- Chimera-users - RBVI Mailing Lists

MultiFit is not working
by Smirnova, Julia 03 Nov '16

03 Nov '16

Dear Chimera-team, I was trying to use a MultiFit service of Chimera (to fit two models into my cryo density map), and it gives me the following error: Wrote /tmp/tmp_rSyaW/INSRT_model2.pdb Wrote /tmp/tmp_rSyaW/1x1n.pdb Traceback from web service request (connection setup): Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 52, in _setup md = self.sudsClient.service.getAppMetadata() File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 280, in __getattr__ port = self.__find(0) File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 315, in __find raise Exception, 'No services defined' Exception: No services defined 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 "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/appWebService.py", line 48, in _initApp self.backend = Backend(service, url) File "/opt/UCSF/Chimera64-1.11.2rc/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:MultiFitWebService' is unavailable. See Reply Log for more details. Could you please give me a clue what might be a problem. I do have an internet connection (checked by 'Fletch by ID... ' function) Thank you for your support, Julia

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Re: [Chimera-users] How to accurately and proportionally adjust structure size
by Cathy Lawson 03 Nov '16

03 Nov '16

Hi Xiaoyan, Tom Goddard had provided some useful hints when I asked a similar question last month. This has worked really well, though does require fitting a set of coordinates into each map that you want to compare. After following the suggestion set the focus always to all (or some element) of the aligned model for a consistent view across a set of maps. see http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-October/012767.html

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How to accurately and proportionally adjust structure size
by Zhu, Xiaoyan 02 Nov '16

02 Nov '16

Hello, I am trying to compare the cryoEM structures of radial spoke from different organisms. In the mean time, I want to display the same structure from different views. I have trouble to adjust the size accurately and proportional within the same and between different models.? For example, when I adjusted the structure from distal view and then rotated to the proximal view, the distance from screen changed and so the size changed. If I manually adjust the structure after rotation, I don't know how to make the structures from both views identical size. Similar thing troubles me when I want to adjust the size of two independent structures proportionally. Hope I made myself clear. Thank you a lot! Xiaoyan Zhu Ph.D. Candidate Department of Biological Sciences, Marquette University

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select atoms near at least one other atom in original selection?
by Oliver Clarke 01 Nov '16

01 Nov '16

Hi, I’d basically like to perform the equivalent of “hide dust” on an atom selection. I have a bunch of mutation positions that I’ve mapped onto a structure, and I would like to create a subselection containing only those positions which are within lets say 10Å of at least one other postion in the original selection - basically to represent structural clusters of mutations on the structure. Does anyone have any suggestion how to create such a selection using Chimera’s atom selection language? It seems like zr should do it but I can’t quite figure out how. Cheers Oli.

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how to select atom within a rectangular region
by Cherry Dons 01 Nov '16

01 Nov '16

Hi Chimera Developers, This is Dengpan, one of chimera users. I have a question about how to select atoms within a region? For example, I I want to select atoms within a rectangular region x0 to x1, y0 to y1, z0 to z1. Could you please give me a hint how to do it? Thanks. Dengpan Dong -- Department of Materials Science and Engineering, University of Utah

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Headless Chimera Registration Notification
by Healey, Joe 31 Oct '16

31 Oct '16

Hi Chimera Team, For some reason the install I have of headless Chimera as recently started warning me that I'm using an unregistered copy (I have actually registered before via the GUI version installed on my Mac (local machine)). Is there some way I can suppress this message (only purely because it's cluttering the STDOUT in my pipelines and I sometimes want to parse this). Or is there a chimera env variable I can modify to tell it that I am registered? Obviously I can't register in the manner the warning describes, as I'm unable to launch a GUI variant of Chimera on the server I'm using. Thanks! Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>

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How I can use extension in chimera
by b.behkamal＠stu-mail.um.ac.ir 27 Oct '16

27 Oct '16

Hello, I need to work with the extension files which is attached. The attached files is related to SSETracer. I didn't know how I can use them in chimera. Would you mind please help me about this matter and say to me the details of work step by step. Thank you very much in advanced. Regards, -- Bahareh Behkamal Ph. D. Candidate of Computer Engineering Researcher in Structural Bioinformatics Dept. of Computer Engineering Ferdowsi University of Mashhad, Mashhad, Iran

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problem regarding saving a file
by gutta ramadevi 26 Oct '16

26 Oct '16

Good day, I am using chimera following tutorials. I saved the processed receptor and ligand files in pdb format.But the files are not being saved.when i open the saved files i am getting the unprocessed receptor and ligand files. please help me to save the files.

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Definition of residues involved in binding ligand
by Maarten Schledorn 26 Oct '16

26 Oct '16

Dear reader, I have a pdb file of a protein with bound ADP and the file contains nothing but atomic coordinates and a few CONECT lines. If I open the file, the residues involved in binding ADP are shown, but I would like to know how Chimera knows this. I assume it is some VdW vicinity/overlap perhaps, or all residues within a certain distance from the ADP molecule, but I would like to know exactly how it is defined. I have tried to look for it in the documentation but haven't been successful so far. Does someone know the answer or a link to where it has been discussed previously? Many thanks in advance! Maarten

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pythonic version of fitmap tool
by Michał Kadlof 25 Oct '16

25 Oct '16

Is there any pythonic way of running fitmap tool? I would like to use it as a function that return parameters that I can assign to variable without parsing the output. I didn't find anything similar in Midas module. -- best wishes, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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