- Chimera-users - RBVI Mailing Lists

Help Needed
by angshu＠klyuniv.ac.in 03 Feb '15

03 Feb '15

Hi, I need a small help. I need to find out the amino acid residues from one chain of a protein which are within 5A of a specific amino acid residue of some another chain of the same protein. For example: Say I have a protein 1XYZ.pdb containing A, B, C chains. I want to find which amino acids from chain B and C are within 5A distance from ALA 78 belonging to chain A. Please let me know. Thanks. Angshuman

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Using Chimera to measure voxel densities
by Noble, Alex 30 Jan '15

30 Jan '15

Hi all, I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera? Best, -Alex Noble

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Question
by Monete Rajão Gomes 28 Jan '15

28 Jan '15

Hi, I have some problem these days about superimpose templates with matchmaker. I followed this tutorial http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-August/006686.html. There are regions on aminoacids sequences which are identical. So, when I superimpose them, they stay separated. I am sending a screenshot attached. It would be great if you could help me. Best, Monete

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Morph conformations - estimated time to completion in status bar?
by Oliver Clarke 26 Jan '15

26 Jan '15

Hi all - silly little feature suggestion, but I was wondering if it would be possible to add an live-updating “x % complete” or “estimated time to completion” entry in the status bar when running Morph Conformations? When morphing two structures with very large numbers of atoms, morph conformations can take a long time (hours) to complete, and it would be handy to know whether it is nearly done or not (currently it just shows “computing interpolation 1” until it is finished). On a related note, is there any way to speed up morph conformations for large structures? E.g calculating transformations using C-alpha atoms only? Best, Oliver.

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modelling a dimer
by David Norman (Staff) 23 Jan '15

23 Jan '15

I am trying to model a symmetrical dimer using modeller within Chimera. I cannot work out how to present the alignment and pdb. files in oder to do this. Any hints please. Thanks David David Norman Ph.D Nucleic Acids Research Group School of Life Sciences MSI/WTB Complex Dow St. Dundee, DD1 5EH, Scotland, UK. phone +44(0)1382 384798 mobile +44(0)7808572788 E.mail d.g.norman(a)dundee.ac.uk Web site: http://www.lifesci.dundee.ac.uk/people/david-norman The University of Dundee is a Scottish Registered Charity, No. SC015096 The University of Dundee is a registered Scottish Charity, No: SC015096

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how to find non-bonded interactions between a protein and a ligand?
by Sam Paul D. 22 Jan '15

22 Jan '15

Hi, I need to find non-bonded interactions between a protein and a ligand through command line. Could anyone please suggest which chimera command to use with the syntax? With regards, Sam

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Find subsequence programatically
by Thomas Hrabe 22 Jan '15

22 Jan '15

Hi Chimera Team, How can I automate the Sequence View -> Edit -> Find Subsequence Tool programmatically with the Chimera shell or better within python? Thank you, Thomas

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Coot capabilities in Chimera
by Mario J. Borgnia 22 Jan '15

22 Jan '15

Dear all, WIth the advent of atomic resolution maps in Cryo-EM, we find ourselves refining structures. The blunt question is, should I move to Coot and leave behind Chimera for that or are there overlapping functions and what will I be missing if I choose to stay with Chimera. I have some ideas about the answers but would like to read what the developers and power users have to say on the issue. Thanks!!!

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How to predict/model the structure of two known structure proteins
by Phan Trong Hoang 22 Jan '15

22 Jan '15

Dear UCSF developers, I am Hoang, working in IPK in Germany. I am following your series online tutorials about how to use UCSF Chimera. This program is very useful for me. However, I did not see your video showing how to predict/model the structure of a fusion protein that is made by combination of two known structure proteins in PDB (for example gi|534286646|pdb|4KRN| and gi|390136394|pdb|4DDF|A). Is this function available in your software? If yes can you show me how to manipulate with it. I would like appreciate it very much Thank you for your attention and I am looking forward to hearing from you. Best regards Hoang Phan

