- Chimera-users - RBVI Mailing Lists

Re-order models in function of their rmsd regarding a given structure
by Jean Didier Pie Marechal 27 Jan '12

27 Jan '12

Hi everyone, I have a set of protein and would like to morph between them in the smoothy manner. I'd like then, to re-order following the rmsd regarding a given structure. What would be the command-line, script that could do this relatively easily? All the best. JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es

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Re: [Chimera-users] Morph conformation: Starting all movies in the same time
by Elaine Meng 27 Jan '12

27 Jan '12

Hi Damien, You would use the "movie" command to control the recording. That is, your script would include movie commands to start recording before the coordset command, stop recording, and then encode into movie file. Command documentation and example movie command scripts: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples> I hope this helps, Elaine On Jan 27, 2012, at 5:16 AM, Damien Larivière wrote: > Dear Elaine, Tom and Eric, > > Many many many thanks for that! That's perfect! I have been able to clearly see a real difference between two of the 4 morph conformations. RMSD also indicates differences but it is more difficult to interpret. > > Great! > > I have another question: Since it is possible to display the deformation for the 4 models, can we record a movie of all the morph conformations? > > Damien > > ps: Tom, for your information, I tried coordset #0-3 1,100 but it retrurned "Must specify 1 molecule, got 4". I probably downloaded the daily build (windows 64bits) too early ? > > > On 26/01/2012 20:16, Tom Goddard wrote: >> Hi Damien, >> >> I improved the coordset command so you can say >> >> coordset #0-3 1,100 >> >> in tonight's Chimera daily builds. (Will not be in the Chimera 1.6 release candidate though.) Using multiple commands separated by semicolons or the above single command will play all trajectories in sync. >> >> Tom >> >>> On Jan 26, 2012, at 10:03 AM, Elaine Meng wrote: >>> >>>> You could try putting four coordset commands together with semicolons, e.g. something like: >>>> >>>> coordset #0 1,100; coordset #1 1,100; coordset #2 1,100; coordset #3 1,100 >>>> >>>> That should all be one line... the e-mail program may break it up. You would substitute the model numbers of your morph trajectories and frame numbers as appropriate, and you could include other "coordset" options. >>>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html> >>>> >>>> I'm not completely sure they would start simultaneously, but that's my best guess of what to try. >>> >>> As far as I know, they should start at the same time. If they don't, let us know! >>> >>> --Eric >>> >> >

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Trajectory analysis: RMSD
by George Tzotzos 27 Jan '12

27 Jan '12

Hi everybody, I'm wondering if there's a way to find out per-residue RMSD fluctuation in a trajectory. I'm trying to find the parts of the backbone that show the greatest RMSD fluctuation against a reference structure. A good weekend to you all George

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HDMI connection to 3D-TV and Chimera
by Jani 26 Jan '12

26 Jan '12

Hi, Has anyone tried running Chimera in a system where the monitor is a 3D capable TV connected with an HDMI (version 1.4a) cable? In principle the synchronization signal for the 3D-glasses should be transmitted along the image through the HDMI cable to the TV, like in 3D blu-ray players. We are planning on purchasing a system like this, but before we do I would like to find out if this setup works well with Chimera. --Jani Jani Seitsonen Aalto University Espoo Finland jani.seitsonen(a)aalto.fi

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CC calculation
by Qing Xie 26 Jan '12

26 Jan '12

Hi, Can anyone help me with calculating correlation coefficient from a .pdb model to a .mrc map? Thank you! Qing

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Morph conformation: Starting all movies in the same time
by Damien Larivière 26 Jan '12

26 Jan '12

Dear all, I have 4 MD movies (corresponding to 4 morph conformations) in the viewport like in the image below. Is it possible to start all the movies in the same time? It would be thus possible to better appreciate visually how much far or close are the different deformations. Thanks Damien Chimera

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Creating a single pdb file from multiple pdb files
by Steven Bottomley 25 Jan '12

