- Chimera-users - RBVI Mailing Lists

(no subject)
by Josef Stadelmann 06 Apr '20

06 Apr '20

confirm d9b43160fd8d6219836a2d9e8200e223df7ef733

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Chimera 1.14 Crashes When Attempting to Use the ViewDock Function
by Michael Bielecki 03 Apr '20

03 Apr '20

Hi, Chimera started to crash when choosing a structure for ViewDock. This started to happen after installing ChemOffice (could it be related?). I will be grateful if you could help me troubleshoot this. System: Windows 10, 64bit, NVIDIA GeForce GTX 1650 Sincerely, Mike

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Problems when using pdb2pqr and APBS calculation
by Chen Yinglu 03 Apr '20

03 Apr '20

Hi all, When running pdb2pqr and APBS in chimera, I got some problems. 1. When running PDB2PQR, it came in the ReplyLog at first with “Model 0 (dimer.pdb) appears to be a protein without secondary structure assignments”. I don’t know what does it mean. Is there anything I should do before running pdb2pqr? 2. I tried to calculate the electrostatic surface of my protein with APBS, but the execution ran for about half an hour and had no stop. So I cite the traceback as below. I want to know why it happened. Is there’s anything wrong in the settings? I didn’t change any parameters in the options. Thanks Yinglu Exception in thread Thread-47: Traceback (most recent call last): File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\threading.py", line 801, in __bootstrap_inner self.run() File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\threading.py", line 754, in run self.__target(*self.__args, **self.__kwargs) File "C:\Program Files (x86)\Chimera 1.13.1rc\share\WebServices\opal_client.py", line 205, in _queryStatusInThread status = self.sudsClient.service.queryStatus(jobID) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 521, in __call__ return client.invoke(args, kwargs) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 581, in invoke result = self.send(soapenv) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 613, in send reply = self.options.transport.send(request) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\https.py", line 66, in send return HttpTransport.send(self, request) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 82, in send fp = self.u2open(u2request) File "C:\Program Files (x86)\Chimera 1.13.1rc\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 (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 429, in open response = self._open(req, data) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 447, in _open '_open', req) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 407, in _call_chain result = func(*args) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 1228, in http_open return self.do_open(httplib.HTTPConnection, req) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 1201, in do_open r = h.getresponse(buffering=True) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\httplib.py", line 1121, in getresponse response.begin() File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\httplib.py", line 438, in begin version, status, reason = self._read_status() File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\httplib.py", line 394, in _read_status line = self.fp.readline(_MAXLINE + 1) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) timeout: timed out

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modeling selected protein mutations to a sequence
by Teresa Brito-Robinson 02 Apr '20

02 Apr '20

Hi Chimera users, I am trying chimera for the first time and my question is: - How can I change (substitute) specific amino acids within an uploaded protein sequence to mimic a missense mutation? - Or how can I enter a whole new custom made protein sequence into chimera, so I can probe different variants of a protein sequence. I don't know how to make the file like pdb (protein database) so I can fetch my custom sequence? Thanks! Teresa

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Command History
by Healey, Joseph 02 Apr '20

02 Apr '20

Hi Chimera team, I was wondering if the command history is stored as a (temp?) file somewhere? I presume it must need an on-disk record for the history between startups. Could you let me know where/how to find this on MacOS? It would be useful to do some searching of the file etc. Many thanks, Joe Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB Research Fellow Warwick Medical School University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> Email: J.Healey.1(a)warwick.ac.uk<mailto:J.Healey.1@warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738

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morphing
by Francesco Malatesta 30 Mar '20

