- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] structural movement when removing ligand
by Elaine Meng 31 Jan '12

31 Jan '12

On Jan 30, 2012, at 6:24 PM, Benny Lo wrote: > Hi, Elaine: > I am using chimera to remove ligand from the protein structure and am curious why there are structural movement of the protein? > Thank you for your response, > Ben Hi Ben, If you are just deleting some atoms, the other atoms should not move. To say anything else, would need more details on what you actually did. Questions should be sent to chimera-users(a)cgl.ucsf.edu, or if you believe it is a bug, you should use Help... Report a Bug in the Chimera menu to send us everything needed to reproduce the problem (for example attaching your input file and describing each step that you did). 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

1 0

Biology infrastructure at the XFEL
by Tim Wiegels 31 Jan '12

31 Jan '12

The European Molecular Biology Laboratory (EMBL) and the European X-ray Free Electron Laser (XFEL) at DESY, Hamburg, Germany, have a keen interest in the development of FEL-based applications in structural biology. Within this framework the EMBL, together with international collaborators from Russia, Sweden and Germany, propose to construct a biology infrastructure at the XFEL facility (expected completion in 2016) to enable biological experiments using the high brilliance, ultrashort pulse duration and high repetition rate coherent X-ray radiation. The proposed biological sample infrastructure facility will provide: - support to the international life-science community in generation and handling of challenging samples in immediate proximity to XFEL instruments. - appropriate selection, quality control and evaluation of samples, including correlative imaging, immediately prior to XFEL experiments. - standardized technology for data interpretation, including computation and validation of structural models. In order to ensure efficient operation of the facility and provide optimal services for the international biological community we seek your input to identify the requirements necessary to support these novel biological imaging experiments. We would appreciate your input in the web-based questionnaire available at http://www.embl-hamburg.de/xfel_cgi-bin/questionnaire The results of this survey will be used to identify the most pressing needs that should be taken into account during planning and construction of the infrastructure. We thank you in advance for your cooperation. __________________________________ Tim Wiegels Predoc @ Lamzin Group, EMBL Hamburg __________________________________ EMBL Hamburg c/o DESY Notkestrasse 85 DE-22603 HAMBURG GERMANY Phone 0049 40 89902-184 Fax 0049 40 89902-149

1 0

Regarding Bonding Pattern and all residue
by Vivek Keshri 30 Jan '12

30 Jan '12

Dear Sir / Madam, I Vivek Keshri writing from Uttar Pradesh India, I am opening docked PDB file in Chimera 1.5.3 and want to identify all residue of receptor and ligand which are involved in binding. Waiting for favorable response... Yours Sincerely, Vivek Keshri +91-8005261512

2 2

Minimisation error
by Kyle Morris 30 Jan '12

30 Jan '12

Hi, I get a minimisation error - Atom type "Br" is not supported by MMTK - when trying to minimise a PDB that contains a bromonaphthalene covalently bound ligand. I have read the post by neelagiri.d at gmail.com and note the Cl substitution does make this work but my Br is part of the molecule and so GAFF/Antechamber should be able to handle it I thought? Really appreciate any help. Best wishes, Kyle

5 4

Re: [Chimera-users] pythonw.exe error
by Gutheil, William 30 Jan '12

30 Jan '12

Im am getting the same error as noted in this post: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-December/005790.html Is this a graphics problem? Any suggestions to fix? THanks

3 3

Images
by George Tzotzos 30 Jan '12

30 Jan '12

Hi everybody, When I'm saving images either as tiff or pgn, the void around the image can ON OCCASIONS be quite large. The example attached below. Is there a way of reducing the void space? Regards George

2 1

Chimera output into Collada .dae file format
by Evan Kantrowitz 30 Jan '12

30 Jan '12

Hi, This is the way I got it to work, I exported Chimera scene to VRML (.wrl). Next you need blender. You can download it from http://www.blender.org/download/get-blender/ Then Open Blender. In the upper right corner in the Scene section right click on Lamp and delete it right click on Cube and delete it right click on Camera and delete it Save this file so you don't have to do this every time. I called mine empty_blender_file.blend Either open empty_blender_file.blend or continue from above and read in the the .wrl file from Chimera File -> import->X3D Extensible 3D (.x3d/.wrl) this reads in the file In Blender you need to delete the three lights that came in from Chimera called TOPO, TOPO.001 and TOPO.002 In the upper right corner in the Scene section right click on TOPO and delete it right click on TOPO.001 and delete it right click on TOPO.002 and delete it Now you need to move around the viewport to get it centered In the upper right corner in the Scene section click on the Viewport then press number pad 0 Press the cube icon below the Scene section Now in the transform section move the location x,y,z. When you have it the way you want it is ready for export. File->export->collada (.dae) Done. This file will read into iBooks Author and have somewhat uniform lighting. By the way, .dae files can be opened an checked in Preview. Its easier than going back and forth into the iPad, since you can rotate the image in Preview. Here is a link to a .dae file of 1crn that you can import into iBooks Author or Preview http://dl.dropbox.com/u/4300550/1crn2_mod.dae Hope this helps, let me know if it works for you and if you have any suggestions. Finally, someone needs to write a one step VRML and/or X3D to collada converter that will work with PyMol and Chimera etc. PS It was a little easier from PyMol, if your interested see the post at https://discussions.apple.com/thread/3670156?start=0&tstart=0 PSS. Okino Computer Graphics makes a .wrl and .x3d to .dae converter http://www.okino.com Have fun! ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu<mailto:evan.kantrowitz@bc.edu> Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow<http://www2.bc.edu/~kantrow> Chestnut Hill, MA 02467 -------------------------------------------------------------------

4 3

Re: [Chimera-users] Chimera output into Collada .dae file format
by Chris Tomlinson 28 Jan '12

28 Jan '12

Hello, I've tried generating several Collada dae files via Meshlab from stl files exported from Chimera and consistently get: The 3D file “benzene.dae” wasn’t added. The scene couldn’t be loaded. I've tried very simple ones as above and more complex ones such as 1CRN.pdb with no success. I also tried generating an xsd file and then converting to dae via Meshlab and got the message: The 3D file “2HHB.pdb.dae” wasn’t added. The files assets could not be consolidated Perhaps the iBooks Author isn't ready to handle these sorts of files as of yet. Chris

1 0

Re: [Chimera-users] Chimera output into Collada .dae file format
by Chris Tomlinson 28 Jan '12

28 Jan '12

Hello, I've tried generating several Collada dae files via Meshlab from stl files exported from Chimera and consistently get: The 3D file “benzene.dae” wasn’t added. The scene couldn’t be loaded. I've tried very simple ones as above and more complex ones such as 1CRN.pdb with no success. I also tried generating an xsd file and then converting to dae via Meshlab and got the message: The 3D file “2HHB.pdb.dae” wasn’t added. The files assets could not be consolidated Perhaps the iBooks Author isn't ready to handle these sorts of files as of yet. Chris

1 0

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

3 2

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 >>> >> >

2 1

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

2 1

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

3 2

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

2 2

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

4 3

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

3 3

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

2 1

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

1 0

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?

2 2

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?

1 0

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". :-)

1 0

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

2 2

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

2 1

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

2 1

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

2 2

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

2 1

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

2 1

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

3 3

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

2 1

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

2 3

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.

