- Chimera-users - RBVI Mailing Lists

Small molecules and orbitals/ESP's
by Kenward Vaughan 30 Aug '14

30 Aug '14

Hi all, I am searching for a way to show small molecules with orbitals and potential surfaces from their associated QM calculations, in stereos display using our planned 3D vision setups. Cross eye works well for some in a class, but mant students simply never get it. It doesn't appear that any small molecule viewers are out there with such capability. Is there some way to pull such information into Chimera to do this? Kenward -- In a completely rational society, the best of us would aspire to be *teachers* and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca

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Question: how can I render pseudobonds visibly when saving as Chimera-highres-image]
by Dietlind Gerloff 29 Aug '14

29 Aug '14

Dear Elaine and Tom and other Chimera-developers/maintainers, I cannot tell you how much I admire (and appreciate) what you have done with Chimera !!! I am just getting the last touches on a collaborative paper with colleagues from the University of Edinburgh and I used Chimera for much of the modelling of a large protein (Condensin) and for lovely images as well. We'll make sure we give you proper credit! One thing I'm having problems with - I am now trying to save image in high-resolution (600dpi) that show pseudo bonds Each pseudobond highlights a distance constraint, i.e. they are drawn by the distance function/monitor and are visible beautifully on the screen. However, when I save (as .png, .jpg or whatnot) the pseudo bond doesn't scale, i.e. becomes so thin compared to the regular bonds that it cannot be seen unless one zooms in like mad. Doesn't matter how wide I ask the pseudo bond to be on the display. Is there a way to change the preferences for how (thick) pseudo- bonds are rendered when I save an image using Chimera-rendering? Sorry to bug you so close to Labor Day weekend but if you had a quick answer (even if there isn't) that would help. Alternatively I could maybe draw lines/bonds but it seems such a pity since the pseudobonds are so beautifully telling the story on my screen ... in the worst case, we'll screen shot for now, of course ;-) Cheers and again I have become a Chimera fan recently and I am now telling students and coworkers to use it instead of PyMOL - also because of the amazing tutorials and help pages. W-O-W !!! Dietlind *Elaine, in case you don't remember me - I was a postdoc with Fred Cohen when you were in Tack's lab in the Midas days a long long time ago :-) -------------------------------------------- Dietlind L Gerloff, PhD Senior Fellow Foundation for Applied Molecular Evolution (FfAME) Gainesville, FL 32604 email: dgerloff(a)ffame.org --------------------------------------------

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scan and minimization of dihedral angle
by Milo Westler 28 Aug '14

28 Aug '14

Hi, I want to to a potential energy scan of a dihedral (of a small organic molecule) by setting a dihedral angle, fixing those atoms involved, and doing a minimization. Then incrementing the angle and repeating. I can currently do all of this by using the gui (set torsion angle in build_structure,minimize with selected atoms fixed , then save and edit the final energies for each angle in reply log). I'm sure that this can be done with python. I am wondering if there is an available script to do this all. As input I would have a set of torsion angles and as output I would like a table of angle and energy. -- -- Milo =================================================== National Magnetic Resonance Facility at Madison An NIH-Supported Resource Center W. Milo Westler, Ph.D. NMRFAM Director Senior Scientist and Adjunct Professor Department of Biochemistry University of Wisconsin-Madison DeLuca Biochemistry Laboratories 433 Babcock Drive Rm B160D Madison, WI USA 53706-1544 EMAIL: milo(a)nmrfam.wisc.edu PHONE: (608)-263-9599 FAX: (608)-263-1722 ======================================================================= ========

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Re: [Chimera-users] Edge visualisation
by Tom Goddard 28 Aug '14

