- 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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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>

2 2

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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cannot save a Chimera session
by ouyang 06 Aug '14

06 Aug '14

Dear All, I use Chimera1.9 in WindowsXP. I failed to save Chimera session neither by using the 'save' command nor 'file/save session (or save session as)' menu. Somehow, the file menu choice 'save session' is always displayed in gray and not clickable. Could anyone know what problem it would be and how to fix it? Thanks a lot! Best. Ouyang

2 1

Delphi electrostatic potential visualization
by Joshua Broyde 04 Aug '14

04 Aug '14

Hi, My name is Joshua Broyde, and I am a big fan of Chimera. I have recently been using Chimera to visualize Delphi outputs (i.e. .phi files).As per your advice here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-March/000710.html I have been using Delphi itself and visualizing the output in Chimera, rather than using the DelphiController within Chimera. Chimera seems to not consistently be able to visualize the output of Delphi on the surface of the proteins. After coloring 2 different protein models with the delphi electrostatic output, I tried to color the third protein surface I was examining with the Delphi output, and Chimera simply colored it gray. To double check that this was not a Delphi problem, I then took this protein structure and created a separate chimera session with it, and then Chimera was able to visualize the Delphi output on the protein surface. Is this a bug or something? Is there a way around this? I want to be able to visualize many Delphi outputs at once on Chimera. Thanks so much, you guys are great! Sincerely, Joshua Broyde

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Chimera script specify filetype
by Thomas Hrabe 02 Aug '14

02 Aug '14

Hi everyone, I have a donwload option on our page for chimera python scripts - one example is attached. When you open it, chimera asks for the filetype. How can I hardocde it’s a PDB file? Thanks, Thomas

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Setup for 3D workstations?
by Kenward Vaughan 30 Jul '14

30 Jul '14

Hello all, I apologize if this is skewed for the list; please correct me if so. I am putting together a proposal to set up a 3D/computational lab at our school for the STEM area, with Chimera at the top of the list of applications using it. The general idea is to have 10 workstations and one workstation-server (the server side being used for computational work), with students at each station doing their own things. Does anyone have an idea of the best setup for each station with respect to hardware for viewing in 3D?? I expect our Dell-camp school to go with something like an Inspiron T5610, using an nVidia K4000 card. I was thinking that the nVidia 3D vision system made sense, but honestly don't know if that would work with 10 different ones going at once. I am unfamiliar with other options. Would someone help me with this? There would be two or three students at each station, FWIW. Am I out in left field in my thinking? Cheers, 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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About MD movie problem
by rama david 30 Jul '14

30 Jul '14

Dear Friends, I completed the simulation of peptide ligand and receptor in gromacs. I want to make the simulation movie. I am using latest version of chimera. I also converted the trajectory files into single pdb movie in gromacs. I did following process: 1. Through tool----> Md movie-- I choose the gromacs option and load the tpr and trr/xtc files. But the software shows that the memory is not enough. ( Frame 4000 and atoms 8000) 2. For second time I chose the PDB option for Mdvie. I load the PDB & now I am getting following message : Residue 4.C not in the first model on line 17718 of Md.pdb file. I am pasting the few lines of md.pdb starting from line 17718 ATOM 8852 N NH2 C 4 61.241 96.447 51.027 1.00 0.00 ATOM 8853 H1 NH2 C 4 61.539 97.208 50.457 1.00 0.00 ATOM 8854 H2 NH2 C 4 61.923 95.899 51.517 1.00 0.00 END Could you please help me in the above problem, I will be a very thankful to you for your help. This is very Important movie for my work. I am looking for reply, With best Wishes Rama David

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Changing Structure/Sequence Associations by a command
by Marek Basler 28 Jul '14

28 Jul '14

Hi, I'd like to be able to change an association between a sequence in a multiple sequence alignment and an opened structure model by a chimera command. I have a model that is a multimer and I'd like to color code one of its subunits according to its sequence conservation ... but I need to reassign the automatic association that Chimera does after opening of a fasta file. Any idea? Thank you!! Best regards, Marek

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[External] import error from module: Togl
by Mike Sivley 25 Jul '14

25 Jul '14

I apologize in advance if this becomes too system-specific, as I believe an automatic update of our server's python libraries may be to blame for this error. However, my hope is that others may have run into the issue as well and have already found a solution. I have a python/chimera script that generates Chimera scenes with various annotations assigned to residues in a protein structure. This script worked without issue for several weeks. I returned from a week of vacation and now the script fails with the following error: ImportError: No module named Togl File "/ant2/Bush_eQTL/sivleyrm/bin/UCSF-Chimera64-2014-05-13/share/chimera/tkgui.py", line 73, in <module> import Togl Togl appears to be a deprecated library, so my best guess is that it was removed during some automatic update (possibly of PyOpenGL?) applied to our servers. However, Chimera is distributed with its own python executable and libraries, so I'm unsure how this type of change could have affected it. I am using the nightly headless linux build of Chimera from 05-13-2014. I have reinstalled chimera from the original .bin file, and I have also installed the most recent nightly headless build. Neither resolved the issue. I'm additionally confused because the exception is raised by tkgui.py, which by naming convention seems like it shouldn't even be called given that I am passing the "--nogui --silent --script" parameters to chimera. The specific call to chimera is this: chimera --nogui --silent --script 'lib/PDBMapVisualize.py 1hho 1 maf temp/61098856282.TEMP 1.000000 0.000000 data/rcsb/biounit/coordinates/all/1hho.pdb1.gz results/pdbmap_1kg_1hho_20140725-11 -' Where lib/PDBMapVisualize.py is my script and everything following are arguments to that script. Nothing about this call or the script it is calling have changed between when chimera ran successfully and now. Any help or advice in resolving this issue would be greatly appreciated. Thanks! Mike Sivley PhD Student in Biomedical Informatics Center for Human Genetics Research Vanderbilt University Medical Center

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distance between two residues in multiple pdb files
by Mahendra B Thapa 24 Jul '14

24 Jul '14

Dear Chimera users, One of the ways to find distance between two residues (say, residue no 10 and residue no 15 of a pdb file) is the use of command 'distance' in the command line of Chimera. How can I use the command 'distance' for a multiple pdb files (say, 20 pdb files which are generated by simulation of a protein)? I mean, may I need some scripts for looping? Any other alternatives will also help me a lot. Thank you, Mahendra Thapa University of Cincinnati,OH

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DNA nucleotide bases representation as long sticks
by roz orchidea 23 Jul '14

23 Jul '14

Dear all, I am trying to make nice DNA images with Chimera. I would like to have my nucleotide bases shown as long sticks like in this image: http://www.nature.com/cr/journal/v23/n2/images/cr2012170f1.jpg Does anybody know how to do that? Thanks in advance for you answer! Alexandra

2 1

surface color by conservation among different sequences
by 李智海 21 Jul '14

21 Jul '14

Hi, I want to show a model in surface style which represents the conservation based on a series of sequences by its color. I have got a result of sequence alignment (.fas file). How can I apply this alignment result to the surface coloring in Chimera? Thanks! best wishes! Zhihai Li

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Re: [Chimera-users] Chimera-users Digest, Vol 135, Issue 20
by Boaz Shaanan 21 Jul '14

21 Jul '14

Hi, On top of what Elaine wrote there is also the interface between Consurf (http://consurf.tau.ac.il/) and Chimera, which is also a very nice option. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Monday, July 21, 2014 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 135, Issue 20 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. surface color by conservation among different sequences (???) 2. Re: surface color by conservation among different sequences (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 21 Jul 2014 23:20:45 +0800 From: ??? <21620101152414(a)stu.xmu.edu.cn> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] surface color by conservation among different sequences Message-ID: <211F19AF-2CA8-4E66-81D4-0F9BC20A868A(a)stu.xmu.edu.cn> Content-Type: text/plain; charset="us-ascii" Hi, I want to show a model in surface style which represents the conservation based on a series of sequences by its color. I have got a result of sequence alignment (.fas file). How can I apply this alignment result to the surface coloring in Chimera? Thanks! best wishes! Zhihai Li

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disulfide bonds ?
by Marek Maly 15 Jul '14

15 Jul '14

Hellow, I just visualized my Amber MD trajectory with protein containing several disulfide bonds. These bonds as well as all the other bonds are written in the given Amber topology (*.prmtop) file, which is read in by Chimera. Moreover the distance of sulfur atoms connected by disulfide bond is in all cases quite reasonable ( 2-2.1 A). In spite these facts Chimera draws some of those bonds in "stick" and some of them in "dashed line" style, even if one sets globally "stick" or "ball & stick" representation. Please see the attached illustrations. Why Chimera is doing such unwanted differences in graphical representations here ? It is possible, to force Chimera to draw all of those bonds unanimously in "stick" representation ? Thank you in advance for your help, Best wishes, Marek Maly -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Calculate RMSD over SSE of NMR ensemble
by Markus Heller 14 Jul '14

14 Jul '14

Hello, The subject says it all. How do I calculate the RMSD of secondary structure elements of an NMR ensemble? I did RTFM, but I'm hoping that I can avoid spelling out the residues comprising the SSEs ... Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller(a)cdrd.ca<mailto:mheller@cdrd.ca> | www.cdrd.ca [cid:image002.png@01CF9C4B.5C0363C0] Follow us: [Description: cid:image003.jpg@01CD86A6.39B41A10] <https://twitter.com/C_D_R_D> [Description: cid:image005.jpg@01CD86AE.B197F5D0] <http://www.linkedin.com/groups/CDRD-3186016/about?report%2Esuccess=3NcE4iZo…> [Description: cid:image009.png@01CD86AE.B197F5D0] <https://www.facebook.com/pages/The-Centre-for-Drug-Research-and-Development…> [Description: cid:image010.png@01CD86AE.B197F5D0] <http://www.youtube.com/user/CDRDCVI?view_as=public> This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email.