2 3

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

2 2

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

2 1

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/

1 0

modeller chimera interface
by Mahmoud Soliman 13 Jan '12

13 Jan '12

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: <class 'urllib2.HTTPError'> Exception in Tk callback Function: <function command at 0x10a113848> (type: <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) <class 'urllib2.HTTPError'>: 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 ************************************ 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 ********************************** Please find our Email Disclaimer here: http://www.ukzn.ac.za/disclaimer/

2 1

Electrostatics potential of amino acid residues
by Ankush Sharma 13 Jan '12

13 Jan '12

Regards all, i wanted to calculate the calculate the Electrostatics potential associated with a specific part of the protein and differentiate from the other part of protein. How can it Possible . is there any method apart from MD to plot a graph of both to diffrentiate Quantitatively the The Potential Thanks in advance Ankush Sharma On Fri, Jan 13, 2012 at 5:54 PM, <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. issue in the installation (kaushlesh mishra) > 2. Fwd: Re: issue in the installation (Greg Couch) > 3. going through saved scenes (Bala subramanian) > 4. modeller chimera interface (Mahmoud Soliman) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 12 Jan 2012 19:37:50 +0530 > From: kaushlesh mishra <kaushelesh.mishra(a)gmail.com> > To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] issue in the installation > Message-ID: > <CAOMCm+pMFrOJfGnk6v7-+ULpVs8XMJDC+6RW1eqZkZj_k03qGw(a)mail.gmail.com > > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > I?ve tried hardly to intall the last Chimera version for Windows (chimera > 1.5.3), but at the phyton execution time, I have this message: "Unable > to execute file: C\Archivos de programa\Chimera 1.5.3rc\phyton.exe > Create process failed; code 14001" > Ifound this error and it possible solution in internet, without any > success. Could you help me? > > -- > Regards > > Kaushlesh Mishra > > > > ------------------------------ > > Message: 2 > Date: Thu, 12 Jan 2012 13:11:59 -0800 > From: Greg Couch <gregc(a)cgl.ucsf.edu> > To: Chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] Fwd: Re: issue in the installation > Message-ID: <4F0F4C9F.8050703(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > FYI > > -------- Original Message -------- > Subject: Re: [Chimera-users] issue in the installation > Date: Thu, 12 Jan 2012 12:58:39 -0800 > From: Greg Couch <gregc(a)cgl.ucsf.edu> > To: kaushlesh mishra <kaushelesh.mishra(a)gmail.com> > > > > On 01/12/2012 06:07 AM, kaushlesh mishra wrote: > > Hi, I?ve tried hardly to intall the last Chimera version for Windows > > (chimera 1.5.3), but at the phyton execution time, I have this > > message: "Unable to execute file: C\Archivos de programa\Chimera > > 1.5.3rc\phyton.exe Create process failed; code 14001" Ifound this > > error and it possible solution in internet, without any success. Could > > you help me? > > Hello, > > The last time I saw this, it was because the computer didn't have the > Microsoft Visual Studio 2008 runtime installed. Please try installing > the runtime from Microsoft at > > http://www.microsoft.com/downloads/en/details.aspx?FamilyID=9b2da534-3e03-4… > < > http://www.microsoft.com/downloads/en/details.aspx?FamilyID=9b2da534-3e03-4… > > > and then see if the chimera installation works. > > HTH, > > Greg > >

3 7

going through saved scenes
by Bala subramanian 13 Jan '12

13 Jan '12

Friends, I save several scenes with 'scene name 01, scene name 02' etc. I wanted to go through the saved scenes one by one and record a movie. But i dnt know how to do it. Please enlighten me on this. I tried fly command to go through the scenes in succession with 'fly 01 02 03' but it throws me the following error IndexError: list index out of range File "/home/cbala/.local/UCSF-Chimera-2012-01-12/share/Fly/fly.py", line 73, in view_parameters for mid,xf in positions[pnames[0]][5].items(): Thanks, -- C. Balasubramanian

2 1

Fwd: Re: issue in the installation
by Greg Couch 12 Jan '12

12 Jan '12

FYI -------- Original Message -------- Subject: Re: [Chimera-users] issue in the installation Date: Thu, 12 Jan 2012 12:58:39 -0800 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: kaushlesh mishra <kaushelesh.mishra(a)gmail.com> On 01/12/2012 06:07 AM, kaushlesh mishra wrote: > Hi, I´ve tried hardly to intall the last Chimera version for Windows > (chimera 1.5.3), but at the phyton execution time, I have this > message: "Unable to execute file: C\Archivos de programa\Chimera > 1.5.3rc\phyton.exe Create process failed; code 14001" Ifound this > error and it possible solution in internet, without any success. Could > you help me? Hello, The last time I saw this, it was because the computer didn't have the Microsoft Visual Studio 2008 runtime installed. Please try installing the runtime from Microsoft at http://www.microsoft.com/downloads/en/details.aspx?FamilyID=9b2da534-3e03-4… <http://www.microsoft.com/downloads/en/details.aspx?FamilyID=9b2da534-3e03-4…> and then see if the chimera installation works. HTH, Greg

1 0

issue in the installation
by kaushlesh mishra 12 Jan '12

12 Jan '12

Hi, I´ve tried hardly to intall the last Chimera version for Windows (chimera 1.5.3), but at the phyton execution time, I have this message: "Unable to execute file: C\Archivos de programa\Chimera 1.5.3rc\phyton.exe Create process failed; code 14001" Ifound this error and it possible solution in internet, without any success. Could you help me? -- Regards Kaushlesh Mishra

1 0

Re: [Chimera-users] Measure relative orientation of molecules
by Tom Goddard 10 Jan '12

10 Jan '12

Hi Ed, Yeah for chains A and B in a single PDB file use match :.A :.B move false show true which will report in the reply log Motion from original file coordinates Matrix rotation and translation 0.86421485 0.50312170 -0.00112044 0.02930667 -0.50311880 0.86421463 0.00213137 0.02433383 0.00204064 -0.00127825 0.99999710 48.44760893 Axis -0.00338844 -0.00314144 -0.99998932 Axis point -0.30430942 0.18590569 0.00000000 Rotation angle (degrees) 30.20700574 Shift along axis -48.44726749 This requires a Chimera daily build http://www.cgl.ucsf.edu/chimera/download.html#daily since the 1 year old production release (1.5.3) does not allow matching two parts of the same molecule. The above will only work if chains A and B have identical atoms. If they differ in any way you can try specifying equivalent sets of atoms, for example CA only, "match :.A@CA :.B@CA move false show true". If the sequences differ then you will need to use MatchMaker and it still requires two separate models and you could use two copies of the same PDB file. Sorry I read your original question too quickly. Tom > Hi, > There is actually no map involved. The PDB coordinate system has the > axis at x=0, y=0 (along z). I am not trying to fit these, only to look > at the angles within this PDB file. > Regards, > Ed > > On 1/10/2012 6:31 PM, Tom Goddard wrote: >> >>> Hi, >>> It is not obvious to me if there is a simple way to do this in >>> Chimera. Given a PDB file containing a number of chains of identical >>> molecules arranged into a helix, but without exact helical symmetry, >>> is there some way to measure the rotation between adjacent chains? I >>> imagine that I can use MatchMaker, and then convert the resulting >>> rotation matrix to the angle about the helical axis... >>> Regards, >>> Ed >> >> Hi Ed, >> >> If PDB models #1 and #2 are fit to a filament map you can use >> Chimera command >> >> measure rotation #1 #2 >> >> which will produce output in the Reply Log (menu Favorites / Reply >> Log) like >> >> Position of 1mwk (#2) relative to 1mwk (#1) coordinates: >> Matrix rotation and translation >> 0.89907669 -0.42653054 -0.09865501 -14.80260678 >> 0.38452015 0.87709721 -0.28782762 9.59677669 >> 0.20929731 0.22084426 0.95258724 -47.13790770 >> Axis 0.50580078 -0.30621414 0.80647286 >> Axis point 19.41814624 18.14474471 -0.00000000 >> Rotation angle (degrees) 30.18795070 >> Shift along axis -48.44128198 >> >> This specifies the rotation in PDB #1 coordinates, not the >> coordinates of the map these two molecules have been fit into. It is >> described as a 3x3 rotation matrix and a translation (4th column of >> above matrix). And it is equivalently described as an axis, point on >> the axis, rotation angle and shift along the axis. The command will >> also show in the graphics window the axis of rotation for this latter >> specification. >> >> Unfortunately there is not an option to express this rotation in the >> map coordinate system which is probably what you are interested in. >> Here's a way to do that though. Fit the first molecule in the map. >> Then write out that PDB file using the map coordinates using Chimera >> menu File / Save PDB... with the "Relative to model mymap.mrc" option >> enabled. Now close that fit molecule and open the saved PDB. It has >> the same coordinate system as the map. Open a second copy of that >> PDB and fit it in another position in the map. Then use the "measure >> rotation #1 #2" command (can be shortened to "me rot #1 #2"). >> >> I'll see if I can easily add an option to the measure rotation >> command to report the result in the map coordinate system. >> >> Tom >> >