28 Aug '14

Hi Petr, You are right about the Measure and Colors Blobs tool — the “Show principle axis box” option shows a box aligned with the moment of inertia principle axes. I was mistaken in my previous email. The behavior is described in the documentation (almost every Chimera feature is described in great detail) — just press the Help button on the Measure and Color Blobs dialog to see: "Show principal axes box [color well] - whether to show a bounding box in the specified color (default green) for each subsequently picked blob. A blob's bounding box is aligned with its principal axes of inertia, calculated assuming a constant mass per unit surface area.” The Laplacian filtering is again described in the documentation. If you use the Volume Filter dialog press the Help button to see the documentation, or if you use the “vop laplacian” command you can see the documentation with command “help vop”. Anyways here’s what the docs say: "Laplacian filtering. The Laplacian operation is a sum of second derivatives. Laplacian filtering is useful for edge detection but amplifies noise, so it may be necessary to perform smoothing such as Gaussian filtering beforehand. Finite differences v(i-1)-2*v(i)+v(i+1) along each axis are used, and voxels at the edge of the box are set to zero.” You referred in your email to “second derivatives” and comparing them to zero. I thought you meant the six independent second derivatives that make up the Hessian. I guess meant the Laplacian (sum of second derivatives along x, along y, and along z. When you run Laplacian or Gaussian filtering or any other map filter in Chimera it makes a new copy of the map. Chimera does not save maps in session files. So if you want that Laplacian map to appear in the session file you need to save the map to its own file before saving the session. You do this with the Volume Viewer dialog menu File / Save Map As…. This is a pain, and some day we will allow the option to save the maps in the session file (even though they can be very large). The session also does not save information about how to recalculate your Laplacian map, so you have to save that map separately for sessions to restore it. Tom On Aug 28, 2014, at 1:08 AM, Petr Brazda wrote: > Hello Tom, > > Thank you for your answers and comments. I will try to work on this evaluation with my colleague, who is a skilled programmer. I think that measure and color blobs tool works differently (at least the boxes are not aligned with the data axes) - it finds the largest diameter and puts it as the "x axis", then finds the largest perpendicular diameter (y axis). I got two more questions: > > 1) how exactly is the laplacian calculated? I found this > https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/gaus…. If I understand it well it says that it calculates only non-mixed differences along x, y, and z axes (no diagonal direction, no dxdy...) and you write that the second derivative is in fact Hessian. Could you please precise this? > > 2) I wanted to save a session where I have overlapped density and its lapacian filter and I had to save this filter to be able to save the session. However, when I reopened the lapla. filtered data, there was only one bar in the histogram in the surface style, which makes the map unusable for me so now I have to do the filtering and subregion setting each time I begin with the analysis. Is there a possibility to add another bar into the histogram? > > Thank you, > > Petr > > -- > ________________________________________ > Petr Brazda > Institute of Physics of the ASCR, v.v.i. > Cukrovarnicka 10/112 > 16200 Prague 6 > Czech Republic

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Molecular Representations
by Jian Guan 28 Aug '14

28 Aug '14

Dear all, I have one question about the Molecular Representations. In chimera, molecule can be represented by ball and sphere. Sphere is with the VDW radius for atoms and stick bonds. What about the ball? What is the ball size? I tried to measure the distance between two molecules. I used command line of "measure distance #1 #2". It shows closest distance between two sets of atoms. When I made surface map for the same two molecules, I used the same command, it showed different number. I understand it is the distance of VDW. But what is the distance between atoms if I used PDB file instead of surface map? Which one is more reliable? Thanks, Jian

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Adding Hydrogens to Dexomethasone Misses 1 Atom
by BATUHAN KAV 27 Aug '14

27 Aug '14

Dear All, I am trying to add hydrogen atoms to dexomethasone ligand. In the original PDB file, there are two dexomethasone molecules. So, I create split them into two different PDB's. Then, I load them and use addH option. In one PDB (sil.pdb), everything works fine and all hydrogens are added successfully. However, in the other pdb (which I name as other.pdb), one hydrogen atom is missing. I will use these files for further parametrization in AMBER, so this is really important. I looked through the files over and over again but couldn't find any reason for this apparent difference. What am I missing? I also attach the files. Any help would be greatly appreciated. Cheers

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Re: [Chimera-users] Edge visualisation
by Tom Goddard 26 Aug '14

