? 3. I do this on a helix belonging to a GPCR, with the loops firstly broken for rotation and then perhaps need to rejoin them. How to join them back? 4. After joining, should I just redo energy minimization for the loops concerned? Much thanks!

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displacing atoms following a given vector
by Jean-Didier Maréchal 22 May '08

22 May '08

Dear All, I have been flying through the developer's guide but can't find what I look for, sorry. I have a given molecule and a vector in cartesian coordinates (e.g. a normal mode but not necessarily) indicating a direction of displacement for the different atoms of the molecules. I would like to write a script that displaces the atoms following this vector. I am prettysure that some modules of chimera should allow me to do that, but I can't find which ones. Could you give me a hand on this please? ALl the best JD El jue, 22-05-2008 a las 12:00 -0700, chimera-users-request(a)cgl.ucsf.edu escribió: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.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. Stereo projection (Magali Cottevieille) > 2. Stereo projection (Steven Ludtke) > 3. Re: Stereo projection (Greg Couch) > 4. Re: findhbond/5750 (FindHBond failure) (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 21 May 2008 16:06:07 -0400 > From: Magali Cottevieille <mc3077(a)columbia.edu> > Subject: [Chimera-users] Stereo projection > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <483480AF.9020604(a)columbia.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > Is there any way, with two projectors piloted by two graphic cards, to > send from Chimera the stereo left eye view onto one, and the stereo > right eye view onto the other one ? These two projectors are meant to be > used with filters and special glasses to create a 3D view. > Thanks for your help! > > -- > Magali Cottevieille, Ph.D. > Howard Hughes Medical Institute, > Department of Biochemistry and Molecular Biophysics, > 630 W 168th St, P&S Black Building 2-221 > New York, NY 10032 > > Ph: (+1) 212-305-9521 > Fax: (+1) 212-305-9500 > > Email: mc3077(a)columbia.edu > magali.cottevieille(a)gmail.com > > > > ------------------------------ > > Message: 2 > Date: Wed, 21 May 2008 16:18:26 -0500 > From: Steven Ludtke <sludtke(a)bcm.edu> > Subject: [Chimera-users] Stereo projection > To: chimera-users(a)cgl.ucsf.edu > Cc: mc3077(a)columbia.edu > Message-ID: <0F963AC8-7667-4B76-B8E2-0DC9855E406C(a)bcm.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Yes, we have done this before, though I don't remember with absolute > certainty if we > did it with chimera. You don't use 2 video cards normally, but rather > 1 card with 2 > outputs. Also, you will need one of the 'professional' cards where the > driver supports > stereo in a window ie- NVidia Quadro (we didn't try ATI). The NVidea > stereo drivers then > have a mode for this type of stereo, or at least that's my memory, it > was a year or two > ago when we demonstrated this. You need: > > 2 identical projectors which permit geometry correction so their > corners can be exactly aligned > 2 polarizer plates. we got (http://www.3dstereo.com/viewmaster/pj-pfilt-3x3.html > ) for $20 a pair > linear polarizing glasses (from the same site) > Quadro or similar GFX card > > Note that with this type of stereo, you could technically make this > work with any old dual > output 3-D card, but you would have to write the visualization > software so it would open > 2 display windows with slightly different orientations that you could > then manually (or > automatically) position on each of the 2 projectors. > > We did this just as an initial proof of concept, and haven't managed > to get back to it again, > though we keep meaning to, as it is MUCH cheaper than the commercial > solutions. Oh, one warning, > the polarizer plates mentioned above are plastic, and the light energy > put out by your typical > projector is quite substantial. We actually melted one of the > polarizers on our first attempt, > despite using much of it's 3x3 inch surface area. ie - use a low power > projector, or put the > polarizer between thick glass plates or somesuch... > > > From: Magali Cottevieille <mc3077(a)columbia.edu> > > Date: May 21, 2008 3:06:07 PM CDT > > To: chimera-users(a)cgl.ucsf.edu > > Subject: [Chimera-users] Stereo projection > > > > Hi, > > > > Is there any way, with two projectors piloted by two graphic cards, to > > send from Chimera the stereo left eye view onto one, and the