1 0

Measure relative orientation of molecules
by Tom Goddard 10 Jan '12

10 Jan '12

> Hi, > It is not obvious to me if there is a simple way to do this in > Chimera. Given a PDB file containing a number of chains of identical > molecules arranged into a helix, but without exact helical symmetry, > is there some way to measure the rotation between adjacent chains? I > imagine that I can use MatchMaker, and then convert the resulting > rotation matrix to the angle about the helical axis... > Regards, > Ed Hi Ed, If PDB models #1 and #2 are fit to a filament map you can use Chimera command measure rotation #1 #2 which will produce output in the Reply Log (menu Favorites / Reply Log) like Position of 1mwk (#2) relative to 1mwk (#1) coordinates: Matrix rotation and translation 0.89907669 -0.42653054 -0.09865501 -14.80260678 0.38452015 0.87709721 -0.28782762 9.59677669 0.20929731 0.22084426 0.95258724 -47.13790770 Axis 0.50580078 -0.30621414 0.80647286 Axis point 19.41814624 18.14474471 -0.00000000 Rotation angle (degrees) 30.18795070 Shift along axis -48.44128198 This specifies the rotation in PDB #1 coordinates, not the coordinates of the map these two molecules have been fit into. It is described as a 3x3 rotation matrix and a translation (4th column of above matrix). And it is equivalently described as an axis, point on the axis, rotation angle and shift along the axis. The command will also show in the graphics window the axis of rotation for this latter specification. Unfortunately there is not an option to express this rotation in the map coordinate system which is probably what you are interested in. Here's a way to do that though. Fit the first molecule in the map. Then write out that PDB file using the map coordinates using Chimera menu File / Save PDB... with the "Relative to model mymap.mrc" option enabled. Now close that fit molecule and open the saved PDB. It has the same coordinate system as the map. Open a second copy of that PDB and fit it in another position in the map. Then use the "measure rotation #1 #2" command (can be shortened to "me rot #1 #2"). I'll see if I can easily add an option to the measure rotation command to report the result in the map coordinate system. Tom

1 0

minimization using python
by divya neelagiri 10 Jan '12

10 Jan '12

Hello, I am using python to go through all the files in a directory and minimize them using chimera. But the problem is I get and error when I try to minimize a file having Br. I have a lot of files in that directory. So is there any way by which I can skip the file that has error and go onto the next file? Any suggestion would br greatly appreciated. Thank you, Divya On Sat, Jan 7, 2012 at 2:51 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi George, > I didn't have a problem when I tried Intersurf, so must be something > specific. > > To report a problem, please use Help... Report a Bug in the Chimera menu > and include any information (you can attach a session file or structure > file and describe all steps you did) needed to reproduce the problem. > > The chimera-users email address is for meant discussion and questions, not > bug reports. > > Thanks, > 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 Jan 7, 2012, at 10:15 AM, George Tzotzos wrote: > > > Hi Elaine, > > > > I've done so. It kick an error message "AttributeError: 'NoneType' > object has no attribute 'atoms'". Please see below. > > > > Many thanks for your help > > > > George > > > > > > #0, chain A: odorant binding protein > > #0, chain B: odorant binding protein > > <type 'exceptions.AttributeError'> Exception in Tk callback > > Function: <function command at 0x12e233f50> (type: <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 438, in command > > getattr(s, buttonFuncName(txt))() > > File > "/Applications/Chimera.app/Contents/Resources/share/Intersurf/Intersurf.py", > line 173, in Apply > > bias, prune, pruneDistance) > > File > "/Applications/Chimera.app/Contents/Resources/share/Intersurf/Intersurf.py", > line 179, in doApply > > m1_list = SurfMaker.GetAtomList(m1, m2, pruneDistance) > > File > "/Applications/Chimera.app/Contents/Resources/share/Intersurf/SurfMaker.py", > line 69, in GetAtomList > > rList = _pruneResidues(rList, prune, pruneDist) > > File > "/Applications/Chimera.app/Contents/Resources/share/Intersurf/SurfMaker.py", > line 46, in _pruneResidues > > rCentroids = _getCentroids(rList) > > File > "/Applications/Chimera.app/Contents/Resources/share/Intersurf/SurfMaker.py", > line 33, in _getCentroids > > for a in r.atoms: > > <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute > 'atoms' > > > > AttributeError: 'NoneType' object has no attribute 'atoms' > > > > File > "/Applications/Chimera.app/Contents/Resources/share/Intersurf/SurfMaker.py", > line 33, in _getCentroids > > for a in r.atoms: > > > > On Jan 7, 2012, at 7:01 PM, Elaine Meng wrote: > > > >> Hi George, > >> Make sure you have the pruning option turned on (check the box for > "Residue centroid distance pruning") or else the distance setting won't > have any effect. That is probably the problem. > >> 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 Jan 7, 2012, at 9:48 AM, George Tzotzos wrote: > >> > >>> Hi everybody and happy New Year > >>> > >>> I'm using Intersurf to define the interface between two sub-units of a > protein. > >>> > >>> Intersurf selects the atoms which appear to be far from the interface. > Changing the prune distance from the default value of 30 to, say 10 or less > has no effect on the atom selection. Is this right? Is there a way to > select atoms that lie, say 5 Angstrom on either side of the interface. > >>> > >>> Thanks and best regards > >>> > >>> George > >>> > >> > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

2 1

Attribute Error!
by Asma Tahir 10 Jan '12

10 Jan '12

Greetings! I encountered error while using the Modeller tools from the Structure Menu. I have tried this function using .aln , .pir, .ali files but i encountered problem. The error is as below: *Attribute Error: Templateseq instance has no attribute 'status'.* ** If I will try to fetch PDB through ID, it is giving me error of "Error during PDB fetch". I read the archives of the chimera on site and changed the www.rcsb.org to the IP Address, as written, in init.py and fetch.py but still the same error. I am using Windows 7. The downloaded chimera version is 1.5.3 win 64. Kindly advice. Thanks in advance, *Asma Ishaq Tahir* *Research Technical Assistant*

2 1

superimposing an all-atom structure to a reduced one
by Damien Larivière 10 Jan '12

10 Jan '12

Dear all, I have two instances of the same protein. One is the original pdb structure which has been locally deformed and saved as the second pdb structure. I would like to match the 2 pdb structures. However, one structure is a reduced version of the other in that it contains only the carbon-alpha trace plus one or two atoms of the side chain. I get an error message when I use MatchMatcher. What can I do to superimpose the all-atom structure onto the reduced one? Many thanks for your help! Damien ps: I can join the two pdb structures if necessary