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SDF file
by Hernando J Sosa 22 Jan '15

22 Jan '15

I have an sdf file with a small ligand molecule in 2D (it looks flat when opened in chimera). What would be the best way to make it 3D (i.e. assign/minimize the proper bond angles & distances). Is it possible to do it in chimera? Thanks

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How can one create a sculpted view of a cellular assembly?
by Kenward Vaughan 21 Jan '15

21 Jan '15

As I slowly approach the operational realization of my computational/visualization lab, I received your lovely holiday card. This seriously elevated my dreams of larger scale possibilities for chemistry and biology students through the cellPack resources. In playing with it, I found myself wanting a more robust version of a clipping plane which would have several characteristics: 3 dimensional - take a cell and hack out 1 or 2 adjoining octants relative to its center to give a sliced view similar to what is found in some texts (also often used in geology books to depict the earth's internal structure--see http://www.the-science-site.com/earths-interior.html for an example). Being able to leave the nucleus alone while the surface strips away the cytoplasm would be cool, much like the referenced image above showing the core of the earth. Likely a difficult one to actually implement? Have the clipped surface not be flat, but rather allow a component to stay visible as the surface is moved past it until some determined relationship at which point it vanishes (perhaps when it has passed entirely through the clipping surface?). The clipped surface would thus show structure of a sort. Have the choice of the clipping surface being static with the assembly (it could rotate with the assembly, keeping the same internal view), or separately static (how a clipping plane behaves now--as I know it--where rotating the structure causes things to move through the unmoving plane. One approach I can imagine would be the use of a spherical or ellipsoidal (?) surface of specific size at a specific distance from the center of the cellular assembly. Is this already implemented in a way that can be manipulated to achieve at least the major aspects of this effect (e.g. logical ANDing of clipping by 3 intersecting planes)? Sorry for the long question... ;-/ 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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Ringer/Chimera/IDLE
by Alejandro Virrueta 21 Jan '15

21 Jan '15

Hello, I am modifying some Ringer files for my own needs, but I am running into a weird issue. If I run Ringer via typical means: $RINGER/ringer/ringer -i ringer_in_${pdb_ID}.txt -o ringer_out_${pdb_ID}.txt it works fine. However, when I step through it in what I think is my version of IDLE ("$CHIMERA_HOME/bin/chimera --nogui --nostatus --script `which idle2.7` /usr/bin/idle2.7", with `which idle2.7` returning "/usr/bin/idle2.7"), I run into this error: Traceback (most recent call last): File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 233, in <module> main() File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 161, in main move_set, pdb = structureFile(parameters, path) File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 65, in structureFile pdb = chimera.openModels.open(parameters.pdbfileName) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1817, in open checkForChanges=False, noprefs=noprefs) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1644, in add makePseudoBondsToMetals(realMolecules) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1961, in makePseudoBondsToMetals cmPBG = mol.metalComplexGroup(issueHint=True) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 119, in _getMetalPbg am.color = preferences.get(MOLECULE_DEFAULT, MOL_COMPLEX_COLOR) File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 608, in get forPrefSave=forPrefSave) File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 179, in get return self._options[name].get(forPrefSave=forPrefSave) File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 80, in get return self.prefToVal(self.value) File "/Applications/Chimera.app/Contents/Resources/share/chimera/tkoptions.py", line 1229, in _prefToColor return getColorByName(pref) File "/Applications/Chimera.app/Contents/Resources/share/chimera/colorTable.py", line 87, in getColorByName color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0) ValueError: missing default material Any suggestions? Cheers, Alex

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Alternate conformations in residues
by Alejandro Virrueta 21 Jan '15

21 Jan '15

Hello all, Is there a way to get the all the information for an alternate conformation from a residue object? I have res.altLocs resulting in set([a,b]), but how can I get chi1-4 for conformation b for example? Thanks! Alex