25 Jan '12

Hi It is possible to create a single (preferably weighted) protein structure (pdb file) from two or more related protein structures (pdb files)? I guess that this would be something like creating a single (weighted average) of NMR ensemble structures but using any chosen pdb file. Thanks for any help! Regards Steven

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how to make rotation slabs smaller
by Moumita Dutta 25 Jan '12

25 Jan '12

Hello, I am trying to measure rotation using the "measure rotation showslabs t" command in chimera which gives very large slabs. How can I make the slabs smaller ? Any help gratefully appreciated. Thanks

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show viewdock models via command line
by Eric Pettersen 24 Jan '12

24 Jan '12

On Jan 24, 2012, at 6:59 AM, Alex Schneider wrote: > Is there a way to activate/show (...not only select) a loaded > dockview frame using the chimera COMMAND LINE (show frame 1, show > frame 10, show frame 20 ...)? I tried different commands, using > models.submodels combinations, no success, I can select different > submodels, but, I cannot bring them on the screen without clicking > on the dockviewe window. You can show a viewdock model with the 'modeldisp' command, e.g.: modeldisp #0.5 modeldisp turns display of the entire model on without changing the display state of individual atoms, so that if you had undisplayed hydrogens previously for instance, hiding the model with ~modeldisp and then showing it with modeldisp would keep the hydrogens hidden. With tonight's daily build you can activate a model for motion with select 0.5 (and deactivate it with ~select). Prior to tonight's build there was a problem parsing submodel numbers in the select command and you would have to use this kludgey alternative: select 0.5-5 --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Intersurf
by George Tzotzos 24 Jan '12

24 Jan '12

've used intersurf to show the interface area between two different protein sub-units. I'm attaching an image. Is it possible to increase the transparency of the interface area shown in red? I found no way to do so. Many thanks in advance for any suggestions Regards George PS. No attachment as it is 33.5 Mb. By the way, is there a way to reduce the size of tiff images without compromising the quality?

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Intersurf + one more question
by George Tzotzos 24 Jan '12

24 Jan '12

've used intersurf to show the interface area between two different protein sub-units. I'm attaching an image. Is it possible to increase the transparency of the interface area shown in red? I found no way to do so. Many thanks in advance for any suggestions Regards George PS. No attachment as it is 33.5 Mb. By the way, is there a way to reduce the size of tiff images without compromising the quality?

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Re: [Chimera-users] Chimera-Viewer IDEA
by Eric Pettersen 23 Jan '12

23 Jan '12

On Jan 20, 2012, at 6:00 AM, Alex Schneider wrote: > Is there a standalone Chimera-Session-viewer or a way to create such > an viewer? It should be a small tool which can only display, zoom, > rotate a chimera-py-session-file with its bondstyle, background > color AND dockview conformers WITHOUT having the comprehensive > options of the full chimera package, f.e. (options just imaginary): > > chimera-viewer.exe peptidewithhbonds.py -fullscreen > chimera-viewer.exe peptide_10conf_20picosec.py -startmovie > > The idea is to use the small tool just to view a chimera-session > without changing the style or without manipulating bonds or anything > else, JUST VIEW (o:. You could use that tool for presentations at a > conference. > > Normally I manipulate my molecules with chimera and export a vrml- > file for that task. BUT: > > I want to view my dynamic results as rotatable trajectory. I use the > dockview tool for that task. > > Ok, I know, I can just use the full chimera package to visualize my > results, but I just want to tell you my idea. Hi Alex, We don't have plans for the "Chimera Lite" you describe, but we do have some plans that nonetheless may be of some help. One thing we have right now (in the 1.6 daily build) is "WebGL" export [under File...Export], which modern browsers can show directly without any plug-ins (though many browsers currently need to have this cutting- edge capability explicitly "turned on" by the user, see: get.webgl.org) This may be more convenient than showing VRML. The generated HTML file, when shown in a browser, supports the normal "embedded trackball" Chimera mouse motions for rotating and scaling. We are actively working on improving the performance of exported WebGL, but it still can be slow for large systems. We also intend to leverage WebGL further and implement a subset of Chimera directly as HTML displayable in modern web browsers. This will take some time to get going and even then display of trajectories is doubtful. It's a lot closer to your Chimera Lite idea though. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu P.S. Thanks for the compliments in the original mail! I trimmed them off the above so that other people just got the "meat". :-)

