- Chimera-users - RBVI Mailing Lists

Opening DESMOND trajectories in Chimera,
by Shriyash Upadhyay 28 Jul '17

28 Jul '17

Hello, I am a researcher using DESMOND to run molecular dynamics simulations of protein-DNA interactions. However, I and others in my lab are most comfortable viewing trajectories and creating images in UCSF chimera. Is there a way to export DESMOND trajectories in a format that Chimera can open, either from maestro or some intermediate program like VMD? Thanks, Shriyash Upadhyay

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Incomplete Surface Model
by Bosung Kim 25 Jul '17

25 Jul '17

Hello, Do you know why my surface model is incomplete? I have attached picture. Thanks

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Program close during AutoDock Vina Session
by Nannette Yount 21 Jul '17

21 Jul '17

Hi, I had a computer shutdown during an Autodock Vina session (via Opal server) during the "execution in progress" stage. These sessions typically take between 5-6 days to complete, and now upon computer restart - when opening Chimera, I see no evidence that the session is still ongoing. The "get information" icon - where I could check Autodock status is also greyed out. Is there any way to get this session back - since it's probably still running on the server (process was about 3 days into the session)? Thanks, Nannette Nannette Y. Yount, Ph.D. Infectious Diseases Department of Medicine Harbor-UCLA Torrance, CA 90502

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morph interpolation
by Souroprobho Chowdhury 20 Jul '17

20 Jul '17

Hello, I am trying to use morph interpolate on two (for this post) PDBs (I2.pdb and I3.pdb, attached) but something peculiar is happening. The Hydrogen on the HIS 1082 (N1) does a ‘cork-screw’ like movement. Essentially, instead of interpolating directly from position A to B, it is taking a more round-about angle. A similar movement is observed for the O3 in the T1 O ligand. This problem has come up recurrently in my work and I am yet to find a solution. I have used most of the options that apply on morph interpolate that are mentioned on the chimera website without much improvement. I am using Maestro by Schrodinger to model my structures. Please find attached I2.pdb , I3.pdb and mov_all.pdb. mov_all.pdb is the trajectory file, works on Pymol (I am attaching a pymol script called auto-script.pml as well for selection of the correct residues, and a reasonable representation). The chimera interpolation script is also attached. Thanks! Souro

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Re: [Chimera-users] Define Plane
by Eric Pettersen 18 Jul '17

18 Jul '17

Hi Catherine, Remind me how exactly you are creating the axis in Chimera, and send me whatever script you are using to compute it yourself… —Eric > On Jul 18, 2017, at 8:24 AM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu> wrote: > > Hi Eric, > > I am able to generate the axis. Like you said, we used the x,y,z axis subtracting it from centroid position and did the SVD. > For most cases, the axis is same as Chimera but for few it is little different. I checked the number of atoms used between both and it is same. > Are you using all the atoms or only specific atoms or is there any other thing I am missing? > > Thanks, > Catherine > > On Fri, Jun 30, 2017 at 7:13 PM, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: > Chimera simply calls numpy.linalg.svd (singular value decomposition) on an array of the xyz coordinate (after the centroid position has been subtracted from them). The documentation for numpy.linalg.svd is here: > > https://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.svd.html <https://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.svd.html> > > It looks like it in turn calls LAPACK routine_gesdd, which is documented, in general, here: > > https://software.intel.com/en-us/mkl-developer-reference-c-singular-value-d… <https://software.intel.com/en-us/mkl-developer-reference-c-singular-value-d…> > > It’s an implementation of singular value decomposition, described in general terms here: > > https://en.wikipedia.org/wiki/Singular_value_decomposition#Relation_to_eige… <https://en.wikipedia.org/wiki/Singular_value_decomposition#Relation_to_eige…> > > The math is pretty complicated. > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > > >> On Jun 30, 2017, at 10:09 AM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu <mailto:catrajen@umail.iu.edu>> wrote: >> >> Hi Elaine, >> >> Thank you for helping me understand it. Can you give me more details about how PDB file is decomposed to find the plane and normal. Like, how the eigenvectors are calculated from the atomic coordinates. >> >> Thanks, >> Catherine >> >> On Thu, Jun 29, 2017 at 7:23 PM, Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >> >> >> > On Jun 29, 2017, at 2:14 PM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu <mailto:catrajen@umail.iu.edu>> wrote: >> > >> > Hi, >> > >> Hi Catherine, >> >> > I am trying to understand how the plane is defined in chimera. Can you please help me with that? >> > >> > "Define a plane for the specified atoms. Eigenvectors/values are calculated from the atomic coordinates after subtracting the position of their non-mass-weighted centroid. The plane is anchored at the centroid and aligned with the first two eigenvectors (the third eigenvector is normal to the plane)." >> > >> > Define a plane for the specified atoms. >> > - specified atoms, i use 'sel protein’ >> >> OK, so if using the graphical tool (Axes/Planes/Centroids) it uses the selected atoms, meaning all the protein atoms if you had used “sel protein.” If using the “define” command, you can just specify “protein” directly in the command to use all the protein atoms, without making a selection. >> > >> > Eigenvectors/values are calculated from the atomic coordinates >> > - atomic coordinates, so x,y,z coordinates of all atoms. (Can you please explain a bit more like how and what you read from PDB file to define plane). >> >> For the atoms you specified, there are ATOM lines in the PDB file with X,Y,Z coordinates. Each atom is a point in 3D (X,Y,Z). >> >> > >> > after subtracting the position of their non-mass-weighted centroid >> > - how is non-mass-weighted centroid is calculated >> >> It is the centroid of the points (atomic positions), not sure how else to say it. The average position of all the atomic points is the centroid. Non-mass-weighted just means all the atomic points are treated equally, instead of heavier atoms being treated as more important than lighter atoms. >> > >> > The plane is anchored at the centroid >> > - which centroid is this? Is the protein moved to the origin(0,0,0) position? >> > >> The centroid is the same centroid as in your previous question. Nothing is moved. >> > >> > Thanks, >> > Catherine >> >> You’re welcome. I hope this helps, >> Elaine >> ---------- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > >

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PROBLEM ABOUT BLAST PROTEIN
by Rosie Spera 18 Jul '17

18 Jul '17

Dear support, I am trying to open Chimera's Blast Protein, but everytime I receive this error: Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.11.2\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.11.2\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.11.2\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 1.11.2\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 1.11.2\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 1.11.2\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 1.11.2\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 1.11.2\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 1.11.2\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 407: Proxy Authentication Required 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 Blastp request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.11.2\share\blastpdb\ParserBlastP.py", line 361, in _initBlast self.opal = OpalService(self.ServiceName) File "C:\Program Files\Chimera 1.11.2\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. 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. Blast web service appears to be down. See Reply Log for more details. I have configured Chimera to use the proxy server and I have saved the setting. I hope any help. Best wishes Inviato da Outlook<http://aka.ms/weboutlook>

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1st CfP "From Virtual Reality to Immersive Analytics in Bioinformatics"
by baaden＠smplinux.de 18 Jul '17

18 Jul '17

Dear Colleague, 1st CfP "From Virtual Reality to Immersive Analytics in Bioinformatics", February 2018, Burlingame, California, USA ************************************************************************ Special Session at the Stereoscopic Displays and Applications XXIX, Burlingame, California Special Issue of the Journal of Integrative Bioinformatics, vol 15, de Gruyter Berlin ************************************************************************ Bioinformatics usually deals with the smallest entities of life, therefore, visualization plays an important role in this field. Stereoscopic rendering has already been used for a long time for visualizing biological structures, dating back to the first hype of virtual reality technologies 25 years ago when the CAVE was invented and Head-Mounted Displays (HMD) became affordable. Triggered by the success of new, modern HMDs such as Oculus Rift and HTC Vive, Virtual Reality has recently gained a lot of attention again. On the other hand, a new generation of large-scale "computational microscopes" is being established, such as the CAVE2, representing large, nearly 360 degree-spanning visualization facilities. At the same time, advanced "Visual Analytics" solutions have become an important tool in all areas of scientific data analysis, combining visualization, data mining and analysis methods, and user interaction. Uniting both VR and VA, "Immersive Analytics" now starts to make use of new technologies, immersing the scientist into the data, and, in the best case, enabling advanced insights. This special issue will focus on: - What is the legacy of the past? - Which approaches (partly) failed, and which success stories were triggered by Virtual/Augmented Reality in the context of Bioinformatics? - Which new ideas exist to approach now immersive analysis of biological data? - Which methods, technologies and/or applications are expected to change the way we see and perceive biology? More info: http://VR2IAinBioInf.immersive-analytics.org Stereoscopic Displays and Applications XXIX, 28 Jan - 1 Feb 2018, Burlingame, California ************************************************************************ Since 1990, SD&A focuses on developments covering the entire stereoscopic 3D imaging pipeline from capture, processing, and display, to perception. SD&A XXIX will be held as part of the 2018 IS&T International Symposium on Electronic Imaging: Science and Technology at the Hyatt Regency San Francisco Airport, Burlingame, California, USA. The conference brings together practitioners and researchers from industry and academia to facilitate an exchange of current information on stereoscopic imaging topics. http://stereoscopic.org Scope of the Special Session ************************************************************************ Molecular biology produces huge amounts of