26 Aug '14

Hi Petr, Chimera doesn’t have much to help you measuring nano-crystals, since it is designed for molecular visualization. First I think the chance that Laplacian filtering will help you find edges of the crystals is small, because even a small amount of noise will be amplified greatly by the second derivative calculation. Perhaps by doing Gaussian smoothing first, followed by Laplacian filtering you can get something useful, but it depends on your data. The Chimera “measure and color blobs” tool only finds a bounding box aligned with the data set axes (density map x, y, and z axes). It has no capability to rotate to find the tightest box. There is a “measure intertia” command that computes the principle moment axes of atoms or a surface, which might find the nanocrystal axes if you could produce a surface of just one nano-crystal. But then there is no tool to use those axes and find the tightest box. Chimera does not have a specific capability to find a surface of a density map located where second derivative is near zero and first derivative is large. You could attempt to code something like this as a Python script for Chimera but I think it would be unlikely to work unless you have perfect data. I think you will get holes in the surface because of places where the second derivative becomes too large or first derivative too small. Your idea is good in theory, but I just don’t think it is likely to work with real noisy data. A few more comments about looking at a surface where the second derivative is near zero. If you want to show a range of second derivative values near zero, then that defines a volume, maybe a thin shell, not a surface. You can show that as bounding isosurfaces at the minimum and maximum allowed second derivative values. The second derivative is a 3x3 matrix (Hessian) so I think you probably are actually interested in the second derivative along the gradient direction being zero. Chimera doesn’t have any tool that analyzes the second derivative along the gradient direction. Your requests are all specialized and outside the realm of what Chimera is designed for. So Chimera doesn’t do these things, and quite likely no other software does either. To try your ideas will likely require that you do some programming. Tom On Aug 25, 2014, at 5:33 AM, Petr.Brazda(a)seznam.cz wrote: > Hello Tom, > > thank you for the answer. I have now a more complex question. I would like to extract dimensions and volumes of the nanocrystals embedded in a matrix. The problem is that the edges of the crystals are blurred and the density of the whole particle (crystals+matrix) increases slightly towards the centre of the particle. I started to use inflection point as a point where the crystal ends/begins. I found out that there is a Laplacian volume filter in Chimera, which would help me with the analysis. However, there are some problems. > > 1) Theoretically, the second derivative of the inflection point (where the particle ends/begins) is zero, but unfortunately it is also (close to) zero for the matrix and crystals in their "cores". Therefore, is it possible to visualize points, which have nearly zero (including the adjustment of the density (value) limits how far I want to go from zero) second derivative while having the first derivative "far" from zero (with possible adjustment of the density (value) "far")? I think that this filtering would show the real edges of the crystals (maybe there is a better option, as I said I am a complete newbie). > > 2) I would like to use "measure and color blops tool" for measuring the dimensions of the crystals. The crystals have developed crystal faces. Crystal structure is orthorhombic, so using three orthogonal axes for the measurement is optimal for me. However, the setting of the box axes is usually useless for me, because the axes of the box are not parallel with the crystallographic ones. Is it possible to rotate/adjust the box so it would measure the distances I want? Or is there an other option how to measure dimensions of a crystal in three orthogonal directions? > > 3) As I said in the beginning I also need the volume of the particles. Therefore, it would be optimal if Chimera would connect voxels with 2nd derivative about zero and 1st derivative far from zero and define them as the "surface" of the particle. Is such tool available in Chimera? There is a problem when the maximum in the 1st derivative is not so sharp and "noisy" so it is possible that there will be some range where the 2nd derivative will be close to zero/oscillate about zero so some "real minimum on the 2nd derivative" will be maybe necessary. > > Petr > > > ---------- Původní zpráva ---------- > Od: Tom Goddard <goddard(a)sonic.net> > Komu: Petr.Brazda(a)seznam.cz > Datum: 22. 8. 2014 17:58:21 > Předmět: Re: [Chimera-users] Intensity range shift > > > Yes, you can shift the density values with volume dialog menu Tools / Volume Filter, filter type Scale. Or you can do it with the volume operation command, e.g. "vop scale #0 shift 100” described in the manual > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#scale > > Tom > > On Aug 22, 2014, at 5:22 AM, <Petr.Brazda(a)seznam.cz> <Petr.Brazda(a)seznam.cz> wrote: > > > Hello, > > > > I would like to ask whether there is a possibility in Chimera to shift the intensity range. I have tomography data, which range from -32000 to 10000 in intensity. A would like to gradually erase parts of the tomogram with volume eraser but it is not possible because the intesity range does not start at zero. It is not possible to do the job with subregion selection. Is there a way to shift the intensity range? > > > > Petr > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Assigning pre-calculated attribute to B-factor column of pdb
by Oliver Clarke 26 Aug '14

26 Aug '14

Hi all, Is there an easy way to assign a pre-calculated attribute (for example, ramachandran probability) to the b-factor (or occupancy) column of a pdb file using chimera? I’d like to do this so I can color a pdb by ramachandran probability (or other custom attributes, e.g map-model correlation) and use it as a guide while rebuilding in Coot (which has options for coloring by b-factor or occupancy, but no other capacity for custom coloring of molecules). Best, Oliver.

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Export data to .xplor format
by Petr.Brazda＠seznam.cz 26 Aug '14

26 Aug '14

Hello, I would like to ask if it is possible to export the density map (.rec) to . xplor format. Petr

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Movie trajectory/restart header greater than 80
by Francesco Pietra 25 Aug '14

