- Chimera-users - RBVI Mailing Lists

the fastest way to convert a pdb to density map
by 李智海 22 Jan '16

22 Jan '16

Hi, Here I want to calculate a model-to-map FSC curve. If I am not wrong, firstly I am supposed to convert the pdb file to a density map. So I was just wondering in Chimera, how to use command molmap to generated a map with the same pixel size and dimensions as the corresponding map? Any help will be high appreciated. Best, Zhihai Li

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Select residues with missing atoms?
by Oliver Clarke 19 Jan '16

19 Jan '16

Hello, Is there any way to select/color all protein residues with incomplete sidechains? This would be very helpful when looking at a structure and deciding whether it is necessary to run dock prep to fill them in prior to performing other calculations (e.g. sometimes I am only concerned with what is going on around a ligand binding site). Cheers, Oliver.

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question
by A G Szabo 15 Jan '16

15 Jan '16

I have to admit that my understanding of the various commands to use for very specific functions in Chimera is difficult for me to find the correct command. I know how to color a specific residue using the sequence table and the color chart. So how do I color a specific atom in a residue. For example I am interested in coloring the nitrogen of the Asn amide side chain say color red. How can I do this? When I highlight a residue and visualize it as a ball and stick, then color it different from the color of the helix, the color of that part of the helix changes to the color of the ball and stick, different from the color of the rest of the helix. How can I reset the color of the helix location of that residue, leaving the ball and stick as another color. Thank you Arthur Szabo Professor Emeritus Chemistry and Biochemistry Wilfrid Laurier University Waterloo Canada.

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Geometric Center
by tobias.eilert＠uni-ulm.de 15 Jan '16

15 Jan '16

Hello, I want to translocate a protein such that its geometric center is the origin. Finally I want to save this new configuration in a pdb-file, so it is conserved like this. Do you have any suggestions? With kind regards Tobias Eilert

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save command
by Dougherty, Matthew T 11 Jan '16

11 Jan '16

The FILE pull down menu allows for "save" and "save as". The command "save" allows for two options: with or without a session_name. Without a session_name, a dialog box is presented and effectively I am doing the "save as" in the FILE menu at that point. With a session_name, it functions as a 'save as' without the dialog box. How do I create the same effect as FILE pull down menu "save", using the save command? Looking for a generic approach for any session, not knowing the file/session name apriori, & having to type the session name everytime. I suppose there is a python method to get the session filename & path, then build the command string. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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header intact
by maozhouhe 08 Jan '16

08 Jan '16

confirm 4cb1de59074527102f482c8970f4d33506347705

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Re: [Chimera-users] [chimera-dev] Volume Eraser: Recentering the eraser
by Tom Goddard 07 Jan '16

07 Jan '16

Hi Mohan, Here are a few more details about how to erase the density inside the capsid of a virus density map. The trick as you’ve seen is getting the sphere centered at the center of the virus and having the correct radius. Here’s how I do this. First I adjust the volume eraser sphere radius so it visually looks about the same radius as the outside of the virus map. Then I move the sphere with the mouse to try to center it on the virus. I rotate to look at it from different view angles and center with the mouse at each view direction. It helps if the radius of the sphere is set so that just a little bit of the density pokes through so you can visually see whether the same amount of density is poking through on all sides. Now I have the right centering and I try to get the radius I want. For this it helps to clip the map and sphere using menu Favorites / Side View and move the left vertical yellow line to the right to clip the models. I move the clip plane to cut through near the center of the virus, then adjust the sphere radius. In this view you can see the sphere size relative to the concentric layers of density. It helps here to make the sphere not transparent by clicking the color square in the Volume Eraser dialog and setting the A (opacity) channel to 1. I’ve attached a pickture. To do this in a more precise way I create a sphere and mask using it with commands shape sphere radius 240 center 0,0,0 coordinateSystem #0 color blue mask #0 #2 invert true This requires that the origin of the map is set to the center of the virus capsid. You can choose this center grid point using Volume Viewer menu Features / Coordinates setting the Origin Index. Tom > On Jan 7, 2016, at 9:38 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hello Mohan, > If you read the Help for Volume Eraser (press the Help button on the dialog to see it), it explains how to move and resize the eraser sphere. Or, you can see this information on our website: > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleras…> > > Basically you can set which mouse button will be used to move the sphere, and then use the mouse to move it to where you want, including with Shift to move in Z (toward or away from you). There isn’t a feature to automatically put it at the center of the capsid. > > For user questions, the better address is chimera-users(a)cgl.ucsf.edu (not this address chimera-dev, which is more for programming questions). > > 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 Jan 6, 2016, at 9:01 AM, Mohan Sudabattula <mk.sudabattula(a)gmail.com> wrote: >> >> Hello, >> >> My name is Mohan Sudabattula, I am fairly new at using Chimera so please excuse my lack of understanding the program. >> >> I am currently utilizing the Volume Eraser tool and am trying to employ it erase the internal structure of a viral capsid. Upon opening the Volume Eraser it always seems to orient itself to the "frontmost face of the current display region". This is problematic because it is now only partially erasing what I am needing to be erased. >> >> Instead I am looking to have it oriented so that it is in the center of my virus. Is there any way to reorient the eraser so that this may be the case? >> >> Thank you! >> Mohan Sudabattula >> > > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >

