- Chimera-users - RBVI Mailing Lists

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 20 Apr '15

20 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 09 Apr '15

09 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 07 Apr '15

07 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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