- Chimera-users - RBVI Mailing Lists

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 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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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 07 Aug '10

07 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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UCSF Chimera Visual Identity
by Jessen Vernon Bredeson 07 Aug '10

07 Aug '10

To whom this may concern, I downloaded the UCSF Chimera 1.4.1 update for Mac OS X and noticed that the Chimera symbol had a grey outline around it, likely due to multiple alpha channels in rendering the image into .ICNS format, so I recomposed the image in higher quality and it is attached below. Also below is an accompanying symbol for MS Windows format (.ICO). These icons are free of charge, keep up the good work. Jessen Bredeson Fourth-Year Genetics, Genomics & Development Molecular and Cellular Biology University of California, Berkeley

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model panel: add/edit note
by Dougherty, Matthew T 03 Aug '10

03 Aug '10

Is there a command to be able to modify notes on the model panel? If not, it would a useful addition when creating a command file to load in & color datasets.

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Small molecules and antechamber
by Jon Rumbley 02 Aug '10

02 Aug '10

I have several small organic molecules constructed in ChemDraw and converted in Chem3D to .mol2 files. I can open them in Chimera but cannot seem to add charges to. I was simply using the add charge menu commands and AM1-BCC and assuming the structures would be read as nonstandard but antechamber reports an error with residue ****. The error log has no real indication of what the trouble might be. Are there additional steps I must take before assigning charges? The structures already have hydrogens added. An example .mol2 file is below: @<TRIPOS>MOLECULE **** 44 45 1 0 0 SMALL USER_CHARGES @<TRIPOS>ATOM 1 C -2.8306 2.5311 -0.9622 C.2 1 **** 0.0000 2 C -2.8728 1.1718 -1.0363 C.2 1 **** 0.0000 3 C -4.0552 0.3840 -0.9622 C.1 1 **** 0.0000 4 C -1.6082 0.4134 -1.1450 C.2 1 **** 0.0000 5 N -5.0052 -0.2769 -0.8917 N.1 1 **** 0.0000 6 O -1.8883 -0.9222 -1.2800 O.3 1 **** 0.0000 7 O -0.4722 0.8459 -1.1451 O.2 1 **** 0.0000 8 C -0.8034 -1.8901 -1.1282 C.3 1 **** 0.0000 9 C -0.3965 -1.8485 0.3585 C.2 1 **** 0.0000 10 C -1.4383 -3.2075 -1.5077 C.3 1 **** 0.0000 11 N 0.6925 -2.6041 0.6991 N.am 1 **** 0.0000 12 O -1.0062 -1.1536 1.1745 O.2 1 **** 0.0000 13 C 1.2426 -2.6055 2.0833 C.3 1 **** 0.0000 14 C 2.4273 -3.5343 2.1380 C.ar 1 **** 0.0000 15 C -3.9592 3.4353 -0.8741 C.ar 1 **** 0.0000 16 C -3.7802 4.6664 -0.1923 C.ar 1 **** 0.0000 17 C -4.8234 5.5702 -0.0757 C.ar 1 **** 0.0000 18 C -6.0611 5.2454 -0.6673 C.ar 1 **** 0.0000 19 C -6.2633 4.0447 -1.3692 C.ar 1 **** 0.0000 20 C -5.2063 3.1490 -1.4690 C.ar 1 **** 0.0000 21 O -7.0408 6.1768 -0.5154 O.3 1 **** 0.0000 22 C 3.5525 -3.2801 1.3388 C.ar 1 **** 0.0000 23 C 4.6333 -4.1642 1.3545 C.ar 1 **** 0.0000 24 C 4.6017 -5.2952 2.1768 C.ar 1 **** 0.0000 25 C 3.4888 -5.5395 2.9865 C.ar 1 **** 0.0000 26 C 2.3994 -4.6635 2.9668 C.ar 1 **** 0.0000 27 H -1.8332 3.0176 -0.9495 H 1 **** 0.0000 28 H 0.0351 -1.5845 -1.7993 H 1 **** 0.0000 29 H -0.6942 -4.0150 -1.5686 H 1 **** 0.0000 30 H -1.9272 -3.1457 -2.4932 H 1 **** 0.0000 31 H -2.2150 -3.5214 -0.7935 H 1 **** 0.0000 32 H 1.1669 -3.2048 0.0167 H 1 **** 0.0000 33 H 1.5395 -1.5662 2.3712 H 1 **** 0.0000 34 H 0.4439 -2.9024 2.8058 H 1 **** 0.0000 35 H -2.8085 4.9012 0.2576 H 1 **** 0.0000 36 H -4.7042 6.5169 0.4530 H 1 **** 0.0000 37 H -7.2285 3.8279 -1.8322 H 1 **** 0.0000 38 H -5.3406 2.2282 -2.0442 H 1 **** 0.0000 39 H -7.9024 5.8992 -0.9622 H 1 **** 0.0000 40 H 3.5844 -2.3950 0.7014 H 1 **** 0.0000 41 H 5.5045 -3.9710 0.7250 H 1 **** 0.0000 42 H 5.4465 -5.9867 2.1870 H 1 **** 0.0000 43 H 3.4659 -6.4183 3.6333 H 1 **** 0.0000 44 H 1.5299 -4.8643 3.5946 H 1 **** 0.0000 @<TRIPOS>BOND 1 1 2 2 2 1 15 1 3 1 27 1 4 2 3 1 5 2 4 1 6 3 5 3 7 4 6 1 8 4 7 2 9 6 8 1 10 8 9 1 11 8 10 1 12 8 28 1 13 9 11 1 14 9 12 2 15 10 29 1 16 10 30 1 17 10 31 1 18 11 13 1 19 11 32 1 20 13 14 1 21 13 33 1 22 13 34 1 23 14 22 2 24 14 26 1 25 15 16 2 26 15 20 1 27 16 17 1 28 16 35 1 29 17 18 2 30 17 36 1 31 18 19 1 32 18 21 1 33 19 20 2 34 19 37 1 35 20 38 1 36 21 39 1 37 22 23 1 38 22 40 1 39 23 24 2 40 23 41 1 41 24 25 1 42 24 42 1 43 25 26 2 44 25 43 1 45 26 44 1 Thanks for any help you can provide. Dr. Jon N. Rumbley Assistant Professor Dept. of Pharmacy Practice and Pharmaceutical Sciences University of Minnesota-Duluth 127 LSci 1110 Kirby Dr. Duluth, MN 55812 Phone: 218-726-6047 email: jrumbley(a)d.umn.edu

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model panel: color patch
by Dougherty, Matthew T 31 Jul '10

31 Jul '10

using a command or python file, how do I set the color patch on the model panel?

