- Chimera-users - RBVI Mailing Lists

Command line problem
by Luca Pellegrini 03 Feb '15

03 Feb '15

Hi, I am having the following problem when I try to use the command line. When I select ‘Command line’ from the ‘Favorites’ menu, the command line window appears, but I can’t type anything in it. Or rather, I can type in it, because if I hit return the command gets executed, but I can’t see what I type. Any idea of what’s going on? I suspect that it might be something to do with Yosemite 10.10.2, since this problem arose after upgrading the MacOSX operating system. I am using Chimera 1.10.1, build 40415. Thanks for any advice. Kind regards, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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Error: UnboundLocalError: local variable 'i' referenced before assignment
by Letizia Meregalli 03 Feb '15

03 Feb '15

Hi, I have a tRNA molecule and I would like to measure the angles between two nitrogenous bases. I created two planes, each for each base. When I select both planes, in order to measure the angles between them (Structure Measurements Axes/Planes/Centroids) I get following message: <type 'exceptions.UnboundLocalError'> Exception in Tk callback Function: <bound method SortableTable._browseCmd of <CGLtk.Table.SortableTable instance at 0x117990638>> (type: <type 'instancemethod'>) Args: ('1',) Traceback (innermost last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/Chimera.app/Contents/Resources/share/CGLtk/Table.py", line 1043, in _browseCmd self.userBrowseCmd(self.selected()) File "/Applications/Chimera.app/Contents/Resources/share/StructMeasure/Geometry.py", line 268, in _tableCB self.feedback(sels) File "/Applications/Chimera.app/Contents/Resources/share/StructMeasure/Geometry.py", line 113, in feedback diff = " ".join(words2[i:]) <type 'exceptions.UnboundLocalError'>: local variable 'i' referenced before assignment UnboundLocalError: local variable 'i' referenced before assignment File "/Applications/Chimera.app/Contents/Resources/share/StructMeasure/Geometry.py", line 113, in feedback diff = " ".join(words2[i:]) See reply log for Python traceback. I really don’t know how can I solve this problem.. I’d be really grateful if you could help me or give me some hints! thank you a lot Letizia

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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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need guidence
by Maria Saqib 08 Jan '15

08 Jan '15

Dear user i am using chimera for some images of protien .I have a problem while labelling i want to change font colors , How can i label it with different font colors? Waiting for your reply Maria

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VR in Chimera?
by Andrey Malyutin 07 Jan '15

07 Jan '15

Good morning, With recent resurgence in virtual reality technology, such as Oculus Rift and Samsung Gear VR, is it possible that we'll see support for VR headsets in future releases of Chimera? Thank you, Andrey

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Distance Grid SES calculation available?
by Hurt, Darrell (NIH/NIAID) [E] 06 Jan '15

06 Jan '15

Hi Chimera friends, This question is probably for Tom Goddard, but I'm happy to hear from anyone. I'm really interested in using Tom's code for "distance grid SES" calculations as described here: http://www.cgl.ucsf.edu/chimera/data/surface-oct2013/surface.html The above page suggests that this code will be part of Chimera 2, but I'm wondering if it is available now for surface calculations. Too many of my surface calculations are failing for our production server using Chimera. This would help immensely. Molmap is a decent alternative in some instances, but for my purposes, distance grid calculations are going to be more MSMS-like, which will be a better solution (cf. the description on the page comparing the internal pockets formed by molmap vs MSMS surfaces). Is there some way to call the routine, especially in a script? Python maybe? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 5601 Fishers Lane, 4A31 North Bethesda, MD 20852 Office: 240-669-2741 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> , @NIH3Dprint<https://twitter.com/nih3dprint> 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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Parsing a new 3D file format
by ros 05 Jan '15

