May 2022 - Chimera-users - RBVI Mailing Lists

crystal contacts
by Meital Bachar 12 May '22

12 May '22

Hello, my name is Meital and I am a Ph.D. student at the school of chemistry at Tel-Aviv university. i am trying to identify the crystal contacts of a protein that I am studying. and I was wondering if it is possible to get an output for the calculated crystal contacts in a way that the actual residues are listed. appreciate a lot your response. Meital

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Get rotation between two views?
by Oliver Clarke 11 May '22

11 May '22

Hi, In either Chimera or X, is there a way to obtain the orientational relationship between two views? E.g. if I have two views saved, I would like to be able to say "view 1 is related to view 2 by a 45deg rotation about X and a 25deg rotation about Y" - this would be very useful for figure making/writing purposes. Does this exist? Cheers Oli

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Re: [Chimera-users] Get rotation between two views?
by Elaine Meng 10 May '22

10 May '22

Hi Zhen, Are you using Chimera or ChimeraX? Remember they are two different programs with many differences from each other. Chimera only has a "viewdock" command (no "view" series, but I'm not sure what you mean by that anyway). Also if you are having a problem like your window freezing, instead of sending a message to me or the list, it is better to report it by using menu: Help... Report a Bug (both Chimera and ChimeraX have this) and filling out the dialog. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2022, at 10:31 AM, Gong, Zhen <zg2234(a)cumc.columbia.edu> wrote: > > Hi Elaine, > > Thank you very much for your reply. I was trying to use the “view” series command in chimera 1.13 but always get complaint like “no such file” or “unknow view Dockfile type”. Is that these commands could only be used in ChimeraX but not Chimera? > > By the way, I also had problems using chimera 1.16 on my mac (MacOs Montery version 12.2). The window will just freeze once I clicked on the “command line interface” icon and it will take about half minute to come back. Do you know how to solve this problem? > > Many thanks in advance! > > Best, > Zhen

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Move model with associated map?
by Oliver Clarke 10 May '22

10 May '22

Hi all, Is there any way to apply the same transformation used by matchmaker for alignment to a map? I have two structures (map+atomic model) in different frames of reference. I would like to align one structure on the other, but also move the associated map in the same way. Is this possible? Cheers Oli

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ValueError: can't normalize zero length array
by jyoti vishwakarma 04 May '22

04 May '22

ValueError Exception in Tk callback Function:<function<lambda> at 0x000000000EF38DD8> (type:<type 'function'>) Module:<module 'Tkinter' from 'C:\Program Files\Chimera 1.16\bin\lib\lib-tk\Tkinter.pyc'> (line: 590) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.16\bin\lib\lib-tk\Tkinter.py", line 592, in callit func(*args) File "C:\Program Files\Chimera 1.16\share\chimera\tkgui.py", line 3025, in<lambda> lambda s=self, e=event: s.showLabelBalloon(e)) File "C:\Program Files\Chimera 1.16\share\chimera\tkgui.py", line 3030, in showLabelBalloon objs = self.viewer.pick(event.x, event.y) ValueError: can't normalize zero length array ―――――――――――――――――――― -- Regards, Jyoti Vishwakarma UGC-SRF c/o Dr. R. Ravishankar Biochemistry & Structural Biology Division CSIR-Central Drug Research Institute Lucknow-226031

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Web service issue?
by LaLone, Carlie 03 May '22