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Procedure for modelling a homo-dimer?
by Ashfield, Thomas 23 Jan '12

23 Jan '12

hi, As a novice Chimera user I'm just wondering if it's possible to model a homo-dimer using Modeller with Chimera as the user interface? I'm familiar with the steps required to model the structure of a single chain but I'm not sure how to alter the procedure for a homo-dimer.. Any help is much appreciated, Tom Ashfield / Indiana University

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inertia axis
by Luca Pellegrini 23 Jan '12

23 Jan '12

Hello, Can you please explain how the inertia axis is calculated in: Tools -> Structural analysis -> Structure Measurements -> Define Axes when one uses the 'Selected atoms' and 'Mass weighting' option? Formally one can define three principal axes of inertia for an object, but only one axis seems to be calculated. Thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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save / restore camera angles
by Greenberg, Charles 22 Jan '12

22 Jan '12

I'd like to be able to manipulate things at various angles and be able to return back to a fixed camera view for when I want to save an image. I want to take a series of images with things colored differently, but they won't look quite the same if I have to manually try to move the camera each images. Does that make sense? Thanks. --Charles

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matchmaker
by David Stokes 20 Jan '12

20 Jan '12

Is there a way to align two models based on a subset of residues selected from each model (or even just a subset of residues from the reference molecule). I haven't found it and this would really be helpful. Thanks, David -- David L. Stokes Skirball Institute, NYU Medical Center tel: 212-263-1580 http://saturn.med.nyu.edu/~stokes ---- New York Structural Biology Center tel: 212-939-0660 x9116 http://nysbc.org/ fax: 646-219-0300

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Chimera output into Collada .dae file format
by Evan Kantrowitz 20 Jan '12

20 Jan '12

Hi, The new iBooks Author system uses the collada .dae for its 3D widget. Chimera does not seem to output this format, is that correct? Does anyone know the best way to convert one of the available save scene formats to a collada .dae file. Thanks Evan R. Kantrowitz, Ph.D Boston College

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Is it possible to change the protonation state of only one residue (histidine) of a protein ....
by Sergio Garay 19 Jan '12

19 Jan '12

Hi all I'd like to know if it is possible to change the protonatation state of only one particular residue (histidine) in my protein.. I've been trying to do it using addh tool but with no success, I think it can only work with the protein as a whole, isn' it ? Please, any suggestion is welcomed Sergio -- Sergio Garay Dr. en Ciencias Biológicas Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

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Distance label
by Damien Larivière 19 Jan '12

19 Jan '12

Dear all, I often use the distance tool in order to display the distance between two atoms. It is possible to set several parameters to render the distance (line, stick, color, display the Angstrom symbol or not,...). I would like to increase the size of the label indicating the distance in Angstrom, and eventually to move the label somewhere else in the viewport. Is it possible to do that? Thanks Damien

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DNA Ribbon
by Yoshus Kumka 18 Jan '12

18 Jan '12

Hello, Does anyone know how to assign ribbon attributes to DNA... So I created a stretch of DNA in Spartan and converted the file to pdb which does not contain any attributes such as helical information to automatically have chimera show backbone as a ribbon... I would like to display the DNA backbone as a ribbon and show the bases... But I don't know how to assign the backbone atoms a ribbon property... Please help Thanks

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Minimizing RNA, no MMTK name for H3"
by Tom Goddard 18 Jan '12