05 Jan '15

Hello! I would like to ask for advice and starting directions to be able to parse a new file format in Chimera so I can use Chimera's tools and generate images. The file format that I want to be able to open is generated from the Atoms in Molecules program AIMAll ( http://aim.tkgristmill.com/ ) The AIMAll program of course can also do visualization and is very good at it. I am attaching an example of how a molecule looks. The problem is that if you want to work with big biomolecules (like DNA), the program is not very good to cloak/hide/select atoms so you have to click atom by atom to hide it and make some sense of the visualization. So, I will try to make a parser (or something that you would recommend) to open the file in Chimera and use Chimera's masking rules to select/deselect, hide/show atoms, which is very powerful. The text output generated by AIMAll has an XYZ list for each atom like this: Nuclear Charges and Cartesian Coordinates: ------------------------------------------------------------------------------- Atom Charge X Y Z ------------------------------------------------------------------------------- C1 6.0 0.0000000000E+00 2.3265459100E+00 0.0000000000E+00 C2 6.0 0.0000000000E+00 0.0000000000E+00 1.7647056500E+00 C3 6.0 0.0000000000E+00 0.0000000000E+00 -1.7647056500E+00 H4 1.0 1.6866221200E+00 3.4814514700E+00 0.0000000000E+00 H5 1.0 -1.6866221200E+00 3.4814514700E+00 0.0000000000E+00 C6 6.0 -2.0148478600E+00 -1.1632729600E+00 0.0000000000E+00 H7 1.0 -2.1717143500E+00 -3.2013833400E+00 0.0000000000E+00 H8 1.0 -3.8583364700E+00 -2.8006813000E-01 0.0000000000E+00 C9 6.0 2.0148478600E+00 -1.1632729600E+00 0.0000000000E+00 H10 1.0 2.1717143500E+00 -3.2013833400E+00 0.0000000000E+00 H11 1.0 3.8583364700E+00 -2.8006813000E-01 0.0000000000E+00 H12 1.0 0.0000000000E+00 0.0000000000E+00 3.8040484300E+00 H13 1.0 0.0000000000E+00 0.0000000000E+00 -3.8040484300E+00 That is easy, I think. But as you can see from the attached image, I want to be able to visualize the green spheres (which are called critical points and represents special properties of the electron density, extracted from quantum mechanical calculations). Those points are represented in the output file as: CP# 16 Coords = 5.97894312844235E-20 1.21974356425640E+00 -9.60854463947958E-01 Type = (3,-1) BCP C1 C3 Rho = 2.4067790431E-01 GradRho = 3.5016504866E-18 -2.7948129921E-14 1.7716730860E-14 HessRho_EigVals = -4.4278076226E-01 -4.3836581782E-01 3.5682199801E-01 HessRho_EigVec1 = 1.0000000000E+00 0.0000000000E+00 0.0000000000E+00 HessRho_EigVec2 = 0.0000000000E+00 -6.1321358320E-01 7.8991714842E-01 HessRho_EigVec3 = 0.0000000000E+00 7.8991714842E-01 6.1321358320E-01 DelSqRho = -5.2432458207E-01 Bond Ellipticity = 1.0071370222E-02 V = -2.5219393995E-01 G = 6.0556397216E-02 CP# 18 Coords = 1.05289204670721E+00 3.04112062239339E+00 1.96757752864282E-18 Type = (3,-1) BCP H4 C1 Rho = 2.9524693796E-01 GradRho = 1.0061396161E-16 -1.6479873022E-16 1.6660693347E-18 HessRho_EigVals = -7.9444808957E-01 -7.8708168641E-01 4.1039750300E-01 HessRho_EigVec1 = -5.7017191910E-01 8.2152539989E-01 0.0000000000E+00 HessRho_EigVec2 = 0.0000000000E+00 0.0000000000E+00 1.0000000000E+00 HessRho_EigVec3 = 8.2152539989E-01 5.7017191910E-01 0.0000000000E+00 DelSqRho = -1.1711322730E+00 Bond Ellipticity = 9.3591342377E-03 V = -3.7782718105E-01 G = 4.2522056404E-02 etc etc etc First line indicates the critical point number followed by the XYZ coordinate of the point, and the second line shows which atoms are involved between that critical point. The rest is the electronic properties of the critical point (nothing to visualize there) So, I am guessing that the critical points can be represented as dummy atoms in Chimera following the XYZ coordinates? The idea is that first the molecule coordinates are parsed and the molecule is displayed and then display the critical points of each atom. If possible, show lines joining atoms that have a critical point between them... I know it is a difficult task, but maybe you can provide some starting directions? Anything will help because right now is double clicking 1000+ atoms! Thank you so much and have a good day, Rodrigo. ------------------------- Rodrigo Galindo-Murillo, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 307 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax)

