- Chimera-users - RBVI Mailing Lists

rmsd overlay
by Francesco Pietra 12 Oct '15

12 Oct '15

Hello; Ho to superimpose a fake atom (pdb file available) to a coordiated metal in a protein? I could change the name of the fake atom to that of the metal, but then I need an rmsd overlay. hope it is clear. thanks francesco pietra

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python/model panel
by Dougherty, Matthew T 09 Oct '15

09 Oct '15

I would like to print out the model ID, name and input files as they are listed in the model panel. Can you point me in the direction of how to loop over the model panel ? Such as elevant variables, and what would be a block of code in chimera that I should study. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Re: [Chimera-users] pipes & planks
by Tom Goddard 09 Oct '15

09 Oct '15

Hi Gabe, I've added a "pipes" command to tonight's Chimera daily build, for example, pipes #0 helixColor pink strandColor salmon and to delete the pipes and planks ~pipes #0 Other command options with default values are: helixColor = None, helixEdgeColor = None, helixArrow = True, helixFixedRadius = True, helixRadius = 1.25, helixSplit = False, helixSplitRatio = 2.5, strandColor = None, strandEdgeColor = None, strandArrow = True, strandFixedWidth = True, strandWidth = 2.5, strandFixedThickness = True, strandThickness = 1.0, strandSplit = False, strandSplitRatio = 2.5, displayCoils = True, displayTurns = True, turnColor = None, turnEdgeColor = None, turnResolution = 10, turnWidth = 0.25, turnThickness = 0.25 Colors by default match the ribbon color, or molecule color. Tom > On Oct 9, 2015, at 1:12 AM, Gabriel Lander wrote: > > Hi Tom, > 2 quick questions: > > 1) is there a way to turn generate a pipes & planks model from the command line? > 2) Can the coils in the pipes & planks be depicted as rounded instead of edged? > > Thanks as always, > -gabe > >

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bootstrap wanted boxsize
by Marlovits,Thomas 09 Oct '15

09 Oct '15

Hi Chimera-developers, I am wondering, whether there is a command to generate a new (empty) volume box from scratch? This would be a great help. Many thanks, -Thomas

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Chimera crashes when I try to open a .gro file
by Raag Saluja 09 Oct '15

09 Oct '15

Hi! Chimera crashes when I try to open a .gro file (created through GROMACS). I wanted to open the .gro file and then superimpose it on a .pdb file. Can you please guide? Thank you! Regards, Raag

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display a coordinate system in view
by Byrd, Robert A. (NIH/NCI) [E] 09 Oct '15

09 Oct '15

I would like to represent a xyz coordinate system by the unit vectors on the display with a molecule. Ideally, for a two domain protein, I would like to have two coordinate systems, one for each domain. In an ensemble of structures where one domain changes orientation with respect to the other, one coordinate system would move to the new position. It would be nice to then morph from one position to the next. This is straightforward with a set of structures and the morph utility in CHIMERA. The ability to add the two coordinate systems to the display, and have them ‘move’ or morph from one position to the other, would highlight the geometrical averaging that takes place. Is this possible in CHIMERA? Thanks Andy Byrd

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on command scripts related to movie by chimera
by Smith Liu 09 Oct '15

09 Oct '15

Dear All, I want to learn several commands on chimera movie preparation. Only read the on-line material I find I still meet some difficulty. Suppose I have 2 scripts， each for 1 movie. Will you please tell me by which command in the script I can link the 2 scripts so that the 2 movie will change into 1 movie? Suppose in Chimera I have opened 2 PDB files. Will you please show me the commands to view the structure in the first PDB, then change to view the structure of the second PDB （different from the purpose of morph）? And how about if then we see the 2 structures together, all in a single movie? Best regards. Smith

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3D-visualization of protein chain and mutation
by Elaine Meng 09 Oct '15

