- Chimera-users - RBVI Mailing Lists

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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