25 Aug '14

Hallo: I am trying to replay some old movie of molecular dynamics trajectories (Amber prmtop/dcd). At that time (a couple of years ago I had Chimera of those times) I get the following error message IOError: Trajectory/Restart header line is greater than 80 characters -- invalid! File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 354, in SetupFrame raise IOError, "Trajectory/Restart header line is greater than 80 characters -- invalid! See reply log for Python traceback. The latter reads: <type 'exceptions.IOError'> Exception in Tk callback Function: <function command at 0x315ccf8> (type: <type 'function'>) Args: () Traceback (innermost last): File "/opt/UCSF/Chimera64-1.7/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 704, in OK self.Apply() File "/opt/UCSF/Chimera64-1.7/share/Trajectory/EnsembleLoader.py", line 92, in Apply self.callback) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line 60, in loadEnsemble callback) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line 73, in loadEnsemble ensemble = Prmtop_Traj(prmtop, trajectory, startFrame, endFrame) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 191, in __init__ self.trajectory.addFile(trajectory) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/__init__.py", line 183, in addFile self.trajs.append(self.addFunc(trajFile)) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 190, in <lambda> lambda f: Trajectory(self.prmtop, f)) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 264, in __init__ self.SetupFrame() File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 354, in SetupFrame raise IOError, "Trajectory/Restart header line is greater than 80 characters -- invalid!!" <type 'exceptions.IOError'>: Trajectory/Restart header line is greater than 80 characters -- invalid!! IOError: Trajectory/Restart header line is greater than 80 characters -- invalid!! File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 354, in SetupFrame raise IOError, "Trajectory/Restart header line is greater than 80 characters -- invalid!!" See reply log for Python traceback. <type 'exceptions.IOError'> Exception in Tk callback Function: <function command at 0x4732230> (type: <type 'function'>) Args: () Traceback (innermost last): File "/opt/UCSF/Chimera64-1.7/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 704, in OK self.Apply() File "/opt/UCSF/Chimera64-1.7/share/Trajectory/EnsembleLoader.py", line 92, in Apply self.callback) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line 60, in loadEnsemble callback) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line 73, in loadEnsemble ensemble = Prmtop_Traj(prmtop, trajectory, startFrame, endFrame) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 191, in __init__ self.trajectory.addFile(trajectory) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/__init__.py", line 183, in addFile self.trajs.append(self.addFunc(trajFile)) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 190, in <lambda> lambda f: Trajectory(self.prmtop, f)) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 264, in __init__ self.SetupFrame() File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 354, in SetupFrame raise IOError, "Trajectory/Restart header line is greater than 80 characters -- invalid!!" <type 'exceptions.IOError'>: Trajectory/Restart header line is greater than 80 characters -- invalid!! IOError: Trajectory/Restart header line is greater than 80 characters -- invalid!! File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 354, in SetupFrame raise IOError, "Trajectory/Restart header line is greater than 80 characters -- invalid!!" See reply log for Python traceback. <type 'exceptions.IOError'> Exception in Tk callback Function: <function command at 0x4632758> (type: <type 'function'>) Args: () Traceback (innermost last): File "/opt/UCSF/Chimera64-1.7/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 704, in OK self.Apply() File "/opt/UCSF/Chimera64-1.7/share/Trajectory/EnsembleLoader.py", line 92, in Apply self.callback) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line 60, in loadEnsemble callback) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line 73, in loadEnsemble ensemble = Prmtop_Traj(prmtop, trajectory, startFrame, endFrame) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 191, in __init__ self.trajectory.addFile(trajectory) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/__init__.py", line 183, in addFile self.trajs.append(self.addFunc(trajFile)) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 190, in <lambda> lambda f: Trajectory(self.prmtop, f)) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 264, in __init__ self.SetupFrame() File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 354, in SetupFrame raise IOError, "Trajectory/Restart header line is greater than 80 characters -- invalid!!" <type 'exceptions.IOError'>: Trajectory/Restart header line is greater than 80 characters -- invalid!! IOError: Trajectory/Restart header line is greater than 80 characters -- invalid!! File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 354, in SetupFrame raise IOError, "Trajectory/Restart header line is greater than 80 characters -- invalid!!" See reply log for Python traceback. <type 'exceptions.IOError'> Exception in Tk callback Function: <function command at 0x3bd6500> (type: <type 'function'>) Args: () Traceback (innermost last): File "/opt/UCSF/Chimera64-1.7/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 704, in OK self.Apply() File "/opt/UCSF/Chimera64-1.7/share/Trajectory/EnsembleLoader.py", line 92, in Apply self.callback) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line 60, in loadEnsemble callback) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line 73, in loadEnsemble ensemble = Prmtop_Traj(prmtop, trajectory, startFrame, endFrame) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 191, in __init__ self.trajectory.addFile(trajectory) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/__init__.py", line 183, in addFile self.trajs.append(self.addFunc(trajFile)) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 190, in <lambda> lambda f: Trajectory(self.prmtop, f)) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 264, in __init__ self.SetupFrame() File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 354, in SetupFrame raise IOError, "Trajectory/Restart header line is greater than 80 characters -- invalid!!" <type 'exceptions.IOError'>: Trajectory/Restart header line is greater than 80 characters -- invalid!! IOError: Trajectory/Restart header line is greater than 80 characters -- invalid!! File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 354, in SetupFrame raise IOError, "Trajectory/Restart header line is greater than 80 characters -- invalid!!" See reply log for Python traceback. <type 'exceptions.IOError'> Exception in Tk callback Function: <function command at 0x46cb488> (type: <type 'function'>) Args: () Traceback (innermost last): File "/opt/UCSF/Chimera64-1.7/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 704, in OK self.Apply() File "/opt/UCSF/Chimera64-1.7/share/Trajectory/EnsembleLoader.py", line 92, in Apply self.callback) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line 60, in loadEnsemble callback) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line 73, in loadEnsemble ensemble = Prmtop_Traj(prmtop, trajectory, startFrame, endFrame) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 191, in __init__ self.trajectory.addFile(trajectory) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/__init__.py", line 183, in addFile self.trajs.append(self.addFunc(trajFile)) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 190, in <lambda> lambda f: Trajectory(self.prmtop, f)) File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 264, in __init__ self.SetupFrame() File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 354, in SetupFrame raise IOError, "Trajectory/Restart header line is greater than 80 characters -- invalid!!" <type 'exceptions.IOError'>: Trajectory/Restart header line is greater than 80 characters -- invalid!! IOError: Trajectory/Restart header line is greater than 80 characters -- invalid!! File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 354, in SetupFrame raise IOError, "Trajectory/Restart header line is greater than 80 characters -- invalid!!" See reply log for Python traceback. Thanks for advice as to reply those movies francesco pietra