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Alternate conformations in residues
by Alejandro Virrueta 21 Jan '15

21 Jan '15

Hello all, Is there a way to get the all the information for an alternate conformation from a residue object? I have res.altLocs resulting in set([a,b]), but how can I get chi1-4 for conformation b for example? Thanks! Alex

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Mesh defined by distance to selection
by R. Michael Sivley 21 Jan '15

21 Jan '15

I have a set of residues in a protein structure that each mark the center of a sphere over which a value has been calculated. I can select a subset of residues by value, but the values actually correspond to the sphere around that residue. I would like to visualize this by creating a mesh defined by being within 10A of any selected residue. If a selected residue isn't within 10A of any other selected residue, I would like this to produce two meshes, but if they are within 10A, I would like a single continuous mesh whose boundaries are defined as being 10A from either residue. Zone-selecting residues within 10A of the selection and then showing their surface as a mesh is a close approximation of what I'm trying to convey, but doesn't give me exactly what I'm looking for. I found this in the Chimera help pages, and it seems to be exactly what I need: http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#z… I think I'm missing a first step, though, because I don't understand how to actually create the mesh. I select my residues, open the Volume Viewer, and define the zone radius, but then I'm stuck. How do I actually instantiate the mesh given those values? I've tried showing the surface for the selected residues, but the changes I make in the Volume Viewer don't appear to have any effect on the surface, so I'm assuming these are two separate features. There is no "apply" button in the Volume Viewer, and closing the window does not create a mesh. I've included a screenshot of where I'm stuck, should it be helpful. Could you help me identify the missing step in this process? Thanks! Mike Sivley PhD Student in Biomedical Informatics Center for Human Genetics Research Vanderbilt University

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UHBD map, generated with APBS
by Feldman-Salit, Anna 20 Jan '15

20 Jan '15

My current "strange" problem: I use APBS stand-alone to generate electrostatic potential for a protein in PQR format. What I do is to ask for output in UHBD (GRD not DX) format. Unfortunately, the generated GRD file is not read by CHIMERA, which upsets me... Strange, but VMD seems to be less sensitive to the GRD generated with APBS to visualize the map. Another point: I am very glad that CHIMERA computes potential. Do you think one could save it not only in DX format? Maybe you could suggest me a way to convert DX to UHBD format? Thank you! Have a lovely working day! Greetings, Anna --- Dr. Anna Feldman-Salit Molecular and Cellular Modeling (MCM) Group HITS gGmbH, Schloß-Wolfsbrunnenweg 35 69118 Heidelberg, Germany phone: +49-6221-533-260 fax: +49 6221 533298

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Simply, keep up the good work
by Kevin D. Walker 20 Jan '15

20 Jan '15

I really enjoy using the Chimera program, and I am trying to convince my lab members to make the switch. I hope you get these types of emails all of the time. Your program is duly acknowledged during my seminars. ---------------------------------- Kevin D Walker Associate Professor Michigan State University Department of Chemistry and Department of Biochemistry & Molecular Biology 578 S Shaw Lane; Room 208 East Lansing, MI 48824 Phone: 517 355 9715 x 257 Fax: 517 353 1793 websites: 1) http://bmb.natsci.msu.edu/about/directory/faculty/kevin-d-walker/current-re…

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Creating a cubic box for a density map
by Juan Luis Loredo Varela 18 Jan '15

18 Jan '15

Dear Chimera users When I use the Segment map option to save a specific fragment as .mrc file, Chimera uses the minimal box containing the segment. Does anyone know how to modify the dimensions of a density map to have it in a cubic box that can be used in Flex-EM? Thanks Juan -- Juan Luis Loredo Varela PhD Student Antson Group York Structural Biology Laboratory L0 Department of Chemistry University of York

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Scripting image writing in Mac OSX
by Mike Sivley 16 Jan '15