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Drawing shapes given coordinates
by Oliver Clarke 07 Jan '16

07 Jan '16

Dear Rebecca, I have used Elaine's suggestion before, and it works well, as in the following alias: alias ^pbond dist sel; setattr p label "" sel; setattr p drawMode 1 sel; setattr p radius 0.03 sel which places a thin black cylinder between two selected atoms. To make invisible dummy atoms at arbitrary coordinates, I would use the "mc" accelerator ("ac mc" on the command line), which places and selects a dummy atom at the center of rotation. So something like: cofr x1,y1,z1; ac mc; namesel atom1; cofr x2,y2,z2; ac mc; namesel atom2; sel atom1|atom2; pbond; vdwdefine 0.01 sel; transparency 100,a sel should work. Cheers, Oli. ------------------------------ Thank you! Theoretically if I was to create dummy atoms with coordinates at the locations where I want the cylinders to end, I could connect them with pseudobonds. I can easily shape my data that way, and if it doesn't work the BILD files will probably be fine. Thanks for the help! Cheers, Rebecca On 1/4/16, 5:20 PM, "Elaine Meng" <meng at cgl.ucsf.edu <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> wrote: >*Hi Rebecca, *>*There are two approaches for adding cylinders independent of atomsŠ but I *>*don¹t know if either will be satisfactory: *>>*(1) ³shape cylinder² is command-line and doesn¹t require using atoms as *>*endpoints, but it doesn¹t allow specifying endpoint coordinates directly. *>* A cylinder is specified by only its center, height, radius, and a *>*rotation angle. I don¹t think it is easy to figure out what angle gives *>*the desired endpoint coordinates. (We¹ve discussed the need to improve *>*this, but it may be deferred to our next-generation software in *>*development.) *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_midas_shape.html-23cylinder&d=CwIFaQ&c=TzEZu9LIcihmW3 *>*7vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd *>*4eXf6HdP_BL9dt0gv_zz3oMdq8&s=9vZCIh2K2i-8UrGF7HkSZwZwT7CRFcS9RUZsHUsson4&e *>*= > *>>*(2) BILD-format input allows specifying endpoint coordinates of a *>*cylinder, but it is not a command. You generate a BILD text file *>*describing the objects and read it in to Chimera. BILD format is very *>*simple, however: *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_bild.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r=Z2BqCMu *>*wlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_BL9dt0gv_ *>*zz3oMdq8&s=2A5wPT06BJ7QN1TDyA4kS36ILONzhA703a7xRpdnJKY&e= > *>>*The objects created with ³shape² are surface models, so you can change *>*their colors afterward. The BILD objects are not surface models and *>*cannot be recolored and do not work well with transparency. *>>*There are two approaches that depend on atoms: *>>*(1) pseudobonds can be created with the ³distance² command (or atom pairs *>*can be read in from a file with Pseudobond Reader), but pseudobonds *>*require atoms as endpoints. *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_midas_distance.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w *>*&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP *>*_BL9dt0gv_zz3oMdq8&s=tUGhl0z5yTsTqr2tyEgexdraCTB8o2JtwjuJZTgMwvo&e= > *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_ContributedSoftware_pbreader_pbreader.html&d=CwIFaQ&c=TzEZu9LIci *>*hmW37vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH *>*6akd4eXf6HdP_BL9dt0gv_zz3oMdq8&s=nRvWQ2FPg5n33Obqd9Bee1ovSNmgCCdbaT1EH6Uc1 *>*I8&e= > *>>*(2) the ³define² command (or Axes/Planes/Centroids) tool will show *>*cylindrical axes that are best fits to specified sets of atoms. However, *>*there is currently little control over lengthŠ it is automatically *>*determined from the atomic coordinates. *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_midas_define.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r *>*=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_B *>*L9dt0gv_zz3oMdq8&s=t9I-WC_-VvEvmTfphtU3ey2GT0sMRiFtO62hFkRj7Rk&e= > *>>*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 Jan 4, 2016, at 12:09 PM, Rebecca Swett <Rebecca_Swett at vrtx.com <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> *>>*wrote: *>>>>* Hi all, *>>* I'm trying to add some 3d shapes to a visualization. I was wondering if *>>*it would be possible to draw either a cylinder or tube given starting *>>*and ending coordinates rather than atom names/numbers or centroid? For *>>*example, if I had this coordinate pair: *>>* 6.17 1.10 -15.33 20.82 -0.70 -8.39 *>>>>* What would be the best way to go about drawing a line of some sort *>>*between those two points? I have dozens of pairs of coordinates so *>>*something command line would be ideal. *>>* Cheers, *>>* Rebecca *> This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

