October 2015 - Chimera-users - RBVI Mailing Lists

label residues
by Albert 17 Oct '15

17 Oct '15

Hello: I got a question on label residues in Chimera. Is it possible to use a simple command line to label all protein residue name and number displayed in the workspace? Thanks you very much Albert

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can you provide more opition for webGL?
by Albert 16 Oct '15

16 Oct '15

Hello everybody: I am just fascinated by the webGL function in Chimera and I am googling it today. Here I found something is even more interesting: http://istar.cse.cuhk.edu.hk/iview/ As far as we can see, it provide much more options in the above link. I am just wondering, could the Chimera developer also consider provide more options for the exported webGL file? That's definitely would be very attractive for the users. Thanks a lot Albert

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uneditable format
by Oliver Clarke 16 Oct '15

16 Oct '15

Hi Eric, I had no idea you could do this, it works great and could be very handy!! The colors and lighting (and positions) don’t seem to be preserved though and differ between firefox and safari - see the attached screenshots and test webgl of 1BL* with EDS maps (WebGL link: https://www.dropbox.com/s/jlwt8ynrz59w5qx/test_webgl.html?dl=0 <https://www.dropbox.com/s/jlwt8ynrz59w5qx/test_webgl.html?dl=0>). Oli. > Hi Albert, > Look at the File->Export Scene menu. That allows you to export to various file formats that your recipient may be able to view without any easy ability to save the result as a PDB file. In particular the “WebGL” export can be viewed as a web page in most modern browsers, with the ability to manipulate the structure interactively. > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > > On Oct 16, 2015, at 6:41 AM, Albert <mailmd2011 at gmail.com <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> wrote: > > > > Hello: > > > > I've made a Chimera section which I would like to share with somebody else. However, I don't want the PDB within Chimera section to be exported by others. Is it possible for us to export some special file format so that other users can only visualize my file, but they cannot edit or export file into PDB coordinate? > > > > Thanks a lot > > > > Albert > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

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uneditable format
by Albert 16 Oct '15

16 Oct '15

Hello: I've made a Chimera section which I would like to share with somebody else. However, I don't want the PDB within Chimera section to be exported by others. Is it possible for us to export some special file format so that other users can only visualize my file, but they cannot edit or export file into PDB coordinate? Thanks a lot Albert

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Failure to reproduce complete Consurf output
by George Tzotzos 16 Oct '15

16 Oct '15

Hi everybody, I’m attaching a snapshot of the output of a Consurf job (snapshot1). Trying to save the file in EPS format produces only A PART of the right-hand-side pane of the output. No histogram is produced (see output.eps). I’d appreciate any suggestions as to how to produce a complete output. Thank you in advance George

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Re: [Chimera-users] uneditable format
by Oliver Clarke 16 Oct '15

16 Oct '15

Hi Albert, I'm pretty sure this doesn't exist at present, and I guess it would require substantial changes to make it work - You'd need to make sure that chimera couldn't write out anything after reading that session, and given that Chimera is open source and has many different ways of writing data out that might be tricky. However, that said, I think having a read-only packaged session format would be a very valuable addition (particularly if it incorporated support for maps), because it would solve a long standing issue in peer review of structural biology results - how to provide raw data for inspection to reviewers without providing maps and models with no strings attached, which many PIs are disinclined to do. Cheers, Oliver. >Hello: > >I've made a Chimera section which I would like to share with somebody >else. However, I don't want the PDB within Chimera section to be >exported by others. Is it possible for us to export some special file >format so that other users can only visualize my file, but they cannot >edit or export file into PDB coordinate? > >Thanks a lot > >Albert

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on mrz file
by Smith Liu 16 Oct '15

16 Oct '15

Dear All, Suppose I have 2 mrc files which are similar on the same protein, we call one map A one map B, and suppose onece we open them by chimera, A was in the centre of the window and B was not. By mouse dragging we moved map B almost overlap with chain B, then we fit map B to map A by the chimera "Fit in map" function. Is any way we can save map B, so that when we open map A and the saved map B by chimera, both A and B were in the centre of the Windows and A and B fitted as just before we saved map B? Best regards. Smith

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on scale command
by Smith Liu 15 Oct '15

15 Oct '15

Dear All, If I have used "scale 1.04" to scale up, will you please tell me the factor x in "scale x" by which I can return to the original size before I used "scale 1.04" ? Best regards. Smith

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Suggestion - autofilter history by typed substring?
by Oliver Clarke 14 Oct '15

14 Oct '15

Hi all, Just a suggestion (I guess for chimera 2) - would it be possible to autofilter the command history based on the typed substring? That is if I have typed “sel” and hit the up arrow, to only cycle through those commands in the history that start with “sel”. This would be particularly handy for scrolling quickly through recent “sel” and “color” commands - a similar mechanism is implemented in several shells and it works well. Cheers, Oliver.

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Re: [Chimera-users] Interactive Protein Structure and Sequence Alignment?
by Elaine Meng 14 Oct '15

14 Oct '15

On Oct 13, 2015, at 6:44 PM, Abba Leffler <aleffler(a)alumni.princeton.edu> wrote: > Dear Professor Meng, > I'm a frequent user of Chimera, mostly for visualization of homology models of large complexes. There's one feature I've search for in Chimera and not found. I wonder if you can help me. > > I would like to do two things, which are related. > > First, I would like to be able to visualize where inserts, deletions, and mutations are on the template structure relative to the target sequence. Is there any way to do that? I haven't found one. > > In a related question, I'd like to be able to interactively edit the sequence alignment (i.e. move indels that are in secondary structure elements) and then recompute the homology model to see if the DOPE score gets better or worse. Is that a possibility? > > I've found that many people have told me that alignments have to be "manually corrected", but there don't seem to be many tools out there for doing that in a sane way. If there are any you could recommend, I would sincerely appreciate it. > > All best, > -Abba Dear Abba, (1) Any time you have a structure open in Chimera and associated with some sequence in MultAlign Viewer (Chimera’s sequence viewer), you can easily map between the sequence and structure. It can be an individual sequence or one within a multiple sequence alignment. You can just highlight an area of interest on the sequence with the mouse and it will be highlighted on the structure. See the Sequences and Structures tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html> … and/or the Multalign Viewer documentation, especially the part about sequence-structure association: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> If you used the Modeller interface in Chimera, you already have the target-template sequence alignment open in Chimera. Then you could just use the mouse to highlight where in the sequence there is a mutation or insertion to have it highlighted on the structure(s). Actually this does selection. Then you can use the Actions menu to do something (e.g. coloring) to the current structure selection. While you can’t highlight something in the sequence that isn’t there (a deletion), you could certainly highlight the positions around it. (2) Multalign Viewer does allow for some small amount of manual editing, but it is not optimized for this purpose and other programs should be more suitable for any serious amount of editing. However, I don’t do this myself so I cannot advise... maybe JalView? Here are the instructions for manual editing in Multalign Viewer: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> I hope this helps. I’ve CC’d this reply to chimera-users, which is the address we recommend for asking Chimera questions. 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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