- Chimera-users - RBVI Mailing Lists

saving partial coordinates
by Elaine Meng 21 Jul '03

21 Jul '03

Hi Mark, In the current release of Chimera: if you are on a non-Windows system, you can use the command "pdbrun" to save just the atoms that are displayed. You can see the manual page for this command by typing "help pdbrun" in the Chimera Command Line (by default, Favorites... Command Line). example: pdbrun nouser cat > myzone.pdb Pdbrun literally sends the information for only the displayed atoms in their displayed positions to another command, in this case "cat" to send the information to the file myzone.pdb. If you want the coordinates to be the same as in the original file, first use the command "reset." All the atoms should be in view (i.e. if you are zoomed in and the atoms around the periphery cannot be seen in the Chimera window, they won't be in your output file either). The command "save" (or File... Save Session As... ) doesn't save coordinates, only how they are positioned/colored/displayed, etc. In fact, restarting a saved session will use the original input file(s) for coordinates. The command "write" (same as the function "write PDB" in the Model Panel) saves coordinates into a file. However, these will save the entire coordinates whether displayed or not. If you are on Windows, I am not aware of a solution in the current release. In our working version and thus the next release (late summer or early fall, I believe) there is a delete action. This would allow you to select the atoms/bonds outside a zone, for example, and then actually delete them. (Actions... Atoms/Bonds... delete). Subsequently, a file created with "write" would only contain the atoms/bonds that had not been deleted. I hope this helps, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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I Need Help!
by Mark Cunningham 20 Jul '03

20 Jul '03

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Re: ribbons, chimera, and collagen
by Eric Pettersen 18 Jul '03

18 Jul '03

Hi Randy, You can force Chimera to treat collagen as helical without too much difficulty. First, select a chain or chains (either Select...Chain, or pick an atom or atoms in the graphics window and use up-arrow several times until the chain(s) are selected). Then use the selection inspector (Tools...Inspectors...Selection Inspector, or click the button showing the selection in the lower-right part of the Chimera window). Change what is being inspected to 'Residue' and then set 'in helix' to true. The problem is that the ribbons don't look very good (they're too "twisty") because it's not an alpha helix. Maybe Conrad can suggest something. I don't have any suggestions myself (I tried making them "strands" and that was pretty twisty also). --Eric > I'm trying to make a ribbon plot of collagen using chimera, but it > doesn't > recognize collagen's secondary structure. > Can I just tell it to make a ribbon with the backbone atoms (or peptide > bonds), and not worry about what kind of secondary structure it really > is? > If so, how? > Have a nice day, > Randy

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Delphi and Chimera
by Marco Sette 09 Jul '03

09 Jul '03

Dear all, I have seen Chimera is able to create potential map using Delphi but, in your site, it is stated that this is valid only for unix systems. I have Delphi installed into windows and linux systems: it will be possible in the (near) future to run DelphiController onto these systems ? Thanks a lot for your attention, Best Regards, Marco -- Dr.Marco Sette, Ph.D. Deaprtment of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Re: [Chimera-users] Chimera - Dock grid
by Thomas Goddard 20 Jun '03

20 Jun '03

Hi Joel, The voldata.tar.gz file had a bug. I forgot to do byte swapping on the grid values. So it works on SGI and Mac or on Linux and Windows, but not both. I fixed this problem. The new code is at: http://www.cgl.ucsf.edu/home/goddard/voldata.tar.gz Tom

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Chimera - Dock grid
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi there, I'm quite impressed with chimera and its dock functionality. My query is about dock grid. I can't find any documentation about this ie what the values and their ranges represent. Also I can't seem to turn them off once they are on. And not to be too ungrateful different colours would be handy as well...how can I change those? While I'm at it is there a delete molecule button? Thanks for your help in advance joel -- ________________________________________ Joel Tyndall, PhD Research Officer http://www.imb.uq.edu.au Institute for Molecular Bioscience incorporating Centre for Drug Design and Development Centre for Cellular and Molecular Biology The University of Queensland Brisbane Australia 4072 Tel: +61 7 3346 2988 Fax: +61 7 3346 2101 email: J.Tyndall(a)imb.uq.edu.au

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denbsity maps
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi, I am using chimera to make some pictures of a model docked into a low resolution electron density map. Is there a way to make the mesh lines representing the electron density thicker? Also is it possible to have a cubic grid rather than triangles? Thankyou very much for your help. Suzanne Brewerton University of Cambridge --

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writing Mol2 format
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi David, Writing out Mol2 format can in principle be done, but there are a few caveats. If the original format is Mol2, the original information could be retained and written back out. I don't know how simple/hard this would be to implement (feel free to chime in, other members of the team). When the original format is not Mol2, there is less information in the molecule data than is needed to write the file. Chimera uses a fairly rich set of atom types, but there is still not a one-to-one relationship with all Mol2 types. One would need to create a mapping between the types. Also, I believe Chimera currently knows connectivity but not bond orders, and does not retain any point charge information. The online Chimera Programmer's Guide actually includes an example of code required to write out a mol2 file. I had forgotten about this when visiting your office earlier. It discusses a mapping between atom types (if you use this, you should examine this mapping and make sure it works the way you think it should). The example code writes out all bonds as single. Check it out: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html click the "Examples" link and then "Chimera's Object Model" This example is "writeMol2.py" If you have a molecule open in Chimera, you can view the type assignments using Actions... Label... IDATM type (version 1.1700). A listing/explanation of Chimera types can be seen at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html Best, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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denbsity maps
by chimera-users＠cgl.ucsf.edu 19 Jun '03

19 Jun '03

Hi, I am using chimera to make some pictures of a model docked into a low resolution electron density map. Is there a way to make the mesh lines representing the electron density thicker? Also is it possible to have a cubic grid rather than triangles? Thankyou very much for your help. Suzanne Brewerton University of Cambridge --

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Writing to mol2
by chimera-users＠cgl.ucsf.edu 18 Jun '03

18 Jun '03

Hi, I'm one of your "neighbors" working in the Shoichet lab for the summer. I think it'd be neat if you could output in mol2 format rather than just pdb format, especially if the input is in mol2. Is this in the works? Has it already been done? Is it easy to do? David Minh

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