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Fwd: Visualizing inertia axes as arrows
by Eric Pettersen 31 Jul '10

31 Jul '10

Hi Miguel, Thanks for the corrections! I just fired that one off without testing it. I thought there might be an error or two. I'm glad you find it useful after fixing it. --Eric Begin forwarded message: > From: Miguel Ortiz Lombardía <miguel.ortiz-lombardia(a)afmb.univ-mrs.fr> > Date: July 31, 2010 1:39:33 AM PDT > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Visualizing inertia axes as arrows > > Hi Eric, > > Thanks for this useful script! > > I think I found two errors though: >> >> from chimera.selection import currentAtoms, numpyArrayFromAtoms > > should be: > > from chimera.selection import currentAtoms > from chimera import numpyArrayFromAtoms > > and: > >> for val, vec in zip(vals, vecs): >> bildString += ".arrow %g %g %g %g %g %g .1 .2 .9\n" % ( >> centroid[0], centroid[1], centroid[2], >> centroid[0] + val[0] * vec[0], >> centroid[1] + val[1] * vec[1], >> centroid[2] + val[2] * vec[2]) > > has to be: > > for val, vec in zip(vals, vecs): > bildString += ".arrow %g %g %g %g %g %g .5 1. .9\n" % (centroid[0], > centroid[1], centroid[2], centroid[0] + val * scale * vec[0], > centroid[1] + val * scale * vec[1], centroid[2] + val * scale * > vec[2]) > > (you can ignore the scale thing, that's simply a 50/max(vals) > correction > so the longest axis is 50 A) > > Best, > > > -- > Miguel > > Architecture et Fonction des Macromolécules Biologiques (UMR6098) > CNRS, Universités d'Aix-Marseille I & II > Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France > Tel: +33(0) 491 82 55 93 > Fax: +33(0) 491 26 67 20 > e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. >

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Visualizing inertia axes as arrows
by Jozef Lewandowski 30 Jul '10

30 Jul '10

Hi everybody, Lately, I have been using "measure inertia" command a lot. For my purposes I needed to visualize the inertia axes as arrows instead of the default ellipsoid. I used the vectors from the reply log to write BILD files defining the arrows for the inertia axes. Is there an easy way to script just that? Or differently, is there an easy way to visualize as arrows inertia axes for peptide planes in a protein? Any tips would be appreciated. Thanks, Józef

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Re: [Chimera-users] about transformation matrix
by Tom Goddard 28 Jul '10

28 Jul '10

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 > > > > Hi Julio, > > The details of the fitting algorithm are given in the User's Guide. > > > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht… > > You should definitely read that if you want the best understanding. But > the brief answers to your questions are that the convergence criteria > looks for optimization steps of less than 0.01 grid index to decide > convergence. The user interface does not allow you to change the 0.01 > grid index criteria -- it could be done by editing a line of Python. > The default settings do mask using the contour level of the fit map as > an outer boundary. So that level is important. > > Tom > > >

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Camera parameters
by Tom Goddard 28 Jul '10

28 Jul '10

Hi Matt, The Chimera camera always points along the negative z-axis. The positions of the models are moved/rotated to get different view-points. Do you mean you want camera location (x,y,z) and horizontal angular field of view to the edges of the window (for perspective projection)? I know how to get at these using Python code, but I'm not sure if any Chimera commands report those values. Also I don't know if that info makes its way into X3D or VRML exported from Chimera. Greg Couch would know these answers. He is at SIGGRAPH this week. A quite gruesome way to get the parameters is to find them in the Chimera session file. grep formattedPositions mysession.py formattedPositions = {'p2': (0.3954088241213373, 18.749999499320985, (14.059999585151672, 7.399999618530273, 8.628906249999993), (36.02048479676247, -18.762672296762467), 8.62890625, {(0, 0): ((13.338430482851305, 2.7738552720503122, 6.309792459458727), (0.3889244976446376, 0.8937166155966246, 0.22362545950400858, 33.757570197325826))}, {(0, 0, 'Volume'): (False, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, False, 5.0)}, 4, (29.312384727061698, 10.919780805124898, 8.628906249999993), False), 'p1': (1.0, 18.749999499320985, (14.059999585151672, 7.399999618530273, 8.62890625), (36.02048479676247, -18.762672296762467), 8.62890625, {(0, 0): ((-1.913954659058722, -0.7459259145443079, 6.309792459458727), (0.3889244976446376, 0.8937166155966246, 0.22362545950400858, 33.757570197325826))}, {(0, 0, 'Volume'): (False, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, False, 5.0)}, 4, (14.059999585151669, 7.399999618530277, 8.628906249999993), False)} This is pretty messy and the values depend on which Chimera version saved the file. The values are defined by Python code chimera/share/Midas/__init__.py in the _savePosition() routine: return ( viewer.scaleFactor, viewer.viewSize, cam.center, cam.nearFar, cam.focal, xforms, clips, om.cofrMethod, cofr, viewer.clipping ) If you want a Python script to simply dump the camera positions for all savepos positions I can provide that. Tom > Hi Tom, > > I am creating a workaround for my graphics problem. What I have done in the past is to create a VRML file from Chimera export, extract the openGL camera parameters using a text editor, start up Amira, using TCL I would recreate the same camera view within Amira. At this point I could splice animation clips made by Chimera& Amira using Final Cut Pro. > > It has been a while since I have done this. I am now looking at the exported VRML files and they are lacking the camera info. > > Is there a command I can use to get the camera parameters for the savepos keyframes? > > thanks, Matt > >

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coordinate transformation
by Dougherty, Matthew T 28 Jul '10

28 Jul '10

I was trying to locate details on maxtrix, coordinate transformations & scenegraph, relative to camera transformations.

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about transformation matrix
by Kovacs, Julio A 28 Jul '10

28 Jul '10

Hi, I am doing fitting of two maps and am getting different values of the transformation parameters: the ones given in the window where I specify the options (these seem to be correct), and those given by using the command "matrixget" --- these give a very large translation vector, and moreover, I don't see any relation between that vector and the correct translation. Also, could you tell me what is the order used in Chimera: rotation, then translation? or translation, then rotation? Thank you very much. Julio Kovacs

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Problem
by Reza Heidari 27 Jul '10

27 Jul '10

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Nvidia 3D Vision
by "Christoph Höglinger" 27 Jul '10

27 Jul '10

Dear Chimera developers, I just bought the Nvidia 3D Vision Kit, because i was interested in the 3D Visualisation of it. First I tried it with the latest drivers from Nvidia's Homepage. (Quadro Driver Version: 258.49 & 3Dvision 258.49 ). I changed the Settings in the NV Control Panel (for Stereo output). Sequential Stereo worked fine in an other 3D Application. But when i change the view settings in chimera (sequential Stereo) i get that error: (After The Error MSG ist Quits and displays the Exit Code 3) Runtime Error! Program: C:\Program Files\Chimera\bin\pythonw.exe This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. Then i was looking for hints to solve that problem i found following article. http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005173.html There you mentioned that its probably a problem with the "new" drivers (197.XX). So I installed the driver that had been recommended by you. (Quadro Drv. 191.87 + 3D Vision 191.00). The Problem was that this 3D Vision driver won't support my LCD, its an Acer GD245HQ). I have installing it "manually" it won't activate the shutter glasses when Sequential Stereo is switched "on" in chimera (Shutter doesnt even work in games or any other Application) That means that the 3D-Vision driver is to blame. 197.03 Will recognize my LCD, but that won't work with chimera. Tried also QDRO 191.87 & 3DVision 258.49 (but theres no way to run the 3DVision Setup) Have you got an idea on how to fix that Problem? That would be really great! This is my System Configuration: Intel Pentium E5200 @ 3.5GHz PNY Quadro FX 570 4GB Ram Windows 7 64 Bit Acer GD245HQ Thank you so much for your help! Best regards, Christoph -- GMX.at - Österreichs FreeMail-Dienst mit über 2 Mio Mitgliedern E-Mail, SMS & mehr! Kostenlos: http://portal.gmx.net/de/go/atfreemail

