- Chimera-users - RBVI Mailing Lists

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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