30 Mar '20

Hello I am trying, for teaching purposes, to morph deoxy hemoglobin 1HBA and oxy hemoglobin 1BBB to show the O2-linked quaternary change. I get an obviously wrong morph, attached. Chimera is probably pairing different subunits? Do you think this morph can be done? Thank you Stay safe and well Francesco Francesco Malatesta Professor of Chemistry and Biochemistry FEBS Education Ambassador Department of Biochemical Sciences Sapienza University of Rome Tel: +39 06 49910944 Fax: +39 06 4440062 Cell: 338 6961519 Excellence in Learning and Teaching Biochemistry A FEBS Education Meeting Rome, September 16-17, 2019 www.sites.google.com/uniroma1.it/eltbiochemistry2019 -- ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono strettamente riservate e indirizzate esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non si è il legittimo destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per errore, si prega di restituirlo al mittente e di cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential and intended for the use of the addressee only. If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you have received the message in error, please forward it back to the sender and delete it permanently from your computer system. -- * Emergenza Coronavirus: facciamoci contagiare dalla solidarietà aiutando i nostri ospedali universitari Le donazioni possono essere inviate alla Fondazione Roma Sapienza che devolverà il ricavato al Policlinico Umberto I e Ospedale Sant'Andrea. È possibile donare: – con bonifico bancario (iban: IT72P 01030 03213 000063 259373, bic: PASCITM1R13, beneficiario "Fondazione Roma Sapienza", causale "emergenza coronavirus") – con carta di credito, attraverso il PayPal della Fondazione Sapienza <https://www.fondazionesapienza.uniroma1.it/node/776>

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Keyboard shortcuts for DockView?
by James Wagstaff 30 Mar '20

30 Mar '20

Hi all I am using the DockView extensions to inspect outputs of a virtual screen, and would like to use a keyboard shortcut to (re)assign the state of the currently selected compound. I am not familiar with the inner workings of Chimera so cannot easily see how to do this myself - I am hoping someone else has implemented this! Best James -- James Wagstaff +447910113349

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NMWiz plugin
by George Tzotzos 27 Mar '20

27 Mar '20

Hi everybody, I downloaded the NMWiz Chimera plugin from github: https://github.com/prody/NMWiz-chimera <https://github.com/prody/NMWiz-chimera> From Chimera/Tools/Additional Tools/Add third-party plugin-location, I used the add button to point to the downloaded plugin folder. This doesn’t seem to work. Is there another way to add this plugin? Is it compatible with Chimera 1.14 Thank you in advance for any suggestions

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box face capping
by Giulia Zanetti 27 Mar '20

27 Mar '20

HI all, is there a way to ‘cap high values at box faces’ through the command line? Thanks Giulia

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Re: [Chimera-users] [EXT] Re: Problem with electrostatic surface
by Benedikt Moissl 26 Mar '20

26 Mar '20

Hi Elaine, thank you a lot for your fast response! Your suggestion helped and my problem is solved :-) Best regards Benedikt -----Ursprüngliche Nachricht----- Von: Elaine Meng <meng(a)cgl.ucsf.edu> Gesendet: Dienstag, 24. März 2020 18:27 An: Benedikt Moissl <benedikt.moissl(a)biologie.uni-regensburg.de> Cc: chimera-users(a)cgl.ucsf.edu BB <chimera-users(a)cgl.ucsf.edu> Betreff: [EXT] Re: [Chimera-users] Problem with electrostatic surface Hi Benedikt, You still need to show the surface of your molecule, e.g. with command "surface #0 & protein" (or "surface #1 & protein" since they are the same atomic coordinates). After you do that, it will be listed in the menu of choices of what surface to color in the Surface Color 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 Mar 23, 2020, at 11:35 PM, Benedikt Moissl <benedikt.moissl(a)biologie.uni-regensburg.de> wrote: > > Dear Chimera team, > > I am trying to display color the surface of my molecule according with Poisson-Boltzmann electrostatics using Chimera 1.14. I ran the PDB2PQR tool as described in the user guide and obtained a PDB2PQR file. With that, I ran the APBS tool and obtained a .dx file. As described, the Surface Color panel opens automatically, but here I am unable to choose my structure file for "color surface" (s. attachment 1). I can only choose the .dx file, which does not work. All three models obtained during this process are opened in the model panel though (s. attachment 2). > > Do you have any idea on how to fix this? > > Thank you very much in advance and keep up the great work! > Benedikt Moissl

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