April 2015 - Chimera-users - RBVI Mailing Lists

Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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layering problem
by Joseph Atherton 20 Aug '15

20 Aug '15

Hi! I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this? Cheers, Joe

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Re: [Chimera-users] Request for axes measurements
by Elaine Meng 14 Jun '15

14 Jun '15

Hi, You’re welcome, but I don’t have any further details than what is already given in the manual: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/str…> It’s recommended you send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of me directly, in case others may be able to provide better answers! Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 31, 2015, at 6:26 PM, Jayaraman T <jram(a)pusan.ac.kr> wrote: > > Hi Elaine Meng, > Yes i could figure now the axes as well as angle measurements between them and thanks for your timely help. > > I would be happy if you could tell me the principle on which these axes are calculated. I have noticed that it's from Eigen vector values that are calculated for the coordinates of the set of atoms. > > I'm really interested on the backend for this calculation particularly, might help a bit progressing more for my research. > > Thanks again.

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scale bar
by Dmitry 27 May '15

27 May '15

Dear developers, How are you? I have a question about scale bar. I am not completely sure that the scale bar I drew is correct. What are the scale settings for drawing the scale bar? By the default the scale bar is in Angstroms isn’t it? In ImageJ there is a possibility to set the scale 1 pixel = X value (nm/Å/etc) Is there the same possibility in Chimera? Thank you Sincerely, Dmitry

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depth cue by color for tomogram
by Michael Elbaum 18 May '15

18 May '15

Hello all, I noticed a new sort of 3D color glasses (http://chromatek.com/) that work via blue-red chromatic aberration rather than shifted pairs. I think this would be a useful addition if it isn't available already somehow. The major advantage for a lecture situation is that 2D images are visible also without glasses. I tried to encode depth by color in Chimera but was not successful. I'm using solid style with transparency to see "into" the tomogram, loaded in Volume Viewer. I'd like the deep features to be in one color and the higher parts another, with sparse regions relatively transparent. In the main Viewing panel there's an option for depth cue on the Effects tab, but the cueing is relative to the Side View orientation rather than the real depth. Also there seems to be no option for a color gradient. thanks for any help, Michael Prof Michael Elbaum Dept of Materials and Interfaces Weizmann Institute of Science Rehovot 76100, ISRAEL tel +972 (0)8-9343537 fax +972 (0)8-9344138

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chimera meeting tomorrow
by Greg Couch 29 Apr '15

29 Apr '15

The agenda is available in advance! Thank you Conrad! Conrad says "feel free to add items" :-) https://plato.cgl.ucsf.edu/trac/chimera2/wiki/2015-4-30

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Auto dock Vina Increasing Exhaustiveness
by Tunc Morova 29 Apr '15

29 Apr '15

Hello! I am using UCSF Chimera, Autodock Vina extension for obtaining conformations of my protein and ligand. In this interface, As you know, I can change the exhaustiveness value between 1-8. However, since my system is more than 30x30x30 A, I need to get my exhaustiveness value more than 8 for getting more accurate results. But I can’t make it more than 8 through Auto dock Vina interface in Chimera. How can I increase this exhaustiveness value ? Btw, Instead of using Opal web service, I am using vina locally. Thank you many times for your help Best Regards Tunc Morova

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Converting sdf file into mol2 format
by Mahendra B Thapa 29 Apr '15

29 Apr '15

Dear Chimera users, I am trying to convert sdf file ( downloaded from* diversity set* data from 'http://scs.illinois.edu/htsf/compound_collection/nci.php') into mol2 format. When I ran the command chimera --nogui processSDF.py as given the previous posting ( http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-March/004974.html) I got the following error messages: Cannot find consistent set of bond orders for ring system containing atom #0.73:1@N1 --- Unknown redo atom type: N3 Traceback (most recent call last): Any suggestions for correcting these errors will be a good help for me. Thank you, Mahendra Thapa University of Cincinnati,OH

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Create an artificial bond between ribbons for 3D printing
by David Bhella 28 Apr '15

28 Apr '15

Dear Chimera users, I am trying to prepare a ribbon diagram for 3D printing. As the molecule is a trimer, I would like to create a join between the ribbons such that the model is sent to the printer as a single part. So, I thought that I might be able to create a bond, but I suspect that the current tools may not be able to achieve this. Ideally I don’t want to have to show side chains, moreover the bond needs to be preserved when exported as STL format and finally it will be quite long. The only tool that would seem to come close to my requirement is the distance measure, however I can’t see how to convert that pseudo bond to a cylinder that will be exported. Any suggestions would be gratefully received. Thanks, D. Dr David Bhella MRC-University of Glasgow Centre for Virus Research Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch

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Delete Bug?
by Korbin West 27 Apr '15

27 Apr '15

Hi all, I'm running some code on Chimera to select only certain chains and nearby aspects, but when I try to delete the extraneous information, Chimera freezes up. I'll detail the commands I use below, and for reference I'm interested in the H chain of 1CT1, but it doesn't seem to work with any of its chains. open 1CT1 zonesel :.h 3.5 extend true select invert del sel It then freezes on del sel. I've tried this with other pdb files and it works fine, but for some reason it stops on this one. For example, it works fine on 1PZ3 for its A and B chains. Is this some kind of bug or is there a work-around to this issue? We looked at the residues and couldn't find anything out of place, so we are not sure what is happening. Much thanks in advance. Best, Korbin West? Wabash College

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Making a composite residue
by Repic Matej 23 Apr '15

23 Apr '15

Hello, I wonder if it is possible to construct a composite residue from two existing residues in Chimera? What I would like to do is concatenate residues ALA100 (mid chain) and GLY200 (end of chain) to make a composite residue AGL100. Chimera won't let me set the same residue number via the "resrenumber" command. Preferably, the composite residue would have all the atoms listed where ALA100 was in the original pdb. While I realize there are trivial text editor-based workarounds I would like to know if there is a native way. Thank you all, ---------------------------------------- Matej Repic Ecole Polytechnique Fédérale de Lausanne SB - ISIC - LCBC BCH 4108 CH - 1015 Lausanne ----------------------------------------

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about volume viewer
by 张雷 22 Apr '15

22 Apr '15

Hi, the experts of Chimera, I am a new user of Chimera and have a question to consult you. When I display a 3D model in the volume viewer, I found that there was an original value of the level, as the attached figure shown. If I increased and decreased the values of level, the densities of 3D models were different. Therefore, how to deternime the right value of level for a protein. It is known that the average density of proteins is 1.35 g/cm3; If a protein has a molecular weight of 1350 kDa, and 1 Da = 1.66054E-27 kg; therefore, the protein volume is 1661 nm3.If I want to display the volume of 1661 nm3 in chimera, how can I decide the value of level? In another words, how can I calculate the value of level from the actual volume of a protein? Thank you! Best wishes! Lei Zhang Peking University, Beijing, China

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Re: [Chimera-users] coloring individual segments of a protein
by Greg Couch 21 Apr '15

21 Apr '15

To get a different resolution than 72 dpi, you need to turn on the "Use print units" option in the Save Image dialog, and set the "Print resolution" and pick the image width and height. Or you can use a program like Adobe PhotoShop or GIMP to edit the DPI if you already have an image that you like. HTH, Greg On 04/21/2015 03:01 PM, A G Szabo wrote: > Greg > > Thanks for your reply > > > I had just sent Elaine another question that perhaps you might be able to > answer. > > I am currently writing a book and the editor would like the protein > structure images saved with at 300 dpi. When I saved an image of > Ribonuclease, PDB 5RSA, both as a png file and a Jpeg file the editor > indicated that the resolution was not sufficient and was only 72 dpi. > > Suggestions? > > Thanks > > ags

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Residue Numbers vs. Residue Codes
by Korbin West 21 Apr '15

21 Apr '15

Hi all, I'm trying to determine uncommon ligands in pdb files using a python code, but have run into an odd dilemma. In my code, I open a pdb in Chimera, select the ligand, and write out the residue list. However, the formatting of this list changes depending on how I run the program. If I run the program through xterm, it will print out only residue numbers. If I run the program though Chimera's Idle, however, I will get the residue codes and the residue numbers. For example, I ran this with 3VKG, you can see the results in the attached files, where I show a sample code of what I'm using, the xterm results and the Chimera results. I want to do this for a large number of pdbs, so I'd like to do this --nogui through xterm, but I need the residue codes. Has anyone else ran into this problem or know of a work-around? Thanks in advance. Best, Korbin West Wabash College

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coloring individual segments of a protein
by A G Szabo 21 Apr '15

21 Apr '15

How do I use Chimera to color a protein in the following way: for example: Helix 1 - red Helix 2 - yellow Helix 3 - magenta Strand 1 - dark blue Strand 2 - cyan Etc. A G Szabo

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keyboard accelerators
by Dougherty, Matthew T 21 Apr '15