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Suggested Improvement of Command Line
by Eric Berg 06 Jan '16

06 Jan '16

Hello, I have noticed that when giving the command line a list of residue indexes using the "select" function, the inclusion of white space will cause an error (see attachment). This is technically a pretty small quibble, but it may be beneficial in these instances to include something to filter out white space prior to parsing. Eric

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volume eraser and imod isosurface
by Wouter Van Putte 06 Jan '16

06 Jan '16

Dear, I would like to use chimera for removing some densities manually of an isosurface generated with imod. I've loaded the map/model (.mod) and already used the function 'hide dust' to remove most of the noise. I now would like to use 'volume eraser' to remove the other noise manually. This however doesn't work, probably due to the file format (.mod). I thought saving in another file format would help, but it gave me errors when opening the file. How should I proceed? best wishes, Wouter

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Chimera and imod isosurface (*.mod files) and 'volume eraser'
by Wouter Van Putte 06 Jan '16

06 Jan '16

Dear, I would like to use chimera for removing some densities manually of an isosurface generated with imod. I've loaded the map/model (.mod) and already used the function 'hide dust' to remove most of the noise. I now would like to use 'volume eraser' to remove the other noise manually. This however doesn't work, probably due to the file format (.mod). I thought saving in another file format would help, but it gave me errors when opening the file. How should I proceed? best wishes, Wouter

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Drawing shapes given coordinates
by Rebecca Swett 05 Jan '16

05 Jan '16

Hi all, I'm trying to add some 3d shapes to a visualization. I was wondering if it would be possible to draw either a cylinder or tube given starting and ending coordinates rather than atom names/numbers or centroid? For example, if I had this coordinate pair: 6.17 1.10 -15.33 20.82 -0.70 -8.39 What would be the best way to go about drawing a line of some sort between those two points? I have dozens of pairs of coordinates so something command line would be ideal. Cheers, Rebecca This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

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Identify hinges and rigid groups using Morph Conformations?
by Oliver Clarke 04 Jan '16

04 Jan '16

Hi, I gather from reading the documentation for “Morph Conformations” (https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html) that Chimera identifies hinge regions and rigid groups as part of the procedure (as per http://nar.oxfordjournals.org/content/28/8/1665.long) Would it be possible to expose these to the user (or maybe this is already possible?), such that one can color/label the hinges and rigid entities as desired? This would be helpful for visual simplification of complex conformational changes. Cheers, Oliver.

