- 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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Has the option provided by surfvalues.py script been incorporated into Chimera?
by Boaz Shaanan 21 Sep '11

21 Sep '11

Hi Tom, Here is the plain text version (I keep forgetting that the list has a problem with html formatted messages, but is it always the case? ): A while ago you wrote the very 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 E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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color surface by electrostatic potential from apbs dx file
by matheus froeyen 21 Sep '11

21 Sep '11

Hi I try to show the electrostatic potential calculated by apbs and written to a pot.dx file. This works fine when using the mouse / menus. However I try to do this also using the command line interface because I need to repeat it many times. $ chimera chimera.cmd $ cat chimera.cmd: open prod30.pdb ~ribbon : ~fillring : surface : open pot.dx ~scolor #0 scolor #0 volume #1 cmap rainbow scolor #0 volume #1 cmap -15,red:-5,yellow:0,green:5,cyan:15,blue I don't get an error but the surface is colored by volume data, not by electrostatic potential. Also the popup window "Surface Color" is not updated for the selected colors. In the surface color popup I need to select color surface "MSMS surface" again, change "volume data value" to "electrostatic potential" and then push the button "Color". Then I get what I want, but unfortunately using the mouse again. This should be done by the script too, I guess? I m using the last stable chimera 64 version for unix on redhat. best regards mathy

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Smoothing a trajectory
by Daniel Gurnon 20 Sep '11

20 Sep '11

Hi everyone, For the purpose of making educational content, I'm interested in smoothing out the often jumpy transitions from frame to frame in a MD trajectory. My approach was to write two python scripts (with critical help from Eric of course); one goes through the trajectory and saves pdbs of each desired frame, while the second opens these pdbs and creates a morph, interpolating from one pdb to the next. It seemed like I was almost there, and it looked great when I tried 50 frames.....but Chimera crashed when I tried morphing 200 frames, adding 3 frames of interpolation between each. Is there a better way to add transitions in between (ideally thousands of) frames of an MD trajectory? Thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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segmentation tool
by Jean-Francois Menetret 20 Sep '11

20 Sep '11

Hi, I am using the segmentation tool on a ~15A cryoEM map. I have noticed that the surface of the mrc maps saved from selected areas look pixelated. Any suggestions how to improve the quality of the segmented maps ? Best wishes Jean-François Ménétret

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mailling list hiccup
by Greg Couch 19 Sep '11

19 Sep '11

We had an internal problem with all of our email over the weekend. So if you sent email to chimera-users and it bounced, please resend it. It should work now. -- Greg

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Double coordinates for same residue
by Francesco Pietra 15 Sep '11

15 Sep '11

Hello: Surely a naive question: While beginning to treat a multichain, engineered protein - downloaded from PDB web (1.94 A resolution) - with Chimera, I noticed that many amino acids have such feature as GLU 252 below. Same for many SER, ILE, HIS (two imidazole rings for the same residue number) ATOM 2022 N GLU A 252 15.171 -45.532 45.115 1.00 26.12 N ATOM 2023 CA AGLU A 252 14.023 -44.631 45.214 0.50 26.30 C ATOM 2024 CA BGLU A 252 14.048 -44.592 45.252 0.50 26.30 C ATOM 2025 C GLU A 252 13.983 -43.654 44.050 1.00 25.90 C ATOM 2026 O GLU A 252 12.894 -43.403 43.470 1.00 25.36 O ATOM 2027 CB AGLU A 252 13.974 -43.909 46.559 0.50 26.93 C ATOM 2028 CB BGLU A 252 14.170 -43.759 46.533 0.50 26.77 C ATOM 2029 CG AGLU A 252 13.283 -44.741 47.629 0.50 29.02 C ATOM 2030 CG BGLU A 252 12.874 -43.673 47.313 0.50 29.14 C ATOM 2031 CD AGLU A 252 14.088 -45.948 48.051 0.50 33.10 C ATOM 2032 CD BGLU A 252 12.806 -44.716 48.426 0.50 31.91 C ATOM 2033 OE1AGLU A 252 13.481 -47.014 48.330 0.50 34.82 O ATOM 2034 OE1BGLU A 252 13.394 -44.454 49.504 0.50 31.18 O ATOM 2035 OE2AGLU A 252 15.333 -45.828 48.101 0.50 35.49 O ATOM 2036 OE2BGLU A 252 12.162 -45.782 48.231 0.50 33.14 O ATOM 2037 N GLU A 253 15.141 -43.133 43.683 1.00 24.58 N ATOM 2038 CA GLU A 253 15.225 -42.212 42.559 1.00 25.11 C ATOM 2039 C GLU A 253 14.838 -42.941 41.242 1.00 23.83 C ATOM 2040 O GLU A 253 14.142 -42.383 40.374 1.00 23.54 O ATOM 2041 CB GLU A 253 16.637 -41.603 42.476 1.00 26.18 C ATOM 2042 CG GLU A 253 17.033 -40.722 43.697 1.00 30.81 C ATOM 2043 CD GLU A 253 17.635 -41.491 44.915 1.00 36.16 C ATOM 2044 OE1 GLU A 253 17.540 -42.742 45.032 1.00 35.80 O ATOM 2045 OE2 GLU A 253 18.198 -40.809 45.801 1.00 40.87 O About the protein: SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS MENDOCINA; SOURCE 3 ORGANISM_TAXID: 300; SOURCE 4 GENE: TMOA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: P58KABE; The said residue are not among those not located in the experiment. I am interested in channels, pores and so on in the protein, so that the above issue is of most concern for me. Thanks for aid francesco pietra

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Chimera movie recorder
by Camilla 14 Sep '11