3 4

Directly representing ellipsoids
by Thomas Ouldridge 27 Jul '10

27 Jul '10

Hi, I'm afraid I'm not a crystallographer/protein simulator, and so this question might seem quite naive. I run coarse-grained simulations, and I would like to represent the objects as ellipses in chimera. I have the position (which I am able to use) and the orientation that I would like my ellipses to take, encoded as a matrix relative to (x,y,z) cartesian coordinates. This matrix gives me the principal axes and radii of the ellipse. As I understand, Chimera is designed to display a "Thermal ellipsoid" - I would like this ellipsoid to have the axes and radii given by my matrix. However, it seems that the input (via pdb format files) is interpreted as an "anisotropic temperature factor", and I can't find a way to convert my matrix into the anisotropic temperature factor (I tried some papers online but they seemed to be talking in terms of transformations between lab frame and crystallographic frames, but I cannot see how that applies - what is my crystallographic frame?). In short, is there a way to convert my matrix into the "anisotropic temperature factor" representation so that Chimera can read it and convert it back? I did try just plugging in the matrix elements to the PDB file but got some weird ellipsoids out. Any help would be gratefully appreciated, Tom

2 1

Transparency doesn't look right
by Tom Goddard 27 Jul '10

27 Jul '10

Hi Mitalee This is a Chimera limitation. Two or transparent models will not be shown correctly. Transparency works correctly only when at most one model is transparent. You have the volume data displayed in "solid" style which is a kind of transparent rendering, and you have a surface model which is transparent. How defective the transparency looks depends on the order the models were opened in Chimera (or maybe it depends on which has higher model id number, don't recall). In any case, both orders look seriously wrong. If you reverse the order of opening your two models I think your surface will remain totally invisible until it becomes 0% transparent when it will suddenly appear. This limitation is a rather fundamental design problem in Chimera. Chimera draws the models one at a time. A model that is drawn after another model can only appear in front of the first model. Chimera first draws all opaque models, then draws all transparent models. If you look at the termite gut video I made http://www.cgl.ucsf.edu/chimera/animations/movies/termitegut.mov where surfaces fade in you'll see at the start of the fade in, a black blob suddenly appears representing the object. This is the same bad behavior you see in your case, but your surface is white (the background color) and is in front of the volume data making it look especially bad. This problem has arisen many times in, especially in movie making where transparency is used to fade objects in and out. I have an idea for a solution although it is not yet implemented. But we just hired Daren Weber to work on animation improvements in Chimera and perhaps he can try this. The idea is to enhance the movie command to add a "crossfade" option. You would display the volume, then use a command like "movie crossfade 25" then show the opaque surface. The command would take the image right before the command was issued and the next image and linearly blend them over 25 frames. This would be useful for many fade scenarios. It is limited in that it won't be able to have models moving and a fade occurring at the same time since that is not simply a linearly blending of two images. I'll see if Darren is interested in trying to add this if you are interested. If you do not want to wait for this, another option is to record your movie without the fade -- just have the surface suddenly appear. Then drop the movie into an video editing program like Final Cut and add the crossfade with that software. Tom > Hi Tom, > > I was using the surft command, trying to make a segment appear inside of a > cmap file. Basically, I have a cmap file open and visible, and I want to > show the segmented cell appear slowly. My problem is that when I set the > transparency of the segmented cell to 100 (i.e. surft 100 #0), it doesn't > exactly become transparent, or what I thought would be transparent. When I > enter this command, it makes the entire image transparent at that point > (so the shape of the segmented cell is preserved and matches the > background. I've attached an image of what I got as a result. Is there a > way to make preserve the cmap image and just make the segmented cell > overlay onto it without completely "removing" the section where the > segmented cell will appear? > > Thanks, > Mitalee

1 1

Question about match
by Ibrahim Moustafa 27 Jul '10

27 Jul '10

Dear Chimera developers, I have a question related to the ³match² command. I wanted to align 4 related proteins and I used the default in the match menu. The alignment is fine; but I have a question about the output in the reply log. In the log it says: ³evaluating superpositions across all 439 fully populated columns in the final alignment² Then the pair-wise RMSD between the different pairs (range from 0.7 1.6 A) are given. What is meant by 439 fully populated columns? Does it mean 439 C-alpha atoms for those amino acids in the fully occupied aligned columns? I¹m asking because I want to report these values of RMSD and I want to be more specific and state the number of atoms over which the RMSD value is being reported. P.S. The proteins vary in their length (461,462,460 and 470). Thanks for your reply in advance, Ibrahim

2 2

protonated carboxyl group
by Elaine Meng 26 Jul '10

26 Jul '10

> right now I'm getting stuck on things like adding hydrogens (e.g. I would like a -COOH and not -COO group) Hi, We may make some changes to make this easier in the future, but for now here is the procedure: (a) change the atom type of the oxygen to be protonated to O3. This could be done by Ctrl-clicking to select that oxygen and then using the command: setattr a idatmType O3 sel (b) add hydrogens with command "addh" or the AddH tool (c) if this is in a "standard residue" (amino acid ASP or GLU) and you are also going to assign charges in Chimera, you will also need to adjust the names of the atoms so they will receive the correct Amber partial charge values. If the residue is ASP, you will need to make sure that the sidechain oxygen without the hydrogen is named OD1, the one with the hydrogen is named OD2, and the hydrogen itself is named HD2. If GLU, it is analogous except the names contain E instead of D. Show atom labels for that residue to see the current names (e.g. to show atom labels for residue 9 in chain A, use command: lab :9.a). To rename an atom, you could select it and use a command something like: setattr a name OD1 sel Once the names are correct, charge assignment will give you the correct Amber values for residue ASH (protonated ASP) or GLH (protonated GLU). 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

1 0

map normalization; ccp4 file saving
by Jean-Paul Armache 26 Jul '10

26 Jul '10

hello, i would like to pose two questions: 1. is there a way of adjusting one map so that it's adjusting to the levels of another map? i believe it should be achievable with "vop" command, but i am not sure whether the vop scale is the appropriate thing to use. 2. would it be possible to save the output map as a ccp4 map? currently you're permitting mrc saving, which is not that very much different from ccp4, so i was wondering if it was possible to add this feature. the difference is large enough so that coot does not allow for map loading of mrc files. best regards, jean-paul

2 1

Problem
by Reza Heidari 25 Jul '10

25 Jul '10

1 0

More on extracting data from the reply log
by Jean Didier Pie Marechal 21 Jul '10