data in the post-genomic era. This includes data describing metabolic mechanisms and pathways, structural genomic organization, patterns of regulatory regions; proteomics, transcriptomics, and metabolomics. On the one hand, analysis of this data uses essentially the methods and concepts of computer science; on the other hand, the range of biological tasks solved by researchers determines the range and scope of the data. Integrative Bioinformatics is a new area of research using the tools of computer science and electronic infrastructure applied to Biotechnology. We solicit submissions that describe the use of Immersive Analytics for data analysis in biology and Bioinformatics - potential topics include (but are not limited to): - Virtual and Augmented Reality approaches for data analysis - Semi- and fully immersive data exploration - Metabolic and Regulatory Network Modelling and Simulation - Data Integration and Text Mining Approaches - Signal Pathways and Cell Control - Network Analysis - Medical Informatics, Biomedicine and Biotechnology - Integrative whole cell and molecular modelling - Visual Analytics, Visualization, and Animation Key Dates ************************************************************************ - August 15, 2017: Abstract to SD&A 2018 - January 10, 2018: Full manuscript submission due to JIB - February 1, 2018: Conference Presentation - April 2018: Review and revision process finished - May to June 2018: Publication of accepted papers Organizers and Contact ************************************************************************ - Bjorn Sommer, University of Konstanz, Konstanz/Monash University, Melbourne - Marc Baaden, Institut de Biologie Physico-Chimique, Paris - Michael Krone, University of Stuttgart, Stuttgart - Andrew Woods, Curtin University, Perth If you have any question, please contact us: VR2IAinBioInf(a)immersive-analytics.org Journal of Integrative Bionformatics ************************************************************************ The Journal of Integrative Bioinformatics (JIB) is an international open access journal publishing original peer-reviewed research articles covering all aspects of integrative bioinformatics. It was established in 2004 and joined the Open Access family of de Gruyter - one of the oldest German publishers - in 2017. JIB (ISSN 1613-4516) is indexed by PubMed, DBLP Computer Science Bibliography, SCOPUS and Google Scholar. https://www.degruyter.com/view/j/jib For 2017 and 2018 there is no publication fee for articles accepted and published by JIB! Submission ************************************************************************ Only submit your 500-word abstract to the conference (Deadline: August 15, 2017), use option 2 - presentation only), as the full paper has to be submitted to the Journal of Integrative Bioinformatics in the next step (Deadline: January 10, 2018). http://stereoscopic.org/2018/index.html#submit Please follow the SD&A guidelines for writing the abstract: http://stereoscopic.org/2018/index.html#sag Please submit here your full paper (Deadline: January 10, 2018). https://mc.manuscriptcentral.com/dgjib More info and templates you will find here: https://www.degruyter.com/view/j/jib Review Process ************************************************************************ Each paper submitted to this special issue will be rigorously evaluated in a single-blind peer review process. All accepted papers will appear in a special issue of the Journal of Integrative Bioinformatics (JIB). By submitting a paper, the author(s) agree that, if their paper is accepted, they will: - Submit a final, camera-ready version to the publisher on or before the camera ready deadline. - Register at least one author to attend the conference on or before the registration deadline. - Attend the conference (at least one author). - Present the accepted paper at the conference. -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217

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commands to add red spheres to the ribbon structure
by zhangbin 18 Jul '17

18 Jul '17

Hi Chimera, I would like to know the commands for adding a red sphere to a certain spot in a ribbon structure of a protein (please see the attachment). The command I know worked for older version of the chimera but not this new version 0.1. Thanks, Bin

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axis - length
by Catherine Jenifer Rajam Rajendran 17 Jul '17

