August 2010 - Chimera-users - RBVI Mailing Lists

Chimera List posting
by Hagn, Franz 12 Aug '10

12 Aug '10

Franz_Hagn(a)hms.harvard.edu

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Chimera startup options
by Beale, John 12 Aug '10

12 Aug '10

I have a new installation of Chimera on a Linux box. I am working with a protein/nucleic acid complex. When I start the program with "chimera file.pdb" the ribbon representation of the structure is shown. Also, a plank representation of the nucleic acid is shown. I have to hide the ribbon and select "Actions -> Atoms/Bonds -> Show" to see the atoms. Can someone tell me how to change the startup options so that the ribbon and planks are not automatically generated and that the atoms/bonds are shown by default? Thanks! John John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale(a)stlcop.edu<mailto:jbeale@stlcop.edu>

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64-bit Windows version of chimera available
by Greg Couch 11 Aug '10

11 Aug '10

For users with larger datasets, we now have a 64-bit Windows version of chimera available in the daily builds section on the chimera download page, <http://www.cgl.ucsf.edu/chimera/download.html#daily>. While we believe it is bug-for-bug compatible with the other daily builds, please try it out and let us know if you have any problems. - Greg

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Fwd: Re: Question about selection...
by Yasser Almeida Hernández 11 Aug '10

11 Aug '10

It works!!! Thanks a lot, ;) -------- Original Message -------- Subject: Re: [Chimera-users] Question about selection... Date: Tue, 10 Aug 2010 13:49:55 -0500 From: Elaine Meng <meng(a)cgl.ucsf.edu> Reply-To: Chimera BB <chimera-users(a)cgl.ucsf.edu> To: Yasser Almeida Hernandez <almeida(a)cim.sld.cu> CC: Chimera BB <chimera-users(a)cgl.ucsf.edu> Hi Yasser, if you want to generally select all singleton atoms (atoms not bonded to other atoms), you could use this command: sel @/!bonds this is an example of specification by attribute, described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descri…> 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 Aug 10, 2010, at 7:49 AM, Yasser Almeida Hernández wrote: > Hi... > The problem is that I have hundreds of pdb files with this format: > four models (or less), where each one is an aminoacid and a single > atom. Mostly, the single atom is an heteroatom and i select it with > :/isHet, but sometimes this atom is a protein atom with the ATOM > field and then, the :/isHet selection doesn't work... > There is some tricky way to select this single atom types (ATOM), > according to the structure of the pdb file...??? > Thanks . ----- Terminar mensaje reenviado ----- -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI -------- Original Message -------- Subject: Re: [Chimera-users] Question about selection... Date: Tue, 10 Aug 2010 13:49:55 -0500 From: Elaine Meng <meng(a)cgl.ucsf.edu> Reply-To: Chimera BB <chimera-users(a)cgl.ucsf.edu> To: Yasser Almeida Hernandez <almeida(a)cim.sld.cu> CC: Chimera BB <chimera-users(a)cgl.ucsf.edu> Hi Yasser, if you want to generally select all singleton atoms (atoms not bonded to other atoms), you could use this command: sel @/!bonds this is an example of specification by attribute, described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descri…> 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 Aug 10, 2010, at 7:49 AM, Yasser Almeida Hernández wrote: > Hi... > The problem is that I have hundreds of pdb files with this format: four models (or less), where each one is an aminoacid and a single atom. Mostly, the single atom is an heteroatom and i select it with :/isHet, but sometimes this atom is a protein atom with the ATOM field and then, the :/isHet selection doesn't work... > There is some tricky way to select this single atom types (ATOM), according to the structure of the pdb file...??? > Thanks .

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64-bit Windows version of chimera available
by Greg Couch 10 Aug '10

10 Aug '10

For users with larger datasets, we now have a 64-bit Windows version of chimera available in the daily builds section on the chimera download page, <http://www.cgl.ucsf.edu/chimera/download.html#daily>. While we believe it is bug-for-bug compatible with the other daily builds, please try it out and let us know if you have any problems. - Greg

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64-bit Windows version of chimera available
by Greg Couch 10 Aug '10

10 Aug '10

For users with larger datasets, we now have a 64-bit Windows version of chimera available in the daily builds section on the chimera download page, <http://www.cgl.ucsf.edu/chimera/download.html#daily>. While we believe it is bug-for-bug compatible with the other daily builds, please try it out and let us know if you have any problems. - Greg

