- Chimera-users - RBVI Mailing Lists

ribbons of nucleic acids
by Ann Mullin 01 Sep '04

01 Sep '04

Hello, I am wondering how to adjust the ribbons of nucleic acids so that they follow the path of the phosphates or the sugars, anything but the averaged path they have now. I want to show the backbone as a ribbon with bases projecting out, but now some bases float about the backbone. Thanks for any help. Ann Ann Mullin Research Scientist Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) amullin(a)tulane.edu

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Chimera and building molecules
by Elaine Meng 31 Aug '04

31 Aug '04

Dear Ben, We definitely agree that molecule-building would be a very useful addition to Chimera. Toward this functionality, Chimera includes hydrogen addition; also, the "bond" command has been implemented (and will be available in the next release). Chimera also includes the "swapaa" and "swapna" commands which "mutate" one sidechain or base to another, although they are not very sophisticated. I am not certain what you are referring to in MIDAS, which only had very rudimentary building capabilities and no ability to add hydrogens. The "addgrp" command did allow definition of new amino acid sidechains, but was quite unwieldy and not usable for building in general. Similarly, "addaa" could append one of the standard amino acids to the end of a peptide but was not generalizable to other types of molecules. If you could clarify how you were applying these tools, we might be able to prioritize developments accordingly. Thank you, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu 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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building molecules
by Ben Schuler 31 Aug '04

31 Aug '04

Dear Chimera developers, It seems to me that the manual formation of bonds and building of any type of molecules (not only proteins and nucleic acids), which was a strength of MIDAS, is not supported by Chimera. I would very much welcome an implementation of these features to make Chimera a real replacement for MIDAS. Ben __________________________________________________ Prof. Ben Schuler, PhD Biochemisches Institut, Universität Zürich Winterthurerstr. 190, CH-8057 Zürich Tel: +41 44 635 5535, Fax: +41 44 635 5907 Web: www.biochem.unizh.ch/schuler Email: schuler(a)bioc.unizh.ch

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chimera --send with multiple Chimeras
by Thomas Goddard 22 Jul '04

22 Jul '04

Hi Sandeep, If you have more than one Chimera running on a machine then "chimera --send" sends the file to the most recent one that is accepting connections. Each time you change the Favorites/Preferences/Web Data option to accept connections, that Chimera becomes the most recent. The way this works is there is a list of running Chimera instances that are accepting connections in file (on unix /tmp/chim_webinfo-<username> where <username> is your login name). This file lists the Chimera process id and port number it is listening on. The last line indicates the most recent Chimera that is accepting connections. I wouldn't recommend relying on info in this file since the implementation may change in the future. Tom

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suggest OBJ export option
by Steven McQuinn 19 Jul '04

19 Jul '04

I'm really happy with Chimera, but vexed that every attempt to export a high resolution mesh via the VRML utility ends in a python failure. Have not tried exporting molecular models, only isosurfaces with 250,000+ polygons. What I use instead for export is VMD, which has an .stl export option, providing smaller file sizes than VRML. VMD is buggy on my XP system, requiring several attempts to export correctly. I use Chimera to get my isosurface settings right, then plug these values into VMD. SUGGESTION: If you provided an OBJ mesh export option, nearly every 3d application could utilize the product. The Wavefront OBJ format is the defacto universal exchange format, fairly small file sizes, retaining textures. Should be easy for you geniuses to program. Also, the stereo camera option never "takes." The walleye and crosseye cameras work OK but not the straight stereo pair, which I have to compose from the right and left images. Would like to send the development team some work samples. How do I do that? Please reply to my email address, as I don't read the list. Steven McQuinn _________________________________________________________________ MSN Toolbar provides one-click access to Hotmail from any Web page FREE download! http://toolbar.msn.click-url.com/go/onm00200413ave/direct/01/

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Re: [Chimera-users] PDB-file trajectories
by Eric Pettersen 16 Jul '04

16 Jul '04

I have PDB-file trajectory support working in Movie now. It's only in our internal development version, but I could make a custom snapshot release for anyone who wants to use it immediately. Otherwise, it will be in the next regular release, which will probably be in a month or two. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu > On Thursday, January 8, 2004, at 06:52 AM, amutha ramaswamy wrote: > >> It is possible to make movies with PDB structurers in chimera. this >> would really be helpfull in visualing the conformatinal changes. I >> know chimera has the option for movie with trajectory files. but i >> wish to kow the option with PDB files only. > > Hi Amutha, > I assume you're talking about the situation where you have one PDB > file for each "frame" of a trajectory (or a multi-MODEL PDB file of > the trajectory), rather than a starting and ending PDB file that you > want to "morph" between. Either way, unfortunately, we don't currently > support what you want. However, now that you have pointed out the > usefulness for plain-PDB support in Movie, I can probably add it in > the not-too-distant future. But given my other priorities (including > support for attribute coloring that you mentioned earlier!) the > "not-too-distant future" might still be a couple of months. I'll send > mail when there is at least a preliminary version available.