21 Apr '15

Hi, had a few questions about the documentation. A click in the graphics window may be required. Sometimes it is necessary to click in the graphics window to take back focus from some other dialog so that accelerator or command keystrokes will register. >> is there a way to send accelerators through the Viewing-Side View? I have been dedicating one monitor for the 3D graphics and the other for control, menus, etc. using various USB devices sending accelerators. Would prefer not put to the focus/mouse cursor on the 3D graphics. Accelerators could be shown on menu entries. The keyboard shortcuts could be shown on the corresponding menu entries to make them easier to learn.? >> How? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Help in MD movie
by Ankit Agrawal 18 Apr '15

18 Apr '15

Hi I have trajectory file from gromacs and opened in chimera. Now I am doing inertia calculation. I wrote a python script to show the ellipsoid. But this script is showing only the ellipsoid. I want ellipsoid as well as the molecular structure of that frame, i.e. both ellipsoid and the molecule. so that I can show the how molecule is changing its position. This is like a structure overlay but I want it with ellipsoid. thanks regards Ankit Agrawal

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Reducing the map to a cubic box
by Sushree Tripathy 17 Apr '15

17 Apr '15

Hi, I went through the chimera user's guide and as per the syntax used "vop boxes #0 #0 useMarkerSize true" or "vop boxes #0 #0 size 36" (the simplest case) to create a cubic box from my density map (54, 36, 51). It is neither giving me any error nor giving me the output map. Please help. Thanks Sushree. Sushree Tripathy Graduate Student Department of Physics University at Buffalo

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Generating a map from atomic molecule
by Tom Goddard 17 Apr '15

17 Apr '15

Hi Zhihai, The reason your map surface shows the triangulation is because the grid spacing is large. You made the map with molmap with 30A resolution. By default molmap sets the grid spacing to 1/3 of the requested resolution, so 10 Angstroms in this case. Apparently this is too coarse for your needs. So spedify a finer grid spacing in the molmap command. For instance molmap #0 30 gridSpacing 3 to produce 30 A resolution with 3 A grid spacing. Here is the molmap documentation http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html> Tom > On Apr 16, 2015, at 8:45 PM, 李智海 wrote: > > Hi Tom, > It seems that the low-resolution (about 30A) map generated from atomic model by “molmap" has many artifacts on its surface (see first attached figure), and I can see many rectangle signatures of it in Fourier space (see 2nd attached figure) so that I can not use it as the start map for further reconstruction. > Please tell me how can I get rid of this. Thank you! > > Best wishes! > > > Zhihai Li > > <molmap_30A.png><FFT.png> > > Zhihai Li > > Ph.D student in State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics. > School of Life Sciences, Xiamen University. > Xiang'an Road(South), Xiang'an District, Xiamen City, > Fujian Province, China. > >> On Apr 15, 2015, at 1:28 AM, Tom Goddard wrote: >> >> Hi Zhihai, >> >> If you want the map computed from an atomic model but on a grid that matches a reference map then you should compute the map with molmap and then resample it on the reference map grid. If #0 is the atomic model and #1 the reference map. >> >> molmap #0 8 edgePadding 50 >> vop resample #0 onGrid #1 >> >> Here the 8 is the resolution for the computed map and 50 Angstroms controls how far beyond the molecule bounding to compute the map. >> >> Tom >> >> >> >>> On Apr 13, 2015, at 9:00 PM, 李智海 wrote: >>> >>> hi, >>> here I want to generate a density map from a atomic model in Chimera, then convert the generating map into .pif file to do as the initial map performing in Auto3dem. >>> I have met some questions to successfully finish these work. >>> >>> 1.How can I generate a mol-map from a fitting model with identical dimensions, center coordinates and pixel size of its reference map. I have tried to use “Fit in map”, but the generating map differed from its fitted map in the map size. >>> >>> 2. The mrc map created in Chimera has dimension of even number of columns. If I set the column number to odd number, is it ok (for example, if the origin is off by half pixel?). The reason I am asking such a question is that I will convert this mol-map to pif format, and pif format map has dimension of odd number columns. >>> >>> >>> Thanks in advanced! >>> >>> Best wishes! >>> >>> Zhihai Li >>> >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >> >

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on script which can be read and executed by chimera
by Smith Liu 17 Apr '15

17 Apr '15

Dear All, Will you please introduce to me a web link on how to compile and edit scripts which can be read and executed by Chimera? I am looking forward to getting your reply. Smith

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the "select" funtion of mouse is disable
by sunyeping 16 Apr '15

16 Apr '15

Dear all,I find the "select" funtion of mouse in Chimera is disable. I can not use "ctrl+left mouse button" to select any item in the structure. Have you met this problem before? My systems is windows 7 and the Chimera version is 1.10.1. How to solve this problem? Do I need to change some setting?Best regards,Yeping Sun Institute of Microbiology, Chinese Academy of Sciences

