- Chimera-users - RBVI Mailing Lists

RMSF calculations
by Reza Khayat 12 May '22

12 May '22

Hi, I'm trying to write a script to perform the procedure described here: https://www.cgl.ucsf.edu/pipermail/chimera-users/2017-March/013247.html Can someone help with the command line syntax for associating a structure with a defined sequence? Thanks. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Re: [Chimera-users] [chimerax-users] interface plot
by Elaine Meng 12 May '22

12 May '22

Hi Pranav, If you mean that you wanted a list of the interface residues, you can use the "interfaces" network diagram edge context menu to select the residues, then list them in the Log with "info residues sel" ... and either cut-n-paste from the Log to text file or use "log save" to save it as an HTML file. The "info" command should really allow saving a text file directly, but it doesn't do that yet. I believe we have an open ticket to fix that omission. In the chain-chain network diagram, e.g. when the mouse cursor is over the edge representing the chain B-C interface, context-menu choices include Select Contact Residues of B and C Select Contact Residues of B with C Select Contact Residues of C with B <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html#diagram> Or if you get a new daily build, another way to select the residues is to use menu: Select... Contacts, the Chains section of the resulting dialog: <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html> Then use "info residues sel" and possibly "log save" as mentioned above. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#save> Alternatively, you could use "measure buriedarea" specifying the two chains and "list true", which also reports each residue's buried area. (thus avoiding having to select and use "info") <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> Example: measure buriedarea (/A&protein) with (/B&protein) list true 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 12, 2022, at 9:06 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: > > Indeed! Although, as a suggestion, would it be possible to highlight > in the description that in order for the plot to inherit residue > colors, one needs to invoke the plot _after_ the residues have been > identified and colored? Also, could I save the output of the analysis > to a text file? > Best, > Pranav > -- > Pranav Shah > Postdoctoral Research Fellow. > > Division of Structural Biology, > Wellcome Trust Centre for Human Genetics, > University of Oxford, > Roosevelt Drive, Oxford OX3 7BN, > UK > > On Thu, May 12, 2022 at 4:53 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> haha, glad you like it!! >> >> Best, >> Elaine >> >>> On May 12, 2022, at 8:27 AM, Pranav Shah via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> <3 >>> <3 >>> <3 >>> <3 >>> <3 >>> >>> Best, >>> Pranav >>> -- >>> Pranav Shah >>> Postdoctoral Research Fellow. >>> >>> Division of Structural Biology, >>> Wellcome Trust Centre for Human Genetics, >>> University of Oxford, >>> Roosevelt Drive, Oxford OX3 7BN, >>> UK >>> <image.png>_______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>

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use of the program UCSF Chimera
by GABRIELLE LUPETI DE CENA 12 May '22

12 May '22

Goodnight! My name is Gabrielle, I am a Master's student at UNIFESP (Federal University of São Paulo), SP, Brazil. I'm using UCSF Chimera to analyze the secondary structure of some peptides that I'm studying. When I load the .pdb file in the program, it generates a different structure than the one desired. In the examples below, we have two structures alpha helix and random coil, but the images generated are different and I don't understand why. Could you help me, explaining what is happening, or what I should do to have the image as in the first figure (NATTP_05 chimera). Thanks -- ---- A Universidade Federal de São Paulo segue a política de e-mail Institucional disponível em https://sti.unifesp.br/documentos/termos-de-uso-do-email <https://sti.unifesp.br/documentos/termos-de-uso-do-email> <https://sei.unifesp.br/sei/publicacoes/controlador_publicacoes.php?acao=pub…>

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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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Questions in ChimeraX comparing with Chimera
by Long Gui 27 Apr '22

27 Apr '22

Dear Chimera users, I have been recently transferring to ChimeraX from the conventional Chimera and I am currently struggling with two features existing in Chimera but not in ChimeraX. 1. How could I combine two or several different ChimeraX files? I have been doing in Chimera as I was opening new chimera files by "Files...Open...", this is a window pop-up as the following and if I click "No", the new Chimera will be added to the cold Chimera as the old one was not closed. However, when I performed the similar operation in ChimeraX, there is no such window and the new ChimeraX would REPLACE the old one. I wonder if there is a way (probably using command to open? but I did not find the correct open options.) to open the new ChimeraX without closing the old one? [cid:23bcde4a-3b02-4fc4-9b5e-7b034cd22a9f] 1. I am also working with tomogram slices and cellular segmentation. Previously, in Chimera I can set this Transparency value to 0 and the Plane of the tomogram will be totally opaque. Now in ChimeraX I have used the command "transparency #2 0" (#2 is the tomogram files) but it still look quite different from my previous images in Chimera. Is there a way to set it up in ChimeraX so it could look similar as before? [cid:1e2eb72a-f2e5-4c83-b4e4-81b881b9dc67] Thanks again and I am very grateful if any advice or help could be provided. Long Gui, Ph.D. Postdoc Researcher, Nicastro Lab University of Texas Southwestern Medical Center Long.Gui(a)utsouthwestern.edu Tel: (214)-645-1561 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Re: [Chimera-users] Help and guidance on using chimera
by Tom Goddard 27 Apr '22