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3D printing a viral capsid
by Jeremiah Gassensmith 22 Aug '14

22 Aug '14

Hello I’m trying to produce an STL file from a model I have built in Chimera but it comes out incredibly deformed. I have created the model from a PDB file of a viral coat protein such that it is fully assembled into the proper capsid structure. You can see the model I’ve created here: https://dl.dropboxusercontent.com/u/9856122/CAPSID.py Problem is, when I export to STL and open in Blender I get a squished unrecognizable “clump” looking thing and not a beautiful sphere. Any help would be lovely! Thanks! Jeremiah

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Re: [Chimera-users] 3D printing a viral capsid
by Tom Goddard 22 Aug '14

22 Aug '14

Hi Jeremiah, The symmetry for your capsid is 222r, not 222. These both have 2-fold symmetry axes along x,y,z but they differ by a rotation by 90 degrees about z which puts the 5-fold symmetry axes in different locations. To figure out the right simmetry I used the Chimera Icosahedron Surface dialog (menu Tools / Higher-Order Structure) to show an icosahedral cage and then I try different standard orientations to find the one that matches. Tom On Aug 22, 2014, at 2:31 PM, Jeremiah Gassensmith wrote: > Many thanks. Using the OBJ did indeed work to get it into Blender (Freeware) to convert it to STL. > > Related to Tom’s suggestion I tried (before I emailed the listserv): > > >molmap #0 4 symmetry i,222 > > but I’m not sure why that didn’t work (that should be the right symmetry…?) > > molmap #0 4 sym biomt works, however. > > > > Again, Many thanks. > > Jeremiah > > > On Aug 22, 2014, at 4:27 PM, Tom Goddard <goddard(a)sonic.net> wrote: > >> Here’s the molmap capsid image. >> >> Tom >> >> <capsid.jpg> >> >> >> On Aug 22, 2014, at 2:25 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >>> Hi Jeremiah, >>> >>> The STL export of your virus capsid multiscale model is giving just one asymmetric unit and that is a Chimera bug. I’ll make a bug report and see if I can fix that. >>> >>> Here’s another suggestion about how to print it. Make a single density map for the entire capsid with the Chimera molmap command >>> >>> molmap #0 8 sym biomt >>> >>> This makes an 8 Angstrom resolution map using the asymmetric unit of the capsid PDB model #0 and uses the symmetry specified in the PDB file BIOMT remarks. I’ve attached an image of what it looks like. If you print on a single color printer this surface exported as STL is likely to work better than the Chimera Multiscale surfaces which may not be touching enough to hold together. Also it gives a better (and very different) appearance because it is single color. You can try different resolution values and see what works best. The resolution of 3d printers isn’t too good, so having too much detail doesn’t produce the best printed model. >>> >>> Tom >>> >>> >>> On Aug 22, 2014, at 10:33 AM, Hurt, Darrell (NIH/NIAID) [E] wrote: >>> >>>> Hi Jeremiah, >>>> >>>> I got a good import of your scene in Blender by exporting an OBJ from Chimera. Maybe give that a try. You can then convert to STL using Blender's tools. >>>> >>>> Hope it helps! >>>> Darrell >>>> >>>> >>>> From: Jeremiah Gassensmith >>>> Date: Friday, August 22, 2014 10:15 AM >>>> To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> >>>> Subject: [Chimera-users] 3D printing a viral capsid >>>> >>>> Hello >>>> >>>> I’m trying to produce an STL file from a model I have built in Chimera but it comes out incredibly deformed. I have created the model from a PDB file of a viral coat protein such that it is fully assembled into the proper capsid structure. You can see the model I’ve created here: >>>> >>>> https://dl.dropboxusercontent.com/u/9856122/CAPSID.py >>>> >>>> Problem is, when I export to STL and open in Blender I get a squished unrecognizable “clump” looking thing and not a beautiful sphere. Any help would be lovely! >>>> >>>> Thanks! >>>> Jeremiah >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users(a)cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >