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WebGL viewer
by Thomas Hrabe 05 Jan '15

05 Jan '15

Hi everyone, I am trying to implement a EM density viewer in a HTML page based on the chimera webgl & html export feature. The original page chimera exports when you save a webgl / html scene has been modified to load multiple JSON objects with densities as they come from chimera. The bar at the bottom of the page essentially performs a coarse density sliding similar to chimera. Almost all works great but what I am missing is how to connect the rotation that was applied to one model and to propagate it to all other models. What is happening now is that when one rotates one model and slides the bar, the next model will not be rotated but will be in it’s original position. Here’s my page I am currently working on http://localize.pytom.org/php/displayWebGL.php?jobID=tutorial I tried catching the mouse event with a loop, but it seems it fails to propagate the rotation to the other models. Check the block at line 916 in the code try { var rotMat = vsphere(mouse_position, new_position); var camera = this.camera; var matrix = new Mat4; matrix.$translate(camera.target[0], camera.target[1], camera.target[2]); matrix.$mulMat4(rotMat); matrix.$translate(-camera.target[0], -camera.target[1], -camera.target[2]); for (var i = 0, models = this.scene.models, l = models.length; i < l; ++i) { var elem = models[i]; elem.matrix = matrix.mulMat4(elem.matrix); } } Thank you in advance for your help, Thomas

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mmaker usage with md-movie perframe
by Bala subramanian 02 Jan '15

02 Jan '15

Friends, I have a crystal structure of a protein (370aa). I have a trajectory of a similar protein (not same) with (210aa). I opened the crystal structure and the trajectory via md-movie tool. In the perframe analysis, i gave the following command (#1 my traj, #0 crystal.pdb) *mmaker #1 #0 computeSS false* mmaker uses different number of atom pairs for rmsd calculation. If there are say 150aa that match between my target and crystal, then mmaker should make the rmsd firt for 150 atom pairs in every frame. Why does it use different no. of atom pairs. Do i need to give some extra options ? Thanks, Bala -- C. Balasubramanian

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Add reasonable bonds from command line
by Enrico Ronca 29 Dec '14

29 Dec '14

Dear Sir. I'm Enrico Ronca a post-doc researcher at the National Research Council of Italy in Perugia. I'm contacting you because I often work with metal atoms and not always chimera show me bonds. I solved the problem removing all bonds and pseudo bonds and adding "reasonable bond between selected atoms" in the adjust bonds menu of chimera. Is there a way to run the same procedure from the command line so that I could automate it by a script? Thank you in advance for your reply. I'm looking forward to hearing from you Enrico

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Re: [Chimera-users] Customizing Chimera
by Eric Pettersen 25 Dec '14

25 Dec '14

On Dec 22, 2014, at 1:08 AM, Michał Kadlof wrote: > Hello, > > I'm currently work on proteins with disulfide bonds. I'm very often do the same sequence of tasks in Chimera: > > 1. open structure > 2. Select -> chemistry -> functional group -> disulfide > 3. extend selection to have selected all atoms of Cys-Cys bridge > 4. Show selected atoms > > Is there any way to wrap it into one-click button on toolbar? Hi Michał, While it is literally possible to put what you want on the toolbar, it's a bit easier to make a menu item instead. To do that, you create a command alias for the actions, and put that in a file that Chimera reads at startup so that it is always available. Details: The alias would be alias ^showbridge sel disulfide; sel up; disp sel This creates an alias named "showbridge" which is only expanded if typed at the beginning of a line -- that's what the ^ indicates. Such beginning-of-line aliases are also placed in an Aliases menu that appears after the Favorites menu (if you have any such aliases). To get the alias read by Chimera at startup you would put it in any of the files listed in the "Files to read at startup" section of the Command Line preferences (Favorites->Preferences). This is also described in more detail here: Command Line. Finally, if you really want it on the toolbar instead, that will involve making your own (simple) plug-in in Python. I can provide more detail about that if you like. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Can't open the CASTp site
by Lei Jinmin 18 Dec '14