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Can't open the file generated by NORMAD-REF
by Mahendra B Thapa 14 Jul '14

14 Jul '14

Dear Chimera users, I can't open the pdb file (one of them is attached) generated by NORMAD-REF( http://lorentz.immstr.pasteur.fr/decoys/submission.php) in chimera (version 64-1.9). The format of the pdb file looks like ok while trying to follow the former posts like " http://www.cgl.ucsf.edu/pipermail/chimera-users/2012-June/007704.html". Please help me to find the errors which might have remained unnoticed to me. Thank you, Mahendra Thapa Doctoral Student,Physics University of Cincinnati,OH

2 1

local cross-correlation coefficient
by 李智海 08 Jul '14

08 Jul '14

Hi, I performed tool "Fit in map” to calculate the correlation value, i was wondering whether the value is the same as local cross-correlation coefficient (local CCC). Thanks in advance for your help! Best wishes for you! Zhihai Li

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Chimera Using Problem
by christophe 08 Jul '14

08 Jul '14

Hi,I'm trying to import chimera in python but when i try to make it i've bug, it said to me the following thing just after have execute:>>>from chimera import *Traceback (most recent call last): File "C:\Python27\Lib\site-packages\Chimera 1.9\share\testMM.py", line 1, in <module> from chimera import * File "C:\Python27\Lib\site-packages\Chimera 1.9\share\chimera\__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, XformImportError: No module named _chimeraI'm on windows 8 64 bits and i have chimera 1.9 and python 2.7.7 i've this following structure of directories:C:\Python27\Lib\Site-packages\chimera 1.9And i've run my script under the python.exe of chimera.So can you said to me what is wrong to fix it cause of i need chimera to made a script using superposition ( so with MatchMaker)? Cordially,Christophe Linhard.

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Suggestion - secondary structural element as an additional level in the selection hierarchy?
by Oliver Clarke 07 Jul '14

07 Jul '14

Greetings, Currently, the selection hierarchy in Chimera is as follows - atom<residue<chain<model<all. I don’t know how complicated it would be to implement, but perhaps it might be desirable in a future version of Chimera to include “secondary structural element” (being coil, helix or strand) as an additional level, between residue and chain? This would enable easy/quick selection/coloring of specific loops, helices or strands in a structure. E.g, say I am working on a helical repeat protein like an importin, and I want to color all the helices on the concave, inside surface one color, and all the helices on the outside surface another color - to do that at present is possible, but somewhat laborious, as it is necessary to explicitly specify the boundaries of each helix, and if there are many helices in the desired selection that are not sequence-adjacent then this becomes complicated. If SSE was a level of the selection hierarchy, I could select one residue in each helix on the desired surface, press the up arrow once to broaden the selection and all the helices on the inner surface would then be selected, without needing to know the location in the sequence of each helix. It seems like there would be quite a lot of use cases where this might save time - selecting individual surface exposed loops, or a specific set of helices or strands that form a binding surface for a ligand or partner protein, for example. Best regards, Oliver.

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Change default display settings?
by rswett＠chem.wayne.edu 07 Jul '14

07 Jul '14

Hi, I was wondering if there was a way to change my startup preferences so that the default is to show only ribbons? No atoms?

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How to install chimera as a python module
by Ivan Castro 07 Jul '14

07 Jul '14

Hi everyone, Looks like Chimera can be installed as a python module, but I can't find the first steps to do that. Anyone can suggest me a tutorial or webpage for this purpose. Thanks. -- Iván Castro, B. Sc (Hons). M. Sc Student - Biology at Universidad del Valle, Colombia. Member of Grupo de Estudios en Genética, Ecología Molecular y Fisiología Animal. Member of Fundación Colombiana para la Investigación y Conservación de Tiburones y Rayas.

2 1

how to connect broken ribbon
by Pu Qian 07 Jul '14

07 Jul '14

Hi there, Sometime, when I use chimera to make a ribbon presentation of protein, the helix region will either broken or does not present properly. Similar thing can be happened in Pymol. But, Pymol provides a command called "alter". When I rebuilt it after altering, broken helix can be repaired. I'm wondering is there similar function in Chimera, or is there a suitable method which can be used to deal with it. Thanks Best regards Pu Qian

2 1

Measure correlation for rotated map positions
by Tom Goddard 03 Jul '14

03 Jul '14

Hi Rakesh, The “measure correlation” rotationAxis option only accepts a specification of two atoms to define the rotation axis. This is explained in the Chimera documentation. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlat… Specifying 3 numbers is not enough since you need both a direction and a point on the axis. If you have a center x,y,z position and axis vector ax,ay,az then you could use the “turn” command to do the rotations and the “measure correlation” command without the rotationAxis option as follows. perframe "turn 0,0,1 10 center 0,0,0 coord #1 model #1 ; measure corr #0 #1" frames 36 This does a rotation by 10 degrees about center 0,0,0 and axis 0,0,1 using map #1 coordinates then measures the correlation between map #1 and #0, repeating this 36 times (covering 360 degrees). Results are reported in the reply log. Tom On Jul 3, 2014, at 2:56 PM, Rakesh Ramachandran wrote: > Hi, > > I wanted to know how can I measure correlation starting from a fit and rotating the model around an axis with respect to the map. I tried calculating the centroid of the model and then rotate it using measure correlation but it did not work, the rotationAxis field was not taking the x,y,z position of the centroid of the model. > > Regards > Rakesh

1 0

Structure editing
by George Tzotzos 02 Jul '14

02 Jul '14

I’m dealing with a X-ray model in which some of the residues are shown in two conformations. Is it possible to edit the structure keeping the higher occupancy conformation ONLY? Another question is whether it is possible to delete all waters but the selected ones (e.g. HOH molecules in the binding pocket that are conserved). I’ve been doing this manually using an editor and I wonder if there is better way of doing this. Thanks in advance for your advice Regards George

2 1

suggested improvements
by Dougherty, Matthew T 02 Jul '14

02 Jul '14

1) first suggestion on the sym command the following is defined icosahedral symmetry I[,orientation] around center Example: i,n25 where orientation can be: 222 (default) - with two-fold symmetry axes along the X, Y, and Z axes 2n5 - with two-fold symmetry along X and 5-fold along Z n25 - with two-fold symmetry along Y and 5-fold along Z 2n3 - with two-fold symmetry along X and 3-fold along Z 222r - same as 222 except rotated 90° about Z 2n5r - same as 2n5 except rotated 180° about Y n25r - same as n25 except rotated 180° about X 2n3r - same as 2n3 except rotated 180° about Y In the chimera tool->higher order structure -> the icosahedral structure it defines similar orientations, assume in the same order. It would be helpful on the selections to include the sym syntax as part of the icosahedral structure text ie {222} xyz 2 fold {2n5} x 2 fold z 5 fold 2) second suggestion When reading an MRC file I occasionally see situations that make me question whether the file is EMDB complaint. It would be good to have the means to dump the MRC header, even if chimera refuses to read the file in its entirety. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Re: [Chimera-users] Attaching a Probe to Modify an Existing Amino Acid
by Eric Pettersen 02 Jul '14