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How to send files to Chimera
by Thomas Goddard 02 Jul '04

02 Jul '04

Hi Sandeep, To open files in an already running Chimera from your program you can use the chimera --send option. For example, chimera --send myfile.mrc You need to tell Chimera to accept "web data" for this to work. You do this using Chimera menu entry Favorites/Preferences, category Web Data, set "Accept web data" to true. Press the Save button if you want this setting to apply to all future Chimera sessions (saved in ~/.chimera/preferences). If you don't set this preference, the --send command-line option will just start another copy of Chimera. This is described in the Chimera manual where command-line options are described: http://www.cgl.ucsf.edu/chimera/1.1951/docs/UsersGuide/options.html You can do fancier things, like send Python code (*.py files) or Chimera commands (*.cmd or *.com files) to Chimera to show your data in a certain way. You would still use the --send option to send the Python file. These remote control features were added to Chimera so that a web browser link can cause commands and files to be sent to Chimera and this is described in the Chimera manual: http://www.cgl.ucsf.edu/chimera/1.1951/docs/ContributedSoftware/webdata/chi… The hard part here is that volume data display options like threshold levels do not have simple Chimera commands to set them. Instead you have to dig around in the VolumeViewer Python code (in the share directory) in order to see what Python functions set these things. This is not easy to figure out. I can help you if you have specific questions about the Python functions for volume data display. Tom > Date: Fri, 2 Jul 2004 10:01:40 -0600 > From: Sandeep N Seshadri <sandeep(a)nmsu.edu> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Re: [chimera-dev] regd error when opening a .mrc file > > Hi Tom, > sorry for being very confusing . i am trying to open up files generated from my > program . as of now all i do is chimera test1.mrc > > and next time i generate another file i would open it as chimera test2.mrc > > so it would open a new chimera window and show the next .mrc file . what i would > like to do is when i open the second file test2.mrc i would like to see it open > in the already opened chimera window for test1.mrc. > > do you think i can do this ? Please let me know > > Sandeep Seshadri

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[Chimera-users] Re: [chimera-dev] regd error when opening a .mrc file
by Thomas Goddard 01 Jul '04

01 Jul '04

Hi Sandeep, This error indicates that the mrc file data values are all zero. The error occured when making the histogram that is shown in the Volume Viewer dialog, when it was trying to scale it to fit the width of the dialog. Of course, our code should not generate an error in this case. I will fix it for the next release. If you will be opening mrc files that may be all zero you can change chimera/share/VolumeViewer/histogram.py line 26 hscale = float(cheight) / max_height to if max_height == 0: hscale = 1 else: hscale = float(cheight) / max_height Then you will not get any error and the histogram will display correctly. Thanks for pointing out this problem. I am not familiar with pdb2mrc so I do not know why it is generating a volume consisting of all zeros. Tom > Date: Wed, 30 Jun 2004 21:33:12 -0600 > From: Sandeep N Seshadri <sandeep(a)nmsu.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: [chimera-dev] regd error when opening a .mrc file > > i am getting the following error when i try to open a .mrc file . i generated a > .pdb file and use a pdb2mrc to generate a .mrc file . i tried opening the .pdb > file it works fine but when i try to open the .mrc file it gives the error. > > if anyone has any idea on why this error occurs please let me know > > thanks > sandeep > > > Error while processing test-helix.mrc: > ZeroDivisionError: float division > (see reply log for Python traceback info) > Traceback (most recent call last): > File "/home/sandeep/chimera/share/__main__.py", line 56, in ? > value = chimeraInit.init(sys.argv) > File "/home/sandeep/chimera/share/chimeraInit.py", line 275, in init > prefixableType=1) > File "/home/sandeep/chimera/share/chimera/__init__.py", line 886, in open > models = func(filename, *args, **kw) > File "/home/sandeep/chimera/share/VolumeViewer/ChimeraExtension.py", line 30, > in open_cb > d.add_data_sets([g]) > File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 175, in > add_data_sets > self.redisplay_cb() > File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 459, in > redisplay_cb > self.show_using_dialog_settings(self.focus_region) > File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 380, in > show_using_dialog_settings > tp.update_histograms(data_region) > File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 1142, in > update_histograms > cw.update_histogram(data_region, read_matrix, self.dialog.message) > File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 1465, in > update_histogram > h.show_data(Numeric.log(s.counts + 1)) > File "/home/sandeep/chimera/share/VolumeViewer/histogram.py", line 26, in > show_data > hscale = float(cheight) / max_height > ZeroDivisionError: float division

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Is it possible to undo an action?
by Lesheng Kong 30 Jun '04

30 Jun '04

Hi, Is it possible to undo an action in Chimera? I notice that some actions in Chimera can be undid, such as "undo selection" or "undo move". Can every action be undid in Chimera? For example, I colored a selection zone in a different color. But I want to undo this action and recover each atom's previous color. Thank you very much! With best regards, Lesheng

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Re: Chimera questions.
by Thomas Goddard 30 Jun '04

30 Jun '04

Hi Matt, Support for DCD trajectories is in our current Chimera development version, but is not in the most recent release, Chimera 1.1951. It is described in the development version of the Chimera manual: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html If you like, I can give you the new Python code for DCD trajectories. I have not yet tested whether it will work in Chimera 1951, but I can test it. Otherwise, you can get it in our next release which is at least a few months away. To reposition a PDB model using Python code see the Programmer FAQ: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q4 Tom > Date: Wed, 30 Jun 2004 16:53:00 +0000 > From: Matthew Baker <mlbaker(a)gmail.com> > To: goddard(a)cgl.ucsf.edu > Subject: Chimera questions. > > Tom, > > Two quick questions: > 1. Is there a reader/display for DCD or netCDF trajectory files in > Chimera? I see that you can read AMBER trajectory files in the > Molecular Dynamics module. > > 2. How do you update a PDB file loaded into Chimera? I have a PDB file > and I want to apply a transformation to it and have the updated > coordinates applied in the viewer. > > Thanks, > > Matt

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