2 2

APBS -> Chimera plugin - why not?
by Boaz Shaanan 09 Jan '12

09 Jan '12

Hi Elaine, Following on the recent exchange of messages: I've actually been wondering for quite some time why there isn't an APBS plugin for Chimera. Is it because of no interest on the APBS side? Should we ask them to develop one? I'm sure we can collect enough votes to promote that. For example, I find the Consurf and Castp plugins (maybe interfaces, whatever they should be called) very nice and useful, so why not APBS too? Happy New Year to you all (still not too late). Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Friday, January 06, 2012 2:22 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 105, Issue 5 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: APBS (Elaine Meng) 2. Re: APBS (Elaine Meng) 3. Re: APBS (Anjana Ramnath) 4. Re: How to place a metal ion in protein model (Suneel N.A.) 5. Re: How to place a metal ion in protein model (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Thu, 5 Jan 2012 12:04:22 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Anjana Ramnath <anjanaram1(a)gmail.com> Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] APBS Message-ID: <4CE9538A-80A1-4A3B-B99D-D4F401A73A6E(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hello Anjana, Are you sure you're using Chimera? As far as I know there is no APBS plugin for Chimera, only for Pymol. In Chimera, (A) there are several ways to show distances, including selecting two atoms (Ctrl-click on one atom, Shift-Ctrl-click on the second atom) and using command: distance sel (B) there is no tool especially for aromatic interactions, but you can use the tool Find Clashes/Contacts or command findclash to identify contacts between two sets of aromatic residues. For example, to identify contacts between aromatic amino acids in chain A and aromatic amino acids in chain B, command: findclash :.a&aromatic test :.b&aromatic overlap -1 hb 0 (You would probably also want to display all atoms so you can see where the contacts are.) The same thing could be done using the Find Clashes/Contacts graphical interface, in the menu under Tools... Structure Analysis. GUI documentation: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas…> Command documentation: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.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 On Jan 4, 2012, at 9:02 PM, Anjana Ramnath wrote: > Hello all, > My question is simple: im trying to install the APBS plugin but have so far been unsuccessful. I am also trying to show the interactions between aromatic residues on a PDB molecule. how do i do this? im also having trouble with showing the distance between 2 residues. im using Fedora 12 and also WindowsXP. please do let me know. thank you very much! > sincerely, > Anjana. ------------------------------ Message: 2 Date: Thu, 5 Jan 2012 12:23:49 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Anjana Ramnath <anjanaram1(a)gmail.com> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] APBS Message-ID: <5BAFC2C8-8868-4D58-A577-C2EE7DD1C6CE(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi Anjana, After showing a surface, you can either (A) open an electrostatic potential (ESP) map previously calculated with some other program (DelPhi, Grasp, UHBD, APBS) in Chimera and then use it to color the surface with "Electrostatic Surface Coloring" (in menu under Tools... Surface/Binding Analysis) or command "scolor" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolo…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html> or (B) use the "Coulombic Surface Coloring" tool (in same menu as above) or command "coulombic" to calculate Coulombic ESP and color the surface based on those values <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombi…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html> ... for example, as in this tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> 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 Jan 5, 2012, at 12:14 PM, Anjana Ramnath wrote: > thanks so much for your prompt response! well actually, i was wondering if there was a way to show the electrostatic surface in chimera? > ------------------------------ Message: 3 Date: Fri, 6 Jan 2012 01:56:19 +0530 From: Anjana Ramnath <anjanaram1(a)gmail.com> To: Chimera BB <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] APBS Message-ID: <CAAwO1H_Lt3ZRSnjqTNx+qXDpYa7jhF3=-hf+F5TMM1QRjGnj8w(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" thanks so much Elaine! let me just say that Chimera user support is waayy better than any other popular graphics program ive come across! youve got a chimera fan here now. :) On Fri, Jan 6, 2012 at 1:53 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Anjana, > After showing a surface, you can either > > (A) open an electrostatic potential (ESP) map previously calculated with > some other program (DelPhi, Grasp, UHBD, APBS) in Chimera and then use it > to color the surface with "Electrostatic Surface Coloring" (in menu under > Tools... Surface/Binding Analysis) or command "scolor" > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> > < > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolo… > > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html> > > or > (B) use the "Coulombic Surface Coloring" tool (in same menu as above) or > command "coulombic" to calculate Coulombic ESP and color the surface based > on those values > < > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombi… > > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html> > > ... for example, as in this tutorial: > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> > > 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 Jan 5, 2012, at 12:14 PM, Anjana Ramnath wrote: > > > thanks so much for your prompt response! well actually, i was wondering > if there was a way to show the electrostatic surface in chimera? > > > >

5 5

Intersurf
by George Tzotzos 07 Jan '12

07 Jan '12

Hi everybody and happy New Year I'm using Intersurf to define the interface between two sub-units of a protein. Intersurf selects the atoms which appear to be far from the interface. Changing the prune distance from the default value of 30 to, say 10 or less has no effect on the atom selection. Is this right? Is there a way to select atoms that lie, say 5 Angstrom on either side of the interface. Thanks and best regards George

2 4

Phosphorylation
by Tombline, Gregory 07 Jan '12

07 Jan '12

Hi I noticed the script/plugin for no natural amino acids... Is it possible to substitute phosphorylated residues? Ie. and see the phosphate Thanks, Greg Sent from my iPhone

2 2

automated selection of most N-terminal residue in model
by michel dedeo 06 Jan '12

06 Jan '12

Hi, I'm trying to measure the distance between the N-termini (or the first known residue) of a batch of dimeric proteins. The two proteins are different chains. I know how to do this by hand, but am exploring different ways to script it. It may be best to avoid using chimera entirely, but I thought I'd check to see if anyone knows a clever way to select the residue closest to the N-terminus when it's not residue #1. Thanks for your help. Michel

3 2

Re: [Chimera-users] APBS
by Elaine Meng 05 Jan '12

05 Jan '12

Hi Anjana, After showing a surface, you can either (A) open an electrostatic potential (ESP) map previously calculated with some other program (DelPhi, Grasp, UHBD, APBS) in Chimera and then use it to color the surface with "Electrostatic Surface Coloring" (in menu under Tools... Surface/Binding Analysis) or command "scolor" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolo…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html> or (B) use the "Coulombic Surface Coloring" tool (in same menu as above) or command "coulombic" to calculate Coulombic ESP and color the surface based on those values <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombi…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html> ... for example, as in this tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> 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 Jan 5, 2012, at 12:14 PM, Anjana Ramnath wrote: > thanks so much for your prompt response! well actually, i was wondering if there was a way to show the electrostatic surface in chimera? >

2 1

APBS
by Anjana Ramnath 05 Jan '12

05 Jan '12

Hello all, My question is simple: im trying to install the APBS plugin but have so far been unsuccessful. I am also trying to show the interactions between aromatic residues on a PDB molecule. how do i do this? im also having trouble with showing the distance between 2 residues. im using Fedora 12 and also WindowsXP. please do let me know. thank you very much! sincerely, Anjana.

2 1

movie quality
by Ernesto Arias 04 Jan '12

04 Jan '12

Hi everyone, I've made some movies using the current Chimera alpha version (alpha version 1.6 build 35109, 2011-12-24) in an ubuntu 10.04 laptop. I've noticed that the quality of the movies is worse that in the version 1.5.3, and I have generated the movies using the same chimera session and the same script. I've seen this for at least avi and mp4 formats. The movie options I'm using in the script are: *movie record supersample 3 movie encode output movie.avi bitrate 5000 framerate 25 mformat avi* Does anybody know why the quality is worse in the newer Chimera version? Thanks in advance, Ernesto.

