September 2011 - Chimera-users - RBVI Mailing Lists

importing chimera module question
by Lockwood, Svetlana 23 Sep '11

23 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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