02 Jul '14

Hi Shana, Well, you might be able to get away with just setting that atom's "name" attribute to "SD", but since you are writing Python code anyway and residues hold their atoms in a name-indexed structure, it would be better to do it the right way by removing the atom from the residue, renaming it, and putting it back. Assuming you have the CYS residue in a variable named 'cys': s = cys.findAtom("SG") cys.removeAtom(s) s.name = "SD" cys.addAtom(s) --Eric On Jun 19, 2014, at 11:25 AM, Shana Burstein <sburstei(a)haverford.edu> wrote: > Hi Eric, > I was able to move the CN atoms from the CN residue to the CYS residue and call it MSCN. I actually need it to be called MSCN in order for the modified residue to be recognized by a force field in an MD simulation. My only problem now is that the S atom of cysteine is labeled as "SG" and I need it to be called "SD." I know how to do this by going through the Tool menu, but is there a way to automate that? > > Thanks, > Shana > > > On Wed, Jun 18, 2014 at 2:35 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Hi Shana, > If you were starting from scratch, the procedure to add the CN would probably be simpler by using chimera.molEdit.addDihedralAtom() to add the C and then the N at the appropriate bond length, angle and dihedral and then rename the residue with: r.type = "MSCN". Nonetheless, you have come a long way down the road with your script and probably would not prefer to start over from scratch! So let's suppose you have your two relevant Residue instances in variables named 'cys' and 'cn'. The code to do what you want would be: > > for a in cn.atoms: > cn.removeAtom(a) > cys.addAtom(a) > cys.type = "MSCN" > # empty residues are problematic in various parts of Chimera, so... > cn.molecule.deleteResidue(cn) > > If you don't know how to get the 'cys' and 'cn' variables but you know an atom specifier that selects each, you can use this code to set the variables: > > runCommand("sel atom-spec-for-cys") > cys = chimera.selection.currentResidues()[0] > runCommand("sel atom-spec-for-cn") > cn = chimera.selection.currentResidues()[0] > > There's a couple of further relevant things here. Strictly speaking, 4-letter residue names are not legal in PDB format (while there is a column where a 4th character could go, according to the format definition that column is supposed to be blank). Therefore if you export your modified structure to other software programs, they may or may not be able to handle the 4-character residue name without problems. Therefore I recommend you use the same residue name that the PDB uses for this moiety, 4CY (which can be found in the 3or0 entry). > Along the same lines, 4CY can actually be found in the SwissSidechain rotamer library plugin for Chimera (SwissSidechain - A database of non-natural side chains) and therefore if you install that plugin then the entire substitution process becomes a single command: swapnaa 4CY cysteine-atom-spec. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Jun 18, 2014, at 6:50 AM, Shana Burstein <sburstei(a)haverford.edu> wrote: > >> Hello, >> I am an undergraduate student at Haverford College and I am attempting to attach thiocyanate probes onto different sites along a protein by first replacing the existing amino acid with a cysteine and then by adding a C and N onto the S- of the Cys residue. I know it is possible to carry this out manually using Tools>Structure Editing>Modify Structure, but I am hoping to automate this process by calling an external .py script that will primarily contain a list of preexisting Chimera commands. >> >> I have been successful at converting the targeted amino acid to Cys using "swapaa," building a CN residue called MSCN (using the createMolecule.py as a guide), combining the two models into one ("combine selected close True") and forming a bond between the Cys S and CN C atoms ("bond"). >> >> At this point, I am seeking help in automating the renaming of the modified residue to MSCN. Currently, Chimera sees this residue as two different separate residues called CYS and MSCN. Is there a way to combine these two structures so that the label corresponds to MSCN and the residue number corresponds to CYS? >> >> Sincerely, >> >> Shana Burstein >> Haverford College '15 >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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Making a hole in a volume
by Dieter Blaas 01 Jul '14

01 Jul '14

Hi, I am trying to make a small hole in a volume with 'erase octant' but either it cuts away some of the volume at the wrong place or the hole created is much bigger than the green box. Sometimes it does not do anything until I make the box bigger. What might I am doing wrong ? (chimera 1.6.2) Thanks, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Re: [Chimera-users] Fo-Fc electron density maps
by Oliver Clarke 30 Jun '14

30 Jun '14

Actually adding a second arg works well, thanks! So now I have: alias normalize_to_rms vop scale $1 rms 1 modelID $2; close $1; volume $2 capfaces false style mesh meshlighting false squaremesh false color blue; sop cap off alias split_diff_map vop scale $1 rms 1 modelID $2; close $1; volume $2 capfaces false style mesh meshlighting false squaremesh false level -3 color red level 3 color green; sop cap off Where the first one just normalizes to rms and colors blue, and the second one also normalizes but creates two appropriately colored contours, and I can call these as e.g. split_diff_map #0 #1, where #0 is the input map number and #1 is the desired output map number. Cheers, Oliver. On Jun 30, 2014, at 5:06 PM, Tom Goddard <goddard(a)sonic.net> wrote: > Making a macro create map #1000 does not work well, since the second time you use it it will try to make another model #1000. You could add a second argument to your macro that specifies the output model number. Or you make your macro that sets all the volume settings (mesh, capfaces, …) take a model number. None of the choices is very good. > > Tom > > On Jun 30, 2014, at 2:01 PM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > >> Ah right - that’s okay then, I can just assign it to modelID 1000 then, on the assumption that I’ll never have 1000 models open at the same time. >> >> Thanks! >> >> Oliver. >> On Jun 30, 2014, at 4:59 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >>> There is no special variable to indicate the last created map for use in Chimera commands. In a vop command you can include an option “modelId #5” to assign the id number of the new model. So your macro could take the model id you want for the new map. If you use the vop (volume operation) command to create a new map and don’t specify the modelId option then the new map has the lowest unused model number. There are no output values assigned to variables in the Chimera command language, so it is quite limited. >>> >>> Tom >>> >>> >>> On Jun 30, 2014, at 11:32 AM, Oliver Clarke wrote: >>> >>>> Thanks Tom and Elaine, that’s very helpful! >>>> >>>> While we’re on the topic of macros/aliases, is there any way to refer to the model ID of an output map of a command as a variable in an alias? >>>> >>>> For example, in the normalize_to_rms macro below, I would prefer to apply all the volume settings to just the map I am normalizing, rather than all open maps, but I can’t predict the model ID of the output map because it depends on how many maps I have open. >>>> >>>> This would be handy for stringing together multiple map/model manipulations in a single macro - e.g. to normalize a map to rms, generate two contours and color them appropriately, without disturbing any other open maps. >>>> >>>> Cheers, >>>> Oliver. >>>> >>>> On Jun 30, 2014, at 2:00 PM, Tom Goddard wrote: >>>> >>>>> Hi Oliver, >>>>> >>>>> To simplify your Chimera macros a bit you can put multiple options in one volume command. Instead of >>>>> >>>>> volume # capfaces false; volume # style mesh; volume # meshlighting false; volume # squaremesh false >>>>> >>>>> you can change settings for all open maps with >>>>> >>>>> volume # capfaces false style mesh meshlighting false squaremesh false >>>>> >>>>> Tom >>>>> >>>>> >>>>> On Jun 28, 2014, at 3:14 PM, Oliver Clarke wrote: >>>>> >>>>>> Dear Egor, >>>>>> >>>>>> In addition to Elaine’s suggestion of unchecking “Cap high values at box faces", I use the following aliases to make difference maps more familiar in style to a crystallographer: >>>>>> >>>>>> First, to just normalize the map to RMS (as per coot etc) and adjust to get a mesh, turn capping, mesh lighting off etc: >>>>>> >>>>>> alias normalize_to_rms vop scale $1 rms 1; close $1; volume # capfaces false; sop cap off; volume # style mesh; volume # meshlighting false; volume # square mesh false >>>>>> >>>>>> Second, to split the map into two maps (one positive, one negative), which can then be colored green and red respectively: >>>>>> >>>>>> alias split_diff_map vop threshold $1 minimum 0; vop threshold $1 maximum 0; close $1; sop cap off; volume # style mesh; volume # meshlighting false; volume # squaremesh false; >>>>>> >>>>>> I add these two lines in a “chimera_aliases.com” file, which you can tell Chimera to read at startup under Favorites—>Preferences—>Command Line. >>>>>> >>>>>> You can then run these commands from the chimera command line, e.g. normalize_to_rms #1 or split_diff_map #1 if your map number is 1. Then just adjust the contours and colors in the volume viewer and you are good to go. >>>>>> >>>>>> I don’t know how to automatically color the resultant maps, because there does not seem an obvious way to predict their model numbers, but I am sure there is a way to do that too, perhaps via some python trickery. >>>>>> >>>>>> This is all kind of a work around of course - there may be a way to color a map by density value (such that all positive regions are green, and all negate regions are red), but I couldn’t figure out how to do it. >>>>>> >>>>>> Best, >>>>>> Oliver. >>>>>> _______________________________________________ >>>>>> Chimera-users mailing list >>>>>> Chimera-users(a)cgl.ucsf.edu >>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>>> >>>>> >>>> >>>> >>> >> >> >

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Re: [Chimera-users] Fo-Fc electron density maps
by Oliver Clarke 30 Jun '14

30 Jun '14

Dear Egor, In addition to Elaine’s suggestion of unchecking “Cap high values at box faces", I use the following aliases to make difference maps more familiar in style to a crystallographer: First, to just normalize the map to RMS (as per coot etc) and adjust to get a mesh, turn capping, mesh lighting off etc: alias normalize_to_rms vop scale $1 rms 1; close $1; volume # capfaces false; sop cap off; volume # style mesh; volume # meshlighting false; volume # square mesh false Second, to split the map into two maps (one positive, one negative), which can then be colored green and red respectively: alias split_diff_map vop threshold $1 minimum 0; vop threshold $1 maximum 0; close $1; sop cap off; volume # style mesh; volume # meshlighting false; volume # squaremesh false; I add these two lines in a “chimera_aliases.com” file, which you can tell Chimera to read at startup under Favorites—>Preferences—>Command Line. You can then run these commands from the chimera command line, e.g. normalize_to_rms #1 or split_diff_map #1 if your map number is 1. Then just adjust the contours and colors in the volume viewer and you are good to go. I don’t know how to automatically color the resultant maps, because there does not seem an obvious way to predict their model numbers, but I am sure there is a way to do that too, perhaps via some python trickery. This is all kind of a work around of course - there may be a way to color a map by density value (such that all positive regions are green, and all negate regions are red), but I couldn’t figure out how to do it. Best, Oliver.