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Question about selection...
by Yasser Almeida Hernández 10 Aug '10

10 Aug '10

Hi chimerians... I have this pdb file with some models... MODEL ATOM 1 N ARG 2 75 3.566 -4.680 2.408 1.00 27.73 N ATOM 2 CA ARG 2 75 3.319 -3.762 1.307 1.00 27.44 C ATOM 3 C ARG 2 75 4.363 -2.641 1.381 1.00 27.43 C ATOM 4 O ARG 2 75 4.900 -2.249 2.434 1.00 26.54 O ATOM 5 CB ARG 2 75 1.901 -3.115 1.361 1.00 29.76 C ATOM 6 CG ARG 2 75 0.685 -4.005 1.574 1.00 30.19 C ATOM 7 CD ARG 2 75 1.021 -5.453 1.347 1.00 32.01 C ATOM 8 NE ARG 2 75 1.567 -5.689 0.064 1.00 35.22 N ATOM 9 CZ ARG 2 75 2.123 -6.788 -0.467 1.00 37.99 C ATOM 10 NH1 ARG 2 75 2.301 -7.901 0.253 1.00 37.85 N ATOM 11 NH2 ARG 2 75 2.343 -6.799 -1.796 1.00 37.02 N TER ATOM 1 OE1 GLU 3 561 2.565 -3.602 -1.919 1.00 35.57 O TER ENDMDL MODEL ATOM 1 N ARG B 75 3.153 -4.497 2.431 1.00 25.72 N ATOM 2 CA ARG B 75 2.895 -3.593 1.311 1.00 26.52 C ATOM 3 C ARG B 75 3.980 -2.519 1.148 1.00 26.28 C ATOM 4 O ARG B 75 4.530 -2.055 2.176 1.00 26.18 O ATOM 5 CB ARG B 75 1.566 -2.890 1.541 1.00 30.04 C ATOM 6 CG ARG B 75 0.249 -3.353 1.047 1.00 33.78 C ATOM 7 CD ARG B 75 -0.666 -3.815 2.137 1.00 37.95 C ATOM 8 NE ARG B 75 -0.707 -5.248 2.257 1.00 42.21 N ATOM 9 CZ ARG B 75 -0.886 -6.067 3.286 1.00 44.76 C ATOM 10 NH1 ARG B 75 -1.060 -5.717 4.569 1.00 44.33 N ATOM 11 NH2 ARG B 75 -0.888 -7.403 3.027 1.00 45.78 N TER ATOM 1 OE1 GLU 3 561 2.565 -3.602 -1.919 1.00 35.57 O TER ENDMDL MODEL ATOM 1 N ARG H 75 2.710 -4.027 1.931 1.00 41.50 N ATOM 2 CA ARG H 75 2.475 -2.983 0.948 1.00 38.30 C ATOM 3 C ARG H 75 3.422 -1.785 1.027 1.00 39.34 C ATOM 4 O ARG H 75 3.907 -1.419 2.105 1.00 38.57 O ATOM 5 CB ARG H 75 1.022 -2.521 1.055 1.00 41.90 C ATOM 6 CG ARG H 75 0.718 -1.195 0.370 1.00 48.73 C ATOM 7 CD ARG H 75 -0.639 -0.637 0.779 1.00 50.05 C ATOM 8 NE ARG H 75 -1.742 -1.354 0.145 1.00 56.64 N ATOM 9 CZ ARG H 75 -2.422 -2.353 0.705 1.00 57.10 C ATOM 10 NH1 ARG H 75 -2.121 -2.773 1.928 0.00 56.09 N ATOM 11 NH2 ARG H 75 -3.413 -2.931 0.040 0.00 56.09 N TER ATOM 1 OE1 GLU 3 561 2.565 -3.602 -1.919 1.00 35.57 O TER ENDMDL MODEL ATOM 1 N ARG K 75 2.718 -3.987 1.949 1.00 40.34 N ATOM 2 CA ARG K 75 2.510 -2.935 0.974 1.00 40.91 C ATOM 3 C ARG K 75 3.439 -1.730 1.052 1.00 41.44 C ATOM 4 O ARG K 75 3.779 -1.257 2.143 1.00 44.22 O ATOM 5 CB ARG K 75 1.045 -2.492 0.991 1.00 46.88 C ATOM 6 CG ARG K 75 0.759 -1.285 0.109 1.00 57.01 C ATOM 7 CD ARG K 75 -0.722 -0.981 -0.005 1.00 64.03 C ATOM 8 NE ARG K 75 -0.939 0.301 -0.673 1.00 70.73 N ATOM 9 CZ ARG K 75 -0.576 1.482 -0.173 1.00 75.39 C ATOM 10 NH1 ARG K 75 0.025 1.563 1.009 1.00 75.51 N ATOM 11 NH2 ARG K 75 -0.798 2.594 -0.862 1.00 77.70 N TER ATOM 1 OE1 GLU 3 561 2.565 -3.602 -1.919 1.00 35.57 O TER ENDMDL How can i select the 1 OE1 GLU atom in each the model? Any hint... Thanks... ;) -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI

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64-bit Windows version of chimera available
by Greg Couch 10 Aug '10

10 Aug '10

For users with larger datasets, we now have a 64-bit Windows version of chimera available in the daily builds section on the chimera download page, <http://www.cgl.ucsf.edu/chimera/download.html#daily>. While we believe it is bug-for-bug compatible with the other daily builds, please try it out and let us know if you have any problems. - Greg

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Re: [Chimera-users] Ramachandran Plots
by Conrad Huang 10 Aug '10

10 Aug '10

Actually, you can now bring up a Ramachandran plot via the user interface in the Chimera daily build (http://www.cgl.ucsf.edu/chimera/download.html#daily). If you pop up the Model Panel (Favorites -> Model Panel), there should be a "Ramachandran plot..." button that displays a plot for each selected model. This is still an early implementation, so please send us bug reports and suggestions. Conrad On 8/9/2010 5:53 PM, Daniel Gurnon wrote: > Conrad, This script isn't working for me- I get the following error: > > Traceback (most recent call last): > File "C:\ProgramData\Chimera\ram3.py.txt", line 2, in <module> > from Plotdialog import PlotDialog > ImportError: No module named Plotdialog > > > Can you tell me how to make it work? > Thanks > Dan > > > On Mon, Jun 7, 2010 at 1:55 PM, Conrad Huang <conrad(a)cgl.ucsf.edu > <mailto:conrad@cgl.ucsf.edu>> wrote: > > It's been on our list for a while now. In the mean time, try out > this script. It generates a Ramachandran chart for the first open > molecule. > > Conrad > > > On 6/3/10 8:55 AM, James Nettles wrote: > > Does Chimera do Ramachandran Plots and I'm missing something > obvious? > > I like doing just about everything else in Chimera :-) > > Thanks, > > Jim _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > -- > ____________________________ > > Daniel Gurnon, Ph. D. > Assistant Professor of Chemistry > DePauw University > Greencastle, IN 46135 > > p: 765-658-6279 > e: danielgurnon(a)depauw.edu <mailto:danielgurnon@depauw.edu>

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Fitting with constrained motion
by Tom Goddard 06 Aug '10

06 Aug '10

Hi Julio The Chimera fitting code does a full 3-degree-of-freedom rotational search. It cannot search fewer rotational degrees of freedom. It would be nice to adapt the code to be able to consider only rotations about an axis. The needed changes would be in the FitMap Chimera module not the fitnogui.py script. Optimizing using only two rotational degrees of freedom that are Euler angles seems like a bizarre case and we are not likely to ever handle that. Please post future questions to the chimera-users mailing list so others can answer and read the answers. Tom > Hi Tom, > > Sorry to bother you again. Is there a way fix one of the Euler angles > for the fitting? Since we have a small theta, we would like to fix > psi=0, and optimize on phi and theta only, plus the translations. I'm > using the fitnogui script. > > Many thanks, > Julio > > > On Jul 28, 2010, at 5:13 PM, Tom Goddard wrote: > >> >> Hi Julio, >> >> I guess you are using the fitnogui.py script. >> >> >> http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/fitnogui.py >> >> The parameters are right near the top -- ijk_step_size_min is the one >> you're interested in. >> >> The initial contour level is set as described in the documentation: >> >> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum… >> >> The "volume" command can set the contour level: >> >> volume #0 level 27.6 >> >> Tom >> >>> Hi Tom, >>> >>> Thanks again. Editing the line of code would be perfect for us, >>> since we are calling Chimera from our program with the "nogui" >>> option. Could you point me the place where I need to change that 0.01? >>> >>> What happens with the contour level when I'm calling Chimera in that >>> way (nogui)? Can I similarly set it somewhere in the code? Or with >>> an option in the command line? >>> >>> Best, >>> Julio >>> >>> >>>

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Chimera-users August 2010