2 2

Grid on image
by Sukanya Punthambaker 04 Jan '12

04 Jan '12

Hello, I have a quick question about Chimera. When I save an image from Chimera it displays a grid on top of the image. How do I get rid of the grid? Thank you, -Sukanya Punthambaker.

2 1

Re: [Chimera-users] SURF for large proteins
by Tom Goddard 03 Jan '12

03 Jan '12

Hi Vijay, Chimera molecular surface calculation (using MSMS) fails for most molecules larger than 5,000 atoms. The main trick that can help is to split large multi-chain models into a separate model for each chain using the split command (e.g. "split #0"). Then use a separate molecular surface on each chain. The attached photo shows the result of that for chaperone 1aon with 21 chains with one subunit colored yellow so you can see its shape. If you use Coulombic Electrostatic Coloring (menu Tools / Surface & Binding Analysis) doing it on the split model gives a slightly different result than with an unsplit model. The potential on each surface is just the potential for one chain. Doing the calculation without split would use the potential for the entire model. The split version can be more useful if you are interested in complementary charges on interfaces between chains. Sometimes you can get a molecular surface computation that fails on one computer to work on another computer. Mac Chimera produces surfaces for larger models, and Windows Chimera has the most failures, and the failure rate for 64-bit Windows Chimera is much higher than 32-bit Windows Chimera which is higher than Mac (all versions). Not sure where Linux fits in. Another approach is to use a different kind of surface, one generated from a density map made by placing Gaussians at each atom. The molmap command creates this surface (e.g. "molmap #0 5" for a 5 Angstrom resolution surface). You'll probably want to use a high resolution (< 5A) since the electrostatics can vary on short distances. You might want to use the molmap "gridSpacing" option to get a finer mesh for the surface (e.g. "molmap #0 5 gridSpacing 1" for a 1 Angstrom grid). Currently only molecular surfaces can be colored by Chimera's Coulomb potential coloring code, so that won't work on these molmap surfaces. You would need an externally computed potential (e.g. from APBS or DelPhi) and then use the Chimera Electrostatic Surface Coloring tool (menu Tools / Surface & Binding Analysis) which uses those externally computed potential grids. Those external potential calculations can take a long time and a huge amount of memory for large models. I submitted a Chimera enhancement request to allow the Chimera built-in Coulomb coloring to work on any surface, but Eric who wrote that code has many other things to work on, so it probably won't happen soon. Tom -------- Original Message -------- Subject: SURF for large proteins From: Vijay Reddy To: Tom Goddard Date: 1/3/12 7:32 AM > Hi Tom, > > Happy New Year! Wish you the best for you and yours in the New Year! > > I was wondering if are there tricks to calculate and display MSMS > surface for large proteins, even with the coarse representations. I am > trying to display electrostatic potential. > > Many thanks, > Vijay > >

2 1

Hbond analysis in trajectories
by George Tzotzos 20 Dec '11

20 Dec '11

I'm trying to analyse Hbond formation during a 2ns AMBER trajectory involving receptor ligand complex. The trajectory loads as expected. I've selected the ligand and I checked the boxes "Only find H-bonds with at lease one end selected" and "Write information to file" . The output hbond.info contains information of a single frame. My question is whether there's a way by means of which information of ALL frames can be printed out. Many thanks and best regards George

3 2

minimization error
by divya neelagiri 20 Dec '11

20 Dec '11

Hello, I got this error when I was trying to minimize a structure. please tell me what went wrong. Executing testchim.py...Opening test1_chimera.mol2...1 model opened Traceback (most recent call last): File "/data/pgm/chimera/chimera_1.2422/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 298, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1253, in open File "CHIMERA/share/chimera/__init__.py", line 746, in _openPython File "testchim.py", line 10, in ? rc("minimize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") File "CHIMERA/share/chimera/__init__.py", line 1912, in runCommand File "CHIMERA/share/Midas/midas_text.py", line 60, in makeCommand File "CHIMERA/share/MMMD/ChimeraExtension.py", line 29, in cmdMMMD File "CHIMERA/share/Midas/midas_text.py", line 281, in doExtensionFunc File "CHIMERA/share/Midas/midas_text.py", line 1885, in _getRealKw MidasError: Keyword 'nsteps' doesn't match any known keywords Error while processing testchim.py: MidasError: Keyword 'nsteps' doesn't match any known keywords (see reply log for Python traceback info) This is my program. I tried to execute it from command line using chimera --nogui testchim.py import os import chimera from chimera import runCommand as rc from chimera import replyobj os.chdir("/data2/di/database_build/outputs/outputs_mol2_sdf") fn = "test1_chimera.mol2" rc("open " + fn) rc("minimize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") rc("write format mol2 0 min/" + fn) rc("close all") rc("stop now")

3 4

Rotating a model by exactly 90 degrees
by Konrad Hinsen 20 Dec '11

20 Dec '11

Hi everyone, I need to rotate a model by exactly 90 degrees around the Y axis. Mouse precision is not enough. I spent some time searching the command list for something appropriate, but without success. Is there really no way to do this? Thanks in advance, Konrad. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Moléculaire, CNRS Orléans Synchrotron Soleil - Division Expériences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: research AT khinsen DOT fastmail DOT net http://dirac.cnrs-orleans.fr/~hinsen/ ---------------------------------------------------------------------

3 3

Surface not including all molecules?
by Gustaf Olsson 20 Dec '11

20 Dec '11

Hello I'm trying to create a "cavity" model for visualization, I've done it before (a long time ago) and it worked great. But this time I'm having some problems. When trying with all molecules, I got some error regarding the calculation, so I split the model up into pieces and now it almost works. The problem I'm having is when I try creating a surface of one of the molecular species, I only get three "blobs" and not one big surface for all molecules. Any suggestions are most welcome. Don't know if it works, but I'll attach the PDB file for the molecules not being displayed as a surface properly.

4 8

Chimera 1.53 64bit and 12-16-2011 alpha both segmentation fault
by Starr Hazard 16 Dec '11

16 Dec '11

Folks, I have a chimera 1.41 running on an oldercluster head node with RHEL 4 something so its been a while since I did this procedure.... I have a newer cluster based on RHEL 6.1. When I try to launch either 1.5.3 or the alpha daily build I see the initial chimera banner but then only a text message reporting segmentation fault. Should these chimera's crash due to the fact that they are RHEL 5 compatible or is it something in my X11 setup? Will there be a log file anywhere that would provide clues? Where would that file be located? Thanks Starr

2 1

Posing Small Molecules
by Yoshus Kumka 15 Dec '11

15 Dec '11

Hello, I was wondering if there is a way to place in a molecule into a DNA and then minimize that structure either with chimera or in combination with other programs using chimera. For example, on page "1928" of the paper I attached they discuss posing a small molecule in between bases of the DNA. Here's the paragraph and the underlined sentences are of interest to me. If you are wondering why I don't use DeepView for this, my answer is that it is very unstable and crashes more often then producing useful results. Thanks for your help in advance. In a second stage, the crystallographic receptors were replaced by canonical B-DNA with similar sequences, generated with X3DNA.49 Since structural changes in the macromolecule are not allowed during docking, one canoni- cal oligomer was previously modified to include an “inter- calation gap”. In this way, Swiss PDB Viewer was used to pose an ellipticine molecule between two base pairs of canonical DNA, parallel to the base rings. After that, the complex was minimized by the steepest descent method, using the GROMACS package with the GROMOS 53A6 force field. The result was a modified B-DNA in which the base pairs flanking ellipticine were separated by 6.50 Å. Ellipticine was removed from the complex, and the modified B-DNA (see Figure 6B/F) was used as a target for docking with ellipticine. The sequences of the X3DNA generated oligomers are d(CGCAATTGCG)2 (without gap) and d(CG- GCATGCCG)2 (with gap, indicated in bold) .