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Re: [Chimera-users] Reducing the map to a cubic box
by Tom Goddard 15 Apr '15

15 Apr '15

In Chimera “atoms” means an atomic model, for example from a PDB file, not a density map. If you want to reduce your map to a cube by cropping and it is size 54,36,51 use command volume #0 region 0,0,0,35,35,35 That gets the lower left corner. To get the center part volume #0 region 9,0,7,44,35,42 The 6 numbers are imin,jmin,kmin,imax,jmax,kmax where i,j,k are indices along the 3 map axes. You can also do this with the Volume Viewer dialog menu entry Features / Region Bounds, or interactively with the mouse using Features / Subregion Selection. For more info about map manipulations http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html Tom > On Apr 15, 2015, at 1:17 PM, Sushree Tripathy wrote: > > Hi, > > Thanks for your prompt reply. What I am trying to do is I have a map which I have loaded in chimera as #0. Now I want to reduce it to cubic size. Since the syntax is "vop boxes <> volume-spec atom-spec <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> size d", so I am choosing #0 for my volume and all the atoms in that volume. so #0 again. Please correct me if I am wrong. > > > Thanks > Sushree. > > Sushree Tripathy > Graduate Student > Department of Physics > University at Buffalo > > On Wed, Apr 15, 2015 at 4:13 PM, Tom Goddard wrote: > Hi Sushree, > > Why does your "vop boxes” command use model #0 for both the map and the markers? That can’t be right. If your marker(s) are in model #1 you would need “vop boxes #0 #1 size 36”. What are you trying to do? > > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#boxes <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#boxes> > > Tom > > > >> On Apr 15, 2015, at 1:03 PM, Sushree Tripathy wrote: >> >> Hi, >> >> I went through the chimera user's guide and as per the syntax used "vop boxes #0 #0 useMarkerSize true" or "vop boxes #0 #0 size 36" (the simplest case) to create a cubic box from my density map (54, 36, 51). It is neither giving me any error nor giving me the output map. >> >> Please help. >> Thanks >> Sushree. >> >> >> Sushree Tripathy >> Graduate Student >> Department of Physics >> University at Buffalo >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > >

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Reducing the map to a cubic box
by Sushree Tripathy 15 Apr '15

15 Apr '15

Hi, I went through the chimera user's guide and as per the syntax used "vop boxes #0 #0 useMarkerSize true" or "vop boxes #0 #0 size 36" (the simplest case) to create a cubic box from my density map (54, 36, 51). It is neither giving me any error nor giving me the output map. Please help. Thanks Sushree. Sushree Tripathy Graduate Student Department of Physics University at Buffalo

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generating a map from a atomic model with the same size of its reference map
by 李智海 14 Apr '15

14 Apr '15

hi, here I want to generate a density map from a atomic model in Chimera, then convert the generating map into .pif file to do as the initial map performing in Auto3dem. I have met some questions to successfully finish these work. 1.How can I generate a mol-map from a fitting model with identical dimensions, center coordinates and pixel size of its reference map. I have tried to use “Fit in map”, but the generating map differed from its fitted map in the map size. 2. The mrc map created in Chimera has dimension of even number of columns. If I set the column number to odd number, is it ok (for example, if the origin is off by half pixel?). The reason I am asking such a question is that I will convert this mol-map to pif format, and pif format map has dimension of odd number columns. Thanks in advanced! Best wishes! Zhihai Li

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generating a map from a atomic model with the same size of its reference map
by 李智海 14 Apr '15

14 Apr '15

hi, here I want to generate a density map from a atomic model in Chimera, then convert the generating map into .pif file to do as the initial map performing in Auto3dem. I have met some questions to successfully finish these work. 1.How can I generate a mol-map from a fitting model with identical dimensions, center coordinates and pixel size of its reference map. I have tried to use “Fit in map”, but the generating map differed from its fitted map in the map size. 2. The mrc map created in Chimera has dimension of even number of columns. If I set the column number to odd number, is it ok (for example, if the origin is off by half pixel?). The reason I am asking such a question is that I will convert this mol-map to pif format, and pif format map has dimension of odd number columns. Thanks in advanced! Best wishes! Zhihai Li

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Fitting pdb model into difference map
by Chinaza Egbuta 13 Apr '15

