July 2013 - Chimera-users - RBVI Mailing Lists

Software Chemistry Linux
by giovanni.ortosecco＠libero.it 09 Jul '13

09 Jul '13

Dear List, kindly would like to know if there is an open-source software for advanced molecular modeling for use with Linux (Ubuntu, CentOS, Debian) along the lines of ChemDraw or ChemSketch. Thanks for Your attention. Best Regards, Giovanni Ortosecco Dr. Giovanni Ortosecco Institute of Biostructures and Bioimaging National Research Council Naples - Italy Posted by: Ubuntu 13.04 Raring Ringtail http://www.ubuntu.com/about/ Use free software!

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Software Chemistry for Linux
by giovanni.ortosecco＠libero.it 09 Jul '13

09 Jul '13

Dear List, kindly would like to know if there is an open-source software for advanced molecular modeling for use with Linux (Ubuntu, CentOS, Debian) along the lines of ChemDraw or ChemSketch. Thanks for your attention. Best Regards, Giovanni Ortosecco Institute of Biostructures and Bioimaging National Research Council Naples - Italy

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color by height
by p.j.depablo 08 Jul '13

08 Jul '13

Hi everybody I am interested in coloring an EM volume by height. In this option you can change the origin and the axis of coloring. Specifically, I rotate t the structure untill a desired orientation. Then, I would like to choose the axis of coloring to be the same as the view axis, but can not find the viewing axis coordinates. Is there possible to find this informaton anywhere? Thank you in adavance. Pedro

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camera horizontal field of view
by Dougherty, Matthew T 08 Jul '13

08 Jul '13

The camera settings allow for a horizontal field of view of 1-179 degrees. Wikipedia states that human horizontal field of view is ~180 degree. using 179 is not anything I normally recognize, looks like star trek enterprise going to warp. In cinematography books, lenses are sometimes referenced at around 20 degrees. For chimera I have found 10-30 gives nominal viewing on LCD. Setting it 1 is effectively orthographic. For DTI in a dome projection (as opposed to dome camera), I frequently will use 80-110, unless I am looking for a orthographic look, then lower values. For the mono & DTI cameras on a flat display, what are the values or the process to determine the values, for the most accurate mapping to normal human vision? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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ergonomics
by Dougherty, Matthew T 08 Jul '13

08 Jul '13

a few suggestions on placement 1) on viewing dialog, change the location of "view all" from the sideview window, relocating it to the bottom next to reset/restore/etc buttons. having additional orthogonal buttons (x,y,z) would be avoid having to do a lot of text commands. 2) on the volume viewer dialog, saving dialog preferences is accessed through its pulldown menu; having it act like other dialogs would be helpful (ie, at the bottom like viewing dialog). 3) the main 3d graphics window when dominant , causes the default pulldown menus to appear such as when chimera starts up. when accessing volume viewing, the overall chimera pulldown menus change. The only way to get the original/main pulldown to return is to put the mouse on the 3d graphics window and doing a left click twice. Since the volume viewing has its own pulldown menus, getting this overall switch of pulldown menus eliminated would help avoid a lot of unneeded mouse movements, particularly for the situation when two displays are used, one dedicated to 3D graphics, and the other having the viz controls. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Creating Average Structure from PSF/DCD --> Include metal ions in final structure
by Peter Murphy 08 Jul '13

08 Jul '13

Hi, I am trying to create an average structure in chimera 1.7 using the built in MDtools (loading a PSF/DCD file to get the trajectory). I am able to create an averaged structure for a select number of frames easily, but it doesn't appear that the metal ions are included when the averaging occurs. Is there someway to force the ions to be included? or alternatively, is there a script to create an average structure that includes selected atoms? Thanks, Peter -- Peter Murphy, Ph.D. Candidate Department of Biochemistry and Molecular Biology Dalhousie University Halifax, NS Canada

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icosehedron enhancement
by Dougherty, Matthew T 08 Jul '13

08 Jul '13

for the mesh adjustment, it would be good to be able to enter the radius of the mesh tubes. currently I have to select the item, go to the inspector to set the radius. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Re: [Chimera-users] [chimera-dev] Trouble with Saving New Atom Attributes
by Elaine Meng 05 Jul '13

05 Jul '13

Hi Juliette, PDB format does not include atom-type information, as you have seen. The only sure way to save your atom type changes is to save the Chimera session. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sessions.html> However: Chimera applies chemical perception to try to figure out the atom types when a structure is read in from a file. The Mol2 format does have some atom-type information, but the SYBYL Mol2 types are not related 1-to-1 to the types in Chimera. You could try saving in Mol2 format and reading it back in to see if the information you want is retained. Further, if you have added all hydrogens before writing the file (PDB or Mol2) the chemical perception is more well-determined and it is possible that it will assign the types you intended. If those do not work, however, the session is the way to go. If you just wanted a list of the assignments rather than the assignments per se, you could use "File... Save Attributes" from the menu of Render by Attribute (itself in menu under Tools... Depiction). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html…> This seems more like a "user" question than a developer (programmer) one; it's not necessary to email both lists. 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 Jul 5, 2013, at 2:34 PM, Juliette Cao wrote: > Hi All, > I was successfully able to change a few atom types using the setattr command. > I checked to see that the atoms I changed were correct (by selecting the atoms and then then clicking the IDATM type option.) > I saved the .pdb file > When I opened up the saved .pdb file and checked the atom types, they had reverted back to their original type. > Is there a specific way to save files after using setattr command? > Regards, > Juliette Cao > University of Houston

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Trouble with Saving New Atom Attributes
by Juliette Cao 05 Jul '13

05 Jul '13

Hi All, I was successfully able to change a few atom types using the setattr command. I checked to see that the atoms I changed were correct (by selecting the atoms and then then clicking the IDATM type option.) I saved the .pdb file When I opened up the saved .pdb file and checked the atom types, they had reverted back to their original type. Is there a specific way to save files after using setattr command? Regards, Juliette Cao University of Houston

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force field for G-quadruplexes
by Gilmar Salgado 05 Jul '13

05 Jul '13

Hello, recently I was looking into the capabilities of Chimera minimization tools to minimize the structure of a DNA G-quadruplex molecule. The problem is that all G-quadruplexes have an ion (K+ or Na+) in-between and stabilizing the tetrads. I wonder if the force field available in chimera are "decent" to water-minimize this kind of structures? ...and which one is more adapted, after all those are non-conventional DNA structures. Thanks in advance for your input Gilmar Salgado Université Segalen Laboratoire ARNA (INSERM U869) Institut Européen de Chimie et Biologie 2 rue Robert Escarpit 33 076 Pessac Cedex FRANCE +33(0) 540 0022 24 +33(0) 557 571 015 (fax)

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