2 1

problem with match function (superposition)
by Ken Shimo 14 Dec '11

14 Dec '11

Hello, I'm working with evolutionary algorithms applied to protein-protein docking. I'd like to calculate de RMSD between the native complex and the complex achieved with my docking model. For that I was trying to make the superposition of the complexes using the match function through the Chimera command line. I called the function as: match #0 #1 and got the following message: Atoms in each selection must be in the same model I'd like to know what am I doing wrong, or if there is anyway other way to obtain the RMSD and the superposed complexes. I'm using the complex code PDB 1CHO. Thanks for any help, -- Helder Ken Shimo BSc in Biomedical Informatics (University of São Paulo - Brazil) MSc candidate in Bioinformatics (University of São Paulo - Brazil) -- "When I get sad, I stop being sad and be awesome instead." (Neil Patrick Harris as Barney Stinson)

2 1

Error in using Chimera
by Poornima Josyula 13 Dec '11

13 Dec '11

Hi, I installed Chimera 1.5.3 in my system today. I have a Windows 7 64-bit machine with a processor that is, Intel i7-2600, CPU@ 3.40 GHz. After I open the image, I get the following error. I copied this from the debug window of Chimera. * initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions Return code: -1073741819 Press return or enter to to exit* I would be glad if anyone can help me fix this issue. Thank you. -- With best regards, Poornima Josyula Ph.D. Scholar Fluid Mechanics Laboratory Dept. of Applied Mechanics IIT, Madras India E-mail: poornima.josyula(a)gmail.com

2 1

Regarding estimation of volume in 2D
by Poornima Josyula 13 Dec '11

13 Dec '11

Respected Sir/Madam, My name is Poornima and I am a Ph.D. student from India. My area of research is Biofluid Mechanics. I am modeling bubble transport in bifurcating microchannels. I am performing 2D simulations for the above problem using a commercial Computational Fluid Dynamics (CFD) software called ANSYS Fluent. ImageJ is currently used for the purpose of post processing. But, I haven't entirely been successful in estimating the volume accurately. Please find attached a snapshot of the simulation. In that snapshot, my region of interest (ROI) is the red colored area whose volume I have to find out. Is there a way Chimera can help me estimate this volume? Please let me know your suggestions. Thank you for your time and patience in reading my mail, despite your busy schedule. Kindly excuse me for any inconvenience caused. Look forward to receive a positive response at the earliest. Have a good day. -- With best regards, Poornima Josyula Ph.D. Scholar Fluid Mechanics Laboratory Dept. of Applied Mechanics IIT, Madras India E-mail: poornima.josyula(a)gmail.com

3 3

how to change the atom type in chimera
by Hina 13 Dec '11

13 Dec '11

Dear All, Can you kindly let me know how to change or edit atom typing in chimera and how to visualize the ligands in the form that double bond single bonds aromatic centers are clearly seen.

2 1

making movie with animation utility
by Bala subramanian 13 Dec '11

13 Dec '11

Friends, I am using chimera build 34374 (downloaded on 9/1/2011). I opened * tools-utilities-Animation* and added a number of scenes. I want to make a movie out of these scenes that were added into the Animation panel. When click *setting-save*. It says the category animation is saved, however i dnt find any animation saved on my system. In brief, i want to make a movie out of the scenes saved in Animation panel, Kindly write me how to do it. Cheers, Bala

2 1

Simple distance to .txt scripting question
by Andrew Hagen 09 Dec '11

09 Dec '11

Hi everyone, I'm trying to write a script that opens a set of .pdbs, measures the distances between certain atoms, and then writes the distance to a text file for later analysis. It's easy enough to do something like... >>> runCommand("distance #0:519.A@NZ #:1.Y@O4") ...which executes the command and appends the info to the reply log ("Distance between #0 LYS 519.A NZ and #5 X01 1.Y O4: 2.33"). What I'd like to do is have that actual measured distance (2.33) be stored in a variable that I could then write to a text file (I know how to do this bit). Thanks for any thoughts! --Andrew -- Andrew Hagen PhD candidate - Plant and Microbial Biology UC Berkeley - Keasling group

2 1

helix anomaly
by larif sofiene 09 Dec '11

09 Dec '11

Greeting sir I'm studying a protein mutation effect using M.Dynamics, and when got results a used chimera to view my protein. in this snapshot http://imageshack.us/photo/my-images/839/errya.jpg/ you can see the first arrow (helix distortion, which predicted as a mutation effect ) and a second arrow showing the discontinuity the helix,where its final turn is replaced by a coil. My question is this coil a secondary structure detection bug in chimera,because when using other tools (pymol, vmd ) they detect this final coil as a helix. thanks

2 1

problem
by Sidra Saleem 09 Dec '11

09 Dec '11

i have downloaded ucsf chimera many times but its not working and giving a window named chimera error the error is unable to contact UCSF computer graphics lab to check for new version(network disconnected) kindly help me urgently

2 1

Axis vs map rotation
by Nicolas Coudray 09 Dec '11

09 Dec '11

Hi, I'm using the "Feature >> Plane" options of the "Volume viewer tool" to show contour lines in planes of density maps. For the plane, there are 3 options: "X-axis", "Y-axis", and "Z-axis". The plane I'm interested in is none of those. I try to rotate the maps, but the X, Y and Z axis are also rotating... Do you know if there's a way to rotate the "axis" and the "map" independently, please? Thanks in advance, Nicolas *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*

2 4

Re: [Chimera-users] MD plots
by Elaine Meng 06 Dec '11

06 Dec '11

Hi Luis, This is a new feature added after the 1.5.3 release --- you would need to use a Chimera daily build to try this feature. Daily build download: <http://www.cgl.ucsf.edu/chimera/download.html#daily> List of new features since the 1.5 release series: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html> Enjoy! 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 Dec 6, 2011, at 4:33 PM, lecan wrote: > Hi Elaine. > I was following this item that George asked about the plotting of distances in a MD and I got interest in plotting distances as well. But I can not find the plot button in Chimera 1.5.3. Could you please tell where is the plot button in this version? In the MD movie window at the analysis pull down only appear "Calculate occupancy", "Cluster" and "RMSD map". > > Thank you in advance, > > Luis L. > > > On Mon, 5 Dec 2011 13:18:09 -0800, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> Hi George, >> The distance command is for showing the distance monitor (dashed line >> and angstrom label). For MD movie plotting, you need only select the >> two atoms and then click the Plot button on the dialog. In the image >> you sent, the dialog is showing an error message that suggests you do >> not have exactly two atoms selected (i.e. either fewer or more atoms >> than two seem to be selected). Try clearing the selection before you >> select the two atoms. Also make sure your selection is really getting >> only two atoms. >> >> For example, realize ":124@H" could select more than one atom. There >> might be residue 124 in both chain A and chain B, and/or in model 0 >> and model 1, etc. >> >> You can see how many atoms are selected, for example by clicking the >> green magnifying glass on the lower right corner of the Chimera window >> to open the Selection Inspector. >> 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 >> >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

1 0

Flip maps
by Mario Dejung 06 Dec '11

06 Dec '11

Hi everybody, since the newest version of chimera, it is not longer possible to flip a map via the Voxel Size. In older versions, I could just write 2 2 -2 and my map was flipped. Is there still a way to flip my map within Chimera, or do I have to flip it in a different program and load this new map into chimera. Thanks Mario

