- Chimera-users - RBVI Mailing Lists

Chimera/auto dock vina
by Maketansky, Grace M 10 Nov '16

10 Nov '16

Hello, I am contacting you due to an error message that repeatedly gets displayed upon attempt to use auto dock vina through chimera. I have had no issues with running chimera on my mac, however I cannot get auto dock vina to work properly (I attempted to install and input the proper commands but cannot seem to get it to work). Attached is a screen shot of the error that keeps occurring. Any help would be greatly appreciated! Thank you! [cid:BD8D0978-A4C1-41ED-BDAA-54FFB6EA5958@res.enc.edu]

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Surface calculations difficulties
by Sarah Piper 10 Nov '16

10 Nov '16

Hi everyone, I’ve been struggling with getting the structure surface of my molecule shown (actions surface - show). Even after going through a list of suggestions of how to overcome this problem (e.g. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html ), I can’t get all needed surfaces displayed. Some other .pdb files work without a problem, but mine doesn’t or just works partially (e.g. just one chain instead of all chains), without seeing any apparent differences in the .pdb files or molecule sizes. A while ago I did not encounter this problem (using the same molecule/file), so is this maybe a chimera version problem? Or do the .pdb files have to be in a certain format? I usually get the following errors: "Surface calculation failed, mscalc returned code 2. Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface. If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed. More details are given at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html” My main use of surfaces in chimera is to display electrostatic potential files (or hydrophobicity plots) calculated in APBS and others. I’m using Chimera v1.9 on a Mac (but I had the same problems on a Linux workstation). I'd appreciate any feedback or reply! Many thanks for your help, Sarah ………………………………………………………………….. Sarah Piper, PhD student University of Queensland, St Lucia, 4072 QLD, Australia Phone: +61 7 3346 2325 Email: sarah.piper(a)uq.edu.au<mailto:sarah.piper@uq.edu.au>

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Measuring SASA of ligand
by George Tzotzos 09 Nov '16

09 Nov '16

I’m dealing with two separate trajectories involving: 1. Ligand A in complex with the monomeric subunit of a given protein A 2. the same ligand in complex with the dimer of protein A I would like to measure the buried (or solvent accessible) surface area of ligand A in both cases. I referred to a relevant posting in the list (http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-June/012472.html) but I’m not sure how this could apply in the above case. I’d be grateful for any suggestion on how to deal with this type of measurement. Many thanks in advance for any suggestions George

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Help for downloading UCSFchimera
by Rosaura Padilla 07 Nov '16

07 Nov '16

Hello, I am unable to down chimera onto my mac book pro. I get the following message: “Chimera” can’t be opened because the identity of the developer cannot be confirmed. Can you please help me Thank you so much. Rosaura -- *Rosaura Padilla-Salinas, PhD* Research Associate, Yin Lab University of Colorado BioFrontiers Institute Boulder, Colorado Rosaura.Padilla(a)Colorado.edu

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I need SSEBuilder and SSEHunter plug in
by b.behkamal＠mail.um.ac.ir 07 Nov '16

07 Nov '16

> Hello, > > I am a Ph.D. candidate of computer engineering in structural bioinformatic from Ferdowsi University of Mashhad, Iran. I'm working on cryo-em modeling. I necessary need the "SSEBuilder and SSEHunter plug in" in chimera to build the SSEs and continue my work. Would you mind please help me about this matter. > > Thank you very much in advanced. > > _Sincerely,_ -- 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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FW: request for operating delete option
by Williams, Joanne 07 Nov '16

07 Nov '16

Mr. Rama needs help. Please read below. Thanks! jo From: gutta ramadevi <ramadevi364(a)yahoo.co.in<mailto:ramadevi364@yahoo.co.in>> Reply-To: gutta ramadevi <ramadevi364(a)yahoo.co.in<mailto:ramadevi364@yahoo.co.in>> Date: Monday, November 7, 2016 at 2:09 AM To: "chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>" <chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>> Subject: request for operating delete option Good day, I have two same molecules saved in pdb file. I want to delete one molecule from the saved pdb file. How to do it when i open in chimera software. Iam attaching the concerned file. Please help me how to delete one molecule. Thanking you, G.Rama Devi.

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Upgrade chimera?
by Michał Kadlof 07 Nov '16

07 Nov '16

Hello, is it possible to upgrade built-in numpy in chimera python from version 1.7.0b2 to current version 1.11.2 in close future? This week preferably? -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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Depiction of backbone CA atoms as spheres
by George Tzotzos 05 Nov '16

05 Nov '16

I’m trying to depict selected backbone atoms as spheres with a smaller vdw radius. Residue side chains should not been shown. I checked the list and found an option that appears to do the job, e.g sel :77-80, 91-94 repr bs @ca vdwdefine +1.0 @ca But this didn’t work for me. Grateful for any suggestions Thanks in advance George

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Re: [Chimera-users] How to install package in chimera python?
by Jaime Rodríguez-Guerra 04 Nov '16

04 Nov '16

Hi! My favorite way to do this is via pip. 1. First grab the pip installer from https://bootstrap.pypa.io/get-pip.py wget https://bootstrap.pypa.io/get-pip.py 2. Install pip in Chimera chimera --nogui --script get-pip.py 3. Call the newly installed pip to install your package, ie. scipy chimera --nogui --script `chimera --root`"/bin/pip install scipy" That's it!