13 Apr '15

I generated an Fo-Fc difference map using CCP4i and was able to superimpose the PDB model structure onto the map in Coot but I am unable to do so with Chimera. The model and map are offset/rotated away from each other and I have not been able to fit the model into the map with Volume Viewer --> Tools --> Fit in Map. Please let me know how I can get around this issue. Thank you. CE

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Extracting masked map region using selected sop piece?
by Oliver Clarke 13 Apr '15

13 Apr '15

Hi all, I find the sop command (particularly 'sop split' and 'sop hideDust metric volume rank') to be very useful for viewing a molecular envelope at a low threshold in an otherwise noisy map. I would like to save the volume enclosed by a single sop piece as a separate volume, but it does not seem like this is possible - when I select a sop piece and use 'volume nameregion’ to assign it a name, and then attempt to write just that region to an mrc, it saves the whole map. Is there some way to do this that I am missing? I realize that a similar outcome can be achieved with segger, but for larger maps this can be very slow (and potentially involve multiple cycles of selection and regrouping), whereas sop operations are almost instantaneous, so I feel it would be a valuable adjunct capability to that offered by segger. Also, the behaviour of sop split seems a little counterintuitive to me. When I use 'sop split' on a volume, it generates a new model with a different ID for the split map - fine so far. However, the original map seems to be completely invisible - it is listed as displayed in the model panel, but if I undisplay the split map in the model panel and toggle display of the original map in the model panel, nothing happens. If I go to the volume viewer, the original map is listed as displayed, and if I toggle it off and then on again there, it reappears. It seems like it would be maybe simpler for the user to just automatically undisplay the original map upon creation of the sop split map, but not to prevent the user from redisplaying it in the model panel. Here is a link to a screen recording demonstrating what I mean: https://www.dropbox.com/s/g40u9dhj0xslcbf/sop_split.mov?dl=0 <https://www.dropbox.com/s/g40u9dhj0xslcbf/sop_split.mov?dl=0> Best, Oliver.

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Fitmap on overlap/correlation only within bounds of smallest map
by Oliver Clarke 13 Apr '15

13 Apr '15

Hi, I am trying to fit a set of large (whole protein) maps to a map corresponding to a single domain of the protein (extracted using ‘vop zone minimalbounds true’ with an atomic model of the domain in question. It works fine, except that it takes rather a long time (~2000 steps), and the final correlation is 0.33, which is strange because the overall correlation between the two complete maps is ~0.95, and I can see that the final overlap between the aligned maps is good. It seems like ‘fitmap’ is calculating the correlation/overlap based on all grid points in the map that I am aligning, which has a much larger box size than the map to which I am aligning it. Is there any way to restrict the metric analysis to just consider points within the smaller box of the reference map? I cannot find such an option in the documentation for fitmap. The use case for this is when one has multiple conformations of a protein (for example, EM volumes after 3D-classsification) and would like to align them on a single reference domain. Best, Oliver.

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Ways to minimize data loss during resampling?
by Oliver Clarke 13 Apr '15

13 Apr '15

When one has multiple maps corresponding to the same protein in different conformations, it is convenient to save aligned copies of each map, for easy comparison later or for transfer to other programs. This requires interpolating the map to be aligned on the grid of the map to which one is aligning, e.g. using “vop resample x ongrid y” in Chimera. This step involves a certain degree of data loss, which is mostly insignificant but occasionally affects the quality of the resultant map in a way that is visually noticeable. Does anyone have any tips for minimizing this data loss, or is that impossible? E.g., if I oversample the map to which I am aligning by lets say 4 times, resample my map on that grid, and then save at gridstep 3 will that help, or is the data loss an unalterable consequence of the interpolation procedure? Best, Oliver.

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Re: [Chimera-users] [chimera-dev] Using Chimera to display family shuffling information.
by Elaine Meng 10 Apr '15