14 Sep '11

Hi, My name is Camilla and I'm an undergrad student at UNC-CH. I've been using Chimera to create models of fibrinogen polymerization. I discovered that I could make movies of my models to be able to see them from all views. However, my videos are very choppy and since I rotate the model by mouse, the movies are very poorly made. Is there a specific command I could use where I can get the model to rotate 360 degrees by itself to make this movie more smooth and to be able to still see the model all the way around one axis? Thank you, Camilla

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question regarding using molmap with symmetry option
by Janet Iwasa 14 Sep '11

14 Sep '11

Hello! I've been working with some virus models, and was hoping to use molmap with the symmetry option. The main reason I'm not using multiscale models is so that I can create a single surface for several of the different chains in the capsid. I've been having a little trouble getting this to work, and I'm not sure if I'm doing it correctly: molmap :.A-C 10 symmetry biomt Is this correct? Doing this gives me the error: "Keyword 'symmetry' doesn't match any known keywords" Advice? thanks, Janet

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uninstalling production release after installation of daily build (Windows)
by Boaz Shaanan 12 Sep '11

12 Sep '11

Hi, I noticed that after installing a daily build, the (very useful) uninstall feature disappeared from the pull-down of the production release (currently 1.5.3). I wonder how it can be removed once a new production release is available. I noticed that this cannot be done through the add-remove feature in the control panel either. BTW, I keep the daily build and production release in separate directories, to be on the safe side. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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Re: [Chimera-users] structure editing query
by Bala subramanian 12 Sep '11

12 Sep '11

Thank you Elaine and Mary, Now i am able to do the modification now. It is wonderful to have an option to adjust the newly added bonds. Bala On Mon, Sep 12, 2011 at 7:11 AM, MARY VARUGHESE <maryvjes1985(a)yahoo.co.in>wrote: > hi, > consider creating bonds only after checking their valencies and bondtype > like single or double bond. > Hope this will help you. > > Mary > > --- On *Sat, 10/9/11, Bala subramanian <bala.biophysics(a)gmail.com>* wrote: > > > From: Bala subramanian <bala.biophysics(a)gmail.com> > Subject: [Chimera-users] structure editing query > To: "chimera-users BB" <chimera-users(a)cgl.ucsf.edu> > Date: Saturday, 10 September, 2011, 4:17 PM > > > Friends, > I am trying to modify the sugar of a nucleotide. I am interested in making > a linkage of two carbons in the sugar as in the attached pdb. I tried to use > the Build structure -> modify structure option but it does not work in the > sense that when i select carbon atom (c2') and tried to connect it to an > oxygen, chimera says that it is already bonded and hence some bonds to > create a new one. Is there any way to make such linkages as in the pdb ? > > Thanks, > Bala > > -----Inline Attachment Follows----- > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu<http://mc/compose?to=Chimera-users@cgl.ucsf.edu> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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НА: Re: problem in coloring a selected region
by Sp 12 Sep '11

12 Sep '11

Отправлено с моего коммуникатора HTC

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chimera rotation mode
by Jean-Francois Menetret 12 Sep '11

12 Sep '11

Hello, for some reason, the default rotation option in the viewing window always comes back to "independent" when I restore a session; how could I change the default to be "center of models" for example ? Jean-Francois

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atom order in RMSD calculations
by Elaine Meng 10 Sep '11

10 Sep '11

Hi Kristen, I'm CCing chimera-users since this is more of a user question than developer/programmer (chimera-dev) issue. The serial number is not the main factor in pairing the atoms. As mentioned in the "rmsd" documentation, <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> "If atom order is not specified... the atoms within a residue are ordered first by name, and where these are identical, by alternate location identifier, and where these are also identical, by serial number." As for residues, if your models have multiple residues I believe they are compared in order. However, if your structures have exactly the same atom names and in the same order, I believe the rules above would pair the atoms in the epected order. The only other issue I can think of is that chemically symmetrical pairings are not tried, for example, if you had two phenyl rings or two carboxylates that exactly match in space but the atom names are in "flipped" positions, you would still get a higher RMSD. If it seems Chimera is not pairing the atoms as advertised, please use "Help... Report a Bug" in the Chimera menu and attach a session file with the two models, and give a short description and an email address if you'd like to hear back. There are a couple of ways to explicitly give the atom order, but if your structures have many atoms, they would be difficult/tedious: (a) interactively pick the atoms one by one from the graphics display in the correct order and then use the word "sel" to specify them in the command, as described in more detail in the documentation (link above) (b) specify all the atom names in order in the command 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 10, 2011, at 11:44 AM, Kristen Eisenberg wrote: > [chimera-dev] Calculating RMSD > > Hi, > I want to calculate the RMSD between two mol2 structures in place. The two > structures are different forms of the same structure. I haver modified the > mol2 so that the two of them have the same serialNumber in their respective > atoms. The problem is that when I use the command rmsd #model1 #model2, it > return an incorrect value of the rmsd, as the value showed is too high, > about 5, when it should be about 1 (the two structures are very similar). Is > there any way to calculate the RMSD value in place correctly or I am doing > anything wrong? > > Thanks for your help. > Kristen Eisenberg

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structure editing query
by Bala subramanian 10 Sep '11

10 Sep '11

Friends, I am trying to modify the sugar of a nucleotide. I am interested in making a linkage of two carbons in the sugar as in the attached pdb. I tried to use the Build structure -> modify structure option but it does not work in the sense that when i select carbon atom (c2') and tried to connect it to an oxygen, chimera says that it is already bonded and hence some bonds to create a new one. Is there any way to make such linkages as in the pdb ? Thanks, Bala

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path to an object displayed in a chimera session
by Jean-Francois Menetret 09 Sep '11

09 Sep '11

Hello, how can one find out the path to an object displayed in a chimera session ? Best wishes Jean-Francois

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