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Calculating ASA for side chain
by saadraza＠bs.qau.edu.pk 29 Jun '14

29 Jun '14

Respected Admin I would like to know if there is any way to modify the calculation of Accessible Surface Area (ASA) to calculate only the ASA for the side chain or a particular group of atoms in chimera. If not possible could someone guide me to some other tool. I will be obliged if someone sort this problem for me Regards Saad Raza

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Fo-Fc electron density maps
by Egor Tchesnokov 28 Jun '14

28 Jun '14

Hello, Is there a way to display Fo-Fc electron density maps so that "red/negative" and "green/positive" densities are displayed at the same time. Thank you Egor

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Urgent: surface calculus
by Olivier Sire 27 Jun '14

27 Jun '14

Hello, I am in a hurry to generate a surface object with 2FJG complex to be exported in a STL format for 3D printing. This item will be presented for a local event organized by the Ligue contre le Cancer. I have download Chimera as absolute beginner and I am facing a need for splitting the (too big ?, multi-chain) complex. The function Action / Surface / show generates the splitting solution. Could you help me and guide me ? Thanks in advance Regards Olivier Sire -- *Olivier SIRE * / Professeur à l'Université de Bretagne-Sud / ------------------------------------------------------------------------ Laboratoire d'Ingénierie des Matériaux de Bretagne Campus de Tohannic BP575 56017 VANNES cedex Tél. 02 97 01 71 48 Fax. 02 97 01 70 70 Mob. 06 89 48 25 24 olivier.sire(a)univ-ubs.fr UNIVERSITÉ DE BRETAGNE-SUD http://www-limatb.univ-ubs.fr/ <http://www.univ-ubs.fr/>

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Build a quadruplex
by sette＠uniroma2.it 26 Jun '14

26 Jun '14

Dear all, Im interested to create a rough model of a quadruplex molecule using a specific sequence. One possibility could be to load a pdb structure of a quadruplex and « mutate » each nucleotide with the correct one. Is this feasible with Chimera ? Alternative suggestions are appreciated as well. Thanks for your help, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it e-mail: m77it(a)yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 www.rete29aprile.it ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it

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Rainbow by secondary structural element?
by Oliver Clarke 26 Jun '14

26 Jun '14

Hi all, Currently, the rainbow function can operate at the levels of per residue, per chain or per model. I was wondering whether it would be feasible in a future release to add an additional level, coloring per secondary structural element? This would be particularly handy for structures of membrane proteins, where it is often desirable to color each helix/strand a different color, while not varying the color along the helix (and not coloring residues in loops etc). Even better would be to have separate “rainbow helix” “rainbow strand” and “rainbow secstruc” commands for finer control, but this is probably not really necessary. Cheers, Oliver.

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Color by height from surface?
by Oliver Clarke 25 Jun '14

25 Jun '14

Hi all, I’m wondering if there is any way to use scolor to color by height from another surface rather than from a plane, axis or point? Specifically, I’d like to color a molecular surface by distance from the surface of the low-res model generated using multi-scale models, in order to highlight cavities in the surface of the protein. Best, Oliver.

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Chimera scripting with --nogui can't write pdb files
by rswett＠chem.wayne.edu 24 Jun '14

24 Jun '14

Hey guys, i've been trying to put together a command line only set of scripts that will do some selection processing and save a pdb without going through the gui. If I use the command chimera --nogui --script close.py pdb1.pdb pdb2.pdb where close.py contains select #0 za<3 & #1:HOH write selected 1 output.pdb I should get the residues that match that selection criteria saved as the pdb output.pdb, correct? I get SyntaxError: invalid syntax for line 2 even though this works OUTSIDE a script. as in, if I just run chimera command line and enter those commands sequentially, it works. I also noticed that within the gui I need "#1" and outside it only works with '1" as the model number. I've also tried doing this with a python script: chimera --nogui --nostatus --script "close.py pdb1.pdb pdb2.pdb output.pdb" this should pass whatever I enter as $1 $2 $3 as arguments to my script, correct? So close.py for this version contains open (sys.argv[1]) open (sys.argv[2]) select #0 za<3 & #1:CVX write selected 1 (sys.argv[3]) which also pukes on the pdb write. I couldn't find any other way to write a pdb using python syntax, I assume the way i'm doing it is wrong, but I couldn't find a write.pdb function during my digging. Does anyone have suggestions for writing a pdb based on a selection without going through the gui? I plan on batching this up for a huge number of files and directories and going through the gui would be far too time consuming. Rebecca

2 1

making capsid map from asymmetry unit.
by Jian Guan 24 Jun '14

24 Jun '14

Dear All, I want to make a capsid map from asymmetry unit. The PDB ID is 3iyj, the L1 protein of BPV. The BPV is a T=7, icosahedral capsid. Does anybody know how to make it? Thanks a lot. Sincerely yours, Jian

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side view crash
by m.maletta＠nki.nl 23 Jun '14

23 Jun '14

Dear all, I installed the latest stable Chimera 1.9 on a 64bit ubuntu precise 12.04 and I noticed that every time I try to use the side-view applet, in the viewing control, Chimera just crash. Other function seems to work just fine. I should add that on the same machine the Chimera 1.6 does not crash. Can anyone share a similar experience in Linux? chimera Segmentation fault (core dumped) Any hint what may be the problem? Best Max __________________________________ Massimiliano Maletta post-doc in NKI Netherlands Cancer Institute -Antoni van Leeuwenhoek Hospital Plesmanlaan 121 B6 1066CX Amsterdam group of Peter Peters www.nki.nl/research/peters/ | www.necen.nl m.maletta(a)nki.nl Tel : +31 20 512 2022 Fax : +31 20 512 2029

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Icosahedral model
by 李智海 20 Jun '14

20 Jun '14

Hi， I have a density map of an icosahedral capsid, and now i want to make a icosahedral model to represent the capsid. In this model, every corner represent a capsomere. what can i do to display this in Chimera ? Do I require any plug-in? Thank you！ Best wishes! Zhihai Li School of Life Sciences, Xiamen University. Xiang'an Road(South), Xiang'an District, Xiamen City, Fujian Province, China.

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Fwd: CCL: Coordinate system rotation
by Elaine Meng 19 Jun '14

19 Jun '14

On Jun 19, 2014, at 8:33 AM, "Radoslaw Kaminski rkaminski.rk,+,gmail.com" <owner-chemistry(a)ccl.net> wrote: > Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]=[gmail.com] > Dear All, > > A trivial question. I have a XYZ file with a molecule in some coordinate > system. I would like to have a Z axis be in a certain direction along A...B > atoms. Is there any program that can easily change my coordinate system by > choosing some 3 atoms? I can of course do all transformations by hand (for > example in Excel) but its tedious. I know that ADF is capable of transforming > the coordinates to some specified coordination system (Prof. Baerends' CCL post > from several years ago), but is there any other program that can just make such > transformations quickly? > > Thanks in advance, > Radek From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: Re: CCL: Coordinate system rotation Date: June 19, 2014 9:57:00 AM PDT Hi Radek, With Chimera you could align 2 atoms front->back and then save a PDB file with the transformed coordinates. Not sure if that is exactly what you needed, or whether it is quick enough, but you could automate looping through multiple files with a little bit of Python. (1) open XYZ file (e.g. menu File…Open, choose file.xyz, or command "open file.xyz") <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/xyz.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html> That will automatically assign unique atom names by element and order in file, for example the first C will be C1, the first N will be N1. (2) use "align" command to put atoms A,B in center of view along the line of sight (laboratory Z axis) with A in front and B in back (e.g.: align @c1@o1) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/align.html> (3) save PDB with transformed coordinates (e.g. menu File…Save PDB, un-check "use untransformed coordinates" or command something like "write #0 file.pdb") <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> (4) close structure (e.g. command "close #0" or "close all") … if multiple structures to process, loop back to step 1. See here for writing looping scripts for Chimera: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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split
by John Mercer 19 Jun '14

