- Chimera-users - RBVI Mailing Lists

Measuring dihedral angles using chimera
by Aswani Kumar Kancherla 02 Sep '14

02 Sep '14

Hello Chimera Users, I have recently installed chimera version 1.9 in Linux OpenSuSe 11.4 and am trying to get acquainted with its features. I am trying to measure dihedral angles (specifically the angle chiSS defined by Cb-Sg-Sg'-Cb' about disulfide bonds) for a list of pdb files containing NMR structure ensembles. I was trying to do this using a script (kindly given by a friend and pasted below) to which I can pass the coordinates of the four atoms and get the measured values for the "reply log" information. I need to put the files in a directory called pdb_files, open chimera and call the script and retrieve information from the "reply log". However, there is a problem: Since the coordinates of (Cb,Sg, etc ) will be different for each of the ensemble (since each ensemble is structure of a different molecule), I need to pass the coordinates dynamically for each pdbid. I have found from Chimera User group archives that reply log can be saved using a function. http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003184.html So that should solve one issue. I can save the reply log and parse it later. What is the best way to measure specific dihedral angles from multiple pdb files ? Is it possible to invoke chimera in tty mode and make it execute functions? In that case, I could probably write a shell script to invoke chimera once for each pdb and ask it to execute python script having appropriate atom coordinates. I apologize for slightly long an e-mail. Any hints or directions to enable me figure out how to get this done efficiently in chimera will be of great help to me. with regards, Aswani *script:* *================================================================* *import os* *import Matrix* *from chimera import openModels, selection, runCommand* *#angle #0:resno@CB :resno@SG :resno@SG :resno@CB 34.6289* *# Directory containing PDB files* *directory = 'pdb_files'* *# Get paths to all files in the specfied directory * *paths = [os.path.join(directory,f) for f in os.listdir(directory) if f.endswith('.pdb')]* *for pdbfilename in paths:* * filename = pdbfilename.split("/")[1]* * openModels.open(pdbfilename, baseId = 0) # Open as model #2* * runCommand('angle #0:863@CB :980@SG :1130@SG :1235@CB') # calculate torsion angle* * runCommand('close #0') # close molecule and map* *=================================================================* -- K.Aswani Kumar Graduate Student Molecular Biophysics Unit Indian Institute of Science Bangalore-560012 Karnataka, India.

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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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