18 Dec '14

Hi, I have to use CASTp tool for research sake, but I can't open the site anymore( http://sts-fw.bioengr.uic.edu/castp/index.php ). I remember it worked a couple of weeks ago. Does anyboday know when it begins working again? Thank you in advance! Best, Jinmin Lei Researh assitant Aalto University, Finland

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constrain measurement of rotation to a particular axis?
by Elaine Meng 18 Dec '14

18 Dec '14

Begin forwarded message: > From: Tom Goddard <goddard(a)sonic.net> > Subject: Re: [Chimera-users] constrain measurement of rotation to a particular axis? > Date: December 18, 2014 11:07:57 AM PST > > I think the sensible thing is to report the hinge angles without trying to use a common rotation axis. I can think of different ways to define the common rotation axis (you have to align all the structure in some way, then say how much the observed rotation about the axis for a particular structure translates into a rotation about a slightly different common axis), all of them arbitrary and hard to explain, and even harder to compute, so I wouldn’t go that way. > > Tom > >> From: Oliver Clarke <olibclarke(a)gmail.com> >> Subject: [Chimera-users] constrain measurement of rotation to a particular axis? >> Date: December 17, 2014 2:36:45 PM PST >> To: Mailing List <chimera-users(a)cgl.ucsf.edu> >> >> Hi all, >> >> When using the “measure rotation” command, is there any way to constrain the rotation to be measured about a particular axis? >> >> I am thinking specifically of a case where I have multiple structures of a protein with different inter domain hinge angles - I can use chimera to measure the hinge angle, but for each pair of structures it chooses a slightly different rotation axis, whereas I would like to keep the same axis so I can directly compare the rotation observed between pairs of structures. >> >> Or perhaps there is there another way to do this that would make more sense? Suggestions are welcome... >> >> Best, >> Oliver. >>

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How to change colour of H-bond between atoms
by Mahendra B Thapa 18 Dec '14

18 Dec '14

Dear Chimera Users, There is a hydrogen bond between, say, H20 of a ligand (LIG,res no: 240; this H-atom is attached with N atom of LIG) and O atom of GLU 120 residue. There are other hydrogen bonds too, but I am interested to change the color of that H-bond only to, say, red. I tried some like bondcolor red :240@H20 But, it is not working. Any suggestion might help me. Also, is there any way to change width of the H-bond? Thank you, Mahendra Thapa University of Cincinnati,OH

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constrain measurement of rotation to a particular axis?
by Oliver Clarke 17 Dec '14

17 Dec '14

Hi all, When using the “measure rotation” command, is there any way to constrain the rotation to be measured about a particular axis? I am thinking specifically of a case where I have multiple structures of a protein with different inter domain hinge angles - I can use chimera to measure the hinge angle, but for each pair of structures it chooses a slightly different rotation axis, whereas I would like to keep the same axis so I can directly compare the rotation observed between pairs of structures. Or perhaps there is there another way to do this that would make more sense? Suggestions are welcome... Best, Oliver.