10 Apr '15

On Apr 8, 2015, at 5:11 PM, Matthew Tiffany <matt.tiffany(a)icloud.com> wrote: > To Whom It May Concern: > I am interested in displaying results from DNA shuffling experiments on a crystal structure. Here is a graphical tool that I have found to do this: http://qpmf.rx.umaryland.edu/XoverDemo.html > > What I would like to do is input an alignment of parental sequences and separately a chimeric protein that is derived from the parental sequences by domain shuffling. Then color code a related structure based upon which domain of a parent the chimeric protein came from. The Xover program does this in a graph, but I would like to be able to do this in 3D space. It is similar to color coding by conservation in MultiAlign, but not exactly. Is there any existing plugin that you may be aware of that does this already or a potential backbone plugin that I can use as a starting point to try and code it myself. > > Regards, > Matthew Tiffany > Postdoctoral Fellow > Mark A. Kay Laboratory > Stanford University Hi Matthew, I’ve CC’d the chimera-users list since my answer doesn’t involve programming... Chimera itself includes a lot of sequence-structure interactivity and related features. Certainly you could do it semi-manually: (1) open your 3D structure and sequence alignment in Chimera. You can just the “File… Open” dailog. Chimera understands several sequence alignment formats. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> (2) associate the structure with a sequence in the alignment. I don’t know exactly what your data look like, and so this requires some judgment calls and deciding amongst different strategies. My thought is at least initially, don’t worry about which sequence is associated with the structure, just try to get it associated with any sequence so that the 3D mapping along the alignment as a whole is correct. — approach A: just use sequence window menu Structure… Associations to force association with any one of the sequences, if it didn’t already associate automatically — approach B: add the sequence of the chimeric protein to your sequence alignment, sequence window menu Edit… Add Sequence, use From Structure (if it adds it poorly you may have to go through a few cycles of Edit… Delete Sequences/Gaps to remove it and then adding it back with different alignment parameters) … I’m leaning toward approach B as the better approach, but you can see whether one or the other works better for your situation… <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> (3) then you can select the different parts of the structure for coloring by using the mouse in the sequence window to select the appropriate ranges of residues in the structure-associated sequence <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> Another approach to #1-2 above would be to start with a sequence of just your structure (for example, open the structure, use Favorites… Sequence to show its sequence) and Blast against the PDB, then load in the Blast alignment. However, you already have your own alignment so I don’t think it would get you much further. Further, there is a newish “mda” command that performs multiple steps including blasting against PDB, automatically loading in the structures and Blast alignment, and conveniently laying out the structure hits N->C (based on alignment to query) in the 3D display. This also wouldn’t get you much further toward the color mapping of your chimeric structure, but the layout stuff is cool. It might not work if your shuffled cassettes are pretty short though. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mda.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Atomspec balloon don't show up
by LINA MARCELA PEDRAZA CASTILLO 10 Apr '15

10 Apr '15

Hi. (Sorry about my english, it's not my language) Dear users: I'm working on my thesis, and I use Chimera ucsf for everything, and suddenly, one day, it stops showing the atomspec balloons, (when the cursor is paused over an object (atom, bond, surface, *etc.*), whether to show the corresponding label information in a balloon in the graphics window, and PDB chain information, if available, in the status line <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/chimerawindow.html#statusli…>.) OK, That's what's no happening anymore, and I need it, so... Can you help me please with this issue? I already read the docs and I did the modifications at preferences menu, and modify: Labels *Label font* (*Sans Serif* - *Normal -* *16* *Labels on top* (*true* *Show atomspec balloon* (*true* *Atomspec display style* (*simple* Please, help me with this. Thanks. I will appreciate it.

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Mapping predicted secondary structure and solvent accessibility on structure or homology model?
by Oliver Clarke 09 Apr '15

09 Apr '15

Hi, I noticed that in the multalign sequence viewer, Chimera has the option to show predicted secondary structure, but it doesn’t seem to work, at least for my sequence (it seems to work initially, but when I show predicted helices/strands there is nothing to see). I think that incorporating modern secondary structure, solvent accessibility and disorder prediction (e.g. using JPRED, which I believe has an open API) would be a very valuable addition to Chimera for structural analysis - it would be particularly helpful for evaluating homology models and models that are based on low resolution crystallographic or CryoEM data, to pick up places where there might be a register error. Maybe this is something to consider for Chimera 2 (or maybe there is a way to load such data in now, if I could create it externally and load it in as a set of attributes…). Best, Oliver.

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openGL error.
by Mosavverul Hassan 08 Apr '15

08 Apr '15

Hi, I am trying to get chimera run remotely on a linux server while logging into it from a mac terminal. I get the following error libGL error: failed to load driver: swrast X Error of failed request: GLXBadContextTag Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1386 Current serial number in output stream: 1386 glxinfo gives me the following name of display: localhost:13.0 libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/tls/swrast_dri.so libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so libGL: driver does not expose __driDriverGetExtensions_swrast(): /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so: undefined symbol: __driDriverGetExtensions_swrast libGL: Can't open configuration file /mnt/raidc2/mhassan/.drirc: No such file or directory. libGL: Can't open configuration file /mnt/raidc2/mhassan/.drirc: No such file or directory. libGL error: failed to load driver: swrast display: localhost:13 screen: 0 direct rendering: No (If you want to find out why, try setting LIBGL_DEBUG=verbose) server glx vendor string: SGI server glx version string: 1.4 It seems to run fine from a linux computer but has problems with a mac. I am using X11 forwarding when I log in. I have X11 on my mac. Could someone please help me out? Regards, Mosavverul Hassan.