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Include "perframe" command as action in Animation panel?
by Oliver Clarke 30 Dec '15

30 Dec '15

Hi, I really like the animation panel of chimera because it makes it incredibly easy to create a nice looking movie, but transitions are still a bit limited compared to what one can do in a script - e.g. smoothly transitioning from one contour level to another, moving along a chain and highlighting specific residues, etc. On the command line, it is easy to do this and a bunch of other iterative processes using the “perframe” command. Perhaps it might be worth considering inclusion (in ChimeraX presumably) of an equivalent of the “perframe" command as an action in the animation GUI (One could call it “Custom” or “Script” to avoid confusion), to enable mixing in code snippets into the animation GUI? It would only need to have a couple of parameters - the frame range, variable range, interval, and command to execute (with a checker to catch invalid syntax prior to execution). Alternatively/additionally, it would be nice to have the option to export the current animation setup as an editable script, to provide a starting point for a more complex movie, although I am not sure whether this is feasible given the way the animation tool incorporates scenes. Cheers, Oliver.

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HLS color adjustments?
by Oliver Clarke 30 Dec '15

30 Dec '15

Hi all, Suggestion for ChimeraX: Allow tweaking (not replacing) color of selection, to adjust hue, lightness or saturation of selection (which could contain multiple colors). This would be handy when creating duotone images, where one selection is one color and another selection is a lighter (or darker) version of the same color; Or for creating Goodsell-style images where carbons are one color and heavier elements are a darker version of the same color. In general this would also be useful in cases where you want to edit a color that is close to but not quite the desired one - currently, launching the color editor defaults the selection to black, and it can sometimes be difficult to locate the exact color one had previously, so a way to edit colors in place would be useful for this purpose. Another suggestion to consider - would it be possible to allow exporting to a format (perhaps SVG?) where both vector and bitmap information can be edited separately? Specifically, I’m envisioning a three-layer file, with a bitmap + text and lineart, where lineart would include pseudobonds and potentially silhouettes. This would allow easy adjustment of the thickness, style etc of silhouettes and pseudo bonds post-Chimera, and editing/reformatting of text labels. I am not sure how practical this is, but if it is feasible to implement eventually it would certainly be useful. Cheers, Oliver.

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Can Chimera specifically superimpose renamed atoms of a ligand ?
by Yogendra Ramtirtha 29 Dec '15

29 Dec '15

I have to detect the presence of a ligand in many PDB files. So I have renamed all the Carbon atoms of the "HETATM" entries in these PDB files and I have also renamed the Carbon atoms of the file with known ligand. Can I use Chimera to specifically superimpose these renamed atoms ? If yes, can you tell me how can I do this ? In general, can Chimera superimpose ligands in 2 PDB files ? Thank you

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SaveScene Error
by Alvaro Rossan De Brandão Prieto Da Silva 28 Dec '15

28 Dec '15

I can't save UCSF Chimera sessions with saved scenes. What should I do in order to circumscribe this error? My ReplyLog Error in after-models callback: KeyError: (-1, 0) File "C:\Program Files\Chimera 1.10.2\share\Animate\SceneState.py", line 1252, in modelsLookup mList = [ m for m in SimpleSession.modelMap[ref] See reply log for Python traceback. -- Dr. Álvaro Prieto, D.Sci PqC-IV *Biologia Molecular de Toxinas Animais* Laboratório de Genética Tel +55 11 26279721 Mob. +55 11 982227144 email alvaro.prieto(a)butantan.gov.br

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Fwd: Fit to segments
by Elaine Meng 24 Dec '15