09 Oct '15

> From: "Coci, Emanuele" <Emanuele.Coci(a)akh-celle.de<mailto:Emanuele.Coci@akh-celle.de>> > Date: Friday, October 2, 2015 at 8:54 AM > Subject: 3D-visualization of protein chain > > Deat Chimera team, > my name is Emanuele Coci, MD PhD. > > I would kindly ask you for help about Chimera software in solving the following technical issue. I want to visualize the 3D-structure of a mutated protein chain. > > Which of the chimera tools is more indicated to visualize the 3D structure? > Is the toll open source? > Which software do I need to download the tool on my PC : JAVA, …? > > Best regards and many thanks in advance? > Emanuele Coci Dear Emanuele Coci, Chimera is a free download for any noncommercial use (research, education, …) and is available for Windows, Mac, and Linux. You should not have to download any other software to use it. All you need is a reasonably modern computer. See Chimera homepage and download links: <http://www.rbvi.ucsf.edu/chimera/index.html> <http://www.rbvi.ucsf.edu/chimera/download.html> I’ve CC’d chimera-users(a)cgl.ucsf.edu — that is the proper address for user questions. There are many possible styles of displaying a protein, and you have to use your own judgement and artistic taste to decide which style is best for what you want to see for yourself or show to others. There are several step-by-step tutorials for learning how to use Chimera, including “getting started” for beginners and some example image tutorials: <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> For showing a mutation, the first thing you could do is just show the location of that amino acid on the structure (without mutating it), for example coloring it differently than the rest of the structure. It may be helpful to show the sequence of the protein so that you can identify the correct position (Chimera menu: Favorites… Sequence). You can choose a residue with the mouse in the sequence window, which will automatically select-highlight it in the structure. Secondly, you could try “mutating” that residue computationally. This could be done with the Rotamers tool (in menu under Tools… Structure Editing) or the “swapaa” command. There is an example of using the Rotamers tool in the “Structure Analysis and Comparison” tutorial: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/rotamer…> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html> However, Chimera will not predict any larger-scale changes in the structure from the mutation or calculate changes in stability or affinity. It will only change the sidechain and not move anything else. You can use Rotamers to analyze the H-bonds and clashes (bad contacts) of different conformations of the sidechain, which may allow you to hypothesize whether the mutation would be disruptive to the stability or interactions of the protein. 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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Newlines in labelopt string
by Repic Matej 07 Oct '15

07 Oct '15

Hi everyone, I have pretty long atom labels and it would be nice if I could split them with newlines. I set labels with labelopt info %(name)s %(ee).2f %(ea).2f %(er).2f # what I have C3 0.41 0.22 0.14 # what I want C3 0.41 0.22 0.14 The obvious \n does not work. Any ideas? Thank you, ------------------------------------------------------ Dr. Matej Repic Ecole Polytechnique Fédérale de Lausanne Laboratory of Computational Chemistry and Biochemistry SB - ISIC LCBC BCH 4108 CH - 1015 Lausanne ------------------------------------------------------

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Joining Models + Avoiding Steric Clashes
by Carlos Gonzalez Oliver, Mr 06 Oct '15

06 Oct '15

Dear Chimera, I have been trying to use Join Models to make a C-N bond between the globular domain of a protein and a region of it (a C-terminal tail) whose structure I simulated using MD. However, when I do the joining with Join Models C-N bond option, I get some serious steric clashes. I have tried to resolve them by hand by adjusting the bond's torsion and angles but it is too complicated. Other than trying to use other software to minimize clashes, I think I might have to use a brute force method and try a bunch of the structures my MD generated until one of them works. So what I am trying to do now is write a script to do the model joining automatically with many different structures that I generated, and return the one with the least number of clashes. But I haven't been able to find a command line equivalent of the Join Models window.. I was wondering if you know if such a command exists, if not what combination of commands would work? (for repositioning the models and forming the bond) Thanks! -- Carlos G. Oliver M.Sc. Student Vogel Lab Department of Biology McGill University Montréal, QC, Canada

