- Chimera-users - RBVI Mailing Lists

Ribbon Structures From Gaussian Output
by Michael Lodewyk 30 Sep '11

30 Sep '11

Hello, I'm interested in using Chimera to visualize oligopeptide structures computed with Gaussian09 as ribbon structures... that is I'd like to be able to render an alpha helix backbone as a ribbon and then select specific residues/ligands to be rendered as tube or ball & stick models. While I can save or convert the Gaussian output file to a variety of formats, they do not inherently contain the information necessary for such a rendering of the structure, as one would find in a true .pdb file. So my question is... Is Chimera the correct place to start for creating such representations? If so, can you please point me to any documentation that would assist me in doing so? Thank you, Dr. Michael Lodewyk Tantillo Group, UC Davis

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Using addaa at the N-terminus?
by Tosan Omabegho 30 Sep '11

30 Sep '11

Hi, I read in the manual that addaa can be used at the N-terminus. I'm not having any luck doing this. I've been assigning the amino acid to add at the N-term with a lower number, like: addaa cys,5,alpha :6.a The error message says 'Can only add to last residue'. Is there something I may be doing wrong? Thanks, Tosan

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Chimera for Mac 10.7
by Michael Chou 27 Sep '11

27 Sep '11

Hi Chimera Team, Which version of Chimera do you recommend I download in order to use for Mac 10.7? I downloaded chimera-1.5.3-mac.dmg<http://plato.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=mac/ch…>. Although it opens, I cannot use any of the features such as any of the actions or presets. Thank you, Michael

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Protein
by sanabaseer＠sbcglobal.net 27 Sep '11

27 Sep '11

Hello, Please help me with managing the chimera program. I have created an image of a protein, but would like to view the active site complex. How can I highlight that in my image? Thank you, Sana Sent from my U.S. Cellular BlackBerry® smartphone

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ribbon display of circular DNA structures
by jens j birktoft 26 Sep '11

26 Sep '11

Hi Everybody How can I display a circular DNA structure with three helices without a break at the places where the ends meet according to the numbering system. In the real structure there is no break in the covalent structure Best Jens *+++++++++++++++++++++++++++++++++++++++++++++++++++++++* * * *Jens J. Birktoft New York University, Department of Chemistry. **e-mail: jb160(a)nyu.edu <jens.knold(a)gmail.com> **Phone: 212-749-5057 *

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matrices
by Dougherty, Matthew T 26 Sep '11

26 Sep '11

I was doing something with crystallographic point group matrices. Does Chimera allow for improper rotations and inversions? Or does it rectify them as proper rotations? I would like to go from Model 0.0 1 0 0 0 0 1 0 0 0 0 1 0 TO Model 0.0 -1 0 0 0 0 -1 0 0 0 0 -1 0 Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ________________________________________

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importing chimera module question
by Lockwood, Svetlana 22 Sep '11

22 Sep '11

Hi to everybody! I am new to Chimera. I've just installed Chimera and trying to run a python script. I get the import error: no module named chimera. My OS is Win7 and Chimera 1.5.3. I checked my path under enviromental variables and added Chimera folder in there. Still nothing changed. There must be an easy fix to this. Please let me know what could be done. Thanks!

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Re: [Chimera-users] Has the option provided by surfvalues.py script been incorporated into Chimera?
by Tom Goddard 22 Sep '11

22 Sep '11

Hi Boaz, Ok, I added today a "Report value at mouse position" option to the Surface Color dialog. If you are showing electrostatic potential on a surface with that dialog the numbers are reported in the status line as you move the mouse over the surface. It works for all the modes of coloring surfaces (radius, cylinder radius, height, volume data value, volume gradient, ESP value). It will be in tonight's Chimera builds. Tom Boaz Shaanan wrote: > Hi Tom, > > A while ago you wrote the ver useful surfvalues.py script to show > actual potential values while wandering with the mouse over the > surface. I wonder whether it has been incorporated into the Chimera > version by now. I couldn't figure out whether it has. > > Thanks, > > Boaz > /Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > /

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Re: [Chimera-users] SASA calculation in Chimera
by Elaine Meng 21 Sep '11

21 Sep '11

Hi Horacio, Chimera is using MSMS to generate the surface and give surface area values per atom. There is more information and an MSMS reference here: <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfa…> 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 Sep 21, 2011, at 9:01 AM, Horacio Pérez-Sánchez wrote: > We have developed a fast and accurate new GPU based SASA calculation method. It can bring information about SASA per atom and also grid per atom necessary to graphically render the molecular surface. We are new to Chimera but we would like to know: > > a) where could we find information about the SASA method Chimera uses so we can test with our own method > b) same question for the method Chimera uses to graphically render the molecular surface > > Thanks in advance, > Horacio > >

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Re: [Chimera-users] Atom selection by number ?
by Marek Maly 21 Sep '11

21 Sep '11

Thanks a lot Victor it works ! Best wishes, Marek Dne Wed, 21 Sep 2011 14:47:36 +0200 Victor Muñoz <chewaka.87(a)gmail.com> napsal/-a: > you should try using: > > select @/serialNumber=31 > > Best wishes, > > Victor Muñoz > > > > __________ Informace od ESET NOD32 Antivirus, verze databaze 6481 > (20110921) __________ > > Tuto zpravu proveril ESET NOD32 Antivirus. > > http://www.eset.cz > -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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