24 Dec '15

Begin forwarded message: > From: Greg Pintilie <gregdp(a)gmail.com> > Subject: Re: [Chimera-users] Fit to segments > Date: December 24, 2015 at 9:38:59 AM PST > > […] that’s a good question… some comments below. > >> Begin forwarded message: >> >> From: Luca Pellegrini <lp212(a)cam.ac.uk> >> Subject: [Chimera-users] Fit to segments >> Date: December 18, 2015 at 4:07:08 AM PST >> To: chimera-users(a)cgl.ucsf.edu >> >> Hi, >> I am using ‘Fit to Segments’ to fit a crystal structure into the appropriate segment of an 18A EM map of a larger protein complex. The structure is one subunit of the complex. >> >> After initial manual alignment of the structure, fitting to the selected segment works well and produces what I believe is the correct orientation of the structure in the map. However, the fitting stats (Corr/At. Incl.) for the wrong hits are almost as good (within a few percent points), even though for some of them the structure is clearly misplaced in the segment. >> > > This can happen quite often especially at lower resolutions, so I’m not too surprised. Try looking at the Z-score as well. For more details see the “Docking Scores” section at http://ncmi.bcm.edu/ncmi/software/segger/docs. It like won’t be too high either in this case though. In such cases it’s often useful to argue that this is the correct fit using other experimental evidence. >> Can anyone please comment/advise on this? It looks like fitting and relative statistics are calculated relative to the entire map rather than the selected segment. I am using Chimera 1.10.1, build 40415. >> > > Yes, it is true the scores are calculated using the whole map. One way to use only the selected segment is to extract the densities for that segment first and then do the fitting procedure using that segment only.

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2dlab problem
by jrb53 24 Dec '15

24 Dec '15

Hello all, I am making a movie in Chimera and labelling the various proteins as they appear. For some reason I am having trouble with 2dlab If I write 2dlab create kvlab4 text “Voltage-gated potassium channel” size 48 style bold color blue xpos .04 ypos .9 I get the error Keyword 'potassium' doesn't match any known keywords Its like it doesn’t get that the quotes are even there and it sees the label as multiple command line arguments. I get the same error with single quotes. If I use one word labels, it works fine. Any idea? Or am I missing something simple? John

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Chimera User's guide for command ine usage
by Yogendra Ramtirtha 22 Dec '15

22 Dec '15

I would be prefer me a PDF version of the user's guide to run commands through the command line Is the Chimera home page down ? Thank you, Yogendra

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Re: [Chimera-users] multi GPU rendering
by Tom Goddard 18 Dec '15

