- Chimera-users - RBVI Mailing Lists

Enquiry
by Konstantinos P. Zois 17 Jan '25

17 Jan '25

To whom it may concern, I would like to know if there's a way to automatically setup a default way for visualising orbitals/densities... that is, after opening a .cube file, to present the density by a specific colour, transparency etc. Thanks a lot! KPZ -- _______________________________________________ Konstantinos P. Zois, MSc PhD student Institute of Theoretical Chemistry, Währinger Str. 17, A-1090 Vienna Department of Chemistry, Universität Wien _______________________________________________

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RRDistMaps: plot not corresponding to tabulated distance data?
by Dr. Michael Weber 02 Jan '25

02 Jan '25

Hi, I played around a bit with the nice RRDistMaps tool in Chimera v1.17.3 and I am wondering why the output .png plot's size of a single protein structure analysis doesn't correspond at all to the protein length? For a 659 amino acid long protein I was expecting to find a plot in which the distance matrix data area is sized 659 by 659 pixels (or multiples of this) to allow for placing the corresponding grey-scale value for each calculated distance as indicated in the plot's legend. Instead, it appears that the output image's dimensions are actually dynamically adjusted depending on the RRDistMaps's tool window size at the time of generating the plot. As a result, the core data region in the plot can barely accomodate the full data set with regular screen resolutions - at my end at least, it is always smaller (except maybe for very small proteins; I did not check this in more detail, yet). Playing with the sliders and trying to re-export those manually re-formatted images also doesn't seem to solve the problem. Did I miss something here? I just found out about this accidentally while writing a small Python program analyzing the output plots pixel-wise. ;-) I also noticed that the data area appears bordered by a triple line set (single pixel wide, each: grey-black-grey). Please note that I don't question the numeric distance data as exported in .csv/.tsv format - it's all just about the exported .png file. One additional question: Is it possible to run this tool in batch mode from the command line with parameters specifying (forcing) the (correct) output plot size (data region), the input .pdb structure file and all the options available in the GUI plus export the distance data table in .csv format (and maybe even the alignment data)? And finally, it appears that I encontered a possible bug when trying to process more than two sequences using RRDistMaps: The Muscle-based online alignment seems to fail (tried it for two days now) - here is the log: Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.17.3\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.17.3\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.17.3\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 1.17.3\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 1.17.3\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 1.17.3\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 1.17.3\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 1.17.3\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 1.17.3\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 69, in open raise TransportError(str(e), e.code, e.fp) TransportError: HTTP Error 404: Not Found 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 1.17.3\share\WebServices\appWebService.py", line 51, in _initApp self.backend = Backend(service, url) File "C:\Program Files\Chimera 1.17.3\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:MuscleService' is unavailable. See Reply Log for more details. Best regards, Michael. -- Dr. Michael H.W. Weber Rechenkraft.net e.V.

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converting Chimera .py to ChimeraX
by John Price 12 Dec '24

12 Dec '24

Hi, I have looked through the wiki and don't see anything relating to this. Is there a simple way to change the .py or .pyc Chimera to a format that can be used in ChimeraX? Have a great day, JC John C. Price, Ph.D. Professor of Biochemistry Brigham Young University E113 Benson Building 801-422-6040

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Movie from pdb file with 30 models of a conformational change.
by Evan Kantrowitz 02 Dec '24

02 Dec '24

Hi, Can someone give me help with a, I think, simple issue. I have a single pdb file containing 30 MODELS These 30 models correspond to a conformational change. Here is a portion of the Models list When I read it in,I see all 30 models showing in the view. What I want to do is make a movie showing these 30 MODELS one after the other. I have tried coordset and coordset slider but have not got it to work. Thanks Evan PS. This is what the image looks like with the 30 frames.It was generated from the A chain of pdb files 2e2n and 2e2q using the website ViewMotions (viewmotions.bc.edu <http://viewmotions.bc.edu/>). ----------------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu <mailto:evan.kantrowitz@bc.edu> Emeritus Professor of Chemistry Cell: 617-775-9915 Boston College www2.bc.edu/evan-kantrowitz <http://www2.bc.edu/~kantrow> -----------------------------------------------------------------------------

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Issue with Display of Hydrogen Bonds in Find H Bond Tool in Chimera
by GABRIELE SANTOS CEPINHO 12 Nov '24