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Re: [Chimera-users] Request for Source code
by Elaine Meng 16 Dec '14

16 Dec '14

Dear Jayaraman T, You can turn off helical correction and mass weighting using command options, for example with this command: define axis perHelix true helicalCorrection false massWeighting false See: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> I’m just trying to convince you this is the easy way! However, you already also have the source code in your download, as Eric described in his reply: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-December/010574.html> Best, Elaine On Dec 15, 2014, at 6:57 PM, Jayaraman T <jaai.nasa(a)gmail.com> wrote: > Yes Elaine, > > We can use Chimera but there are helical correction and mass weighting options exist. And am trying to get it done for all these helices without these options. > > Anyway let me follow up and write you back if there is a need of further assistance. > > I think it would help us more and thanks again for your kindness. > > Good day. > > On Tue, Dec 16, 2014 at 6:51 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Dear Jayaraman T, > Chimera download already includes the Python code, but why not just use Chimera? It seems like that would be much, much easier than trying to find and understand all the parts of the code to do it. You can script it with Chimera commands “define” to create helix axes cylinders and “angle” to measure the angle between any pair of those. > > See: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html> > > …and information on looping through structures: > <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 > > On Dec 14, 2014, at 6:25 PM, Jayaraman T <jaai.nasa(a)gmail.com> wrote: > > > Dear, > > I'm Jayaraman T pursuing PhD here in Pusan National University. Since we are interested to calculate the interhelical angle and axes for a set of proteins, we found Chimera is really helpful for getting us the results. And i would like to do certain analysis on the basis of these interhelical angles, so i kindly request you to provide me the source code and other requirements for calculating the angle between helices. It would be grateful to you and please help me out at your earliest convenience. > > Thanks > > > > -- > Regards > > > Jram | 201493155 > PhD Student > Bio molecular Engineering Lab > School of Chemical Engineering > Pusan National University. > 30 Jangjeon-dong, Geumjeong-gu, > Busan, South Korea - 609-735. > +8210 9906 3680 > jram(a)pusan.ac.kr >

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Request for Source code
by Jayaraman T 15 Dec '14

15 Dec '14

Dear, I'm Jayaraman T pursuing PhD here in Pusan National University. Since we are interested to calculate the interhelical angle and axes for a set of proteins, we found Chimera is really helpful for getting us the results. And i would like to do certain analysis on the basis of these interhelical angles, so i kindly request you to provide me the source code and other requirements for calculating the angle between helices. It would be grateful to you and please help me out at your earliest convenience. Thanks -- Regards Jram | 201493155 PhD Student Bio molecular Engineering Lab School of Chemical Engineering Pusan National University. 30 Jangjeon-dong, Geumjeong-gu, Busan, South Korea - 609-735. +8210 9906 3680 jram(a)pusan.ac.kr

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different behavior of the Win and OS-X version seen in case of surface calculations
by Marek Maly 15 Dec '14