stereo > > right eye view onto the other one ? These two projectors are meant > > to be > > used with filters and special glasses to create a 3D view. > > Thanks for your help! > > > > -- > > Magali Cottevieille, Ph.D. > > Howard Hughes Medical Institute, > > Department of Biochemistry and Molecular Biophysics, > > 630 W 168th St, P&S Black Building 2-221 > > New York, NY 10032 > > > > Ph: (+1) 212-305-9521 > > Fax: (+1) 212-305-9500 > > > > Email: mc3077(a)columbia.edu > > magali.cottevieille(a)gmail.com > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > ---------------------------------------------------------------------------- > Steven Ludtke, PhD | Baylor College of Medicine > sludtke(a)bcm.tmc.edu | Associate Professor & Co-Director > stevel(a)alumni.caltech.edu | National Center For Macromolecular > Imaging > V: (713)798-9020 | Dept of Biochemistry and Mol. Biol. > F: (713)798-1625 | > | Those who Do, Are > http://ncmi.bcm.edu/~stevel | The converse also applies > > > > > > ------------------------------ > > Message: 3 > Date: Wed, 21 May 2008 14:25:09 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Stereo projection > To: Magali Cottevieille <mc3077(a)columbia.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <Pine.OSF.4.63.0805211409520.1818353(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Wed, 21 May 2008, Magali Cottevieille wrote: > > > Hi, > > > > Is there any way, with two projectors piloted by two graphic cards, to > > send from Chimera the stereo left eye view onto one, and the stereo > > right eye view onto the other one ? These two projectors are meant to be > > used with filters and special glasses to create a 3D view. > > Thanks for your help! > > Chimera supports stereo using workstation graphics cards, i.e., NVidia > Quadro FX and ATI/AMD FireGL cards. We don't have a recent FireGL card > (and driver), so the rest of this email will be about the NVidia Quadro FX > cards and driver. > > The Quadro FX graphics cards have two video outputs and the driver lets > you display the left eye on one output and the right eye on the other. > The higher end cards have SLI support (on FireGL it's called CrossFire) > which lets you use two matched graphics cards together. It is unclear to > me how or if SLI/CrossFire and stereo work together, but I would expect > them to. > > Greg > > > ------------------------------ > > Message: 4 > Date: Thu, 22 May 2008 10:51:29 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] findhbond/5750 (FindHBond failure) > To: Tyler Arbour <tyler.arbour(a)gmail.com> > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <A4A9CFED-F357-4943-AB11-43D644C07DF0(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Tyler, > The problem is that Chimera "knows" the atom types of standard > residues and doesn't try to compute them from scratch. Therefore it > assigns ND1 in HIS a sp2 type, which throws a monkey wrench into the > find-hbond computation as it looks for the planarity of the ND1 and > sees it bonded to nothing! > For what you want to do, you want to get that atom's residue > changed. Do this: > > 1) Control-double click on the ND1 atom > 2) Chose "Modify Atom" from the resulting popup menu. > 3) Change the "Element" to "N"; leave "Geometry" as "tetrahedral" > 4) Change "Bonds" to 3 > 5) In the "Residue Name" section, use the "new residue" option with > "NH3" as the name and chain "het" > 5) Click the Change button > > That should give you what you want. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On May 22, 2008, at 10:25 AM, Tyler Arbour wrote: > > > Wow, I didn't expect a response for this...great! I was actually > > just trying to create a figure representing a computational model > > that I am using. Starting from the crystal structure, I wanted to > > actually change the histidinal N to a simple NH3 molecule. I am > > just trying to get familiar with Chimera--I usually use DS > > Viewerpro for modifying structures, and it doesn't seem like > > Chimera is well-suited to this type of modification. If you have > > any advice on an easy way to make this conversion so that I have a > > nice figure, I'd greatly appreciate it! Thanks. > > > > Tyler > > > > On May 22, 2008, at 11:17 AM, Eric Pettersen wrote: > > > >> Hi Tyler, > >> Your structure seems to have a histidine residue (residue 159 in > >> chain A) that consists solely of an ND1 atom! How did you manage > >> that? > >> > >> --Eric > >> > >> > >> Eric Pettersen > >> UCSF Computer Graphics Lab > >> http://www.cgl.ucsf.edu > >> > >> > > > >

