- Chimera-users - RBVI Mailing Lists

matchmaker
by David Stokes 20 Jan '12

20 Jan '12

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

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

20 Jan '12

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

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

19 Jan '12

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

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Distance label
by Damien Larivière 19 Jan '12

19 Jan '12

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

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DNA Ribbon
by Yoshus Kumka 18 Jan '12

18 Jan '12

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

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

18 Jan '12

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

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

18 Jan '12

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

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

17 Jan '12

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

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MD simulation
by Suda Ravindran 16 Jan '12

16 Jan '12

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

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

15 Jan '12

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

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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/

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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 > >

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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

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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

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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

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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 >> >

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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