15 Dec '14

Hello, I found already several times the differences between OS-X and Win version of Chimera (1.10.). Problem is regarding the ability to calculate molecular surface. There are some cases when Win version of Chimera 1.10 is not able to calculate molecular surface of some more complicated molecular structure (e.g. protein) but on the other hand the OS-X version of Chimera (again 1.10) is able to do it (although writes warning that there was some partial problems). Moreover when I create PY session of such molecule with surface calculated/visualized under OS-X and then I want to open this session under Win version it is opened but without the surface and writes many errors into the log - see below. In both versions I am using default settings (no special changes in parameters important for the surface calc.). How is this different behavior of the same program under Win and OS-X possible ? Do you have any recommendation how to eliminate this problem ? Thank you in advance, Best wishes, Marek Here is the err list after the attempt to load into Win Chimera 1.10 session containing "problematic" molecule with surface calculated under OS-X version of the Chimera 1.10 ***** C:\Program Files\Chimera 1.10\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags Surface calculation failed, mscalc returned code 5. Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface. If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed. More details are given at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html Traceback (most recent call last): File "gB_2G_S16_A.py", line 2669, in <module> restoreCoreModels() File "gB_2G_S16_A.py", line 2654, in restoreCoreModels restoreSurfaces(surfInfo) File "C:\Program Files\Chimera 1.10\share\SimpleSession\versions\v40.py", line 55, in restoreSurfaces elif len(customColors) != len(s.triangleData()[0]): TypeError: 'NoneType' object has no attribute '__getitem__' Error restoring core models: TypeError: 'NoneType' object has no attribute '__getitem__' File "C:\Program Files\Chimera 1.10\share\SimpleSession\versions\v40.py", line 55, in restoreSurfaces elif len(customColors) != len(s.triangleData()[0]): See reply log for Python traceback. Traceback (most recent call last): File "gB_2G_S16_A.py", line 3025, in <module> restoreRemainder() File "gB_2G_S16_A.py", line 3020, in restoreRemainder restoreSilhouettes(silhouettes) File "C:\Program Files\Chimera 1.10\share\SimpleSession\versions\v62.py", line 265, in restoreSilhouettes model = idLookup(modelID) File "C:\Program Files\Chimera 1.10\share\SimpleSession\versions\v23.py", line 162, in idLookup return globals.sessionMap[sesID] KeyError: 27136 Error restoring post-model state: KeyError: 27136 File "C:\Program Files\Chimera 1.10\share\SimpleSession\versions\v23.py", line 162, in idLookup return globals.sessionMap[sesID] See reply log for Python traceback. Warning: Could not restore surface color on surface model with id 0.0 because that surface was not restored. C:\Program Files\Chimera 1.10\bin\lib\site-packages\matplotlib\axes.py:2369: UserWarning: Attempting to set identical left==right results in singular transformations; automatically expanding. left=1, right=1 + 'left=%s, right=%s') % (left, right)) -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Chimera Published Paper
by Kurt Degabriele 08 Dec '14

08 Dec '14

Dear sir/madame, I am a pharmacy student currently undergoing my 4th year pharmacy project at the University of Malta as part of my 5 year study course; I am currently doing research within the Med. Chem. field and would like to ask if you can send me a copy of the following paper so I can include it in my study: UCSF Chimera—A visualization system for exploratory research and analysisEric F. Pettersen, Thomas D. Goddard,Conrad C. Huang, Gregory S. Couch,Daniel M. Greenblatt, Elaine C. Meng andThomas E. Ferrin* Article first published online: 1 JUL 2004DOI: 10.1002/jcc.20084 Regards Kurt

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Re: [Chimera-users] How to use a colour-valued attribute?
by Elaine Meng 04 Dec '14

04 Dec '14

On Dec 3, 2014, at 1:30 AM, Mungo Carstairs (Staff) <g.m.carstairs(a)dundee.ac.uk> wrote: > Thanks all. > Tom, your suggestion of comma- instead or or-delimiter improves speed several times! > Elaine, your point about specifying the chain is noted. > > Conrad, I didn't explain too clearly: my 'real' command is the 'non-contiguous' example (think Zappo colouring with some custom features colours on top). The 'contiguous' example was just what I was using to explore behaviour of setattr / defattr / rangecolor. > (Also by the way the REST API is working fine for me.) > > Instead of 'color' I am now using 'setattr' followed by 'rangecolor'. > I tried both 'setattr' and 'defattr' (passing a temporary file) and didn't see any significant performance difference between them, at the scales I am testing so far (up to 3 models of 1600 residues). > > So I have what I need for now. But I'm still curious to know if / how you get Chimera to 'act on' (display) a colour-valued attribute. > > Best regards, > Mungo Hi Mungo, Setting the color attribute with setattr or defattr does change the color immediately. The problem in what you sent earlier: setattr r color green #0:1-84.B … is that there is no residue attribute named “color". There are atom and molecule-model attributes by that name (setattr a color …) but the only per-residue color setting is ribbon color, name “ribbonColor” … thus you would want something like: setattr r ribbonColor green #0:54.a,76.a … and that would only color the ribbon, not the atoms/bonds. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#respr…> Actually I am mystified as to why this would be any faster than using the color command with the same atomspec (#0:54.a,76.a in the example above), but maybe the others who know more about the “guts” of Chimera can comment. 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

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Commands for multiscale models?
by Hurt, Darrell (NIH/NIAID) [E] 03 Dec '14