21 Jul '10

Hi everyone, I want to write only a part of the reply log in a file. I was trying to use the script you gave to katrina months ago but I have a problem in parsing the reply log text output. If I understand correctly the reply log text is a raw text. I'd like to parse it in "lines" and then only write in the output file a intersting bit, like for example lines that contains "RMSD". I thought it would be enough to split text using the '\n' return character but that does not work. Could you give me a hand please? Best JD def save_reply_log(path): from chimera import dialogs r = dialogs.find('reply') text = r.text.get('1.0', 'end') f= open(path, 'w') i=text.split("\n") f.close() save_reply_log("d:/tmplog.txt") Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Divendres, Juliol 16, 2010 7:33 pm Assumpte: Chimera-users Digest, Vol 87, Issue 13 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: alignment + missing residues (Gesa Volkers) > 2. Re: alignment + missing residues (Gesa Volkers) > 3. Re: alignment + missing residues (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 16 Jul 2010 11:58:48 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402D58.7090906(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Eric, > > thanks for your suggestions. Unfortunately removing the SEQRES > record > did not help. I also downloaded and installed the new chimera- > version > today. The false numbering in the alignment still occurs. Also when > I > remove the SEQRES record and try with the new chimera version the > false > numbering appears. Quite annoying... The pdb-file is not in the > protein > data bank yet. > > Any more suggestions? Could I add "dummy atoms" in the structure? > > Thanks, > Gesa > > > > Eric Pettersen schrieb: > > On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > > > >> Dear All, > >> > >> I observed an issue with the alignment function of Chimera. > >> I loaded a crystal structure where in between a loop is not > modelled > >> due to low electron density- so these residues are missing in > the > >> structure and the numbering also has this gap. When I align this > >> structure with others, the missing residues are not recognized > and > >> chimera just overrides the numbering so after this loop all the > >> numbers in the alignment do not fit anymore to the residues they > >> should belong to although the structure and numberings are shown > in > >> the right way in the graphics window. How can I overcome this > issue? > >> Should I change the pdb-file? In which way? > >> > >> Thanks for all responses! > > > > Hi Gesa, > > I had a similar problem reported with 1JFF 12 days ago and > haven't yet > > worked on fixing it. It seems to only happen for a small subset > of > > structures. 1JFF has a missing loop and also exactly one missing > > residue at the N terminus. Is your structure like that? Is it a > > standard PDB entry (if so, what's the ID code)? I'll add you to > the > > recipient list for the ticket we have open in our bug database > for > > this (#8585) so you will be notified when it gets fixed. It'll > > probably be fairly soon. > > Until then the only workaround that occurs to me is for you to > remove > > the SEQRES records from the PDB file before you open it. Then > the > > Sequence viewer will depict only the residues physically present > in > > the structure -- no gaps (incorrect or otherwise) will be depicted. > > > > --Eric > > > > Eric Pettersen > > > > UCSF Computer Graphics Lab > > > > http://www.cgl.ucsf.edu > > > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 2 > Date: Fri, 16 Jul 2010 12:06:56 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402F40.2010604(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Additionally I downloaded 1JFF and did an alignment with another > tubulin-structure. And still the numbering does not recognize this > gap > between 34 and 61. > > Gesa Volkers schrieb: > > Dear Eric, > > > > thanks for your suggestions. Unfortunately removing the SEQRES > record > > did not help. I also downloaded and installed the new chimera- > version > > today. The false numbering in the alignment still occurs. Also > when I > > remove the SEQRES record and try with the new chimera version the > > false numbering appears. Quite annoying... The pdb-file is not in > the > > protein data bank yet. > > > > Any more suggestions? Could I add "dummy atoms" in the structure? > > > > Thanks, > > Gesa > > > > > > > > Eric Pettersen schrieb: > >> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >> > >>> Dear All, > >>> > >>> I observed an issue with the alignment function of Chimera. > >>> I loaded a crystal structure where in between a loop is not > modelled > >>> due to low electron density- so these residues are missing in > the > >>> structure and the numbering also has this gap. When I align > this > >>> structure with others, the missing residues are not recognized > and > >>> chimera just overrides the numbering so after this loop all the > >>> numbers in the alignment do not fit anymore to the residues > they > >>> should belong to although the structure and numberings are > shown in > >>> the right way in the graphics window. How can I overcome this > issue? > >>> Should I change the pdb-file? In which way? > >>> > >>> Thanks for all responses! > >> > >> Hi Gesa, > >> I had a similar problem reported with 1JFF 12 days ago and > haven't > >> yet worked on fixing it. It seems to only happen for a small > subset > >> of structures. 1JFF has a missing loop and also exactly one > missing > >> residue at the N terminus. Is your structure like that? Is it > a > >> standard PDB entry (if so, what's the ID code)? I'll add you to > the > >> recipient list for the ticket we have open in our bug database > for > >> this (#8585) so you will be notified when it gets fixed. It'll > >> probably be fairly soon. > >> Until then the only workaround that occurs to me is for you to > remove > >> the SEQRES records from the PDB file before you open it. Then > the > >> Sequence viewer will depict only the residues physically present > in > >> the structure -- no gaps (incorrect or otherwise) will be depicted. > >> > >> --Eric > >> > >> Eric Pettersen > >> > >> UCSF Computer Graphics Lab > >> > >> http://www.cgl.ucsf.edu > >> > >> > >> > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 3 > Date: Fri, 16 Jul 2010 10:32:39 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] alignment + missing residues > To: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <CF134751-B951-403B-B9E3-E441DB44644D(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Gesa, > I suspect you are using a Mac, since the daily builds failed last > night for the Mac platforms. You need to get a daily build dated > July > 16 or later. I tried opening the sequence view for 1JFF in one of > the > successful daily builds and it was correct, e.g.: > > > > You can see that the interior gap is correctly recognized now. > Hopefully the daily builds on the Mac platforms will work tonight. > > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > > Ah, the "remove SEQRES records" hack will only work for the single- > sequence viewer, not an alignment. I tested that in the 1.4.1 > release > and it indeed worked as I expected: > > > > The whole sequence is smushed together with no gaps, but the > correspondences are correct. You could then align additional > sequences to the smushed sequence and the correspondences would > remain > correct. Nonetheless it's probably simply better to wait for a > daily > build to succeed than to use the hack now. So make sure you check > the > date in the download table. If you still have problems with a > release > later than July 16, let me know. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Jul 16, 2010, at 3:06 AM, Gesa Volkers wrote: > > > Additionally I downloaded 1JFF and did an alignment with another > > tubulin-structure. And still the numbering does not recognize > this > > gap between 34 and 61. > > > > Gesa Volkers schrieb: > >> Dear Eric, > >> > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > >> > >> Any more suggestions? Could I add "dummy atoms" in the structure? > >> > >> Thanks, > >> Gesa > >> > >> > >> > >> Eric Pettersen schrieb: > >>> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >>> > >>>> Dear All, > >>>> > >>>> I observed an issue with the alignment function of Chimera. > >>>> I loaded a crystal structure where in between a loop is not > >>>> modelled due to low electron density- so these residues are > >>>> missing in the structure and the numbering also has this gap. > >>>> When I align this structure with others, the missing residues > are > >>>> not recognized and chimera just overrides the numbering so > after > >>>> this loop all the numbers in the alignment do not fit anymore > to > >>>> the residues they should belong to although the structure and > >>>> numberings are shown in the right way in the graphics window. > How > >>>> can I overcome this issue? Should I change the pdb-file? In > which > >>>> way? > >>>> > >>>> Thanks for all responses! > >>> > >>> Hi Gesa, > >>> I had a similar problem reported with 1JFF 12 days ago and > haven't > >>> yet worked on fixing it. It seems to only happen for a small > >>> subset of structures. 1JFF has a missing loop and also exactly > > >>> one missing residue at the N terminus. Is your structure like > >>> that? Is it a standard PDB entry (if so, what's the ID code)? > >>> I'll add you to the recipient list for the ticket we have open > in > >>> our bug database for this (#8585) so you will be notified when > it > >>> gets fixed. It'll probably be fairly soon. > >>> Until then the only workaround that occurs to me is for you to > >>> remove the SEQRES records from the PDB file before you open it. > > >>> Then the Sequence viewer will depict only the residues > physically > >>> present in the structure -- no gaps (incorrect or otherwise) > will > >>> be depicted. > >>> > >>> --Eric > >>> > >>> Eric Pettersen > >>> > >>> UCSF Computer Graphics Lab > >>> > >>> http://www.cgl.ucsf.edu > >>> > >>> > >>> > >> > >> > > > > > > -- > > Gesa Volkers > > Institut f?r Biochemie, Molekulare Strukturbiologie > > Felix-Hausdorff-Stra?e 4 > > 17489 Greifswald > > Germany > > +49 (3834)-864392 > > > > > > > > >