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Generating surface for docking models
by fei.wu＠chem.utah.edu 22 Aug '14

22 Aug '14

Dear Chimera team, Is there a way of generating the surface for docking models from ClusPro so I can map electrostatic potential or coulombic potential on it? Since my docking models are composed of three enzymes (2 dimers and 1 monomer), I tried surfacing in "Multiscale Models"but it gave me a very low resolution surface. Thank you! Fei

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Intensity range shift
by Petr.Brazda＠seznam.cz 22 Aug '14

22 Aug '14

Hello, I would like to ask whether there is a possibility in Chimera to shift the intensity range. I have tomography data, which range from -32000 to 10000 in intensity. A would like to gradually erase parts of the tomogram with volume eraser but it is not possible because the intesity range does not start at zero. It is not possible to do the job with subregion selection. Is there a way to shift the intensity range? Petr

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Re: [Chimera-users] mmaker question
by Elaine Meng 21 Aug '14

21 Aug '14

Hi Joshua, If you are fine with CA atoms only, approach (B) may be easier than using the "rmsd" command, especially if the structures have different numbering and/or contain different numbers of residues. The problem with selecting and using "sel" in the command is that unless you picked atoms one by one, it isn't an ordered selection and you wouldn't necessarily get the desired pairing. If you get some ridiculous RMSD, that is definitely the problem. Instead you would need to use specification by residue numbers and atom names in the command line. Whereas mmaker figures out pairing for you, the "rmsd" (and "match") commands do not, and you have to specify the atoms in corresponding orders. For CA-only calculations, approaches (B) and (C ) both done correctly will give the same result. Command-line atom specification: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic> Elaine On Aug 21, 2014, at 11:22 AM, Joshua Broyde <jb3401(a)c2b2.columbia.edu> wrote: > Elaine, > Thanks for the help. I was looking for something like C, so I guess I will just select the C alpha atoms and get the RMSD. > > Sincerely, > Joshua Broyde > > ----- Original Message ----- > From: "Elaine Meng" <meng(a)cgl.ucsf.edu> > To: "Joshua Broyde" <jb3401(a)c2b2.columbia.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Sent: Thursday, August 21, 2014 2:00:44 PM > Subject: Re: [Chimera-users] mmaker question > > Hi Joshua, > Not sure I understand the question. I'll try to answer some possible interpretations, but if I didn't answer your question, feel free to write back! > > (A) To use your own sequence alignment to define the residue pairing for superposition and RMSD calculation, just open your alignment, make sure both structures are associated, and then from the Multalign Viewer menu (the menu of the window showing the sequence alignment) choose Structure…Match. There are some additional options in the resulting GUI. You could use the pairwise alignment from a previous mmaker command with "show true", if that helps. > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > (B) To just calculate the RMSD of structures in their current positions WITHOUT moving them, again starting with an alignment in Multalign Viewer with both structures associated, use the mouse to draw a region (which could be a single box in the alignment, or multiple disjoint boxes if you use Shift-drag) then from the Multalign Viewer menu choose Info…Region Browser. The resulting dialog will show the RMSD for the region you defined with the mouse. > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > (C ) The above use the Multalign Viewer graphical interface, not commands, and use only CA atoms. There is also a "rmsd" command to calculate RMSD between 2 sets of atoms in their current positions without moving (it does NOT calculate the best-fit RMSD, just uses the current positions). It would be harder to use because now you have to specify all the atoms in the command, e.g. if the residue numbering is different in the two structures, you would have to list the residue ranges. You could specify any atoms common to both structures, not just CA atoms. > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> > > Best, > 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 21, 2014, at 8:49 AM, Joshua Broyde <jb3401(a)c2b2.columbia.edu> wrote: > >> Hi again, >> I was wondering if the mmaker command had an option (or if there is some other way within chimera) of reporting the RMSD (as calculated by mmaker) of an alignment without actually superimposing one structure on the other. The reason that I am doing this that for a group of structures I can see with mmaker that they superimpose very well, but I want to show that when you compute the RMSD of those same structures when each is bound to a partner they are not quite as well aligned. >> In essence, what I want mmaker to do is not really realign the structures for me, but to calculated the RMSD of an alignment that I provide it. >> I looked at the mmaker command page but I couldn't seem to find an option for this. >> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html >> >> Thanks again, and Chimera is a wonderful piece of software! >> >> Sincerely, >> Joshua Broyde >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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mmaker question
by Joshua Broyde 21 Aug '14

21 Aug '14

Hi again, I was wondering if the mmaker command had an option (or if there is some other way within chimera) of reporting the RMSD (as calculated by mmaker) of an alignment without actually superimposing one structure on the other. The reason that I am doing this that for a group of structures I can see with mmaker that they superimpose very well, but I want to show that when you compute the RMSD of those same structures when each is bound to a partner they are not quite as well aligned. In essence, what I want mmaker to do is not really realign the structures for me, but to calculated the RMSD of an alignment that I provide it. I looked at the mmaker command page but I couldn't seem to find an option for this. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html Thanks again, and Chimera is a wonderful piece of software! Sincerely, Joshua Broyde