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Re: [Chimera-users] findhbond/5750 (FindHBond failure)
by Eric Pettersen 22 May '08

22 May '08

Hi Tyler, The problem is that Chimera "knows" the atom types of standard residues and doesn't try to compute them from scratch. Therefore it assigns ND1 in HIS a sp2 type, which throws a monkey wrench into the find-hbond computation as it looks for the planarity of the ND1 and sees it bonded to nothing! For what you want to do, you want to get that atom's residue changed. Do this: 1) Control-double click on the ND1 atom 2) Chose "Modify Atom" from the resulting popup menu. 3) Change the "Element" to "N"; leave "Geometry" as "tetrahedral" 4) Change "Bonds" to 3 5) In the "Residue Name" section, use the "new residue" option with "NH3" as the name and chain "het" 5) Click the Change button That should give you what you want. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 22, 2008, at 10:25 AM, Tyler Arbour wrote: > Wow, I didn't expect a response for this...great! I was actually > just trying to create a figure representing a computational model > that I am using. Starting from the crystal structure, I wanted to > actually change the histidinal N to a simple NH3 molecule. I am > just trying to get familiar with Chimera--I usually use DS > Viewerpro for modifying structures, and it doesn't seem like > Chimera is well-suited to this type of modification. If you have > any advice on an easy way to make this conversion so that I have a > nice figure, I'd greatly appreciate it! Thanks. > > Tyler > > On May 22, 2008, at 11:17 AM, Eric Pettersen wrote: > >> Hi Tyler, >> Your structure seems to have a histidine residue (residue 159 in >> chain A) that consists solely of an ND1 atom! How did you manage >> that? >> >> --Eric >> >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >

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Re: [Chimera-users] building linker peptide
by Elaine Meng 22 May '08

22 May '08

On May 21, 2008, at 1:29 AM, Fabian Glaser wrote: > Another question regarding this issue, I succeded to make a new > bond and minimize it between two chains, A and B, in the same pdb. > But this created apparently a problem with the residue numbering > and Nterm recognition, since when I tried to add an additional > linker to the chimera I created, I got the following error message: > > "No MMTK name for atom "H" in standard residue ALA" > > I suspect that this is related to the fact that I still have two > chains, and Chimera does not identified the new bond, or something > similar. > > Is there a way to automatically rename the newly unified chains? > Any suggetion will be highly appreciated. Hi Fabian, There is no automatic way to change chain ID. Only the ugly manual text-editing way, sorry! I guess that the ATOM part of the file no longer agreed with the SEQRES part of the file. It might work to simply delete that atom, if it looks like it is extra. However, I would probably go back to a PDB file saved after you added all your linker residues and edit it to remove all the lines except the coordinates (the ATOM and HETATM lines), remove the chain IDs, and renumber all the residues. It is necessary to renumber the residues because there may be residues with the same number in the different chains, and now there would be no way to tell them apart (for example, two different residues numbered 10, which used to be residue 10 in A and residue 10 in B). Unfortunately you will lose the ability to use the "familiar" residue numbering within the second chain. I attached a fortran (f77) program to do this editing, but I realize you may not be able to use it depending on your computing environment. If you are on some unix-type computer you would just compile it with something like: f77 renum2.f -o renum Then execute it with renum It would ask for the names of the input and output PDB files and what residue number to start with. Then you would have to do the addh/addcharge/minimization stuff again, sorry. I think it would already have the bond you wanted, however. Maybe someone else can think of a more elegant approach. Best, Elaine -------- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Stereo projection
by Magali Cottevieille 21 May '08

21 May '08

Hi, Is there any way, with two projectors piloted by two graphic cards, to send from Chimera the stereo left eye view onto one, and the stereo right eye view onto the other one ? These two projectors are meant to be used with filters and special glasses to create a 3D view. Thanks for your help! -- Magali Cottevieille, Ph.D. Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, 630 W 168th St, P&S Black Building 2-221 New York, NY 10032 Ph: (+1) 212-305-9521 Fax: (+1) 212-305-9500 Email: mc3077(a)columbia.edu magali.cottevieille(a)gmail.com

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Stereo projection
by Steven Ludtke 21 May '08

