- Chimera-users - RBVI Mailing Lists

selecting one water molecule
by hjoseph＠brandeis.edu 31 Mar '08

31 Mar '08

Hi Everyone, I want to select one water molecule but every time I try to do that, all the molecules get selected. Could some one tell me the command line instruction for selecting water 241. Thanks, Helen Josephine

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Re: [Chimera-users] [chimera-dev] Wrapping Chimera in a Java program
by Tom Goddard 31 Mar '08

31 Mar '08

Hi Fabrice, I do not think Chimera could run using Jython because Chimera uses dozens of compiled C/Python modules. You can communicate with Chimera via a pipe. One approach is to start Chimera with a popen() system call and send commands to Chimera's stdin using the ReadStdin capability: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/readstdin/readstdi… It is also possible to talk to an already running instance of Chimera using the "chimera --send <file>" shell command. This is used to have a web browser helper application directly send files to Chimera. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.ht… The implementation uses a socket that Chimera is listening on but it is somewhat tricky to find the right port number. It is saved on the local machine in a file as a security measure to prevent network connections. The details of that implementation are in your Chimera distribution chimera/share/send_to_chimera.py Scooter Morris in our lab has written code to communicate with Chimera from a Java application called Cytoscape. He might be able to provide more advice. Tom Fabrice Jossinet wrote: > Dear developers, > > I would like to launch Chimera from my Java program. I would like to > send messages to Chimera to highlight in its own display selections I > do in my Java program's display. I already did that with PyMOL using a > pipe communication. > > So, several questions: > - is it possible to start Chimera from a classical python distribution > (not the embedded python of Chimera)? One of my ideas is to start > Chimera from Jython, a Java implementation of Python > - is it possible to communicate with Chimera using a pipe ? > - and the most general question: is it possible to communicate with > Chimera from the outside? > > Thank you for your answers > > Fabrice > >

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origin of volume data
by Greg Pintilie 27 Mar '08

27 Mar '08

A question about data origin in densiy maps... I open a map using the python script (in IDLE): >>> import VolumeData >>> gd = VolumeData.mrc.open ( "MRC map file" )[0] looking at the origin of this map: >>> gd.origin (-135.679992676, -135.679992676, -135.679992676) It is different than the origin reported if I open the same map file in Volume Viewer; pasted from the Volume Viewer dialog: -136.75 -136.75 -136.75 Why the difference? As to why I care, it's because if I open the map as in the python script above and then subsequently use it to compute average density values for certain structures, they are different than the average density values reported in the 'Fit Model in Map' dialog. It would give me more peace of mind if they matched... Now to start speculating on why the difference, I've seen that, internally, MRC maps define the origin in terms of a grid value, for example -64,-64,-64 in a 128x128x128 map. So the first value for the origin, as in the script method above, is calculated as if the origin is at the _center_ of the first grid point: origin[0] = -64 * step + step/2 (where step is 2.13669279804), while the second value (showing up in Volume Viewer) is simply calculated right on the grid point: origin[0] = -64 * step What's the right way to think about this? In the worst case, it's really a pretty small offset so not a big deal. Greg

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Collaboratory tool removed ?
by Aurelien Grosdidier 27 Mar '08

27 Mar '08

Hello, I recently noticed that the current production version of Chimera (v1 build 2470) does not have the "Collaboratory tool" anymore. I wanted to give it a try and I am quite disappointed. From a previous changelog (http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2417.html) I read that "Collaboratory removed (use version 1.2309 for this tool)". My question is: can we expect this feature to be back one day, or should I look for an alternative ? Thanks, Aurélien.

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Chimera
by Robert Hilton 27 Mar '08

27 Mar '08

When using Chimera, I want to be able to use XY translation. In the help menu, I found that if I hold down the middle mouse button, I can control XY translation. However, I have a mac, and so have no middle mouse button. How can I control XY translation using a mac? Thanks, Rob Hilton hiltonlds(a)gmail.com

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copy cmd in nogui script
by Nick Horelik 26 Mar '08

26 Mar '08

Hi, This (http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-March/001396.html) answered most of my questions, but I have one more followup question. Is there any way for me to accept the POV-Ray Liscence in nogui mode? I don't have the capability to use the gui at this time. Thanks, Nick -- Tufts University 508.527.9625

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Re: [Chimera-users] using chimera on 3D EM map
by Tom Goddard 26 Mar '08