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problems to start chimera
by torquato.bioq＠epm.br 08 Apr '15

08 Apr '15

Dear collegues !! I'm installed chimera-1.10.1-linux_x86_64.bin on my machine witch controlled by openSUSE 13.2. The installation procedure was fine, but when I try start chimera I got this messege: ricardo@ricardolinux:~$ chimera libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: GLXBadContextTag Major opcode of failed request: 155 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1457 Current serial number in output stream: 1457 Please can some one help T All the best Ricardo

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plane normal axis
by Elaine Meng 08 Apr '15

08 Apr '15

Hi Oliver, If you have a plane defined in Axes/Planes/Centroids, you can write out its information including the normal (Save button on that tool), then place atoms at either end allowing you to define the axis. There are a few steps... In my little test, the plane output information included: Planes plane name, ID, center, normal, radius plane: p1 ( 19.023, 17.733, 7.080) (-0.380, 0.757, 0.531) 24.199 Then I used Tools… Build Structure, Start Structure, add atom at specific coordinates to add two atoms, one at the center of that plane and one to show the normal. The latter's coordinates are (center + normal) coordinates, and you can multiply the normal coordinates by some constant to make the axis longer. For example, I multiplied the normal coordinates by 10 before adding them to the center coordinates to give the position of the second atom as: x 15.223 y 25.303 z 12.390 Then I selected the two new atoms and used them to define an axis in Axes/Planes/Centroids, see attached image. 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 Apr 6, 2015, at 5:01 PM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > Alternatively, would it be possible (or is there some way already) to define a separate axis that is the normal of a plane? In this case I’m working with an ion channel, so I’m looking for a consistent way to represent the change in orientation of particular extramembrane domains with respect to the channel axis. If I could define an axis for the membrane plane normal, I could at least measure the absolute orientation of the principal axes of particular domains or individual helices with respect to the channel axis. It seems like the plane normal is computed already (because there is an option in axes/planes/centroids) to align screen x/y/z to it, but I can’t see a way to generate it as a separate axis that I can use for measuring angles etc. > > Thanks for all your help as always! > > Oliver.

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where is "Save each fit when doing multiple alignments" button
by sunyeping 07 Apr '15

07 Apr '15

Dear all,I am studying the chimera tutorial "fitting to segments" of Segger segmentation tutorials from Greg Pintilie at NCMI (http://ncmi.bcm.edu/ncmi/software/segger/docs_fitting) In the last paragraph, the tutorial states that to align the structure to multiple regions, one needs to check the "Save each fit when doing multiple alignments" button. But where is this button? I cannot find it in the "Fit to Segments", "Segment Map" or other dialogue boxes. Could you tell me where I can find it?Best regard,Yeping Sun Institute of Microbiology, Chinese Academy of Sciences

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how to measure density diameter by chimera
by Smith Liu 07 Apr '15

07 Apr '15

Dear All, Will you please tell me the command or process to measure the diameter of the molecule density in the map by chimera? Smith

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DTI stereo3D
by Dougherty, Matthew T 06 Apr '15

06 Apr '15

?When selecting DTI stereo3D, L&R images are placed side by side, and horizontally rescaled by half, known as SBS-half. I would like to generate SBS-full, ie no horizontal scaling. Is there a way to do that in chimera? Would prefer not to generate stereo pairs and rescale them back to 100% using a video editor. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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segname
by Francesco Pietra 04 Apr '15

04 Apr '15

Hello: May I ask whether there is till a problem in having CHIMERA understanding segname? For those working with XPLOR (NAMD, for example) and multichain proteins, rendering results with CHIMERA becomes very tedious (having to use atom indexes) Thanks francesco pietra

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Autodock vine problem
by Tunc Morova 04 Apr '15

04 Apr '15

Hello, I was trying to use built-in auto dock vina tool of chimera. I came a cross with an error saying service local`c:\”program filex(x86)”\”the scripps research Institute\Vina\Vina.exe` is unavailable. I have been checking forums for a longtime. Unfortunately, i couldn’t run the docking. couple days ago, I think i accidentally ran the docking locally but i am not sure. Is my pathing correct? how can my local auto dock vina be unavaible ? Please help me for finishing my thesis :D Thank you for your support -Tunc

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Opening Gromacs .trr: error with "bham_lr"
by Alan Manning 03 Apr '15