19 Jun '14

Hi All, I understand the use of split as outlined in the tutorial describing how to find the contact region between two chains. file:///Applications/Bioinformatics/Chimera.app/Contents/Resources/share/chimera/helpdir/UsersGuide/frametut.html I don’t know the proper syntax for models with more than two chains, e. g. A, B, C, D, and E where you might like to split the model either as: A, B, D, and E in one group C in the other or A, B, and D in one group and C and E in the other. I would be grateful for a recommendation for the correct syntax to use in the argument list to form two groups to identify the contact surface after further processing (in the same manner as the tutorial). Thanks, -John

2 2

STL Resolution Issues
by Eric Bell 19 Jun '14

19 Jun '14

Hello, I am trying to change the resolution of the atoms for a large molecule packing, but no matter how I change the zoom or the subdivisions property in the viewing effects, it seems to always produce the same filesize (~900 MB, not something our software can handle). Is this a bug or is it something that I'm doing incorrectly? I'm running on a mac, and I have tested this both with a .mol2 and .pdb file. Thanks, Eric

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how to tranfer a .mrc file to .mtz file
by #ZHANG HAIPING# 18 Jun '14

18 Jun '14

Dear chimera user: I have a .mrc file generated by chimera, now I want to convert it to .mtz formate, so I can load to coot, and examine the structure in details. Can anyone tell me how to convert .mrc to .mtz? Best regards, Haiping

3 2

rename a residue?
by Julian Tirado-Rives 18 Jun '14

18 Jun '14

Dear Chimera team, thanks for all the work you put in into a very, very, useful program. I just have a question that I am hoping is just my inability to find the proper command ... is there a way to rename a residue before writing a PDB? I often use chimera as pre-preparation step before getting into some particular calculation packages, which often require different names for residues to indicate tautomers, protonation, etc. and it would be nice to do it from chimera rather than take the PDB's through a rather annoying set of scripts, sed's, or even text editors! Thanks in advance, - Julian - -- ----------------------------------------------------------------- | Julian Tirado-Rives | | | Department of Chemistry | Phone: (203)432-3356 | | Yale University | Fax: (203)432-6144 | | P. O. Box 208107 | email: Julian.Tirado-Rives(a)yale.edu | | New Haven, CT 06520-8107 | | -----------------------------------------------------------------

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Attaching a Probe to Modify an Existing Amino Acid
by Shana Burstein 18 Jun '14

18 Jun '14

Hello, I am an undergraduate student at Haverford College and I am attempting to attach thiocyanate probes onto different sites along a protein by first replacing the existing amino acid with a cysteine and then by adding a C and N onto the S- of the Cys residue. I know it is possible to carry this out manually using Tools>Structure Editing>Modify Structure, but I am hoping to automate this process by calling an external .py script that will primarily contain a list of preexisting Chimera commands. I have been successful at converting the targeted amino acid to Cys using "swapaa," building a CN residue called MSCN (using the createMolecule.py as a guide), combining the two models into one ("combine selected close True") and forming a bond between the Cys S and CN C atoms ("bond"). At this point, I am seeking help in automating the renaming of the modified residue to MSCN. Currently, Chimera sees this residue as two different separate residues called CYS and MSCN. Is there a way to combine these two structures so that the label corresponds to MSCN and the residue number corresponds to CYS? Sincerely, Shana Burstein Haverford College '15

2 1

delete atoms based on their coordinates
by Aranha, Michelle 18 Jun '14

18 Jun '14

Hi , I wanted to know if there is a way in chimera to select and delete atom/atoms based on their position/coordinates in the simulation box. For example delete water 150 at (x, y, z). I tried zone sel, but I couldnt get it to work. Regards, Michelle ?

2 2

com files & animation
by Dougherty, Matthew T 16 Jun '14

16 Jun '14

When executing a com file for animation production, I would like to see the line that is being executed display in the reply log. Is there a way to do that? I would prefer not using echo commands because of the large number of lines in the file being executed. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

2 1

Chimera Plugins
by Eric Bell 16 Jun '14

16 Jun '14

Hello, Does a list exist somewhere of plugins developed for Chimera, or would we need to find them posted separately on a host site? Also, I found recently a software that gives preset .stl mesh resolutions for all atoms of the same element so that when they are 3d-printed, the atoms can all be distinguished from one another: http://cad4.cpac.washington.edu/WinXMorphHome/Cif2VRMLHome/Cif2VRML.htm However, the rest of the software seems lacking in reference to chimera's capabilities, is there any way that Chimera could have a similar feature? Ideally it would allow the "subdivisions" property of the viewing effects apply to every element, similar to how radius applies to all atoms of the same element. Thanks, Eric

3 2

Adding residue to two sides of DNA
by Mehdi Bagherpour 16 Jun '14

16 Jun '14

Dear Chimera Users, I want to add 3 base-pairs to two side of DNA. I tried more about that but I couldn't. Could some one any idea about doing that in chimera or another programs. Best Regards, Mahdi

3 2

QUESTION
by Eifler, Jay Q. (UMKC-Student) 16 Jun '14

16 Jun '14

Wanting to know if we can use charges assigned by define attribute in a file for the purpose of adding ions. Seems like the Add Ions feature will not do this and will only use the built in methods Gasteigter, etc. I have a HYP residue that the Add Charge feature won't do.

2 1

About direct fetching biological assemblies into Chimera
by Boaz Shaanan 16 Jun '14

16 Jun '14

Hi Tom, This is a nice addition but can you ALSO give the option of fetching just one of the biological assemblies? It is my experience that biological assemblies for a particular pdb entry consist of one correct assembly, in the sense of biological function corresponding to the description given by the depositors and other assemblies. I usually flip between the assemblies on the RCSB website before deciding which one to fetch. With your new addition this of course can all be done now in Chimera but if possible, I'd rather not waste time and disk space with meaningless assemblies. What do you think? Cheers, Boaz Message: 6 Date: Mon, 2 Jun 2014 16:53:06 -0700 From: Tom Goddard <goddard(a)sonic.net> To: "Hurt, Darrell (NIH/NIAID) [E]" <darrellh(a)niaid.nih.gov> Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Fetch biological unit? Message-ID: <0086EC78-81D4-4892-9A22-A4177426F74D(a)sonic.net> Content-Type: text/plain; charset=windows-1252 Hi Darrell, I added a Chimera Fetch dialog entry ?PDB biounit? that will fetch all the biological assembly files for a pdb id ? there can be more than one. Also they can be fetched using the Chimera command: open pdbbuID:2bbv Will be in tonight?s daily build. Tom Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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Color by RMSD for multi-chain structure?
by Oliver Clarke 13 Jun '14

13 Jun '14

Hi all, Is there an easy way to color two superimposed structures by RMSD (per C-alpha pair)? I had a quick look through the manual and the mailing list and I couldn’t find any easy way to do so for a structure that consists of more than one chain. I think this would be a very useful addition to either render by attribute or the calculation of a morph (because presumably the paired CA-CA distances are already calculated in the process of generating the morph). I have aligned based on one chain in a complex, and would like to color the entire complex by RMSD (to highlight the parts that move the most between two states of the same complex). I can calculate the per CA RMSD using “rmsd #1 #2”, but I can’t see any obvious way to assign that to a residue attribute using the attribute calculator or setattr etc. Many thanks, Oliver.

2 2

easy way to make alignments in chimera
by Michał Kadlof 13 Jun '14

13 Jun '14

Hello, I would like to ask if there is any quick way to make aligment (with secondary structure score included) beetwen two homologous protein structures, and save them in Stockholm format (information about missing residues is needed). I have houndreds of such pairs, and it would be very helpfull to do it by script for headless Chimera. -- yours sincerely Michael Kadlof University of Warsaw

2 3

Subclass chimera.Molecule
by Jaime Rodríguez-Guerra 13 Jun '14

13 Jun '14

Hello, I am trying to extend the chimera.Molecule class() to add a few methods and attributes, but the followin error arises: TypeError: Error when calling the metaclass bases type '_molecule.Molecule' is not an acceptable base type File "/home/jr/x/gaudi/gaudi/molecule.py", line 51, in <module> class Compound(chimera.Molecule): Is there any workaround? I want my Compound objects to behave like standard chimera Molecules (with all their attributes and stuff), and also be able to call custom methods on that Molecule. Thanks in advance, Jaime.