26 Mar '08

Hi Weimin, Thanks for explaining these problems. We intend to solve all of them (though it will take some time) and perhaps some already have solutions. 1) Volume eraser ball can't be made small enough. The ball can have any floating point radius value > 0. So you should be able to make it as small as you like. I've tried and had no trouble making it tiny. A radius value of 0 is not valid and the ball radius will be left at whatever it was prior to attempting to set it to zero. 2) There is no "undo" in volume eraser. Yes. This is a serious problem we plan on fixing. 3) No way to add density (as opposed to subtracting with volume eraser). I guess you mean you would like to use a 3d ball to mark the density you wish to keep instead of the density you want to erase. It might be easy to make a tool like this where you can paint the volume using a ball (like volume eraser). You could paint using one or more colors and then separate the different colored pieces into separate maps. The underlying code to do this is already in Chimera (color zone tool, and split map by color zone). It requires a way to place a marker that matches the painting ball -- basically just a "Color" button on the volume eraser dialog. Might be able to add this soon. I recently added plane by plane loop drawing for hand tracing surfaces that can be used with the new "mask" command to segment out the enclosed region (in current daily builds). But from what you say that is less useful in your high resolution case. 4) Statistical comparison of two maps. Chimera can report the correlation coefficient between two maps and it can optimize the position of one map within another. This tools was called "Fit Map in Map" in the current Chimera production release (version 1.2470) and is called "Fit in Map" (which also handles fitting models) in current Chimera daily builds. There is also a new option in "Fit in Map" that will update the correlation coefficient in real time as you move one map within the second map. Also there is a new "Fit in Map" option that will compute a simulated map from a PDB at a given resolution (like EMAN pdb2mrc) and will fit the simulated map and report its correlation in the experimental map. Are there other measures besides correlation coefficient that you want? From your example, maybe you want rotations in degrees between two different fits? Tom Weimin Wu wrote: > Dear Prof.: > > I am one postdoctoral in Prof. Wenjiang's group. We have employed > Chimera in our research and really appreciate it. However when our 3D > map goes beyond 5A (see Feb. 28, 2008 Nature paper) which enabled us > to see the boundaries among alpha helices and beta sheets, we meet > some problems in the segmentation which we do think you could help us > out. > > One problem is that the viewer eraser ball is too big even the radius > is set to zero. It prevented us from completely clearing the > neighboring signals. There is no undo option when using the eraser > function. Therefore we have to keep saving the intermediate maps. > > Another problem is that there is no 3D volume editor which can let us > add density in 3D EM map. Sometimes this is the most important for the > segmentation, because it is hard to tell which density should be > included if we go slice by slice, but it is much easier to tell > directly in 3D map with the stereo function. > > Another problem is that there is no statistical tool for analyzing the > slight difference between two 3D EM maps. Therefore it makes hard to > determine the fit quality of one map into the other, for example, when > fitting one subunit into the other, there is some conformation > difference between them, but we need quantitative values to evaluate > the difference and make a story. Something like in two PDBs, we can > fit one domain and check the difference of the other domain. > > If I don't explain the problems clearly, please let me know. Many thanks, > > weimin wu

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Re: [Chimera-users] [chimera-dev] fit map in map -- also fit a/pix at the same time ?
by Tom Goddard 26 Mar '08

26 Mar '08

Hi Stefan, Chimera cannot optimize the volume grid spacing when fitting a molecule model. I agree that would be useful. I'll add it to our requested features list. http://www.cgl.ucsf.edu/chimera/plans.html You can do this scale optimization by hand using the volume dialog Coordinates panel to change the voxel size (press the return key after you change the number), then press the Fit button on the Fit in Map dialog. With small scale changes the fit should converge each time and you can quickly try several different scales. The newer Chimera releases (Jan 31, 2008, 1.2492) available on the daily builds page can make a simulated map for your molecule at the desired resolution and report correlation coefficients which is probably better than average map values for this scale optimization. Tom

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Chimera_v1.2470
by Brittney L. Gurda 26 Mar '08

26 Mar '08

Hello, I have a general question about opening files in the new version. Upon opening my EM maps (in .pif format), my structure is in a solid box which makes viewing difficult. Has anyone encountered this problem before? The older version that I had (not sure which one) never had this issue. Currently I am converting the .pif to a .map file and that seems to work just fine, but I am still curious about where the box is coming from and how I can get rid of it...artificial unit cell perhaps? Thanks, Brittney L. Gurda

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pdb to density map function
by Jeff Triffo 25 Mar '08

25 Mar '08

hi, I think I recall seeing information about a pdb -> density map function (like an MRC density map). is this currently implemented/contained within Chimera? I can use an outside program to do this, but if it is already in Chimera I would prefer to do that. thanks, -Jeff

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