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Problem on Nucleic Acid Ribbon
by Francesco Papi 06 Oct '15

06 Oct '15

Good morning, I'm working on a DNA X-ray structure. The problem I have observed is that the terminal nucleotide of the DNA sequence is excluded from the backbone ribbon, in other terms the backbone ribbon is shown and it is ok, but it is made of all the residues except the terminal one, which is linked to the ribbon by a long phosphodiester bond (see the attached image). Moreover, if I put the representation "Show side (sugar/base)", from the option "Nucleotides", to be "fill/slab", the terminal residue still features an "Atom & Bonds" style. The PDB file seems to be ok, as confirmed by a colleague. Do you how to solve this problem? Best regards Francesco Papi

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solid rendering color voxel by voxel?
by Oliver Clarke 06 Oct '15

06 Oct '15

Hi all, I don’t think this is possible right now, but i just wanted to check and maybe put in a request for addition to Chimera 2 at some point if you think it would be a useful feature. I like generating looping maximum intensity projection movies like the following (using EMDB 2807 as an example): https://www.dropbox.com/s/elt2f5so6azvvhk/emdb2807_example1.mp4?dl=0 <https://www.dropbox.com/s/elt2f5so6azvvhk/emdb2807_example1.mp4?dl=0> https://www.dropbox.com/s/julh586sc9yxl7g/emdb2807_example2.mp4?dl=0 <https://www.dropbox.com/s/julh586sc9yxl7g/emdb2807_example2.mp4?dl=0> Command used to generate representation: #Makes a pseudoprojection style view of the given volume #Usage: volume_project #map_id alias ^volume_project background solid black; volume $1 step 1 sdlevel 0,0 color white sdlevel 20,1 color white style solid projectionMode 3d maximumIntensityProjection true btCorrection true linearInterpolation true; unset depthCue I feel like even at small sizes, this gives a good idea of the overall quality of the electron density, in both mobile and well-ordered regions, due to the non-thresholded nature of the representation. It seems to me that this would be a natural fit for Resmap coloring to color a map by local resolution, as one of the issues I have with the application of Resmap in surface representation is that if you contour the map at a sufficiently low threshold to see the less well ordered parts of the structure, you can’t see the voxels that have the best local resolution (necessitating slabbing of the map). This would also be handy for using Color Zone to color different regions of the map based on the model. Would it be possible to add per-voxel coloring in solid representation at some point, similar to scolor for surface representation, to make this kind of thing possible? Cheers, Oliver.

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Exporting coarse-grained models of proteins
by Hamish Todd 06 Oct '15

06 Oct '15

Hello all, So sorry to bother you all but I've tried googling a lot of things and not found out how to create a coarse grained protein surface like this one <http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/stmvrna/capsid.png>. Creating a *surface* is easy of course, but where does that nice, intuitive, bulbous STMV protein come from? And when I get it, can I export the vertex and polygon data? Hamish -- Hamish Todd 07722 400 806 Personal Website <http://www.musicofthespheresgame.com/?page_id=21>

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Saving images of all scenes in session?
by Oliver Clarke 02 Oct '15

02 Oct '15

Hi all, Apologies for yet another post and thank you for your patience! :-) Feature suggestion (or maybe this exists already?): I would like a way to iterate over all scenes in a session and save an image at each scene, with the same display settings (e.g keep background or make transparent, image format, wall-eye/cross-eye stereo, etc). This would be really very helpful when making, remaking and updating figures. Most of the time, I will have a session, say “Fig1.py”, within which I will have a bunch of scenes corresponding to each panel. It would be really advantageous to be able to take images of each scene all at once, saving each as (for example) Fig1_scene_name.jpg, Fig1_scene_name2.jpg etc. This could work in the same way as saving series of maps or models does now - just have a checkbox in the Save Image dialog for “save images for all scenes in session”, or something similar. It can take quite a while to save each image when on a slow computer, or when using graphics intensive settings such as silhouettes and shadows, so being able to save matched sets of images (e.g. low and hi-res versions, stereo versions, etc) with a couple of clicks would save a lot of time, particularly for example if you realize that the versions you saved the first time were all too low res and you want to go back and save a higher res version of every panel. I realize you guys might not have time to implement this for Chimera 1, as development of Chimera 2 is top priority, so maybe I can write a script to do this in the meantime? Is there any way to return a list of scene names using one of the built in python functions? I guess something in Animate.Scenes ought to do this, but not being much of a python programmer I can’t quite figure it out - any tips much appreciated. Cheers, Oli.