03 Apr '15

Hi I want to import a Gromacs trajectory (a .trr file) in order to create an animation. I'm using the "MD Movie" tool, and I specify the input .tpr and .trr files. However, I get the following error when I try and make the movie: Don't know correct parameters for 'bham_lr' function Does anyone know what this is from? I'm using Gromacs 5.0.4. The complete Reply Log is as follows: using memory mapping VERSION 5.0.4 using floats version 100, generation 26 2613 atoms box o water Don't know correct parameters for 'bham_lr' function Thanks! Regards, Alan Manning

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drawing ribbon
by Hartzell Jr., Criss 03 Apr '15

03 Apr '15

I have a protein with 10 transmembrane domains and would like to make a movie in which the ribbon is drawn in time from the N- to the C- terminus. I wrote a script that does that. But, the 10 transmembrane domains become hard see because they overlap one another. To solve this problem, I wanted to make the first 600 amino acids become 70% transparent after they had been drawn. Then the drawing would continue with the second half of the protein with no transparency. The problem is that the script that I have written to do this draws the first 600 amino acids 70% transparent immediately as they are drawn. Then the second half of the protein is drawn with 0 transparency. I set the wait time to 600 because I want to execute the transparecny command after the first 600 amino acids were drawn. But, instead, the drawing of the first 600 amino acids is tremendously slowed down by this command as if a wait of some duration occurs after each amino acid rather than after all 600 amino acids. I would appreciate your help. Thanks. movie record supersample 4; perframe "ribbon #2:$1" range 1,600; wait 600; transparency 70,r #2:1-600; perframe "ribbon #2:$1" range 601,959; movie stop; movie encode “d:\Dropbox\Chimera_files\movie1.mp4”; Criss Hartzell Professor Department of Cell Biology Emory University School of Medicine Atlanta, GA 30322 404-242-5719 (cell) For Fedex, UPS, other courier: Criss Hartzell 615 Michael St. 535 Whitehead Building Emory University 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).

2 2

New molecule from selection?
by Oliver Clarke 03 Apr '15

03 Apr '15

Hi, This may already be implemented, but I couldn’t find it - the nearest equivalent feature I know of is copy/combine, but that only works on whole models, not taking into account selections. I was wondering if it would be possible to implement a feature creating a new model comprised of all atoms in the current selection? This would be particularly helpful when combining many parts of multiple models, or when creating a separate model consisting of a subselection of the current model. This can be done at present using a combination of copy/combine and selecting and deleting those parts of the copied molecules that are not in the selection, but this gets messy for complicated selections. Best, Oliver.

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select by color (or other display attributes)
by Oliver Clarke 03 Apr '15

03 Apr '15

Hi, one feature I would love to see in a future version of chimera is the capacity to select residues/atoms by color - this would be magic for modifying figures. Example use case: I’ve made a figure in which some complicated selection or set of selections is colored medium blue, and another selection is colored red. I’ve saved the session for the figure, but I (stupidly)didn’t save the corresponding selections, and now I have to remember exactly what selections I used. If there was a “select by color” function, I could simply select all the atoms that are colored medium blue (or some other color ID), and change them to another color, without having to know which residues were in the original selection. Analagously, it would also be handy, although less frequently useful, to be able to select on the basis of whether a residue is displayed, or represented in a particular manner - in particular, being able to restrict selection to displayed atoms/residues would be useful to avoid inadvertent modification of undisplayed models or parts thereof. Cheers, Oliver.

3 4

Smoothly change level of density map in animation?
by Oliver Clarke 02 Apr '15

02 Apr '15

Is there any way to alter the density level in a gradual fashion during an animation? I would like to first show the overall envelope of a cryoEM map, and then smoothly change to a higher contour level where I can see helices etc. Many other parameters, such as the presence of a MSMS surface or the position of a clipping plane, seem to automatically gradually transition between two key frames of an animation, but density level doesn’t seem to do so. Oliver.

2 2

mclip suggestion - match to arbitrary plane
by Oliver Clarke 02 Apr '15

02 Apr '15

Hi, Currently the mclip command can be used to match a model specific clipping plane to the global near/far clipping planes, or the per model clipping plane of another model. I think it would be a handy addition to a future chimera version to be able to match the per model clipping plane to an arbitrary plane, pre-defined in axes/planes/centroids - e.g. “mclip #1 match p2” would match the per model clipping plane of model #1 to the plane named “p2”. This would be useful because it allows one to easily generate a per-model clipping plane that intersects a certain set of atoms, which also facilitates precise description of a figure. Cheers, Oliver.

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