18 Dec '15

Hi Ben, One more bit of useful info regarding rendering large maps with solid style. The “perpendicular to view” projection mode is not the same as the mode “x, y, or z planes”. The perpendicular mode uses an OpenGL graphics 3d texture and slices the map perpendicular to the viewing direction and uses trilinear interpolation on the graphics card. The x,y,z planes mode uses OpenGL 2d textures perpendicular to one of the x, y, or z axes. While the perpendicular mode seems better the trouble is that 3d textures are generally not used in video games, so this is a very obscure graphics feature that may not be well optimized in the graphics driver, it may be slow (e.g. be done with no hardware acceleration), it may have limits to the size of the volume. On the other hand 2d textures are used in every video game and are optimized to the hilt — they are what is used to put color patterns on any surface. With some graphics cards and drivers the 3d textures will work as well as 2d textures, particularly the high-end cards, but you will only find this out by trial and error. The default “auto” projection mode never uses perpendicular to view because it is a bad choice on many low-end graphics cards. Tom > On Dec 18, 2015, at 1:38 AM, Benoît Zuber <benoit.zuber(a)ana.unibe.ch> wrote: > > Hi Tom > > Thanks for the additional info. I didn't know about the projection mode option. I was wondering before why under some conditions z planes were super thin when viewed perpendicular to z axis and why sometimes the gaps were filled. This was a bit problematic for some data sets where we actually mainly look in this orientation. Now using projection mode "perpendicular to view" instead of auto forces the planes to be rendered thick. great. > > watching nvidia-smi outputs confirms that only one GPU is used for rendering. Watching is also very useful to know how much the volume must be cropped before switching to the next step size without saturating the GPU memory. > Now I got it, if we want to watch bigger volumes, we just need to get a top geforce with 12 Gb instead of 3 Gb (Santa if you can hear me) > > Cheers > Ben > On 18.12.2015 01:02, Tom Goddard wrote: >> Hi Ben, >> >> From what I read both Nvidia SLI and AMD CrossFire for using multiple graphics cards both require hardware jumpers between the cards. >> >> The Chimera solid benchmark makes a cube shaped volume and times rendering it. A 1024 cubed volume takes 2 Gbytes on the graphics card because each grid point takes two bytes, one for the gray level and one for the transparency. An important thing to know about the solid rendering with really big volumes is that by default when you rotate it will make up to 3 full copies of the data — so up to 6 Gbytes in the benchmark example. It makes a copy when you rotate to viewing a different face of the cube. It then treats it as slices parallel to that face. So for a cube shaped map you will see a freeze when you rotate beyond 45 degrees. For non-cube maps I think the rule is it uses the face of the box that is showing the most area. For big volumes if you don’t care so much about looking at it along x and y directions then you might change projection mode the Features / Solid Rendering Options from “auto” to “z planes”. You probably want to know what auto does — it uses z planes if the volume is a thin slab, but "x, y, or z planes” if it is not a thin slab. Thin means x or y at least 4 times larger than z (I pressed Help on Volume Viewer dialog to learn that bit, even though I wrote the code). Once “projection mode” is “z plane” then you won’t get any of the extra copies. >> >> For really big volumes I could probably the transparency and use one byte per grid point. I could just scale transparency with intensity (which is what volume viewer does anyways). That makes the data of the graphics card half as big so it would be possible to show larger maps. I’ll try that in our next generation ChimeraX software — would be a nice improvement. >> >> Back to using multiple graphics cards — I don’t think the driver can possibly split the volume solid rendering data (2d OpenGL textures) — it will try to put all of it on both graphics cards — so you won’t get more memory by using more cards. >> >> Tom >> >> >>> On Dec 17, 2015, at 2:39 PM, < <mailto:benoit.zuber@ana.unibe.ch>benoit.zuber(a)ana.unibe.ch <mailto:benoit.zuber@ana.unibe.ch>> <benoit.zuber(a)ana.unibe.ch <mailto:benoit.zuber@ana.unibe.ch>> wrote: >>> >>> Hi Tom >>> >>> Thanks for your thorough reply. I am not in front of the workstation but I’ll use the gpu activity monitor to guess if chimera is using the three GPUs. I have some doubts that the OS / openGL driver is distributing rendering work on each gpu in our configuration. I think that for the SLI to work you need to wire both cards together, which is not the case in our workstation. But anyway, I’ll check activity. >>> >>> The rendering case I was referring to consists of solid rendering. I never try to render the full