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Match two small molecules with command line : "match"
by Jo Sourbron 19 Aug '14

19 Aug '14

Dear, I really appreciate the features that Chimera has (as I read them in yhe user's guide). Though there seem to be a problem: I want to match two small molecules (and in the future maybe more), but If I open the pdb files in Chimera and use the command line match, it says that there is missing an atom spec. Then I looked again in the user's guide and I noticed the "#" that they use. I don't know how what this "#" means. I just want to overlap the two structures and get a percentage of homology or something like that. That would be great. You can always contact me, kind regards, Jo Sourbron PhD Student Laboratory for Molecular Biodiscovery Department of Pharmaceutical and Pharmacological Sciences Katholieke Universiteit Leuven O&N2, Campus Gasthuisberg Herestraat 49, box 824 B-3000 Leuven, Belgium j.sourbron(a)gmail.com GSM. +32 474 94 84 17 TEL. +32 16 37 78 07 http://be.linkedin.com/pub/jo-sourbron/33/496/77a/

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Ligand Problem
by Marcus Fabiano A. Mendes 15 Aug '14

15 Aug '14

Hi, My Name is Marcus, and I am a huge fan of Chimera. Currently, I'm using Chimera to visualize p:MHC complex and it's electrostatic potential map. p:MHC occurs as an α chain composed of three domains - α1, α2, α3, β2 microglobulin and a ligand present in the groove. Chimera automatically recognizes the epitope as a ligand, since they have on average less than 10 amino acids. There's someway to make the Chimera don't recognizes this epitope as a ligand? A option to set the parameters that Chimera uses (ligand = <10 amino acids)? Thanks for All SincerelyMarcus Mendes

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Re: [Chimera-users] Volume viewer chimera
by Elaine Meng 15 Aug '14

15 Aug '14

On Aug 15, 2014, at 2:08 AM, Matteo Allegretti <maallegr(a)biophys.mpg.de> wrote: > Dear prof. Meng, > it would be possible in the future to have more than three panels on the > volume viewer of Chimera? > Thank you so much, > Matteo > -- > Matteo Allegretti > PhD candidate > Max Planck Institut für Biophysik > Max-von-Laue-Straße 3 > D-60438 Frankfurt am Main > Office: +49-69-6303-3015 Dear Matteo, If you mean showing the histograms of more than 3 datasets at the same time, you can already do that. In Volume Viewer menu, choose "Features… Data display options", and then in the resulting options you can increase the “Maximum number of histograms shown” from 3 to some bigger number. It’s better if you send Chimera questions and suggestions/discussion to the chimera-users(a)cgl.ucsf.edu address (CC’d here) instead of directly to me. There are other people who also answer the questions, and I might be gone or not know the answer. Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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does chimara allow changing of the primary sequence of the protein?
by Marta Mikolajczak (BIO) 14 Aug '14

14 Aug '14

Dear Sir/Madam, I am a PhD student working for the University of East Anglia. I have just downloaded the Chimera software and I really like the look of it. So far I have found it very user friendly. I was wondering if the software allows incorporating changes into the protein structure? I am working on the mutant of my protein of interest. I have found, through experimental procedures, that when I mutate one residue it changes the properties of the protein. I was wondering if the effects I am seeing are due to changes in the protein structure. I would like to visualise it. I am not interested in generating crystal structure of the mutated protein or anything like that. I really would like to insert a different amino acid into the structure that already exist. I understand it might be incorrect but all I want to achieve is a "prediction". Would chimera software do that for me? Kind regards, Marta Mikolajczak

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Error with partial charge calculation during minimisation
by Ahir Pushpanath 13 Aug '14

13 Aug '14

Hey there, whenever I try to do a minimisation of a ligand in presence of protein, with a few residues selected as flexible , rest held as rigid, I get past the adding hydrogen box, but it always has a error saying it cant calculate partial charge for the first N-terminal residue, N atom , for example. If I try and delete that residue, it just moves up and says it cant do it for the second one. The PDB file seems fine, and I have opened in Discovery studio and seen it has partial charges assigned fine. Can you enlighten me on what maybe going wrong? I am using the latest build of Chimera. PDB is 1BW9 chain A (only one conformation chosen in multiple conformation residue positions). The ligand is the PPY inside. the flexible residues are all those 5A away apart from NAD. -- Dr. Ahir Pushpanath* PhD.* Senior Biologist, Johnson Matthey.