2 1

Re: [Chimera-users] save density map relative to...
by Tom Goddard 21 Jul '10

21 Jul '10

Hi Jie, You want to save a map that has been rotated relative to another map so that when you open both maps later they align. The difficulty is that the common map file formats like MRC and Spider don't have any place in the file header to specify a rotation. There are two ways to work around this limitation. One is that Chimera does some special trickery and puts the rotation information into a "label" in MRC map files so that when it later reads the file it can restore it in the right position. The trouble is that no other software will recognize that rotated position -- only Chimera. Another difficulty is that Chimera won't record the rotated position when you fit one map in another. The reason for that is because Chimera saves the rotation of the map grid relative to the maps local coordinate system. But fitting doesn't change the orientation of the grid -- instead it moves the local coordinate system (the map coordinate axes move instead of the data moving). Each map has its own set of coordinate axes. I think it would be pretty easy to add a "save relative to" option to the Same Map As... dialog that would take account of both types of rotation. But again, the orientation would only be restored by Chimera. The second method is to resample the rotated map on the grid of the map you fit into and save that resampled map. This will allow other software to open the maps and show the correct alignment. The drawback here is that the resampled map may have degraded quality since it interpolated the original map (trilinear interpolation). The Chimera command to do that looks like vop resample #3 onGrid #2 Here #3 is the id number (shown in Favorites / Model Panel or the volume dialog) of the rotated map that was fit into map #2. This will make a new map that you can save and it will align with map #2 when opened in another session or with other software since they share identical grids. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample Tom > Hi Tom, > > Hope this email finds you well. This is Jie from Joachim Frank's lab. > We met at the UCSF molecular animation workshop. > > I am writing about the "save map as" function in Chimera. Is there a > way to save map relative to another map (like the option available in > "save PDB")? The fitting algorithm ("fit in map" function) in Chimera > is very good, and I sometimes use it to align two density maps. > However, I couldn't save the density map after it was shifted. If > there's no such option, is it possible to add it? > > Best regards, > > > -Jie >

1 0

Re: [Chimera-users] Chimera-users Digest, Vol 87, Issue 13
by Jean Didier Pie Marechal 20 Jul '10

20 Jul '10

Hi again, I'd like to do a mmaker for a region of space leading to something like this: mmaker #(ref-model and part of the selection) #(flex-model and part of the selection) So far I haven't found the correct syntax to do so but I am pretty sure we can do that. any help? Cheers JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Divendres, Juliol 16, 2010 7:33 pm Assumpte: Chimera-users Digest, Vol 87, Issue 13 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: alignment + missing residues (Gesa Volkers) > 2. Re: alignment + missing residues (Gesa Volkers) > 3. Re: alignment + missing residues (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 16 Jul 2010 11:58:48 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402D58.7090906(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Eric, > > thanks for your suggestions. Unfortunately removing the SEQRES > record > did not help. I also downloaded and installed the new chimera- > version > today. The false numbering in the alignment still occurs. Also when > I > remove the SEQRES record and try with the new chimera version the > false > numbering appears. Quite annoying... The pdb-file is not in the > protein > data bank yet. > > Any more suggestions? Could I add "dummy atoms" in the structure? > > Thanks, > Gesa > > > > Eric Pettersen schrieb: > > On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > > > >> Dear All, > >> > >> I observed an issue with the alignment function of Chimera. > >> I loaded a crystal structure where in between a loop is not > modelled > >> due to low electron density- so these residues are missing in > the > >> structure and the numbering also has this gap. When I align this > >> structure with others, the missing residues are not recognized > and > >> chimera just overrides the numbering so after this loop all the > >> numbers in the alignment do not fit anymore to the residues they > >> should belong to although the structure and numberings are shown > in > >> the right way in the graphics window. How can I overcome this > issue? > >> Should I change the pdb-file? In which way? > >> > >> Thanks for all responses! > > > > Hi Gesa, > > I had a similar problem reported with 1JFF 12 days ago and > haven't yet > > worked on fixing it. It seems to only happen for a small subset > of > > structures. 1JFF has a missing loop and also exactly one missing > > residue at the N terminus. Is your structure like that? Is it a > > standard PDB entry (if so, what's the ID code)? I'll add you to > the > > recipient list for the ticket we have open in our bug database > for > > this (#8585) so you will be notified when it gets fixed. It'll > > probably be fairly soon. > > Until then the only workaround that occurs to me is for you to > remove > > the SEQRES records from the PDB file before you open it. Then > the > > Sequence viewer will depict only the residues physically present > in > > the structure -- no gaps (incorrect or otherwise) will be depicted. > > > > --Eric > > > > Eric Pettersen > > > > UCSF Computer Graphics Lab > > > > http://www.cgl.ucsf.edu > > > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 2 > Date: Fri, 16 Jul 2010 12:06:56 +0200 > From: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Subject: Re: [Chimera-users] alignment + missing residues > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <4C402F40.2010604(a)uni-greifswald.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Additionally I downloaded 1JFF and did an alignment with another > tubulin-structure. And still the numbering does not recognize this > gap > between 34 and 61. > > Gesa Volkers schrieb: > > Dear Eric, > > > > thanks for your suggestions. Unfortunately removing the SEQRES > record > > did not help. I also downloaded and installed the new chimera- > version > > today. The false numbering in the alignment still occurs. Also > when I > > remove the SEQRES record and try with the new chimera version the > > false numbering appears. Quite annoying... The pdb-file is not in > the > > protein data bank yet. > > > > Any more suggestions? Could I add "dummy atoms" in the structure? > > > > Thanks, > > Gesa > > > > > > > > Eric Pettersen schrieb: > >> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >> > >>> Dear All, > >>> > >>> I observed an issue with the alignment function of Chimera. > >>> I loaded a crystal structure where in between a loop is not > modelled > >>> due to low electron density- so these residues are missing in > the > >>> structure and the numbering also has this gap. When I align > this > >>> structure with others, the missing residues are not recognized > and > >>> chimera just overrides the numbering so after this loop all the > >>> numbers in the alignment do not fit anymore to the residues > they > >>> should belong to although the structure and numberings are > shown in > >>> the right way in the graphics window. How can I overcome this > issue? > >>> Should I change the pdb-file? In which way? > >>> > >>> Thanks for all responses! > >> > >> Hi Gesa, > >> I had a similar problem reported with 1JFF 12 days ago and > haven't > >> yet worked on fixing it. It seems to only happen for a small > subset > >> of structures. 1JFF has a missing loop and also exactly one > missing > >> residue at the N terminus. Is your structure like that? Is it > a > >> standard PDB entry (if so, what's the ID code)? I'll add you to > the > >> recipient list for the ticket we have open in our bug database > for > >> this (#8585) so you will be notified when it gets fixed. It'll > >> probably be fairly soon. > >> Until then the only workaround that occurs to me is for you to > remove > >> the SEQRES records from the PDB file before you open it. Then > the > >> Sequence viewer will depict only the residues physically present > in > >> the structure -- no gaps (incorrect or otherwise) will be depicted. > >> > >> --Eric > >> > >> Eric Pettersen > >> > >> UCSF Computer Graphics Lab > >> > >> http://www.cgl.ucsf.edu > >> > >> > >> > > > > > > > -- > Gesa Volkers > Institut f?r Biochemie, Molekulare Strukturbiologie > Felix-Hausdorff-Stra?e 4 > 17489 Greifswald > Germany > +49 (3834)-864392 > > > > > ------------------------------ > > Message: 3 > Date: Fri, 16 Jul 2010 10:32:39 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] alignment + missing residues > To: Gesa Volkers <gesa.volkers(a)uni-greifswald.de> > Cc: chimera-dev(a)cgl.ucsf.edu, chimera-users(a)cgl.ucsf.edu > Message-ID: <CF134751-B951-403B-B9E3-E441DB44644D(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Gesa, > I suspect you are using a Mac, since the daily builds failed last > night for the Mac platforms. You need to get a daily build dated > July > 16 or later. I tried opening the sequence view for 1JFF in one of > the > successful daily builds and it was correct, e.g.: > > > > You can see that the interior gap is correctly recognized now. > Hopefully the daily builds on the Mac platforms will work tonight. > > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > > Ah, the "remove SEQRES records" hack will only work for the single- > sequence viewer, not an alignment. I tested that in the 1.4.1 > release > and it indeed worked as I expected: > > > > The whole sequence is smushed together with no gaps, but the > correspondences are correct. You could then align additional > sequences to the smushed sequence and the correspondences would > remain > correct. Nonetheless it's probably simply better to wait for a > daily > build to succeed than to use the hack now. So make sure you check > the > date in the download table. If you still have problems with a > release > later than July 16, let me know. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Jul 16, 2010, at 3:06 AM, Gesa Volkers wrote: > > > Additionally I downloaded 1JFF and did an alignment with another > > tubulin-structure. And still the numbering does not recognize > this > > gap between 34 and 61. > > > > Gesa Volkers schrieb: > >> Dear Eric, > >> > >> thanks for your suggestions. Unfortunately removing the SEQRES > >> record did not help. I also downloaded and installed the new > >> chimera-version today. The false numbering in the alignment > still > >> occurs. Also when I remove the SEQRES record and try with the > new > >> chimera version the false numbering appears. Quite annoying... > The > >> pdb-file is not in the protein data bank yet. > >> > >> Any more suggestions? Could I add "dummy atoms" in the structure? > >> > >> Thanks, > >> Gesa > >> > >> > >> > >> Eric Pettersen schrieb: > >>> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote: > >>> > >>>> Dear All, > >>>> > >>>> I observed an issue with the alignment function of Chimera. > >>>> I loaded a crystal structure where in between a loop is not > >>>> modelled due to low electron density- so these residues are > >>>> missing in the structure and the numbering also has this gap. > >>>> When I align this structure with others, the missing residues > are > >>>> not recognized and chimera just overrides the numbering so > after > >>>> this loop all the numbers in the alignment do not fit anymore > to > >>>> the residues they should belong to although the structure and > >>>> numberings are shown in the right way in the graphics window. > How > >>>> can I overcome this issue? Should I change the pdb-file? In > which > >>>> way? > >>>> > >>>> Thanks for all responses! > >>> > >>> Hi Gesa, > >>> I had a similar problem reported with 1JFF 12 days ago and > haven't > >>> yet worked on fixing it. It seems to only happen for a small > >>> subset of structures. 1JFF has a missing loop and also exactly > > >>> one missing residue at the N terminus. Is your structure like > >>> that? Is it a standard PDB entry (if so, what's the ID code)? > >>> I'll add you to the recipient list for the ticket we have open > in > >>> our bug database for this (#8585) so you will be notified when > it > >>> gets fixed. It'll probably be fairly soon. > >>> Until then the only workaround that occurs to me is for you to > >>> remove the SEQRES records from the PDB file before you open it. > > >>> Then the Sequence viewer will depict only the residues > physically > >>> present in the structure -- no gaps (incorrect or otherwise) > will > >>> be depicted. > >>> > >>> --Eric > >>> > >>> Eric Pettersen > >>> > >>> UCSF Computer Graphics Lab > >>> > >>> http://www.cgl.ucsf.edu > >>> > >>> > >>> > >> > >> > > > > > > -- > > Gesa Volkers > > Institut f?r Biochemie, Molekulare Strukturbiologie > > Felix-Hausdorff-Stra?e 4 > > 17489 Greifswald > > Germany > > +49 (3834)-864392 > > > > > > > > >