03 Dec '14

Hi Chimera friends, I was reading this post from 2009 that indicates that there are no Chimera commands for multiscale models: http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/004009.html Is it still the case that there are no Chimera commands for manipulating the multiscale models? I saw the blue-tongue virus example script for doing something similar using Python itself: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/blueto… I want to script the loading of an arbitrary VIPERdb model and then create multiscale model surfaces for every chain (not just the copies). Can it be done with Chimera commands? Or do I need to work up my Python-fu? 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 Bethesda office: 301-402-0095 Rockville office: 240-669-2741 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> , @NIH3Dprint<https://twitter.com/nih3dprint> 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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volume viewer step value
by Ludovic Renault 03 Dec '14

03 Dec '14

Hi, When I load different EM volumes into Chimera, depending on the size of the box the display step value changes from 1 to 4. Is it possible to force chimera to always load the 3d map with a step value of 1? Or at least change some parameters in preferences to have step 1 loaded with my routine volumes (up to 300 pixel boxes for example). Thanks, Ludo

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show surface fails
by Hartzell Jr., Criss 02 Dec '14

02 Dec '14

I am struggling to show an electrostatic surface on the solvent accessible surface for several related proteins. It works fine in Pymol with APBS but with Chimera I continue to get "surface calculation failed, mscalc returned code 5". I have read posts going back at least 5 years about this problem and I have tried all of the various work-arounds (vdwdef, split, probe radius and vertex density). Has this problem been solved? I am using version 1.8.1 on a PC. Is there a way to identify which part of the protein is causing the problem? Criss Hartzell Professor Department of Cell Biology Emory University School of Medicine Atlanta, GA 30322 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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regarding distance measurement
by abhishek jamwal 02 Dec '14

02 Dec '14

Dear All, I have created a stereoview using chimera where I am showing distance between sidechain atoms of a protein. when I save an image of this stereoview (tiff, 600dpi), the connector lines showing the distances are fading, they are not of same quality in the image as in the original view ! Is there a way to save image without disturbing quality of the connector lines showing distances ? thnx abhishek

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How to use a colour-valued attribute?
by Mungo Carstairs 02 Dec '14

02 Dec '14

Hi, This feels like a basic question but it has stumped me for a day now so here we go... I'm exploring ways of programmatically setting colours to find the most efficient method. This is for the 'custom coloured' case (residue-based colour schemes are not a problem). The simple version is to send as many 'color' commands as there are colours in my (Jalview) sequence: color #ffafaf #0:1.B|#0:5.B|#0:7-8.B|....;color #ffff00 #0:39.B|#0:44.B|#0:47.B|#0:77.B; This works, but doesn't seem to scale up well for large/many structures - I start to see Chimera using 100% CPU for minutes at a time. I'm trying instead to see whether setting a colour-value attribute is faster. I can set the attributes ok with commands like setattr r color green #0:1-84.B etc and confirm they are set with list residues spec #0:1-84.B attribute color but I can't figure out how to get Chimera to use the attribute value as the display colour. 'Render by Attribute' only seems to consider numeric (range-valued) attributes, not colour-valued. I thought perhaps 'my' colour was just hidden in the colour hierarchy, but removing other colours doesn't seem to help. What am I missing? Thanks, Mungo Carstairs Division of Computational Biology University of Dundee http://www.jalview.org The University of Dundee is a registered Scottish Charity, No: SC015096

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Display atoms after multiscale model
by vamsee 02 Dec '14

02 Dec '14

Hello, I am working on a virus capsid and trying to figure out the buried surface area between subunits (similar to what ViperDB has. I have to do this for a few capsids and I am trying to automate this to the maximum possible extent. I have been able to follow the steps in this link Buried surface area calculation <http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-December/001131.html> and manually calculate the information. Are there commands available to do the same? Also, what is the difference between the surfaces created using a multiscale model and surfaces computed from the atom-spec? Would this difference in the surface affect the calculation of the buried surface area? And if it does affect it which one be a more accurate representation? Thank you Vamsee

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