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Surface color by electrostatic potential
by roz orchidea 13 Aug '14

13 Aug '14

Dear all, I am trying to get some images of the electrostatic potential surface of my complex. But I have noticed that by using the same .dx file in chimera and vmd, I am getting different coloring results. Chimera gives more negatively charged areas. I used the -5 0 5 coloring for both. Is it a difference in reading the .dx files between the 2 software? I also think that Chimera colors each side chain by the avg charge. Is it possible to have a more detailed coloring of the surface according the charges? Thanks in advance, Alexandra

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Re: [Chimera-users] [chimera-dev] Feature request
by Elaine Meng 11 Aug '14

11 Aug '14

Dear Xavier, I personally don’t recommend the Chimera/Povray approach… my neon/conic suggestion is better-looking, but not as easy as the feature you request. There is limited programmer time, so I can’t say it will happen, but we can put it on the list of requests. You can enable showing backbone atoms at the same time as ribbon with command “ribbackbone” — then try displaying the carbonyls. You may also need to unchain (avoid drawing long bonds between different carbonyls, e.g. command: setattr m autochain 0). However, the default ribbon path is smoothed, so in some places the backbone atoms will appear to be floating away from the ribbon. You can try reducing that problem by using a different method to calculate the ribbon path, for example, with command: ribspline cardinal smooth strand …but see the manual for other command options and parameters. The cardinal spline tries to follow CA positions, so it is still possible you won’t be able to totally eliminate spaces between ribbon and C atoms. It may be necessary to show the C atoms as balls (slightly larger than stick-ends) to obscure the gapping. The ribbackbone and ribbon path issues are discussed in more detail here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo…> I hope this helps, Elaine On Aug 11, 2014, at 1:48 AM, F.Xavier Gomis-Rüth <xgrcri(a)ibmb.csic.es> wrote: > Dear Elaine & Eric, > thanks again for your and Eric's suggestions. The issue is that the POV-Ray rendering is not as attractive as the CHIMERA rendering. > Would it be possible to kindly and humbly request that this minor feature be implemented at a certain time point in a new version > of the program :-) ? > Another issue I have currently problems with: > it would be very helpful to be able to display the main-chain carbonyls sticking out from the ribbon at the right place. I tried with the > licorize option of the ribbon trace but it was not solving the problem. This is particularly helpful when representing e.g. metal-binding sites. > Thanks again for your help and dedication to constantly improve this fantastic program. > Best wishes, > Xavier > > On 1/8/14 9:11 PM, Elaine Meng wrote: >> A few caveats of the Povray approach: >> In my tests (current daily build), it always makes cylinders with the same aspect ratio regardless of whether I am showing the lines as dotted or dashed in Chimera. Also, it is hard to tell they are cylinders unless you make the linewidth fairly large. >> >> Elaine >> >> On Aug 1, 2014, at 11:28 AM, Eric Pettersen >> <pett(a)cgl.ucsf.edu> >> wrote: >> >> >>> Hi Xavier, >>> In addition to Elaine's neon suggestion, if when you save an image you change the rendering from "Chimera" to "POV-Ray" then any dashed or dotted lines will be converted into equivalent cylinders and spheres in the POV-Ray image. I've attached an image that shows how a distance looks. >>> >>> --Eric >>> >>> > > -- > <fxgr_signanew.jpg>

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huge electrostatic range for APBS
by Dennis N Bromley 07 Aug '14

07 Aug '14

Hi all, I have two proteins models from different points in an MD simulation. I colored the surface by Coulombic Surface Coloring, which ran AnteChamber and such. Then I ran APBS. When I color by the APBS data, they look more or less similar. But when I click the "Set full range" button, the kBTe unit range on one is about +-3 and the unit range on the other is about +-300. Any ideas why one would be so much larger? Or am I misinterpreting something? Both were run with exactly the same parameters, all default except for temperature = 310. thanks- -denny-

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"match" command with serialNumber specifier
by Hiroyuki ISOBE 06 Aug '14

06 Aug '14

Dear Sir: I would like to run “match” with two models by using serialNumber specifiers but fail to specify multiple atoms. I would like to match the following sets of atoms: SerialNumber=14,31,91,74 for model #0 and SerialNumber=74,91,31,14 for model #1 How should I include multiple atoms in the command line? The command for one atom, match #1/serialNumber=14 #0/serialNumber=74 works nicely, but I cannot include, for instance, two atoms with match #1/serialNumber=14,31 #0/serialNumber=74,91 or match #1/serialNumber=14 31 #0/serialNumber=74 91 Could you please let me know the correct commands for this purpose? Thank you for your kind help in advance. Sincerely, Hiroyuki -- Hiroyuki ISOBE Advanced Institute for Materials Research (WPI-AIMR) Department of Chemistry Tohoku University Sendai, 980-8578, Japan Tel: +81-(0)22-795-6585 Fax: +81-(0)22-795-6589 Email: isobe(a)m.tohoku.ac.jp Homepage: http://www.orgchem2.chem.tohoku.ac.jp

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