dataset at full resolution as we are talking about datasets of around 50 Gb. I use a very high step to select a sub region, then I gradually decrease step size and fine tune the contrast transfer function. When I am happy I render at step 2 or step 1, depending on the sub region size. Clearly there is time needed to read data from disk; when reading is done the program still computes stuff for a few seconds. Then I can rotate, zoom, …, the volume. If the sub region is not too large then it is super smooth. But if I select a too large sub volume, then I can rotate some degrees, then it freezes for a while, then it is smooth again, etc. So I guess it corresponds to your description of the problem. >>> >>> I took a look at the benchmark. That’s very useful! Obviously I am not going to get better performance with a quadro (at least one in the benchmark: All quadro except K4000 get worse scores for solid rendering than the GTX 780 Ti. K4000 actually got the same score as the 780 Ti. Only with a GTX Titan would I get a nearly 2x improvement, which makes sense since this card has 2x the memory of the 780 Ti (6Gb vs 3Gb). The GTX Titan X is not in the benchmark yet but it should be even better as it has 12 Gb Ram. Possibly the quadro k6000, which is not in the benchmark either, could have similar or better performance as this one (it also has 12 Gb RAM) but … it costs about 4 times more than a Titan X. Sad that only the quadro work for stereo under linux (but for that we bought a once state of the art quadro on eBay for 150$ and installed it on another PC :-) >>> >>> Cheers >>> Ben >>> >>> De : Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >>> Date : jeudi, 17 décembre 2015 19:22 >>> À : Benoit Zuber <benoit.zuber(a)ana.unibe.ch <mailto:benoit.zuber@ana.unibe.ch>> >>> Cc : chimera users list <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> >>> Objet : Re: [Chimera-users] multi GPU rendering >>> >>>> Hi Ben, >>>> >>>> I haven’t tried Chimera with 2 or more graphics cards working together. I don’t know if it is likely to improve rendering speed. I don’t think applications need any special support to use multiple cards — the system graphics driver distributes the work across 2 or more cards. With Nvidia cards this technology is called SLI and with AMD cards it is called CrossFire. From what I understand they do thing like have each of 2 cards render every other frame — since the graphics are pipelined the current frame and next frame could be rendered simultaneously possibly doubling the speed. I have my doubts that this will improve Chimera rendering speed for large density maps. I think slow rendering of maps in solid (grayscale) style typically happens in Chimera when the map data doesn’t fit on the graphics card, so every frame it has to transfer all the data to the card — the performance plummets once you get a map that big. If the data does fit on the graphics card, it usually renders at full frame rate (60 frames per second), although that isn’t true of all graphics cards. This all relates to the speed rotating the model. When you first load a big map it can take a long time because disk drive speed is slow — a solid state drive helps speed this up. If you explain exactly the case where you see slow rendering I can perhaps advise. >>>> >>>> In general I think the Geforce cards perform better (fewer bugs, faster speed) than the Quadro cards, and would only recommend Quadro if you use stereoscopic display with shutter glasses. Here are Chimera benchmarks for a range of graphics cards: >>>> >>>> <http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks>http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks <http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks> >>>> >>>> Tom >>>> >>>> >>>> >>>>> On Dec 17, 2015, at 5:28 AM, wrote: >>>>> >>>>> Hi >>>>> >>>>> Can chimera make use of more than one GPU for 3D rendering? We have 3 Geforce GTX 780 Ti (mainly used for number crunching) on a particular workstation and would be interested to make full use of them for rendering tomograms or serial block face imaging data. >>>>> >>>>> Another question: has anyone done benchmark comparison for 3D rendering in Chimera between a top of the line Geforce GTX card and a top Quadro card? Is there a strong improvement with the Quadro, which might justify the price gap? >>>>> >>>>> Thanks >>>>> Ben >>>>> -- >>>>> Prof. Benoît Zuber >>>>> Institute of Anatomy >>>>> University of Bern >>>>> Baltzerstrasse 2 >>>>> Postfach 922 >>>>> 3000 Bern 9 >>>>> Switzerland >>>>> <mailto:benoit.zuber@ana.unibe.ch>benoit.zuber(a)ana.unibe.ch <mailto:benoit.zuber@ana.unibe.ch> >>>>> +41 31 631 84 40 >>>>> <http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html>http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html <http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html>_______________________________________________ >>>>> Chimera-users mailing list >>>>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>>> >> >