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how can i register to use chimera
by carlos martinez 12 Jun '14

12 Jun '14

how can i register to use chimera program

2 1

python printing in x3d2collada.py
by Dougherty, Matthew T 11 Jun '14

11 Jun '14

I was delving into the chimera code and wanted to print some variables to better understand how the code works. When I use a print statement I do not see anything in the reply log or the IDLE window. here is an example for filename in args: print filename print >> sys.stdout, "FN: %s" % filename Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Re: [Chimera-users] "ligand" category for selection
by Hurt, Darrell (NIH/NIAID) [E] 10 Jun '14

10 Jun '14

I guess one way to do it might be to use a different specifier for ligands, like maybe: :/numAtoms<100 -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: <Hurt>, Darrell Hurt <darrellh(a)niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Date: Thursday, June 5, 2014 12:41 PM To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] "ligand" category for selection Hi Chimera friends, I'm trying to use the attached MOL file (dopamine) in Chimera and I want to run a Python script on it. My script does some things to the molecule using selection categories. I'm trying to select this molecule as "ligand", but I get a "No atoms specified" error. Alternatively, is there a way in Python to ignore the error if I get it and keep processing the rest of the script? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

3 7

Fwd: STL Output
by Tom Goddard 10 Jun '14

10 Jun '14

Begin forwarded message: > From: Tom Goddard > Subject: Re: [Chimera-users] STL Output > Date: June 10, 2014 at 2:02:27 PM PDT > To: Eric Bell <Eric.Bell(a)oberlin.edu> > > Hi Eric, > > Chimera doesn’t represent molecules as polyhedrons. Are the orange octahedrons each representing one molecule? And what are the red spheres at the corners, with some red spheres out in space? And what are the little attached pink spheres? This kind of display would require a new Chimera plug-in. The graphics would be easy to do in Chimera. I don’t think such a model would hold together very well when printed in 3d. > > The Crystal Contacts tool in Chimera is remotely related, showing contacts between asymmetric units in a crystal > > https://www.cgl.ucsf.edu/chimera/experimental/crystal_contacts/clashes.html > > Tom > > > On Jun 10, 2014, at 1:50 PM, Eric Bell wrote: > >> Dear Tom, >> >> The polyhedral models look something like the attached image. Does chimera do anything like this or would I have to code a separate plugin? >> >> Thanks, >> Eric<polyhedra.jpg> >> On Jun 10, 2014, at 2:15 PM, Tom Goddard wrote: >> >>> Hi Eric, >>> >>> Not sure what kind of CrystalMaker polyhedral models you were thinking about printing. Chimera can show crystal unit cells. Here are 4 unit cells each containing 8 copies of a small protein (1a0m) shown with the Chimera Unit Cell tool (menu Tools / Higher Order Structure / Unit Cell) with the proteins shown as solvent excluded surfaces (menu Actions / Surface) and each unit cell colored differently (selected by hand with a mouse drag, then used menu Actions / Color). >>> >>> Tom >>> >>> <1a0m_2x2_unitcells.jpg> >>> >>> >>> On Jun 8, 2014, at 7:47 PM, Eric Bell wrote: >>> >>>> Dear Chimera Developers, >>>> >>>> My name is Eric Bell, and I am a student at Oberlin College. I have been using Chimera for 3d printing of molecular models because of its ability to handle many of the processes needed for atom editing as well as its ability to export in an .stl format. However, an issue I've run into is that the resolution of those .stl meshes is rather high, and there does not exist an option, to my knowledge, to alter the amount of vertices on the spheres. This causes an issue when we want to print spacefill models of large molecules, because Chimera will output such large files that our software isn't able to properly process the file without serious resource consumption. Is there anything that I as a user can alter to change the resolution of these spheres, or is it a setting that has been compiled so that I can't edit it without recompiling? I am familiar with python so navigating code would not be an issue for me if necessary. Thank you! >>>> >>>> Sincerely, >>>> Eric Bell >>>> >>>> P.S. Another thing we were looking for that has yet to be done is to print polyhedral models like those in programs such as CrystalMaker. As far as I know Chimera doesn't have this functionality but a programming environment called Bsoft is using the native save file format of chimera to do it because of its similarity to XML. >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users(a)cgl.ucsf.edu >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >

1 0

Fwd: STL Output
by Tom Goddard 10 Jun '14

10 Jun '14

> From: Eric Bell > Subject: Re: [Chimera-users] STL Output > Date: June 10, 2014 at 1:50:49 PM PDT > To: Tom Goddard > > Dear Tom, > > The polyhedral models look something like the attached image. Does chimera do anything like this or would I have to code a separate plugin? > > Thanks, > Eric > On Jun 10, 2014, at 2:15 PM, Tom Goddard wrote: > >> Hi Eric, >> >> Not sure what kind of CrystalMaker polyhedral models you were thinking about printing. Chimera can show crystal unit cells. Here are 4 unit cells each containing 8 copies of a small protein (1a0m) shown with the Chimera Unit Cell tool (menu Tools / Higher Order Structure / Unit Cell) with the proteins shown as solvent excluded surfaces (menu Actions / Surface) and each unit cell colored differently (selected by hand with a mouse drag, then used menu Actions / Color). >> >> Tom >> >> <1a0m_2x2_unitcells.jpg> >> >> >> On Jun 8, 2014, at 7:47 PM, Eric Bell wrote: >> >>> Dear Chimera Developers, >>> >>> My name is Eric Bell, and I am a student at Oberlin College. I have been using Chimera for 3d printing of molecular models because of its ability to handle many of the processes needed for atom editing as well as its ability to export in an .stl format. However, an issue I've run into is that the resolution of those .stl meshes is rather high, and there does not exist an option, to my knowledge, to alter the amount of vertices on the spheres. This causes an issue when we want to print spacefill models of large molecules, because Chimera will output such large files that our software isn't able to properly process the file without serious resource consumption. Is there anything that I as a user can alter to change the resolution of these spheres, or is it a setting that has been compiled so that I can't edit it without recompiling? I am familiar with python so navigating code would not be an issue for me if necessary. Thank you! >>> >>> Sincerely, >>> Eric Bell >>> >>> P.S. Another thing we were looking for that has yet to be done is to print polyhedral models like those in programs such as CrystalMaker. As far as I know Chimera doesn't have this functionality but a programming environment called Bsoft is using the native save file format of chimera to do it because of its similarity to XML. >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> >

1 0

STL Output
by Eric Bell 10 Jun '14

10 Jun '14

Dear Chimera Developers, My name is Eric Bell, and I am a student at Oberlin College. I have been using Chimera for 3d printing of molecular models because of its ability to handle many of the processes needed for atom editing as well as its ability to export in an .stl format. However, an issue I've run into is that the resolution of those .stl meshes is rather high, and there does not exist an option, to my knowledge, to alter the amount of vertices on the spheres. This causes an issue when we want to print spacefill models of large molecules, because Chimera will output such large files that our software isn't able to properly process the file without serious resource consumption. Is there anything that I as a user can alter to change the resolution of these spheres, or is it a setting that has been compiled so that I can't edit it without recompiling? I am familiar with python so navigating code would not be an issue for me if necessary. Thank you! Sincerely, Eric Bell P.S. Another thing we were looking for that has yet to be done is to print polyhedral models like those in programs such as CrystalMaker. As far as I know Chimera doesn't have this functionality but a programming environment called Bsoft is using the native save file format of chimera to do it because of its similarity to XML.

