December 2024 - Chimera-users - RBVI Mailing Lists

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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