18 Jan '12

I'm trying to minimize a few RNA nucleotides using Chimera (Tools / Structure Editing / Minimize Structure) but I get the error message No MMTK name for atom H3" in standard residue C. Chimera adds hydrogens and creates this H3" atom on the 3' terminus (O3' atom) of the RNA. Is there some trick to terminate the 3' end of the RNA so MMTK minimization will work? Here's an example of the problem open 2d1b del ~ :39.B min spec #0 nogui true Thanks! Tom

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Using local PDB file for homology modelling
by Steven Bottomley 18 Jan '12

18 Jan '12

Hi Is there any way to use a pdb structure file stored locally for homology modelling using the Chimera interface to Modeller? Presently the only option seems to be an automatic association from the pdb database. I simply want to use my own structure file as a template and not the one in the pdb database. Thanks for your help.

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morph and 2dlabels
by Brunner,Matthias 17 Jan '12

17 Jan '12

Hi, I have generated a movie in which a morph "loop" between volume A and B is running while the volume is rotating...this works fine. Is there a convenient way to fade in a 2D label whenever the volume B endpoint is reached during morphing (at exactly this frame and maybe a few adjacent ones to make it smoother)? Even better would be if it were possible to label both endpoints (as "volume A" and "volume B"). In effect, this should result in a 2dlabels fade-in/out loop that is synchronous with the morph loop. I would greatly appreciate your help! Best regards -- Matthias Brunner <matthias.brunner(a)imba.oeaw.ac.at> PhD student, Marlovits Lab -Research Institute of Molecular Pathology (IMP) -Inst of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3, A-1030 Vienna, Austria Phone: +43 1 79044 4791

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MD simulation
by Suda Ravindran 16 Jan '12

16 Jan '12

Dear list, I am new to MD simulation, so please forgive me.. I am working on membrane proteins and would like to know if Chimera can be used to do MD simulation right from scratch. If yes, can you guide me on how to do it for a protein in (a) free state (i.,e., only with the protein of interest) and (b) protein docked with its ligand... please help me out..!! Best, Suda

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Re: [Chimera-users] modeller chimera interface
by Mahmoud Soliman 15 Jan '12