3 2

alignment + missing residues
by Gesa Volkers 20 Jul '10

20 Jul '10

Dear All, I observed an issue with the alignment function of Chimera. I loaded a crystal structure where in between a loop is not modelled due to low electron density- so these residues are missing in the structure and the numbering also has this gap. When I align this structure with others, the missing residues are not recognized and chimera just overrides the numbering so after this loop all the numbers in the alignment do not fit anymore to the residues they should belong to although the structure and numberings are shown in the right way in the graphics window. How can I overcome this issue? Should I change the pdb-file? In which way? Thanks for all responses! -- Gesa Volkers Institut für Biochemie, Molekulare Strukturbiologie Felix-Hausdorff-Straße 4 17489 Greifswald Germany +49 (3834)-864392

2 5

Positions Available in Electron Crystallography of Membrane Proteins
by Iban Ubarretxena 14 Jul '10

14 Jul '10

Positions Available: Electron Crystallography of Membrane Proteins A number of different positions are available with the Transcontinental Electron Microscopy Initiative for Membrane Protein Structure (TEMIMPS;http://temimps.nysbc.org) TEMIMPS is a new center funded by the NIH Protein Structure Initiative and is composed of five research groups with combined expertise in membrane protein production, 2D crystallization, electron microscopy, image processing, and structure determination. Our center will focus on the development and implementation of high-throughput and high-resolution approaches to structure determination of membrane proteins using cryo-electron microscopy and 2D crystals. We are seeking highly motivated individuals with good communication skills and ability to interact with an interdisciplinary group ranging from biochemists to mathematicians. Individual positions will be available in New York, Cleveland, Seattle and Houston, working in the laboratories of Drs. David Stokes, Iban Ubarretxena, Andreas Engel, Tamir Gonen and Pawel Penczek. These positions include a project manager, postdoctoral associates, software engineers and technical staff; up-to-date descriptions of the individual positions can be obtained at http://temimps.nysbc.org/jobs . Further questions or applications should be sent to temimps(a)nysbc.org. Applications should include a cover letter, a curriculum vitae and contact information for three referees. Applications will be reviewed as they are received and will continue until the positions are filled. Iban Ubarretxena-Belandia, PhD Assistant Professor Dept. Structural and Chemical Biology Mount Sinai School of Medicine Icahn Medical Institute Bldg., Room 16-70E 1425 Madison Avenue, Box 1677 New York, NY 10029 Office: 212-659-5593 Fax: 212-849-2456 Email: iban.ubarretxena(a)mssm.edu WWW: http://www.mssm.edu/physbio/ This e-mail is confidential and may well also be legally privileged. If you have received it in error, you are on notice of its status. Please notify us immediately by reply e-mail and then delete this message from your system. Please do not copy it or use it for any purposes, or disclose its contents to any other person: to do so could be a breach of confidence. Thank you for your co-operation

1 0

volume and area measurements
by Chinthaka Silva 13 Jul '10

13 Jul '10

Hi, Could you please tell me what is the difference between the values we get from the following two options? Volume Viewer: Tools --> Measure Volume and Area Tools --> Volume Mean, SD, RMS Is SD means standard deviation? What is RMS? In the 2nd option, we get 'Surface V and A'. What does 'Surface' mean in here? Thanks, Chinthaka.