16 Jan '15

I have a Chimera script that takes a set of attribute files and generates a collection of scenes images. This script is usually run on Scientific Linux using the Headless Linux 64-bit distribution of Chimera. I'm now trying to run this script on Mac OSX Mavericks and hitting issues with the GUI. If I pass the --nogui flag to Chimera, then the script fails, stating that the GUI is necessary to save images. If I remove the flag, the GUI starts up correctly, but scripted control stops once the new attributes are defined. The user is prompted by the Render by Attribute window, and the script will not progress until the user confirms the changes and closes the GUI. How can I get the script to run start-to-finish without stalling for user-interaction, the way it does in linux? Thanks! Mike Sivley PhD Student in Biomedical Informatics Center for Human Genetics Research Vanderbilt University

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Re: [Chimera-users] dotted lines
by Elaine Meng 16 Jan '15

16 Jan '15

On Jan 16, 2015, at 8:46 AM, Thomas Evangelidis <tevang3(a)gmail.com> wrote: > Hi Elaine, > I don't know why, but none of the 3 approached works, even with the latest Chimera version. > […] Hi Thomas, Your pseudobonds are in stick style. You would have to change the stick to wire before doing those other things; in Chimera there are no “dotted or dashed” sticks, only wires (lines). E.g. in Selection Inspector, inspect: Pseudobond, change bond style to wire. That only changes the specific pseudobond(s) you have selected; if you first select one distance pseudobond, you can press keyboard up arrow to expand the selection to all the distance pseudobonds. Can also be done with setattr command, e.g.: setattr p drawMode 0 Hard to see on white background. Can change color with setattr too: setattr p color black When you first create distances they are normally already in wire style, which is why I didn’t mention the stick/wire issue before. 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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vop add
by Fco Javier Chichón 16 Jan '15

16 Jan '15

Dear all I would like to merge several volumes. Not all the voxels of the two volumes fit, so when I used vop add command, Chimera add the densities instead of average them. Anyone know how to do that? Thanks -- ======================================================= Francisco Javier Chichón García Centro.: Centro Nacional de Biotecnología Dept.: Macromolecular Structure Lab.: S1-S0.1 Tel.: (+34) 91585-5497:4690 =======================================================

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dotted lines
by Thomas Evangelidis 15 Jan '15

15 Jan '15

Greetings, I have created a figure with manually added Hbonds (Tools->Structure Analysis->Distances). Is there any way to make these lines dotted/dashed? thanks, Thomas -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tevang(a)pharm.uoa.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ =============================================================== *Physics is the only real science. The rest are just stamp collecting.* *- Ernest Rutherford*

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Distance measurement in density map
by Maarten Schledorn 14 Jan '15

14 Jan '15

Dear reader, I'm looking at EM tomography data summarised in *.mrc density files. Since there are no atoms defined in these files, the usual distance measurement tool is inappropriate (I suppose). Is there another way to assess the dimensions of the oligomerised protein I'm looking at? With my sincere thanks in advance, Maarten

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shown/hidden state of axes/planes not saved with scene
by Oliver Clarke 14 Jan '15

14 Jan '15

Hi all, Planes seem to be shown by default when I load a scene, regardless of whether they were displayed when I saved the scene. This is not normally an issue, but it is a little problematic when preparing animations using many different scenes - I will often have a plane defined at the start so I can use it to align the x/y/z axes to the normal of that plane (e.g. aligning the fourfold axis of an ion channel), but I do not want the plane displayed during the animation, and I don’t want to have to delete it from each scene and re-arrange the animation timeline if I can avoid doing so. Would it be possible to alter this behavior such that chimera knows the displayed/undisplayed states of axes/planes/centroids when saving a scene or session? Best, Oliver Clarke.

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New to Chimera
by Mike 12 Jan '15

12 Jan '15

This is my first day with Chimera. I'm trying to find how to draw a small molecule, minimize the structure of the small molecule and then have it interact with my protein of interest. However, I don't see any way for me to draw a small molecule (potential drug). Can you provide any direction ? Thanks, Mike

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