2 1

mmView - a tool for mmCIF exploration
by Daniel Svozil 06 Dec '11

06 Dec '11

Dear colleagues, We would like to announce the availability of mmView - the web-based application which allows to comfortably explore the structural data of biomacromolecules stored in the mmCIF (macromolecular Crystallographic Information File) format. The mmView software system is primarily intended for educational purposes but it can also serve as an auxiliary tool for working with biomolecular structures. The mmView application is offered in two flavors: as a publicly available web server http://ich.vscht.cz/projects/mmview/, and as an open-source stand-alone application (available from http://sourceforge.net/projects/mmview) that can be installed on the user’s computer. Petr Cech and Daniel Svozil -- Daniel Svozil, PhD Head of Laboratory of Informatics and Chemistry Institute of Chemical Technology Czech Republic phone: +420 220 444 391 http://ich.vscht.cz/~svozil

1 0

Re: [Chimera-users] MD plots
by George Tzotzos 05 Dec '11

05 Dec '11

Apologies for repeating this. Here are the snapshots On Dec 5, 2011, at 9:58 PM, turk(a)lmb.uni-muenchen.de wrote: > have you tried: > >> distance model_number:residue_A@atom model_number:residue_B@atom > > > George Tzotzos <gtzotzos(a)me.com> wrote : > >> I'm trying to plot the distance between two atoms is a MD trajectory. >> >> I use the command line to select, for example :124@H :121@O >> >> The window in MD Plots fails to show my selection. >> >> Is there something I get wrong? Your help will be much appreciated >> >> Regards >> >> George >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

2 2

Re: [Chimera-users] MD plots
by George Tzotzos 05 Dec '11

05 Dec '11

Thanks for this. I tried, still the result is the same. I'm attaching two snapshots in case it helps with the diagnostics. All the best George On Dec 5, 2011, at 9:58 PM, turk(a)lmb.uni-muenchen.de wrote: > have you tried: > >> distance model_number:residue_A@atom model_number:residue_B@atom > > > George Tzotzos <gtzotzos(a)me.com> wrote : > >> I'm trying to plot the distance between two atoms is a MD trajectory. >> >> I use the command line to select, for example :124@H :121@O >> >> The window in MD Plots fails to show my selection. >> >> Is there something I get wrong? Your help will be much appreciated >> >> Regards >> >> George >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

1 0

MD plots
by George Tzotzos 05 Dec '11

05 Dec '11

I'm trying to plot the distance between two atoms is a MD trajectory. I use the command line to select, for example :124@H :121@O The window in MD Plots fails to show my selection. Is there something I get wrong? Your help will be much appreciated Regards George

1 0

add custom residues to rotamer library or for swapaa command
by Sabuj Pattanayek 05 Dec '11

05 Dec '11

Hi, How do I add custom residues so that they're usable with swapaa or the rotamer tool? Thanks, Sabuj

3 3

CASTp unable to recognise pdb format
by George Tzotzos 03 Dec '11

03 Dec '11

Hi everybody, I used Modeller to generate a structure which I then saved using Chimera. The CASTp server complains that the structure is not in pdb format. I'm attaching the pdb file to help with the diagnostics. Good weekend to all George

2 2

Cando
by poorvi garg 02 Dec '11

02 Dec '11

Hii.., I have generated the json files by sending it to cando . The files we have generated is opened in UCSF Chimera but I am not able to perform any options or operations of the tool . Could you tell me how to perform operations on bld files of the json file obtained. thanks Regards, Poorvi Garg

2 2

volume calculation
by sdimicco 02 Dec '11

02 Dec '11

Dear Chimera developers, is it possible to calculate the volume of the binding site by the softwere? How can I do it? Thank you in advance. Simone

2 1

Multi-align: retract
by George Tzotzos 01 Dec '11

01 Dec '11

I'd like to retract the previous message. I found a way to edit the protein names. It's a bit roundabout but it works. I saved the alignment in Clustal, opened with an text editor, edited the names and saved. Then I opened the file in Chimera. Regards George

2 1

Multi-align
by George Tzotzos 01 Dec '11

01 Dec '11

Hi everybody, I'm wondering if there's a way to edit the protein names in Multi-align. It seems that protein names are generated automatically. An example is attached. The problem is that in scalable eps, sometimes the names overlap with the line numbers. Reducing the ellipsis in Multi-align preferences truncates the names. Thanks for any suggestions George

1 0

PDB splitting
by Milen Raytchev 30 Nov '11

30 Nov '11

Hi everyone, First, thank you Tom for redirecting me. I am trying to split a long single chain which is contained in a PDB file into several shorter chains, each to be contained in individual PDB files. I have tried Chimera (save as) and PDBEditor.jar software to do that but each approach messes the format somehow and I cannot use it in Chimera later (visualization suffers). Could you recommend me a way to do this splitting properly such that the PDB format is not messed up in the resultant 6 AAA domains and I can use the files further in Chimera. The file is attached if of any use. Thank you in advance and I do appreciate your help. Sincerely, Milen Raytchev

3 2

Ice Crystal Surface
by Nancy 30 Nov '11

30 Nov '11

Hi All, I would like to perform molecular simulations with an ice crystal surface; does anyone know if such a structure file can be obtained online? Thanks, Nancy

2 1

shortest distance
by Bishwajit Das 30 Nov '11

30 Nov '11

How to find out the shortest distance between two atom? help me -- * BISHWAJIT DAS* *+91-9433237920* KOLKATA

2 1

help with error message
by Susan Tsutakawa 28 Nov '11

28 Nov '11

I am opening up a pdb that has been generated after MD simulations. Waters have been removed. I am getting an unusual error. I have two pdb files that were generated similarly, but only one gives me the error. Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/tkgui.py", line 343, in openPath mols = chimera.openModels.open(path, type=ftype) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1541, in open models = func(filename, *args, **kw) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 770, in _openPDBModel errOut=errLog) error: radius must be positive Error reading bfactor-911_changed.pdb: error: radius must be positive File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 770, in _openPDBModel errOut=errLog) If someone can help, I would appreciate it.

2 2

Error in viewing trajectories
by George Tzotzos 28 Nov '11

28 Nov '11

Yesterday I posted a message regarding Chimera issuing error messages on trying to open trajectory files. The error was "TypeError: Attempt to form duplicate covalent bond." I believe that the problem arises from the fact that in preparing the topology files with ANTECHAMBER (tleap) in AMBER, I generated disulfide bonds. My guess is that the problem lies there. Has anyone observed similar behaviour? Best regards George

3 4

EM density fitting
by dhacademic 28 Nov '11

28 Nov '11

Hi, I have an EM density map of a protein, as well as several PDB structures, and want to find the most possible structure with the lowest fitting score. Can anyone tell me know how to calculate the fitting score between the EM-density map and a PDB structure in chimera? Many thanks! Best, Hao

2 1

TypeError: Attempt to form duplicate covalent bond.
by George Tzotzos 27 Nov '11

27 Nov '11

Hi everybody, I'm trying to load a trajectory and I get the error message shown above. I'm attaching the error log in case it's of any help. The problem is that I'm able to load the trajectory in VMD without problems (prefer to work on Chimera, though). Any help on how to troubleshoot this would be most welcome. Have a good weekend George