2 2

SAXS Profile
by yann sterckx 13 Jul '10

13 Jul '10

Dear all, I'm trying to run the SAXS Profile Option in Chimera, but it doesn't seem to work properly. Every time I try to run the option, I get the following error message. Error processing trigger "check for changes": HTTPError: HTTP Error 504: Gateway Time-out File "/Applications/Chimera.app/Contents/Resources/lib/python2.6/urllib2.py", line 516, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) See reply log for Python traceback. I work in Snow Leopard. Can anybody help me out? Thanks, Yann

2 2

Fwd: request for stick and ball size in Atoms/Bonds menu
by Bala subramanian 12 Jul '10

12 Jul '10

Friends, I apologize that i sent the following mail wrongly to chimera-bugs. So i am fwdg it to the users list once again. ---------- Forwarded message ---------- From: Bala subramanian <bala.biophysics(a)gmail.com> Date: Mon, Jul 12, 2010 at 7:18 AM Subject: request for stick and ball size in Atoms/Bonds menu To: chimera-bugs(a)cgl.ucsf.edu Dear developers, Greetings. I downloaded a recent daily builds (July 8th) and I am quite happy to see the new additions on the Atoms/Bonds menu. I thank you all for your effort. I would like to request you for the addition the Stick and Ball size settings in the Atoms/Bonds menu. Because when i change the stick/Ball size from preference-New molecules option. I am not able to see the change for the molecule presently loaded in Chimera. It would be of great help to have this option in Atoms/Bonds menu itself. Regards, Bala

2 1

Structural alignment of a protein-ligand complex with other ligands only
by N.R. Jena 09 Jul '10

09 Jul '10

Hi, We are new to Chimera. Can you please let us know, if we have to superpose a protein-ligand complex with other ligands or a DNA-protein complex with few nucleotide-peptide complex, what is the better way to do in Chimera. I guess MatchMaker option is meant for superposition of one DNA or Protein on another DNA or Protein, right?

2 1

Best density map contour level
by Thomas Goddard 08 Jul '10

08 Jul '10

Hi Maria, Unfortunately I don't think your procedure for setting the contour level will work very well. The problem is that the isosurface is not just the outside surface of the capsid. Usually the virus genome has lower density then the protein capsid so there contour surface may show the virus as hollow, or maybe layers of RNA/DNA will appear. So the expected volume is not going to be the volume of a solid ball. There are no well accepted standards for how to set the contour level when showing EM maps. On the other hand there probably is no "right" answer. A good level for looking at the protein capsid will be different from a good level for looking at the genome packing. If a capsid feature of an icosahedral virus does not appear at all 60-fold symmetric locations then symmetry averaged maps will show lower density and you will need a lower contour level to see such features. In practice I believe people analyzing map primarily choose the contour level by eye that best suits their analysis. Tom > Hi Tom, > > Thank you very much for your help. > I'll measure the radius of my 2 d images afterwards I'll use the radius to calculate the volume of my virus and finally > set the contour level so that this volume is enclosed. > > Thanks a lot, > Maria > > >> Hi Maria, >> >> Chimera shows the volume data as an "isosurface" meaning all points >> on the surface are at a specific map value. That map value is called >> "level" in the volume viewer dialog. The values in a map (volume data >> file) determined by electron microscopy are often not normalized in any >> way -- useful values could be 10000 or 0.1 depending on the map. For >> x-ray maps it is common to normalize so that standard deviation over the >> unit cell is 1.0. In EM there no unit cell so the standard deviation >> would depend on how big a box surrounded the virus density -- so this is >> not as useful a normalization. There is no standard accepted EM map >> normalization that I know of. If you knew the expected volume occupied >> by the structure you could set a contour level so that the surface >> encloses that volume. Here's an explanation of how to do that in Chimera >> >> >> http://www.cgl.ucsf.edu/chimera/tutorials/eman07/chimera-eman-2007.html#par… >> >> More often you just visually choose a level that you believe gives a >> surface matching the envelope of the proteins in the structure. The map >> mean, standard deviation and root mean square value can be calculated >> with menu entry >> >> Tools / Volume Data / Volume Mean, SD, RMS >> >> Tom >> >> >> >>> Dear Chimera users, >>> >>> I'm using Chimera to inspect my calculated density maps of viruses. In >>> order to compare different tree d reconstructions I would like to know >>> what the 'Level' value in Volume Viewer dialog means. At present I'm using >>> the level value 1 but I'm not sure if this is correct. >>> >>> Could you please give me some advice how to define the right contouring >>> threshold to present my data in order to inspect it? >>> >>> Thank you for your help, >>> >>> Maria L. >>> >>

1 0

Alternative to the model panel
by Varela, Lawrence Rocco 07 Jul '10

07 Jul '10

Chimera seems to be consistently crashing or slows down drastically when I open the model panel when I have a lot of molecules loaded (200 or more). I'm often times looking at hundreds of small molecules and there relative conformations which requires me to load such big data sets. Is there an alternative to using the model panel? Like for example writing to file all the info that displays in the model panel including most importantly the model ids? Thanks in advanced, --Rocco

2 1

structural alignment
by Bala subramanian 07 Jul '10

07 Jul '10

Friends, I have 10 conformations of the same RNA molecule obtained from 5 separate MD simulations. Now to compare the conformations, I want to make a structural alignment of these conformations and make an alignment map ( something like multiple seq. alignment for protein ) so as to show residues (or residue positions) that higher flexibility among these ten conformations. What is the best way to do it in Chimera. Thanks, Bala

2 4

Parameters choice for match->align and quality assessment
by compchem compchems 06 Jul '10

06 Jul '10

Dear Chimera developers, great thanks to you for possibility to work with your very useful program. I am new in structural alignment studies and have some questions about parameters in match->align. My set cosists of few closely related proteins with same function and conservative spatial structure, but with some divergence in aminoacid sequences except of conservative functional residues. First, what "Residue aligned in column if within cutoff of" influences on and what preferable choice may be in my case. Second, "Superimpose full column" - how can i decide what to select for my set or what play can help me. Third, how can i evaluate quality or correctness of obtained alignment (may be, common procedure). I am sorry for long letter and thanks for your attention to my problem. D. Yegorov.

2 3

(no subject)
by Maria Ingrid Liebl 06 Jul '10

06 Jul '10

Dear Chimera users, I'm using Chimera to inspect my calculated density maps of viruses. In order to compare different tree d reconstructions I would like to know what the 'Level' value in Volume Viewer dialog means. At present I'm using the level value 1 but I'm not sure if this is correct. Could you please give me some advice how to define the right contouring threshold to present my data in order to inspect it? Thank you for your help, Maria L.

2 1

movie panel
by Susan Tsutakawa 02 Jul '10

02 Jul '10

Dear Users List, I apologize for these novice questions. I looked in the archives and could not find it. How do I get a MD molecular movement panel if I accidentally close it or I start a new session? I made a morph and I can see it on the model panel. Another very novice question is how do I delete a pdb in my model panel. Thank you in advance. Sincerely, Susan

2 2

Chimera Installation - NOVELL SUSE Enterprise Linux Desktop 11 (64bit)
by Madhumita Pattanayak 01 Jul '10

01 Jul '10

Request you let me know, whether the following specification will support the installation of Chimera: Operating System Novell SUSE Enterprise Linux 11 (64 bit) Processor Intel® Core?2 Duo Processor E8400 Chipset Intel® Q43 Express Memory (RAM) 4 GB PC-3-10600 (1333 MHz) DDR3 SDRAM Memory Graphics ATI Radeon HD 3470 256MB Appreciate an early reply in this regard. Many thanks for your help. Regards, Madhumita Senior Research Fellow CCMB, Hyderabad India "The person addressed in the email is the sole authorized recipient. Should you receive it in error, immediately notify the sender of the error and delete the e-mail. Any unauthorized dissemination or copying of this e-mail (or any attachment to this e-mail) or the wrongful disclosure of the information herein contained is prohibited. Also note that this form of communication is not secure, it can be intercepted, and may not necessarily be free of errors and viruses in spite of reasonable efforts to secure this medium."

