August 2014 - Chimera-users - RBVI Mailing Lists

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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Chimera-users August 2014