3 2

CASTp data
by Felipe Vasquez 09 Jun '14

09 Jun '14

Hi, I am currently trying to identify certain features from a particular binding cavity, and I decided to use CASTp plugin from Chimera. However, I realized that the data obtained directly from CASTp online server are not the same that those obtained by CASTp from Chimera. Examples include not only the number of pockets, but also the volume and surface area of them. What is the meaning of this confusing results? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

2 1

electrostatic potential based on Swiss-Model
by Jingga Inlora 06 Jun '14

06 Jun '14

Hello, I am a graduate student at the University of Michigan and I am currently trying to obtain images of my proteins with electrostatic potentials for my manuscript. For one of my proteins, there is no solved protein structure (by X-ray crystallography or NMR) and I had to use SWISS-MODEL to predict the structure. I did electrostatic potential calculation using DelPhi but when I visualized it using Chimera, the electrostatic distribution is not what I expected. I did notice the electrostatic potential calculations for other previously solved protein structures took much longer and resulted in bigger files, whereas the SWISS-MODEL-predicted protein contains much smaller .phi file size. I was wondering if you have any idea how accurate it is to calculate the electrostatic potential based on a SWISS-MODEL predicted protein structure, and if there are ways to improve the reliability of the calculated electrostatic potentials for that protein? Thank you very much for your help! Sincerely, Jingga Inlora

2 3

undo
by Antón Vila Sanjurjo 06 Jun '14

06 Jun '14

Hello, I am working with chimera sessions involving a large numer of 70S ribosomes. I keep modifying the sessions over and over, so I save new sessions every day. Much of what I do is labeling interesting residues, measuring distances, coloring these residues, etc. Sometimes I make a mistake, like accidentally selecting and modifying a large portion of the model, and I loose an important amount of information. In these cases, I find that there is no way to go back to the previous state of the system, other than clossing the session and re-opening the latest saved one. Unfortunately, this means loosing a lot of unsaved work. While there is an "undo" option under the "select" tab, it does not really allow one to return to the previous state of the system. In fact, I'm not even sure of what it does. My question is, is there a way to return Chimera to the state ocurring immediately before the last action? In case this does not exist, can it be implemented? best, Antón -- Antón Vila-Sanjurjo, PhD Marie Curie fellow Grupo QOSBIOS, Dept. Química Fundamental Facultade de Ciencias Universidade de A Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain). tlf: (34) 981-167000 ext:2659 e-mail: antonvila.s(a)gmail.com

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Re: [Chimera-users] normalizing attributes through point mutant models
by Elaine Meng 05 Jun '14

05 Jun '14

Hello Ruben, If you were asking how to get consistent coloring for the atomic "overlap" attribute for the different complexes: Just make sure to use the same color for the same overlap value. For example, if you color the first complex with yellow for 0.5 overlap and red for 1.0 overlap, make sure to color the other complexes with yellow for 0.5 overlap and red for 1.0 overlap. You can control which color goes with which value in the Render by Attribute tool, as mentioned in the earlier reply: > in the Render by Attribute tool: you can move the colored bars on the histogram directly with the mouse or by typing in values, change the colors of the bars, etc. as explained here: > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.htm…> ... or if you use the "rangecolor" command, you specify which color goes with which value directly in the command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html> Otherwise, I don't know what you are asking. If I haven't already answered your question, you would need to say more about which Chimera tool you are using to study these interfaces, what values you are trying to display (number of clashes? atomic overlap values?), how you are displaying them (with color? with lines?) and exactly what you mean by weighting or normalizing (are you trying to divide the values by some other values?). Since I already described all the related features I can think of, however, there probably isn't a Chimera tool that does exactly what you wanted. Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

warning: Ignored bad PDB record found on line
by Xiao-Bo Li 05 Jun '14

05 Jun '14

Hello, This morning I kept getting this error "warning: Ignored bad PDB record found on line nnn" whenever I use the python script to try to open a pdb file. The python script I'm using is the usual "chimera.openModels.open(pdbID, type='PDB')[0]". This function call is how I've always been using Chimera, and this morning is the first time I'm getting this issue. I dont see a problem with my internet connection, and I can open the PDB file using File->Fetch by ID, so it doesn't seem like the pdb file has any problems. Only the python script gives me problems. Is anyone else experiencing this problem? Best, XBL

2 2

normalizing attributes through point mutant models
by Rubén Marrero Diaz De Villegas 05 Jun '14

05 Jun '14

Hello I´m working with one antigen/antibody complexes and different point mutations at the interface. I can calculate and draw at the surface attributes like atomic clashes "overlap", but what I don´t know, is how to normalize the calculation output for 2 complexes, neither render such "normalized" attributes in the models. I have tried at Render attribute tool, the option "create corresponding color key", introducing specific clashes boundaries and their coloring values but there is no "apply" button, such the changes doesn't goes to the model. Any help or tip? Thanks in advance Ruben

2 3

Setting the vertex density in a script
by Hurt, Darrell (NIH/NIAID) [E] 05 Jun '14

05 Jun '14

Hi Chimera friends, To save memory and reduce exported geometry sizes, I want to use a script to automatically scale the vertex density of generated molecular surfaces by the size of the molecule. Is there a way to grab the size (number of atoms?) of the loaded molecule(s) and use that with some simple math to set the vertex density value? I know this will reduce surface fidelity, but for very large molecules, the mesh size becomes unwieldy. On a separate, but related note, when loading a volumetric file like electron microscopy data, the "step" size in the Volume Viewer automatically adjusts (1, 2, 4, 8, 16) to optimize visual performance and memory. I'm using a script to import volumetric data and then "Export Scene…". For that export, I want to drop down the step to the next lowest step to get a smoother mesh. I can just set the step value to the minimum with something like "volume #0 step 1 limitVoxelCount false", but this risks maxing out the memory and crashing for very large data sets. Is there a way to use a script to get the current step value and then lower by one step for my export? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

2 5

Re: [Chimera-users] Missing cavities
by Eric Pettersen 05 Jun '14

05 Jun '14

On Jun 5, 2014, at 7:38 AM, sapeptides <sapeptides(a)gmail.com> wrote: > Hi Erik, > > I'm writing because I have noticed that in the new versions of chimera when I create a surface and then try to "cut" it (with the side view tool) to see inside the model I obtain this weird picture (attached), whereas in the old versions (how old I do not remember but I created a stunning images of various active sites) it was possible to check all the cavities inside the molecular structures. > I was wondering if you could suggest how to visualize pockets and clefts when the vdw or solvent accessible surface is present. > > Thanks a lot! > Susanna Hi Susanna, It's best to send questions like this to the chimera-users list rather than me directly so that others can benefit from the answer and since I may not actually be the best person to answer the question. For instance, I have no good ideas about showing cavities effectively with VDW or solvent-accessible surfaces and hope someone else can chime in there. As for the lack of cavities in your image, did Chimera issue a warning when it computed the surface saying that "[c]alculation of some surface components failed" and that "[a] single component of the surface was calculated"? If so, that means that calculation of interior cavities failed and Chimera is showing the exterior surface only (which the error message does say if you read it in its entirety). That would produce the lack of interior cavities you observed. If you didn't get such a message, can you supply the PDB ID for this structure (or PDB file) so I can investigate? Thanks! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

3 2

"ligand" category for selection
by Hurt, Darrell (NIH/NIAID) [E] 05 Jun '14

05 Jun '14

Hi Chimera friends, I'm trying to use the attached MOL file (dopamine) in Chimera and I want to run a Python script on it. My script does some things to the molecule using selection categories. I'm trying to select this molecule as "ligand", but I get a "No atoms specified" error. Alternatively, is there a way in Python to ignore the error if I get it and keep processing the rest of the script? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

2 2

Chimera display problem
by sea 03 Jun '14

03 Jun '14

Hi, I recently changed graphics card. This caused a problem to display image properly in Chimera (see attached screenshot). My new graphics card is MSI RADEON R7 240, chimera version 1.9. Does anyone encounter similar problem, or know how to fix it? Best regards Pu Qian

2 1

Asking Help: Academic User
by Robin Parmar 03 Jun '14

03 Jun '14

Hello, Warm Greetings! Thank you for Allowing me to use Chimera through academic license. Yesterday(June 2nd) I was prompted to update Chimera to 1.9 version. I accepted and installed it successfully on my system (windows7pro). Before that I had removed Chimera 1.8.8. The problem I face is, I can not open certain .pdb/.pdbqt fies saved in my comuter. such files even do not exhibit chimera logo which earlier version did. Even with "choose default program" system can not open these files insted other program (like spdbv) open them. I have not made any change in my system after installing new version. Can I reinstall earlier vrsion(1.8)? Kindly suggest me what best I should do to avail service (Academic Research) of chimera again. Regards. -Robin

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Re: [Chimera-users] Chimera-users Digest, Vol 134, Issue 4
by Boaz Shaanan 03 Jun '14

03 Jun '14

Thanks a lot Tom, This is wonderful. I'll try it as soon as it's on the site. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 Message: 7 Date: Tue, 3 Jun 2014 11:52:46 -0700 From: Tom Goddard <goddard(a)sonic.net> To: Boaz Shaanan <bshaanan(a)bgu.ac.il>, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh(a)niaid.nih.gov> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] About direct fetching biological assemblies into Chimera Message-ID: <2FF03268-945D-4B45-B2BE-1A7B17370069(a)sonic.net> Content-Type: text/plain; charset=windows-1252 Hi Darrell, Boaz, I made a few improvement to the fetching of PDB biological unit files that will be in tonight?s daily build. 1) Made fetching biounit give each assembly a separate top level model id number and separate color. Before all the assemblies were grouped together in Model Panel, and now each assembly is on a separate line in Model Panel. 2) Renamed biounit file type and prefix from pdbbuID to biounitID. So use Chimera command ?open biounitID:1hho?. 3) Allowed specifing a specific biounit by number using pdb id plus "." followed by number, eg. 3fad.2. This works in the Fetch by Id dialog and on the command-line. Also to fetch a few different biounits you can use 3xyz.1.3.8 with each . specifying another assembly number. Used "." instead of comma since commas separate multiple identifiers in the fetch dialog. Tom On Jun 3, 2014, at 5:52 AM, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > Hi Tom, > > This is a nice addition but can you ALSO give the option of fetching just one of the biological assemblies? It is my experience that biological assemblies for a particular pdb entry consist of one correct assembly, in the sense of biological function corresponding to the description given by the depositors and other assemblies. I usually flip between the assemblies on the RCSB website before deciding which one to fetch. With your new addition this of course can all be done now in Chimera but if possible, I'd rather not waste time and disk space with meaningless assemblies. What do you think? > > Cheers, > > Boaz ------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 134, Issue 4 *********************************************