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Problems detecting h-bonds
by Felipe Vasquez 02 Oct '15

02 Oct '15

Hi, I have recently obtained some docking results (I have a complex) and I am trying to detect any protein-ligand h-bonds. Soon, I faced a first problem when I obtain this error message: "More than 2 coplanar positions specified!", and I think I solved it once my ligand was selected and I enter into the command line: "setattr a idatmType sel". However, I obtained later an entire panel (with a big list in it) asking me to indicate the expetd geometries and number of substituents for a large list of atoms, from both ligand and protein. How could I overcome this issue knowing that there is several expected h-bonds to be detected in my complex? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Profesional - 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 Bogotá, D.C., Colombia

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Morphs
by Dr Kereiche 02 Oct '15

02 Oct '15

Dear Chimera team, lately I am facing some problems for creating a movie in which I would like to combine 2 morphs with each other. To make it clearer, I hope, I have 2 Em maps representing 2 states of my structure (vol #1 & vol #2) I did a morph maps (volume/ Morph map) after having recenter and align the 2 maps. it works perfectly. I did similar procedure with 2 pdb files (1.pdb & 2.pdb), corresponding to the fitted molecular structures of the 2 states (vol#1 & vol #2) , using the tool/Structures comparison/ morph conformation. The pbds are aligned with the EM map using VOP command. Now I would like to combine the 2 morphs together to have a final morph of the EM maps with the molecular structure, but I could not find a way to combine them. Thus I would like to know if it is possible to do it ? and if yes how to do it. Moreover is it possible to play the morph of the pdbs in way of the morph of the EM maps back and forth? Thank you in advance, Sincerely Sami

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Angle between pseudobond and principal axis
by Yasser Almeida Hernández 01 Oct '15

01 Oct '15

Hi all, I want to measure the angle between a pseudobond and the X, Y, Z axis. How can I do so? Best Yasser

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Re: [Chimera-users] metal coordination to display off
by Eric Pettersen 30 Sep '15

30 Sep '15

On 9/28/15 6:13 PM, "Luigi Di Costanzo" <dicostanzo(a)rcsb.rutgers.edu <mailto:dicostanzo@rcsb.rutgers.edu>> wrote: > > We have fetched 2MHR with Chimera and noticed that the middle nitrogen > of azide is bonded through a dashed line as following: > > FE2 FEO A 119 N2 AZI A 120 > > From the "structure analysis" tool and "metal geometry" window we are > unable to display off that dashed lines that is incorrect. > > The coordination table does not show that particular link and we can not > deselect it. > > Could you please look into it and provide some suggestions? > > Thanks. Hi Luigi, The spurious dashed line is due to a corresponding CONECT record in the PDB file. So one option is to locate that CONECT record and delete it. The other is to use the Metal Coordination tool to clean up the coordination of that iron. First, it is highly unlikely that the histidine nitrogens coordinating the iron are protonated, so you should select those hydrogens and “del sel” to get rid of them. Then if you bring up the metal coordination tool for the iron it will properly show the nitrogens as coordinating. If you already had the tool up when you deleted the hydrogens then you will have to force the tool to consider the newly deprotonated nitrogens by selecting them and clicking the “Add atoms selected in the graphics window" button. You can now remove the spurious coordination you noted above by first clicking the last atom in the coordination table (HIS 25.A NE2) and then clicking the “Create/Update metal-complex pseudobonds” button. I hope this helps. Let me know if you have any questions. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Chimera
by Scapin, Giovanna 30 Sep '15