03 May '22

Hello, Could you provide advise on how to remedy the issue below? You are now running Chimera version 1.16 (build 42360). Your previous version was 1.15 (build 42258). Check the release notes for new features and other info. (To access the release notes, use the Help menu to bring up the User's Guide. Then click the 'Documentation index' link and you will then see a link for the release notes.) #0, chain X: fatty acid-binding protein, liver Model 1 (m1_Fruit_fly+3stm+X.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 92, in download fp = self.options.transport.open(Request(url)) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\https.py", line 62, in open return HttpTransport.open(self, request) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 67, in open return self.u2open(u2request) File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 132, in u2open return url.open(u2request, timeout=tm) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 435, in open response = meth(req, response) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 548, in http_response 'http', request, response, code, msg, hdrs) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 467, in error result = self._call_chain(*args) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 407, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 654, in http_error_302 return self.parent.open(new, timeout=req.timeout) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 429, in open response = self._open(req, data) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 447, in _open '_open', req) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 407, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 1241, in https_open context=self._context) File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 1198, in do_open raise URLError(err) URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)> 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 web application request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.16\share\WebServices\appWebService.py", line 48, in _initApp self.backend = Backend(service, url) File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:ClustalOmegaService' is unavailable. See Reply Log for more details. Thank you, Carlie Carlie A. LaLone, Ph.D. Research Bioinformatician Great Lakes Toxicology and Ecology Division Office of Research and Development U.S. Environmental Protection Agency 6201 Congdon Blvd. Duluth, MN, 55804 Work: (218)529-5038 BIG NEWS…SeqAPASSv6.0 is now available!!!!! Try the Sequence Alignment to Predict Across Species Susceptibility<https://seqapass.epa.gov/seqapass/> (SeqAPASS) tool and predict chemical susceptibility to hundreds to thousands of species Publications 1. International Consortium to Advance Cross‐Species Extrapolation of the Effects of Chemicals in Regulatory Toxicology<https://setac.onlinelibrary.wiley.com/doi/full/10.1002/etc.5214> 2. Integrative Computational Approaches to Inform Relative Bioaccumulation Potential of Per-and Polyfluoroalkyl Substances Across Species<https://academic.oup.com/toxsci/article-abstract/180/2/212/6112015> 3. Evidence for Cross Species Extrapolation of Mammalian-Based High-Throughput Screening Assay Results<https://pubs.acs.org/doi/abs/10.1021/acs.est.8b04587> 4. In Silico Site-Directed Mutagenesis Informs Species-Specific Predictions of Chemical Susceptibility<https://academic.oup.com/toxsci/article/166/1/131/5060571> 5. Evaluation of the scientific underpinnings for identifying estrogenic chemicals in nonmammalian taxa <https://setac.onlinelibrary.wiley.com/doi/full/10.1002/etc.3456> 6. SeqAPASS: A Web-Based Tool for Addressing the Challenges of Cross-Species Extrapolation <https://academic.oup.com/toxsci/article/153/2/228/2578709> 7. Molecular target sequence similarity as a basis for species extrapolation to assess the ecological risk<https://www.sciencedirect.com/science/article/pii/S0166445X13002312>

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Error in using the "align chain sequences" tool in chimera
by Chara Spanou 02 May '22

02 May '22

Dear all, After performing the structure comparison of 2 structures using the "MatchMaker" tool of the chimera software,I need to run an alignment of the structure sequences using the "align chain sequences" tool of the chimera. Unfortunately, I am getting the following error message in the reply log that persists for weeks: Traceback from web service request (connection setup):Traceback (most recent call last): File "C:\Program Files\Chimera 1.12\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.12\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 92, in download fp = self.options.transport.open(Request(url)) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\https.py", line 62, in open return HttpTransport.open(self, request) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 67, in open return self.u2open(u2request) File "C:\Program Files\Chimera 1.12\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 132, in u2open return url.open(u2request, timeout=tm) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 437, in open response = meth(req, response) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 550, in http_response 'http', request, response, code, msg, hdrs) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 469, in error result = self._call_chain(*args) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 409, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 656, in http_error_302 return self.parent.open(new, timeout=req.timeout) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 431, in open response = self._open(req, data) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 449, in _open '_open', req) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 409, in _call_chain result = func(*args) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 1240, in https_open context=self._context) File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 1197, in do_open raise URLError(err)URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590)> Typically, if you get a TypeError, it's a problem on the remote serverand it should be fixed shortly. If you get a different error orget TypeError consistently for more than a day, please report theproblem using the Report a Bug... entry in the Help menu. Pleaseinclude the traceback printed above as part of the problem description.Traceback from web application request:Traceback (most recent call last): File "C:\Program Files\Chimera 1.12\share\WebServices\appWebService.py", line 48, in _initApp self.backend = Backend(service, url) File "C:\Program Files\Chimera 1.12\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears "NonChimeraError: Web service appears to be down. See Reply Log for more details.Service 'opal:ClustalOmegaService' is unavailable. See Reply Log for more details. Can you please help? Thanks a lot for your time,Chara

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