27 Apr '22

Hi Tommy, Sure those things can be easily be done. I'd encourage you to use ChimeraX instead of the old Chimera program. Also best to email questions to the Chimera mailing list (chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>) or ChimeraX mailing list (chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>). To delete a domain of a protein in ChimeraX that is say residues 151 to 375 of chain B delete /B:151-375 The command syntax would be different in Chimera. To add short linkers is more difficult and I will leave that question to Elaine to advise on the mailing list -- I am not the most knowledgable about how to do that. Tom > On Apr 26, 2022, at 4:45 PM, Tommy Tong <ttong(a)SDBRI.ORG> wrote: > > Dear Thomas, > Good afternoon. How are you? My name is Tommy from San Diego Biomedical Research Institute, CA. I am new to Chimera software and my level of usage has been at the basic level, eg selecting chains and to color label the specific region on the protein. > > May I ask if there is a way to selectively deleting a specific domain on a protein from a pdb file? I want to show graphically how the structure of the molecule will look like without the domain(s). In addition, is it possible to add short amino acid sequence, such as short linkers (eg GSGS) after a domain has been deleted from the protein structure? > > I am currently using UCSF Chimera version 1.16. > > Your help and advice are greatly appreciated. > Thank you for your time. > > Sincerely, > Tommy

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Tomogram display
by Han, Shen 26 Apr '22

26 Apr '22

Hi Elaine, I want to ask some questions regarding displaying tomogram in ChimeraX. is it possible to reveal the density in the tomogram and trace the objects throughout the tomogram (also docking model in the density) in ChimeraX? Best wishes, Shen _________ Dr. Shen Han Postdoctoral Researcher Max Planck Institute for Multidisciplinary Sciences Department of Molecular Biology / Cramer Lab Am Faßberg 11, Göttingen 37077, Germany

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Creating Bonds between Models
by Draven Houser 25 Apr '22

25 Apr '22

Hello, I am trying to build a structure in chimeraX that is a combination of several other known structures. To do this I need to be able to create bonds between different models in the software, but this doesn't seem to be possible for the moment. Can anyone suggest a workaround for this? Thanks! Best regards, Draven Houser

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renumbering sequence with gap
by Haghighijoo, Zahra 25 Apr '22

25 Apr '22

Hi, I am editing a retrieved pdb from homology modeling that has two gaps, is there a way to insert the gaps and renumbering pdb? could you please help me ? Thank you, Zahra

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Open Castp file in Chimera X
by Zhang, Bixia 21 Apr '22

21 Apr '22

Good afternoon, I am trying to open .poc file from CASTP server in Chimera X. And I found this chimeraX recipe https://rbvi.github.io/chimerax-recipes/castp/castp.html. However, when I used the command open<help:user/commands/open.html> read_castp.py, it said No such file/path: read_castp.py. I am working on a Linux unbuntu box and I don't know if this is making any difference. Could you please help with this issue? Thank you so much! Best, Bixia Read CASTP pockets file - ChimeraX Recipes<https://rbvi.github.io/chimerax-recipes/castp/castp.html> We for the ChimeraX atom specifier from chain identifier, residue number and atom name. For example, the above lines are for atoms /A:45@NH2, /B:27@O, /B:27@CG1 in ChimeraX syntax belonging to pockets 2, 1 and 1. rbvi.github.io

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Command for measuring distance between centroids and to show dotted lines depicting the measurement
by Shubham Devesh Ramgoolam 21 Apr '22

21 Apr '22

Hi, I hope you are doing well. Is there a command in chimera that allows us to measure the distance between centroids and also to show dotted lines depicting the measurement? I used the command distance but no lines were shown for centroids. I am considering of using the coordinates of the centroids to place dummy atoms and then, use distance. However, I do not know if there is a command for placing dummy atoms in specified positions. Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Upcoming deprecation of Chimera webservices
by Zach Pearson 21 Apr '22

21 Apr '22

Hello Chimera users, In the next 12 to 18 months, some Chimera tools that depend on web services may stop working: BLAST protein (which is also used by Multidomain Assembler), Modeller comparative and loop modeling, multiple sequence alignment with Clustal Omega and MUSCLE, Small-Angle X-Ray Profile, and 2D Chemical Diagram (used by Structure Diagram and ViewDock). The reason is that some necessary upgrades to our internal systems may break these web services. However, ChimeraX uses a different type of web service that will continue to work, and we have already integrated the following into ChimeraX: BLAST protein, Modeller comparative and loop modelling. In progress: multiple sequence alignment with Clustal Omega and MUSCLE. We wanted to make sure that our users would be prepared for the need to switch to ChimeraX for these features. If you have comments on how to prioritize integrating the remaining services (Small-Angle X-Ray Profile, 2D Chemical Diagram) with ChimeraX, please let us know. Thank you!