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How to install package in chimera python?
by Michał Kadlof 04 Nov '16

04 Nov '16

Hello, how can I add a python package to chimera python? I would like to use scipy inside chimera script. -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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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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Re: [Chimera-users] chimera minimization querry
by Elaine Meng 21 Oct '16

21 Oct '16

On Oct 21, 2016, at 2:42 AM, Shumaila Khan <shumailakhan432(a)yahoo.com> wrote: > > Hello, > I am shumaila khan , M.phil student at Quaid-i-Azam University Islamabad, Pakistan. Attached File is my structure and I want to minimize it. But there occurs an error that "Residue #0.1:165.A (ALA/ alanine) should have either atom HN or H, but not both. Kindly please reply me asap and help me out. > Thanks Dear Shumaila, For future reference, you should use the chimera-users(a)cgl.ucsf.edu email address for questions. For the minimization error, it is probably what the message says! I can only repeat the message: the residue should not have both of those atoms that it mentions, so you would need to delete one of them. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Chimera crashes on Mac OS Sierra (10.12)
by Tom Goddard 20 Oct '16

20 Oct '16

The Chimera developers have received 8 Chimera crash reports on the new Mac OS Sierra (10.12) somehow related to scrollbars. You may want to hold off updating to Sierra if you make heavy use of Chimera. We have not yet been able to reproduce the crash. It is very likely a bug in the Mac Tk window toolkit that Chimera uses, so even when we figure out how to reproduce it it may take time to figure out a fix since the problem is not in our code. Tom

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creating O2 molecule in Chimera
by Elaine Meng 20 Oct '16

20 Oct '16

> Subject: Query about chimera > Date: Thu, 20 Oct 2016 06:47:23 +0000 (UTC) > From: Shumaila Khan <shumailakhan432(a)yahoo.com> > > Hello, > I m student from Quaid-i-Azam University, Pakistan, doing my MS research project and I have some problems while working on chimera. I want some help regarding Attachment of oxygen atom to plant hemoglobin.Kindly please help me out how will I do that. kindly tell me how to draw oxygen molecule on chimera? While drawing Oxygen molecule it has only only Oxygen atom and two hydrogen atoms attached. Kindly help me out. Waiting for your kind response. Hi Shumalia, Your question was forwarded to me — Chimera questions should be sent to this address, chimera-users(a)cgl.ucsf.edu There are several different approaches you could use. One way is to use command: open smiles:oo If you hold the mouse over it you can see a balloon that says the bond length is 1.004. You could change the bond length to a better value by (1) selecting the bond (Ctrl-click on the bond so it has a green outline) (2) using Build Structure to change the length of the bond. Menu: Tools… Structure Editing… Build Structure, and in that dialog change from the “Start Structure” section to the “Adjust Bonds” section. Now you can use the slider or type in a value to change the length to what you want. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> That would make the oxygen molecule a separate model from your hemoglobin. You would probably want to first move the oxygen molecule by hand to the right position, and then (optionally) combine it together with the hemoglobin to make a single model depending on what you are planning to do. If you don’t need them in the same model, there is no need to combine. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> Or, another totally different approach is to find some other hemoglobin structure that already has an oxygen molecule and superimpose the two structures to get the oxygen in the right place, and then delete all the other atoms of the other structure except for the oxygen molecule. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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chimera 1.11.2rc crashes
by Yanni Goudeuk 18 Oct '16

18 Oct '16

Hello Chimera developers I've got the latest chimera (1.11.2rc), installed on windows 7 (64bit). My card is Nvidia Quadro K2000 and is using the latest drivers: 369.49 - *3D OpenGL stereo* is *enabled* under "*manage 3D settings"* in *nvidia Control Panel* My problem is that chimera crashes a few minutes after I open a .pyc file. Sometimes it will crash when I add a map in "*model panel*", sometimes when I rotate the structure, sometimes when I go though the tabs under " *Favourites*" --> "*Side view*". This is happening with other .pyc files too. I can also confirm that this is happening with older versions of chimera. Please have a look at the Application error log from event viewer: The program pythonw.exe version 0.0.0.0 stopped interacting with Windows and was closed. To see if more information about the problem is available, check the problem history in the Action Center control panel. Process ID: ab0 Start Time: 01d2246bcf21dbd4 Termination Time: 46 Application Path: C:\Program Files\Chimera 1.11.2rc\bin\pythonw.exe Report Id: 3c965b43-905f-11e6-bd99-b8ca3a8bb0d4 If you have any suggestions please let me know. Many thanks

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Guidance in finding Interactive Aminoacids with a ligand
by Shreyas Iyer 17 Oct '16

17 Oct '16

Respected Sir, I am unable to find the interactive aminoacids with the ligand present in a protein. Please guide me how to determine interatcive aminoacids. Awaiting a positive reply Yours Sincerely, Shreyas M Iyer

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