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[MGMS-DS]: Molecular Modelling Workshop April 4-6, 2016 in Erlangen, Germany
by Harald Lanig 18 Dec '15

18 Dec '15

Dear list subscribers, I am very happy to announce that the 30th Molecular Modelling Workshop in Erlangen takes place on April, Monday 4th to Wednesday 6th, 2016. Starting on Monday after lunch should allow to avoid travelling on weekend and keeping the expenses at a minimum. This time, the scientific program of the meeting is conducted by Prof. Tim Clark, Technical Director of the Computer-Chemistry-Center in Erlangen, Germany. As usual, the workshop is organised by the German Section of the Molecular Graphics and Modelling Society. ####### Plenary Speakers ####### Over the last few decades computational chemistry, molecular modelling, and chemoinformatics became more and more an integral part of research in various areas of the chemical industry and at universities. A lot of new tools and new approaches together with a huge increase in computer power facilitate this development. We are very pleased to announce Prof. Brian Shoichet University of California, San Francisco, USA and Dr. Marcus A. Neumann Avant-Garde Materials Simulation Deutschland GmbH giving plenary presentations as leading experts their respective fields. ####### Poster and Lecture Awards ####### As in the past years, there will be two poster awards of EUR 100 each and three lecture awards for the best oral presentations: 1st Winner: Travel bursary to attend the Young Modeller's Forum in London, UK, plus a speaker slot option at YMF 2016 (travel expenses are reimbursed up to EUR 500) 2nd Winner: EUR 200 travel expenses reimbursement 3rd Winner: EUR 100 travel expenses reimbursement Only undergraduate and graduate research students qualify for the poster and lecture awards. ####### Registration ####### As every year, an interesting and successful workshop depends on your contributions! Therefore let me invite you to submit talks and/or poster titles via the registration form accessible on the workshop website http://mmws2016.mgms-ds.de/index.php?m=register This website will provide all necessary information about the meeting! The deadline for all submissions is February 26th, 2016. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Please note that the week before the 30th Molecular Modelling Workshop, on Wednesday March 30th to Friday April 1st 2016, a Symposium Commemorating the Life and Work of Paul von Ragué Schleyer will take place at the same venue. If you are interested in this meeting, please follow the link http://schleyersymposium.mgms-ds.de for further information. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ We are looking forward to meeting you in Erlangen soon! -Harald Lanig Chairman of the MGMS-DS e.V. http://www.mgms-ds.de -- ------------------------------------------------------------------------ PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg Zentralinstitut fuer Scientific Computing (ZISC) Geschaeftsfuehrer Martensstrasse 5a, 91058 Erlangen Fon +49 9131-85 20781 harald.lanig(a)fau.de Fax +49 9131-85 20785 http://www.zisc.uni-erlangen.de ------------------------------------------------------------------------

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Fit to segments
by Luca Pellegrini 18 Dec '15

18 Dec '15

Hi, I am using ‘Fit to Segments’ to fit a crystal structure into the appropriate segment of an 18A EM map of a larger protein complex. The structure is one subunit of the complex. After initial manual alignment of the structure, fitting to the selected segment works well and produces what I believe is the correct orientation of the structure in the map. However, the fitting stats (Corr/At. Incl.) for the wrong hits are almost as good (within a few percent points), even though for some of them the structure is clearly misplaced in the segment. Can anyone please comment/advise on this? It looks like fitting and relative statistics are calculated relative to the entire map rather than the selected segment. I am using Chimera 1.10.1, build 40415. Best wishes, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469

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multi GPU rendering
by benoit.zuber＠ana.unibe.ch 17 Dec '15

17 Dec '15

Hi Can chimera make use of more than one GPU for 3D rendering? We have 3 Geforce GTX 780 Ti (mainly used for number crunching) on a particular workstation and would be interested to make full use of them for rendering tomograms or serial block face imaging data. Another question: has anyone done benchmark comparison for 3D rendering in Chimera between a top of the line Geforce GTX card and a top Quadro card? Is there a strong improvement with the Quadro, which might justify the price gap? Thanks Ben -- Prof. Benoît Zuber Institute of Anatomy University of Bern Baltzerstrasse 2 Postfach 922 3000 Bern 9 Switzerland benoit.zuber(a)ana.unibe.ch +41 31 631 84 40 http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html

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dashed distance line
by A G Szabo 16 Dec '15

16 Dec '15

I recently used the distance feature to determine the distance between two alpha carbons in a protein. The view on the image showed a dashed line and the distance in Angstroms. I had managed to change the color of the line and numbers to a dark green, and thicker line. So I then snipped the image and put it in power point. Figure below: As you can see the line and numbers are there. Now look at the Jpeg file that is attached. The dashed line does not show up. No big deal but perhaps there is a setting that I missed when I saved the image. Thank you. Arthur G. Szabo Professor Emeritus Chemistry and Biochemistry Wilfrid Laurier University Waterloo Canada

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