30 Sep '15

Good afternoon I am interested in downloading and installing CHIMERA. Could you let me know if there is any licensing cost involved and if so whom I should contact? Thank you very much Giovanna Scapin Giovanna Scapin Principal Scientist Structural Chemistry Merck & Co., Inc. 2000 Galloping Hill Rd K15-1800 Room B133C Kenilworth NJ 07033 Phone +1 908 740 3632 Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

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Proportional representation of missing segments?
by Oliver Clarke 28 Sep '15

28 Sep '15

Hi all, I think it would be handy, in a future version of chimera, to have an option to represent missing segments in a manner that is proportional to the volume of protein missing - this would be very useful for getting a sense of which chain breaks correspond to very large missing regions (e.g. whole domains), and which correspond to short linkers or loops that are missing. For example, in the structure of the ryanodine receptor, there are missing segments ranging in length from ~5-250 residues in length - it would be very handy to be able to get a quick sense, upon first opening a structure, about what fraction of the crystallized or reconstructed protein is actually present in the model. I can think of a couple of ways of doing this. One way would be to associate an attribute with each missing segment, corresponding to the number of missing residues, and allow the user to scale the radius, color or opacity of the missing segments in proportion to this value (maybe this attribute already exists somewhere internally?). Another way might be to create a completely different missing segment representation - perhaps an ellipsoid, with the ends of the ellipsoid at the N and C-terminal breakpoints, and the volume of the ellipsoid scaled to the volume of a random polymer of the known number of missing residues. I would try to do this myself by creating an extension, but I don’t really know where to start to get the information that would be required - I don’t know how to iterate over all missing segments, calculate the number of residues in each, and create a new representation. I guess there is probably a list somewhere in Chimera corresponding to the missing segments and their properties, but I have no idea how to find it. Cheers, Oliver.

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Forcefields and Molecular Radii
by Cale Martin 25 Sep '15

25 Sep '15

Dear Chimera users, Over the last few days I have been using Chimera 1.9 to model the Poisson-Boltzmann surface potential of a protein. I have been using the APBS software and the two main forcefields I have been using are the TYL06 and AMBER. When I model the chemokine using the AMBER forcefield the result seems to be normal and as expected, but when using the TYL06 forcefield, the final molecule surface seems to have larger molecule radii almost making it look a little more "bubbly" for lack of a better term. Is this a function of the forcefield in any way? Should this be expected from these two different forcefields? Another issue that I have had along the same line involves the APBS program. The settings allow for the selection of a "Smoothed Molecular Surface" and one that is just "Molecular Surface" but when I run the program with every thing the same except these settings, the results look exactly the same. Should this setting affect the visualization of my molecule surface in any way? Thank you, Cale Martin

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FW: How can I find H-bond between ligand and protein residues within selected angstrom?
by Williams, Joanne 25 Sep '15

25 Sep '15

On 9/19/15 1:29 AM, "高木友理子" <kagaribi-firefly(a)bs.s.u-tokyo.ac.jp> wrote: > Dear Chimera creator, > > I use Chimera to analyse protein-ligand interaction. > Especially, I would like to find H-bond between these. > I clicked HBonds and tried to search H-bond within selected distance. > However,I could not. > I guess the reason is that I was not able to understand "Relax > constraints" in H-Bond parameter window. > I ,of course, checked chimera's help. > What is relax constraints? > What does 0.4 angstroms indicate? Is this the Max distance between ligand > and protein residue? > I would like to find H-bond between them within selected angstrom. > What should I do to know that? > Please teach me how to do. > Thank you for being patient with my English. > > Best regards, > > Yuriko Takagi > Tokyo university student

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Way to extract path to file from model ID
by Oliver Clarke 24 Sep '15