1 0

<< creating MOL2 files with different SET records >>
by Hatuey Hack 03 Jun '14

03 Jun '14

Hello, I will like to know if it is possible with Chimera to create MOL2 files that include other MOL2 records like these: @<TRIPOS>SET ATOM$BY_TYPE STATIC ATOMS COLORGROUP SYSTEM 5 1 2 3 4 5 LINK_HS STATIC ATOMS <user> **** 4 2 3 4 5 @<TRIPOS>NORMAL @<TRIPOS>FF_PBC FORCE_FIELD_SETUP_FEATURE Force Field Setup information v1.0 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 NONE 2 0 0 0 0 0 0 0 0 0 0 0 0 Best regards, Hatuey

2 1

Saving Sessions with surface data
by Arjun Dayal 03 Jun '14

03 Jun '14

Hi, I imported several .STL files into Chimera that I generated using TrakEM2. These import as individual surface objects in Chimera. I am then able to color the objects differently and generate some publication-quality screenshots. However, I am unable to save and restore the Chimera session. Upon trying to restore the session, I am presented with a blank screen. The program does not report any errors and even says "Done opening SESSION.py". It seems that the program never loaded the surface files. How does Chimera know where the surface files are located? I saw no mention of their location inside the session PY file. How can I save my session so that next time I open Chimera, all of my surfaces load with the colors, transparency, etc. that I assigned them in Chimera? -- Arjun Dayal Pritzker School of Medicine | Class of 2016 University of Chicago

2 1

rotamers, contacts, H-bonds
by Elaine Meng 03 Jun '14

03 Jun '14

Hello Maryam, This sounds like a chimera-users question (chimera-dev is more about programming), so I CC'd that address. You can use Distance measurements, Find Contacts/Clashes and/or FindHBond to look at the interactions of the residue. See menu under Tools.. Structure Analysis, and instructions: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/str…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findcla…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbo…> For looking at rotamers of amino acids, both same type as native (no mutation) or different type (mutation) you could use the Rotamers tool (in menu under Tools… Structure Editing). The rotamers list also connects to finding contacts and Hbonds through its Columns menu, see "evaluation" in the Rotamers manual page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot…> For examples of measuring distances, identifying contacts and H-bonds, and using Rotamers, I recommend you try the "Structure Analysis and Comparison" tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> Regards, 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 May 28, 2014, at 2:05 AM, "maryam.khoshnejat" <maryam.khoshnejat(a)modares.ac.ir> wrote: > hello > could you help me? > i should model specific mutant residue of protein . i have PDB file and rotamer of mutant residue > how can i find coordination of mutant residue based on backbone and CB coordination of native residue , rotamer and atom bonding distance > i need a code for finding coordination of mutant residue > regards

1 0

Fetch biological unit?
by Hurt, Darrell (NIH/NIAID) [E] 02 Jun '14

02 Jun '14

Hi Chimera friends, The PQS server still works well for downloading the biological unit, but (as noted) it doesn't have every structure in it. The PDB itself provides the biological unit(s) for download in their weird ".pdb1", ".pdb2", etc. format for every entry in the database (even if it is redundant). Is there a way to grab those files from the PDB itself using the Chimera interface? The repository is in: ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Issue with Comparative Modeling Tutorial
by Janan Zhu 31 May '14

31 May '14

Hi, I'm new to Chimera and I've been trying to learn about the various features of the program through the tutorials. I've been having issues with the Comparative Modeling Tutorial from the User Guide (link here <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/frametut.html>) - for some reason, when I try to get updated zDOPE scores after deleting the unaligned termini of the target sequence, the zDOPE scores fail to update, and I only get new RMSD and overlap values. If I try calculating the scores again, I get a message that all models already have scores assigned. I've tried this both with the tutorial structure and some of my own structures and I get the same result. Could anyone possibly provide any assistance with this? Thank you, Janan Zhu -- Janan Zhu Duke University '16

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surface ESP in chimera
by sbasu＠ffame.org 30 May '14

30 May '14

Dear Chimera group, Could you please help us resolving the following issues ? 1. Is there a way to load a pre-computed solvent accessible surface (i.e., coordinates of dot surface points stored in a PDB format against source atom types) on top of a protein molecule ? [kindly see the attached example file] 2. Is there a way to print / write the actual dot surface points generated by Chimera into a file (preferably in a PDB format with the source atom records) ? 3. Is there a way to actually compute the electrostatic potentials (ESP) on the solvent accessible surface by chimera using a Delphi interface ? In that case, how can one set the delphi parameters (e.g., partial charges / atomic radii / percentage grid fills / boundary conditions) according to his likings ? 4. We have computed ESP on solvent accessible surface (MS - connolly) using a standalone version of delphi. When we load the phimap.phi onto the chimera-generated surface to obtain the ESP-colored surface map, we find ambiguities between the surface coloring and the actual values of the potentials (almost the entire surface is showing red / white whereas there are obviously positive patches from the actual numbers) ! We suspect that it is due to the inconsistency between two surfaces. Lastly, 5. A trivial question is how to select residue(s) by residue sequence number (e.g., 108 or 108-VAL) from the select drop-down list ? We do not seem to find that option. thanks and regards, Sankar Basu Post Doctoral Fellow Foundation for Applied Molecular Evolution Gainesville, FL 32601

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Saving an EM map to open at a specific Threshold
by Kevin Huynh 30 May '14

30 May '14

Hello, I have finished processing my cryo-EM map and have set the desired volume to threshold=1 with EMAN2; however, I cannot seem to figure out how to save the map in mrc format so that I can open the map at threshold 1. I am wondering if Chimera can save the map in mrc format so that I can open it at threshold 1? If yes, how can this be done? Thanks, Kevin

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merging 2 pdb files
by Adrian Javaherian 30 May '14

30 May '14

Hi, My name is Adrian. I am a graduate student at Bar Ilan University in Israel. I have 2 pdb files, each containing rRNA sequences and I would like to combine the 2 to make 1 pdb file displaying all of the rRNA subunits. I download the Chimera program. Is it possible to do this on your program and if so, can you please tell me how? Thank you so much, Adrian

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Electron density maps
by lecan 30 May '14

30 May '14

Hello Chimera's users, I would like to know if there are a way to see density maps from .mtz files with chimera. I have tried opening a .mtz file after opening a .pdb file, but I got the next error message after choose CCP4 density map in the Type Selection window: Error reading file abc.mtz format ccp4 File size 631624 too small for grid size (1297373728,929300992,1145110528) and 64 bytes of symmetry operators Does anyone could telling me if what I'm trying to do is possible and what is the way to do it? Thank you for your help, Luis L.

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part-time job for Chimera professionals
by Andrew Voronkov 30 May '14

30 May '14

Dear Chimera users, if anyone may be interested in part-time job and additional income through Chimera usage, please let me know. I am looking for someone, who can regularly make nice-looking Chimera pictures. It can be 2-3 hours per week for example. Best regards, Andrew

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Save to a file
by sette＠uniroma2.it 29 May '14

29 May '14

Dear all, I created a simple text file with a list of distances to be measured How to save in a file the measured distances? The saveFile options does not seems to be the solution. I use 1.7 version of Chimera on Windows 7. Thanks, Marco ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it

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merging 2 pdb files
by Adrian Javaherian 28 May '14

28 May '14

Hi, My name is Adrian. I am a graduate student at Bar Ilan University in Israel. I have 2 pdb files, each containing rRNA sequences and I would like to combine the 2 to make 1 pdb file displaying all of the rRNA subunits. I download the Chimera program. Is it possible to do this on your program and if so, can you please tell me how? Thank you so much, Adrian

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mmCIF support
by Greg Couch 28 May '14

28 May '14

Hello, I'm working on improving Chimera's mmCIF support. So if anyone has a mmCIF file that is not from the PDB and that they are willing to share, please send it to me. Many thanks, Greg

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domain colouring
by ce 28 May '14

28 May '14

Hi, Could You send me instruction about domain colouring (the quickest way if possible) ? Cheers, J.

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