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Loop through hundreds of files and find HBonds
by Samuel Kyobe 19 Apr '22

19 Apr '22

Dear Chimera (and ChimeraX) team I have run a large docking experiment using several ligands to determine the best binders for further analysis in Molecular Dynamics studies and possible wetlab evaluation. I need to find some python example or code snippet capable of looping over hundreds of files and find several .pdb poses from a docking run and find Hydrogen bonds in each one using one receptor. In the process of finding the H bonds, I would like to add Hydrogens, and the protonation state is unspecified. Then at FindHBond, I want to find intermodal Hbonds and write the results to a file. Thanks Samuel Dr. Samuel Kyobe Department of Medical Microbiology, 3rd floor, Pathology/Microbiology BLDG, School of Biomedical Sciences College of Health Sciences, Makerere University. Box 7072, Kampala, Uganda. Mob: +256775468605 Skype: samuelkyobe

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Chimera(X) in Centos stream 9
by Antonio Díaz Quintana 19 Apr '22

19 Apr '22

Dear all, I am unable to install Chimerax and Chimera—yes I still use the old one because its great tools—using the rpm package in Centos Stream 9, because lack of LibOSMesa package in this distribution. I tried using dnf, but a mesa-libGL library (21.3.4...) is already installed Similarly, it seems my OS distribution does not contain python Tk, nor I can get suitable python with Tk-devel from repository, so I get the following message. Could I get any help? Meanwhile I got it on my old Win10, 11 years-old laptop. Both programs work well there. Best, Antonio -- Dr. Antonio J. Díaz Quintana Instituto de Investigaciones Químicas Universidad de Sevilla - CSIC Avda. Americo Vespucio 49 41092 Sevilla Spain Phone: +34 954 48 9631

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Command for selecting aromatic ring
by Shubham Devesh Ramgoolam 18 Apr '22

18 Apr '22

Hello, I hope you are doing well. Is there a command on chimera that will allow me to select for the atoms in aromatic rings? I found a workaround by defining the atoms involved in the aromatic rings and then making my selection. However, I would like to use a command (or perhaps combination of commands) from chimera to select the aromatic atoms. Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Revised Need Help
by Ali Raza Azeemi 14 Apr '22

14 Apr '22

Hi, hope you are doing well? dear, we have a question about making an animation/movie in chimera. I want to add molecular dynamics(MD) movie to the animation timeline, so I am facing difficulty to add on it. Kindly tell me if an option is available for this?. I will be very thankful to you. Thank you -- *Ali Raza Siddiqui* *Jr. Research Fellow* *Computer-Aided Drug Design (CAAD) unit. P-133, PCMD* H.E.J. Research Institute of Chemistry International Center for Chemical & Biological Sciences University of Karachi, 75270 Karachi- Pakistan.

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Question regarding bond angle
by Prathvi Singh 14 Apr '22

14 Apr '22

Hi again Elaine, Is there a way in chimera or chimeraX to change the angle between three atoms A,B,C where atoms A & B are covalently bonded to each other but neither A nor B is bonded to C ? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Need Help
by Ali Raza Azeemi 14 Apr '22

14 Apr '22

Hi, hope you are doing well? dear, we have a question about making an animation/movie. I want to add molecular dynamics(MD) movie to the animation timeline, so I am facing difficulty to add on it. Kindly tell me if an option is available for this?. I will be very thankful to you. Thank you -- *Ali Raza Siddiqui* *Jr. Research Fellow* *Computer-Aided Drug Design (CAAD) unit. P-133, PCMD* H.E.J. Research Institute of Chemistry International Center for Chemical & Biological Sciences University of Karachi, 75270 Karachi- Pakistan.

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Loop through pbd files (ligand poses) and find hydrogen bonds against one template receptor
by Samuel Kyobe 13 Apr '22

13 Apr '22

Dear Chimera (and ChimeraX) team I have run a large docking experiment using several ligands to determine the best binders for further analysis in Molecular Dynamics studies and possible wetlab evaluation. I need to find some python example or code snippet capable of looping over hundreds of files and find several .pdb poses from a docking run and find Hydrogen bonds in each one using one receptor. In the process of finding the H bonds, I would like to add Hydrogens, and the protonation state is unspecified. Then at FindHBond, I want to find intermodal Hbonds and write the results to a file. Thanks Samuel Dr. Samuel Kyobe Department of Medical Microbiology, 3rd floor, Pathology/Microbiology BLDG, School of Biomedical Sciences College of Health Sciences, Makerere University. Box 7072, Kampala, Uganda. Mob: +256775468605 Skype: samuelkyobe

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