1 1

3D custom residue labels
by matheus froeyen 22 Nov '11

22 Nov '11

Hi I tried the command mode options to generate a custom hard coded 3D residue label: labelopt resinfo "ARG 167" rlabel offset 0.,0.,20. :151 however get an error in the labelopt command: "resinfo" keyword does not exist (although it is described in the chimera man pages) Then I tried to bypass this by using the atom labeling labelopt info "ARG 167" label offset 0.,0.,20. :151@CA but again no luck, then is displayed the label "none" in the 3D window the default residue labeling works however. How can I use custom labels without using the menus? I use chimera 1.5.3 build 33475 on mac osx. best regards mathy

2 3

2dlabels with solid background
by Tom Goddard 21 Nov '11

21 Nov '11

Hi Gabe, Unfortunately there is no color key command. Here's another creative solution. Make the label background be another label using unicode squares. 2dlabels create b1 text '\u2588\u2588\u2588' color white xpos .5 ypos .7 size 64 This uses the square unicode character, hexadecimal 2588. This solution has the advantage that you can fade out this background together with the label. In order for the text label to appear on top of background label you have to create the text label after creating the background. I'd recommend making all the labels and backgrounds interactive with the 2dlabel dialog and saving them in a session which you use together with your movie script. The script will show and hide the labels that have already been made, sized, positioned. You can cut and paste the unicode square character, say from web page into the 2dlabel dialog. http://en.wikipedia.org/wiki/Box-drawing_characters This solution doesn't make it easy to make an outline around the background box. Elaine suggested that you just make another slightly bigger background in the outline color. That has the problem that the vertical outline edges are thicker than the horizontal ones if the the background is wider than it is tall. To get uniform thickness outline you could make two extra background boxes one square shorter than the normal background and slide them horizontally them to get vertical outline edges of equal thickness. Tom -------- Original Message -------- Subject: 2dlabels From: Gabriel Lander To: Tom Goddard Date: 11/19/11 6:59 PM > Hi Tom, > Again thanks for the volume tracer settings saver - it's been super helpful. > But now I have another question: > I'm currently making a movie that uses lots of labels, and for the most part the current 2dlabels create& acreate commands work really well. But for certain closeup views the text gets lost in the volume density, and I've been trying to figure out a way to get a box to show up behind the labels (like in the attached image). I've figured out I can get something like this if I use the "color key" option, and then offset the text to fit inside the box, but I can't find a "color key" chimera command that I can put it into my movie script. > I tried using the "shape rectangle" command, but it's a bit too tedious to position the rectangles exactly right for all the labels. > Any ideas? > -gabe >

1 1

Calculating and showing the Mass center of Volume Segments
by Schmidt, Claudius 19 Nov '11

19 Nov '11

Hello, I got a volume map that I segmented in 4 parts. Now I wanted to measure how the parts are coordinated to each other. As the Axes/Planes/Centroids menu can only create planes by atoms I wanted to place atoms in the mass- center of each segment. Is there any way to realize that? Or do you have any other way to measure the angles. To explain what I'm trying to measure: Example you have 4 segments, I call them a b c d. I want to measure how the axis that is formed by a and b, forms an angle to c and d, or how ist he angle of the plane formed by a b and c compared to ab and d . All for segments are basically the same objects just turned and rotated. With best regards C. Schmidt

2 5

D-Proline modeling in Chimera
by Raghavender Upadhyayula 18 Nov '11

18 Nov '11

I am using PyMol for modeling a peptide containing D-aminoacid (D-Proline) residue. I could invert the configuration arounf L-Proline to convert it to D-Proline. But, I want the "Phi" of the Proline to adopt a certain value. When i tried using the torsion command by selecting the bond N-CA of the D-Proline residue, there is no change at all. I want the Phi value to change from -60 deg to +60 deg and use this as the model for further analysis. Also, the "Psi" needs to fixed at 120 deg. Is it possible in any way to carry out the same steps and achieve the desired results in Chimera. Any suggestions on how to carry out this would be highly appreciated. -- U.S.Raghavender, PhD Postdoctoral Fellow SRI International 140 Research Drive Harrisonburg, VA 22802 540.438.6643

3 3

Docking box
by George Tzotzos 18 Nov '11

18 Nov '11

Hi everybody, I'm visualising a cavity generated by CASTp. Ideally I'd like to draw and get the coordinates of a box around the cavity to use in docking simulations. Is this possible with Chimera? Your suggestions would be much appreciated. Regards George

4 5

Structure superimposition - RMSD
by Suda Parimala Ravindran 17 Nov '11

17 Nov '11

**Hi all, I have a set of protein structures (about 10) that I need to superimpose. I have used Matchmaker and superimposed by choosing a reference structure. I want to know how to calculate the overall RMSD of the superimposed structures? Where do I lokk out for it? I have checked the Reply log window, but it gets displayed only for some, whereas for others it does not. Please help.. Thanks, -Suda

2 4

Alignment
by bodvael email 15 Nov '11

15 Nov '11

Hi, I have never used Chimera so please bear with me. I have this short peptide sequence (8 aa) that I want to locate in the secondary structure of a protein which I have opened in chimera. Is there a way to highlight the sequence in a particular color in the 3D model and/or only have the aminoacid numbering in this region? Also, I would like to view a linear alignment of the entire protein sequence with my peptide sequence of interest. I was able to do that and see that the peptide sequence falls in a beta-sheet (green color). Is there any way know which strand it is exactly? It is supposed to be in strand 5 but I don't know how to display strand numbers, or verify with certainty that it is indeed strand 5 and not strand 6 for example. Thanks, Bodvael

4 5

van der Waals surface volume
by Jacob Alan Spooner 15 Nov '11

15 Nov '11

Hello chimera-users, I am wondering if and how I can get a volume for the van der Waals surface of my molecule. I know how to generate the vdw surface, and also how the volume and surface area for the solvent excluded surface, however the same method does not seem to work for the vdw surface as it does not show up in my model panel. I tried setting the probe radius of the MSMS to zero but it does not allow this so I am stumped on how I could obtain the volume of my vdw surface. Thanks in advance Jake Spooner

2 1

Chimera issue
by Jason Mears 15 Nov '11

15 Nov '11

I installed Chimera on my linux machine, and there is an issue when I try to open a session (See attached img). It tells me that I need to update the graphics card, but my card is new and I would think is more than sufficient to run Chimera. Any suggestions? Thanks. - Jason -- Dr. Jason Mears Assistant Professor Department of Pharmacology 216-368-3348 jason.mears(a)case.edu <mears.jason(a)case.edu>

2 1

custom label size
by Francesco Pietra 13 Nov '11

13 Nov '11

Hello: Is it possible to increase the letter size of custom labels? I would like to show the residue number only, saving as a stereo pair. As my stereo pair (a protein complex) works nicely for most people only at a reduced size of the figure (14x4 centimeters, or even smaller), larger letter-size is needed for the labels. thanks francesco pietra

2 1

Visualising disulfide bonds
by George Tzotzos 12 Nov '11

12 Nov '11

Hi everybody, I'm trying to find a way to visualise disulfide bonds in AMBER trajectory files to no avail. Any help how to do so will be very much appreciated. Regards George

2 1

Percent Identity for specified parts of a structure
by Victoria James 08 Nov '11

08 Nov '11

Hi there, I don't know if this command already exists, but I can't seem to find it in the Chimera tools or manual. I'd like to be able to calculate the percent identity of specified parts of 2 matched sequences - in my case the individual transmembrane helices of the structures. I wonder if a command already exists or if there is a way of doing this in Chimera without having to make new .pdb files of each of the areas of the proteins that I want to compare? I think it would be a useful command if it does not already exist. Thanks, Vicky

2 2

rmsd
by sdimicco 08 Nov '11

08 Nov '11

Dear Chimera developers, is it possible to calculate the rmsd between two proteins by the softwere? How can I do it? Thank you in advance. Simone

2 1