15 Jan '12

Dear Eric, Thanks so much for your prompt response. Your suggestion, in deed, sorted the problem out. Best Wishes Mahmoud ************************************ Mahmoud E. Soliman B.Pharm, M.Pharm, MPhil/PhD (Bath, UK) Senior Lecturer - Pharmaceutical Chemistry School of Pharmacy and Pharmacology Faculty of Health Science University of KwaZulu Natal Westville Campus Private Bag X54001 Durban 4000 South Africa Tel. 0312607413 *********************************** Mahmoud E. Soliman (PhD) Computational Chemistry & Modeling Department of Chemistry University of Bath Bath BA2 7AY United Kingdom http://people.bath.ac.uk/mess20/ http://www.bath.ac.uk/person/812559 ********************************** >>> Eric Pettersen 01/13/12 9:30 PM >>> This was also submitted to chimera-bugs (which was the appropriate place for it). For the benefit of anyone searching the mailing-list archive in the future, here is my response on the bug report... The error indicates that you access the web via a proxy server and that you haven't configured Chimera to use the proxy server. Go to Favorites->Preferences and in the resulting dialog change the settings so that Chimera is using your proxy server. Remember to click 'Save' afterward so that the settings will be used in future Chimera sessions. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jan 13, 2012, at 5:59 AM, Mahmoud Soliman wrote: > Dear support, > > I am actually using Chimera as a GUI for modeller and I came across > this nice video tutorial (http://plato.cgl.ucsf.edu/chimera/videodoc/Modeller/ > ) but I keep getting some bugs at different stages as follow: > > 1- When I am trying to fetch ID via UniProt, I get the following bug: > > Exception in Tk callback > Function: (type: 'function'>) > Args: () > Traceback (innermost last): > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/ > site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ > return apply(self.func, args) > File "/Applications/Chimera.app/Contents/Resources/share/chimera/ > baseDialog.py", line 449, in command > getattr(s, buttonFuncName(txt))() > File "/Applications/Chimera.app/Contents/Resources/share/chimera/ > baseDialog.py", line 700, in OK > self.Apply() > File "/Applications/Chimera.app/Contents/Resources/share/chimera/ > fetch.py", line 210, in Apply > func(code, **kw) > File "/Applications/Chimera.app/Contents/Resources/share/ > SeqAnnotations/ChimeraExtension.py", line 27, in showUniprotSeq > self.module().showUniprotSeq(ident) > File "/Applications/Chimera.app/Contents/Resources/share/ > SeqAnnotations/__init__.py", line 291, in showUniprotSeq > acc = mapUniprotNameID(ident) > File "/Applications/Chimera.app/Contents/Resources/share/ > SeqAnnotations/__init__.py", line 61, in mapUniprotNameID > response = urllib2.urlopen(request) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/ > urllib2.py", line 126, in urlopen > return _opener.open(url, data, timeout) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/ > urllib2.py", line 400, in open > response = meth(req, response) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/ > urllib2.py", line 513, in http_response > 'http', request, response, code, msg, hdrs) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/ > urllib2.py", line 438, in error > return self._call_chain(*args) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/ > urllib2.py", line 372, in _call_chain > result = func(*args) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/ > urllib2.py", line 521, in http_error_default > raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) > : HTTP Error 407: Proxy Authentication > Required > > HTTPError: HTTP Error 407: Proxy Authentication Required > > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/ > urllib2.py", line 521, in http_error_default > raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) > > See reply log for Python traceback. > > > 2- I tried to avoid the former step by downloading the sequence file > (FASTA) and read it in chimera. But even when I tried Tools -- > >sequence --> PDB/Uniprot --> tools--> Blast Protein it took ages > and it gives me this message: > > Blast web server appear to be down and that is the reply log: > Traceback from web service request: > Traceback (most recent call last): > File "/Applications/Chimera.app/Contents/Resources/share/ > WebServices/opal_client.py", line 31, in __init__ > self._setup(serviceName, opalURL, sessionData) > File "/Applications/Chimera.app/Contents/Resources/share/ > WebServices/opal_client.py", line 84, in _setup > resp = self.appServicePort.getAppMetadata(req) > File "/Applications/Chimera.app/Contents/Resources/share/ > WebServices/AppService_client.py", line 40, in getAppMetadata > response = self.binding.Receive(getAppMetadataResponse.typecode) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/ > site-packages/ZSI/client.py", line 531, in Receive > self.ReceiveSOAP(**kw) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/ > site-packages/ZSI/client.py", line 416, in ReceiveSOAP > 'Response is "%s", not "text/xml"' % self.reply_headers.type) > TypeError: Response is "text/html", not "text/xml" > > Typically, if you get a TypeError, it's a problem on the remote server > and it should be fixed shortly. If you get a different error or > get TypeError consistently for more than a day, please report the > problem using the Report a Bug... entry in the Help menu. Please > include the traceback printed above as part of the problem > description. > Traceback from Blast request: > Traceback (most recent call last): > File "/Applications/Chimera.app/Contents/Resources/share/blastpdb/ > Parser.py", line 519, in _initBlast > self.opal = OpalService(service) > File "/Applications/Chimera.app/Contents/Resources/share/ > WebServices/opal_client.py", line 43, in __init__ > raise NonChimeraError("Web service appears " > NonChimeraError: Web service appears to be down. See Reply Log for > more details. > > Typically, if you get a TypeError, it's a problem on the remote server > and it should be fixed shortly. If you get a different error or > get TypeError consistently for more than a day, please report the > problem using the Report a Bug... entry in the Help menu. Please > include the traceback printed above as part of the problem > description. > Blast web service appears to be down. See Reply Log for more details. > > > Any help on this matter would be appreciated > > Best wishes > Mahmoud Please find our Email Disclaimer here: http://www.ukzn.ac.za/disclaimer/

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