24 Sep '15

Hi all, I’m wondering, is there any way (presumably via a python function) to get the path to the original file from the model ID? I’ve written a little python jiffy (below) so I can lowpass filter maps to a specified resolution on the fly inside chimera using EMAN, but is quite slow because I need to first write a copy of the map out (so I know where it is) and then modify it. If anyone knows of an easier way to do such things I would be most grateful. Cheers, Oli. Script: def cmd_lowpass(lowpass,args): from Midas.midas_text import doExtensionFunc def lowpass(model,resol): import os from chimera import runCommand import subprocess import sys #You may need to change the below to .bash_profile if on mac. #You must have EMAN2 in your bash path for this to work correctly. #If running multiple times, you need to close the first instance of lowpass.mrc before creating a second. bashrc_path=os.path.expanduser("~/.bashrc") freq=1.0/resol command="cd ~; system mkdir chimera_tmp; cd chimera_tmp; volume "+model+" save ./tmp1.mrc" runCommand(command) pathvar=os.path.expanduser("~/chimera_tmp") os.chdir(pathvar) e2string="--process=filter.lowpass.gauss:cutoff_freq="+str(freq) print(e2string) mrc_in=pathvar+"/tmp1.mrc" mrc_out=pathvar+"/lowpass.mrc" e2command="source "+bashrc_path+"; bash -c \"e2proc3d.py"+" "+mrc_in+" "+mrc_out+" "+e2string+"\"" print(e2command) proc=subprocess.Popen(e2command,stdout=subprocess.PIPE, stderr=subprocess.PIPE,shell=True) out, err = proc.communicate() print 'stdout:', out print 'stderr:', err runCommand("open lowpass.mrc") doExtensionFunc(lowpass,args) from Midas.midas_text import addCommand addCommand("lowpass", cmd_lowpass, help=False)

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Rendering protein molecule to a geometry format by Chimera
by Hsin-Yi Yeh 23 Sep '15

23 Sep '15

Hi, I try to render a protein molecule to a geometry format (from .pdb format to .obj format) by Chimera. I use 'Multiscale models' tool in 'Higher-Order Structure' choice and then make the model by resurfacing at some appropriate resolution. It turns out that the whole protein molecule can be modeled pretty nicely. However, I now have a similar problem; instead of rendering the whole protein molecule, I would like to render the whole structure separately. I want to render the exposed residues (those residues on the surface) and non-exposed/buried residues separately, so I will have two obj files (one for the exposed residues and the others for the non-exposed residues). I haven't been able to figure this problem out yet. Thus, I am wondering could you please give me some direction? Any advice will be greatly appreciated! Thank you, Hsin-Yi (Cindy) Yeh -- Hsin-Yi (Cindy) Yeh PhD Student Parasol Lab, Department of Computer Science and Engineering Texas A&M University Email: hyeh(a)cse.tamu.edu https://parasol.tamu.edu/people/hyeh/

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applying charges calculated by DFT to ligands in protein models
by Anne-Frances Miller 21 Sep '15

21 Sep '15

Dear Sir or Madam, Our protein has a bound FMN and the various tools accessible via Chimera are not able to apply charges to the atoms in FMN. However I have NBO charges for all the atoms from DFT calculations. Is there a way I can provide these to the FMN in my pdb file or in my Chimera session in order to then display a Coulomb electrostatic potential for the protein + FMN? My charges are not simply +1 or -1, but fractional charges for each atom. Can Chimera accommodate this ? If not, no problem, I will still benefit greatly even if all I can do is add -1 to the one atom at which most of the excess electron density is concentrated. Many Thanks, Anne-Frances Anne-Frances Miller Professor of Chemistry Director, Magnetic Resonance Centre University of Kentucky Dept. Chemistry, 505 Rose Street Lexington KY 40506-0055 “You never change things by fighting the existing reality. To change something, build a new model that makes the existing model obsolete.” Buckminster Fuller

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