2 1

renumber model IDs
by Dougherty, Matthew T 24 Jun '10

24 Jun '10

There are a number of times I would like to change the model ID numbers. Sometimes it is because a researcher gives me a session file that has sequences like monomer-b, monomer-d, monomer-a, monomer-c; or sometimes when I got an easy sequence to memorize (monomer-a, monomer-b, monomer-c, monomer-d), I do a colorzone split map that causes sequence names to comeback in a different order (monomer-b, monomer-d, monomer-a, monomer-c). Is there a way using commands to maintain better ID order?

1 0

Re: [Chimera-users] structure based sequence alignment
by Eric Pettersen 24 Jun '10

24 Jun '10

Hi Sonya, On Jun 24, 2010, at 7:39 AM, Sona Vasudevan wrote: > Hello Eric, > > Thanks for all the great features you have added in the last couple > of years since I was last in touch with you. This is a fantastic tool! Thanks! Glad you like it. > I need some help with the alignment editor. > > I am trying to import an alignment in fasta format (fasta aligned) > (see attached). The alignment as you can see has three structures. I > use Load structures from the sequence > window and it brings in all the chains corresponding to teh > structures. It does, but there's a subtlety here that I should point out. The first two sequences in the alignment are for 1XVA, chain A and chain B. Chimera opens two copies of 1XVA and associates one copy with each sequence, but it associates chain A in both, since the sequences of the two chains are identical. It doesn't really look at the sequence name to try to figure out which chain to associate, just how well the sequences match and in this case they both match perfectly. By hovering the mouse over the sequence name you can see which structure/ chain it is associated with. To change the association of the second sequence to use chain B, you need to go to the alignment's Structure menu and choose "Associations...". Thus will bring up a panel showing the association of each structure to a sequence. Change the association of "1xva (#1)" from "chain A" to "chain B" and then click OK. > I then use Matchmaker to align them. I have a few questions: > > 1. Does the match maker use the info from the imported alignment > since the structures are already aligned? In other words is the > structural alignment I am seeing the saem as that was imported. No. MatchMaker is its own tool and doesn't use any open alignments. After all, you could have several alignments involving those structures open. If you want to superimpose the structures based on your alignment, use the alignment's own "Structure->Match" menu item. That brings up a dialog offering a variety of options as to how to carry out the match. I like using the "Iterate" option, but it's totally up to you. > 2. Is there a way to just output the superposed co-ordinates without > the chains that are not being used? There are probably several ways. One that comes to mind is to click on one of the alignment's "Consensus" letters to select all the residues in that column. Then click into the graphics window and hit the up-arrow key to expand the selection to the entire chain. Then either choose Select->Invert or hit right-arrow to invert the selection -- now the unused chains are selected. Actions->Atoms/Bonds- >delete will delete them. You can then write out what's left. Keep in mind that if you want to get model 2's coordinates as superimposed with model 0's original coordinates (for instance) then make sure to use the "relative 0" option in the "write" command or check the "Save relative to" option in the Write PDB dialog and choose model 0. Or you could just write out all models current coordinates. They will all differ from their originals, but they will be superimposed. > 3. Looks like I can add sequences to the alignement. Can I add a > fasta file with many sequences? No. It is on my to-do list but I haven't gotten to it yet. I'll open a feature-request ticket in our Trac database with you on the recipient list so you'll know when it gets implemented. Sorry! > Thanks so much! I have alignment files for 100 families which are > high-qualityas they were manually aligned with Cn3d and I would like > to import them into chimera for further analysis. > > Thanks so much for your time! You're welcome! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Paint a pseudobond....
by Yasser Almeida Hernández 24 Jun '10

24 Jun '10

Hi... I want to connect two atoms that belongs to different models with a pseudobond. It's that possible with Chimera? If it does, how would be the Python API code? 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

2 1

Question about attribute assignment file
by Peng Ni 24 Jun '10

24 Jun '10

Hi, I am trying to use the define attribute function. However, the attribute assignment sheet I generated cannot be read. It reports: "Line 1 of file is either not 'name: value' or is missing initial tab". I cannot spot anything wrong in my txt file, which is also attached in the e-mail. I'd greatly appreciate it if you could help me fix this problem. Regards Peng

2 1

Lost hydrogens when saving mol2 file
by Varela, Lawrence Rocco 23 Jun '10

23 Jun '10

I'm encountering a problem where I'm loosing hydrogens from my small molecules after saving them in Chimera. Here is the situation: the original mol2 file I open has a number of small molecules listed under separate MOLECULE tag identifiers. Using the GUI menu I select "save Mol2", select all the models to save, and select the Save multiple models in "a single file [combined @MOLECULE section] option. When I open the newly saved Mol2 file with the combined MOLECULE section it's obvious that the hydrogens have been removed. How do a save multiple models in a combined MOLECULE section without loosing any hydrogen atoms? Thanks :-) Rocco

2 3

PDB
by Dougherty, Matthew T 23 Jun '10

23 Jun '10

Hi, When PDF files are read by Chimera and the session is written, the PDB data becomes part and parcel with the session files. That is, Chimera does not go back to the PDB files when it reloads the session, it uses the PDB data within the session file instead; as contrasted to density volume files, which are referenced by the session file, and the density volume files reloaded when the session file is read by Chimera. Is there a way to force the session file not to save the PDB internally to the session file, and instead reference and interact with it similar to the way volume files are managed? Matthew

2 4

Grouping Molecules
by Varela, Lawrence Rocco 23 Jun '10

23 Jun '10

Is there a way of grouping molecules in Chimera? Here is my situation. I have 4 molecules A, B, C, and D and I want to group A with B and C with D so that A and B has one center of rotation and C and D has another center of rotation. Rocco

2 1

Fwd: Chimera 3-D viewing
by Eric Pettersen 22 Jun '10

22 Jun '10

Forwarding Ed Pate's question (below) to this list, in the hope that someone who actually knows the answer can chime in! --Eric Begin forwarded message: > From: Edward Pate <edpate(a)hotmail.com> > Date: June 19, 2010 2:39:09 PM PDT > To: <pett(a)cgl.ucsf.edu> > Subject: Chimera 3-D viewing > > Hi Eric: > > I am looking into getting a new workstation for Chimera. In the > past, we have gotten CRT displays in order to do 3-D visualization. > Could you recommend other display options that are available now and > that users have been happy with? Is a CRT still the best option? > > Thanks for the help. > > Ed

3 2

vop binning
by Katrina Lexa 21 Jun '10

21 Jun '10

Hello - Is the volume data (vop) code available somewhere? Particulary the code for binning electron densities? I'm interested in looking at how chimera handles xplor files since I want to find the density of solvent at the edges of my grid. I would love to try to play with the volume code in order see if it can be done through chimera. Thank you, Katrina

2 3