21 May '08

Yes, we have done this before, though I don't remember with absolute certainty if we did it with chimera. You don't use 2 video cards normally, but rather 1 card with 2 outputs. Also, you will need one of the 'professional' cards where the driver supports stereo in a window ie- NVidia Quadro (we didn't try ATI). The NVidea stereo drivers then have a mode for this type of stereo, or at least that's my memory, it was a year or two ago when we demonstrated this. You need: 2 identical projectors which permit geometry correction so their corners can be exactly aligned 2 polarizer plates. we got (http://www.3dstereo.com/viewmaster/pj-pfilt-3x3.html ) for $20 a pair linear polarizing glasses (from the same site) Quadro or similar GFX card Note that with this type of stereo, you could technically make this work with any old dual output 3-D card, but you would have to write the visualization software so it would open 2 display windows with slightly different orientations that you could then manually (or automatically) position on each of the 2 projectors. We did this just as an initial proof of concept, and haven't managed to get back to it again, though we keep meaning to, as it is MUCH cheaper than the commercial solutions. Oh, one warning, the polarizer plates mentioned above are plastic, and the light energy put out by your typical projector is quite substantial. We actually melted one of the polarizers on our first attempt, despite using much of it's 3x3 inch surface area. ie - use a low power projector, or put the polarizer between thick glass plates or somesuch... > From: Magali Cottevieille <mc3077(a)columbia.edu> > Date: May 21, 2008 3:06:07 PM CDT > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] Stereo projection > > Hi, > > Is there any way, with two projectors piloted by two graphic cards, to > send from Chimera the stereo left eye view onto one, and the stereo > right eye view onto the other one ? These two projectors are meant > to be > used with filters and special glasses to create a 3D view. > Thanks for your help! > > -- > Magali Cottevieille, Ph.D. > Howard Hughes Medical Institute, > Department of Biochemistry and Molecular Biophysics, > 630 W 168th St, P&S Black Building 2-221 > New York, NY 10032 > > Ph: (+1) 212-305-9521 > Fax: (+1) 212-305-9500 > > Email: mc3077(a)columbia.edu > magali.cottevieille(a)gmail.com > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Associate Professor & Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-9020 | Dept of Biochemistry and Mol. Biol. F: (713)798-1625 | | Those who Do, Are http://ncmi.bcm.edu/~stevel | The converse also applies

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Re: [Chimera-users] Low resolution surface model
by Elaine Meng 21 May '08

21 May '08

On May 20, 2008, at 10:21 PM, Damien Larivière wrote: > Dear Elaine, > Here is what I would like to do with Chimera : > > From Tools/Structure analysis/sequence, it is possible to copy a > portion of the aminoacid sequence of a protein and then to > highlight in an other color this portion of sequence in a high > resolution surface model (Actions / surface / show). > > I would like to highlight a given portion of sequence but in a low > resolution surface model. I tried High-Order Structure / Multiscale > models with no success. > > Thanks for you help and congratulations for the work you perform. > Damien > ------------------------------------------ > Damien Larivière > Fourmentin-Guilbert Scientific Foundation > 2 Av. du Pavé Neuf, 93160 Noisy-le-Grand, France > Phone : + 33 1 43 03 06 20 > Cell phone : +33 6 82 19 81 32 > damien.lariviere(a)fourmentinguilbert.org > Hi Damien, You can color a low-resolution surface for certain residues, but it takes an additional step as compared to coloring the high-resolution surface. Another difference is that it is done by distance cutoff, because it is no longer clear exactly which atom goes with which point on the surface. (1) First create the low-resolution surface. I can think of two different ways: (a) Multiscale Models - click "Make Models" and that will create a separate low-res surface for each chain. In that dialog, if you select "All" chains you can then edit the resolution value for those surfaces. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/ framemulti.html (b) command "molmap" - it makes a density map from the atomic coordinates, which you can then display as an isosurface. The Volume Viewer tool is automatically opened to show the density; in that tool, you can drag a bar on the histogram to change the contour level. In this case, all the atoms in the structure are used, and so you would get one "blob" (depending on contour level, though) rather than separate surfaces per chain. Volume Viewer has many additional options including surface smoothing (see Features... Surface and Mesh options). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/ framevolumeviewer.html (2) Select the residues and perform the coloring. This can be done exactly the same as for the high-resolution surface, and there are many different ways. To select the residues, you can use the Sequence tool (as you described), or the Select menu, or commands; to perform the coloring, you can use Actions...Color or the "color" command. However, the low-res surface will not be colored yet... (3) Use Color Zone (under Tools.... Volume Data) to color the surface to match the atoms you just colored. This just uses a simple distance cutoff and colors parts of the surface to match the closest atoms. After clicking Color, you can just drag the slider to change the distance cutoff. You're welcome! I hope this helps, Elaine P.S. we are working on better integration of different kinds of surfaces, so this procedure may change in the future ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Chimera-users May 2008