12 Nov '24

Dear Chimera Support Team, My name is Gabriele Cepinho, and I am using Chimera version 1.17.3 for molecular docking analysis in my research. Recently, I encountered an issue with the Find H Bond tool that I have been unable to resolve, and I hope you may be able to assist me. When I use the Find H Bond tool to display hydrogen bonds between molecules, the generated image also shows polar interactions along with the specific hydrogen bonds. However, in the tool’s output file, I can clearly identify which interactions are true hydrogen bonds. My goal is to display only the hydrogen bonds in the image, excluding the polar interactions, but I have not been able to adjust the tool to achieve this. I have tried modifying the distance and angle parameters to restrict the display, yet polar interactions still appear alongside the hydrogen bonds in the visualization. I appreciate any guidance or recommendations you can provide regarding this matter. If there is any additional option to filter these interactions directly in the image, or if there is an update or specific setting available for the Find H Bond tool, I would be grateful to know about it. Thank you in advance for your attention. Best regards, Gabriele Cepinho -- ---- É obrigatória a utilização do e-mail @unifesp em todas as correspondências oficiais, institucionais e no acesso aos equipamentos e sistemas da Universidade Federal de São Paulo, conforme a portaria Reitoria n. 1182/2022 <https://sti.unifesp.br/documentos/termos-de-uso-do-email> que define a Política de e-mail institucional da Unifesp. <https://sei.unifesp.br/sei/publicacoes/controlador_publicacoes.php?acao=pub…>

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Write out SeqRes entry
by David Bhella 07 Nov '24

07 Nov '24

Dear Chimera/ChimeraX team, I have a model for an asymmetric unit of a virus capsid that has three chains of the same capsid protein – but I am having trouble depositing my model in the PDB because it only has a seqres entry for one of the three chains (B). Whatever I do, chimeraX will only write entries for that chain. Is there a way to force chimeraX (or any other program) to write the seqres card for each chain correctly? Thanks D David Bhella Professor of Structural Virology Director, Scottish Centre for Macromolecular Imaging Associate Director, MRC - University of Glasgow Centre for Virus Research +44 (0)141 330 3685<tel:+441413303685> [signature_1350623625] [Logo, company name Description automatically generated]

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Values at Atom Positions
by jp d 01 Nov '24

01 Nov '24

hi, sorry to bother you again, is it possible to run "Values at Atom Postions" from a script where i specify map,pdb and just the output attribute file ? thanks jpd

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ccp4 map from mtz
by Vitali James 31 Oct '24

31 Oct '24

Dear Greg, I just converted my mtz file in phenix to ccp4 maps. Chimera can open the mFo-DFc.ccp4 and 2mFo-DFc.ccp4 but how to fit pdb into the map?. Somehow the map does not appear as continuous crystals as in coot. Can you please explain how to align the pdb structure wuth the map. best James

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About using Chimera(X) in articles
by Elaheh Kashani-Amin 30 Oct '24

30 Oct '24

Dear Chimera developers, We are a research and education group based in Iran and have been using Chimera(X) to teach our students about homology modeling and molecular docking. Recently, we discovered that our access to your website has been denied. Although we can access it via VPN, we would like to inquire if we can legally use Chimera(X) for academic purposes and cite it in our papers. We would greatly appreciate it if you could provide us with legal access to your products. Thank you for your time and consideration. Best regards Elaheh Kashani-Amin PhD, Molecular Medicine

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which file is the Modeller executable on linux?
by Elaine Meng 30 Oct '24

30 Oct '24

Forwarding to chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> so that somebody who knows the answer can respond. I don't know since I'm not on linux and do not use a local installation, sorry. That is the recommended address for asking questions about Chimera. Note that we do not actively develop Chimera any more. ChimeraX is recmomended instead -- it has essentially the same capabilities to interface with Modeller (local or web service) for loop modeling and for comparative modeling. The comparative modeling tool in ChimeraX is better than in Chimera, because it allows modeling multimers whereas the Chimera tool only allows modeling a single protein chain. Here are the help pages for the two ChimeraX tools, Model Loops and Modeller Comparative: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> Also, there is a different address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> for asking questions about ChimeraX. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: > Date: October 29, 2024 at 3:58:41 PM PDT > To: Yassin Ahmed <yassin.ahmed2200m(a)copharm.uobaghdad.edu.iq> > > On 10/29/24 8:12 AM, Yassin Ahmed wrote: >> Please l have download and installed modeller in my Linux system , >> now I want to run modeller locally by Chimera >> Please where can I find the "Modeller executable file location" and also where can I find the "custom Modeller script file location" ? ,,,, >> Because there are many files named modeller and mod in installation folder,so I am confused. Please guide me > > Hi Yassin, I'm not 100% sure what the Chimera developers mean by "Modeller executable file" so I've cc'd Elaine from the Chimera team, but assuming you're running the latest version of Modeller, they probably mean the mod10.6 script. Where that is depends on how you installed Modeller. If you used the RPM, it is /usr/bin/mod10.6. > > In most cases you would not need to change the Modeller script file, instead using that generated by Chimera, so you can leave that box blank, I think. > > Ben Webb, Modeller Caretaker

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