17 Jul '17

Hi, I am trying to display an axis in chimera. I have one point - x,y,z co-ordinates and centroid's x,y,z co-ordinates. I want to extend the length of the axis generated using this two points. I tried to create a bild format file. *.cylinder 0.584 0.048 0.810 20.912 5.823 19.703 1* where, second 3 co-ordinates are centroid. It creates an axis but i want to extend the length from centroid point to the other end too. Or, Is there any other way to define it? Please help me. Thanks, Catherine

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Chimera Dowload
by Lance Patten 15 Jul '17

15 Jul '17

Hello, I have been trying to download Chimera using this link <http://www.rbvi.ucsf.edu/chimera/download.html>, but the website will not allow it to download. Is there another website or place to download the program? Thank you, Lance Graduate Research Assistant Nanoscale Materials and Device Group nano.boisestate.edu In some cases, this email may contain proprietary or confidential information. Emails sent from this address should not be forwarded without permission or full understanding that the message does not include any sensitive information.

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http download links are insecure
by Yuri 14 Jul '17

14 Jul '17

Download site and links here are http: http://www.rbvi.ucsf.edu/chimera/download.html http is susceptible to MITM attacks. Checking md5 signatures help, but I bet majority of people just doesn't do it. You need to make the site and download URLs https to make them more secure. Yuri

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rainbow with atom-spec of a portion of a chain
by Cheng, Micah 14 Jul '17

14 Jul '17

I was trying to rainbow a subset of a chain using the rainbow command and the atom-spec: rainbow #0:34-102.a However when run, the entire chain A was colored with rainbow instead just residues 34-102 running the color command with the same atom-spec: color #FFFFFF #0:34-102.a produced the predicted result of only residues 34-102 being colored white Is there a command to rainbow only part of the chain or are there any workarounds to being able to rainbow only a selected portion of a chain? Thanks in advance Micah CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

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Nvidia Quadro P5000
by Josep TRIVIÑO VALLS 13 Jul '17

13 Jul '17

Hello, I have a brand new computer with a Nvidia P5000. I have not seen anything related with this graphic card but I am not obtaining the expected results when using Chimera. Chimera detects the graphic card and the drivers, and when running the benchmarks it seems like it is working better than, for example, the GeForce GTX TITAN X. I have also been testing with the side view of a large protein, which I can do with a Quadro M4000 on another computer, but with the Quadro P5000 it is not working properly. It works slowly. I am using OpenSuse Leap 42.2 with the newest Nvidia driver 375.66. I have also installed the Cuda libraries. Any hints about what I should do in order to get it working properly? Thanks.

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Command-line equivalents of interative action
by Healey, Joe 13 Jul '17

13 Jul '17

Hi Chimera Team, I've been following this great tutorial: https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html#case1 To render a structure by conservation. I'd like to run this non-interactively for a number of proteins though. Could you tell me what the python or 'chimera code' equivalents would be? For instance, I would provide a structure (or structures in a session) and MSA in fasta format already, so without interactive menus I'd like to: 1. Open the structure(s) and MSA 2. get the conservation from MultAlign (the actual conservation metric doesn't particularly matter to me at the moment) 3. Render any open models by conservation, say using the cyan-maroon colour scale 4. Additionall depict as smooth worms with defined min and max radii If this is possible! Thanks! Joe Joe Healey M.Sc. B.Sc. (Hons) MSRB 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> | ORCID: orcid.org/0000-0002-9569-6738

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Does anyone know how to specify a "MarkerSet Link" to be used for findClash
by Jun Ha Song 11 Jul '17

11 Jul '17

Hello, I want to search whether my models are close enough to be exactly apart from each other by the distance I specify. findClash appear to be tailor-made for the exact task I was hoping to do, but unfortunately, it appear to only search nearby atoms, not the links, even if I select the entire model which has both markers and links incorporated as its component. The only way that I can make my entire MarkerSet to be competent for findClash was to use Tom's *dividelinks.py* script ( http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/dividelinks.…) to add *n* number of marker s along the link of two marker that I selected. Q1. Can I ever specify MarkerSet Link by *atom-spec *commands, to use findClash on the inter-model links as well, not only for the markers? Q2. Is there any other function than findClash that allow me to find any inter-model (never atoms within the same model) atom or link's distance that I specify exist? Best, Jun Ha Song.

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change model ID
by Fabian Glaser 11 Jul '17

11 Jul '17

Hi, Is it possible to change an opened model number? I tried the combine command but could not do it. Thanks a lot, Best, Fabian Fabian Glaser PhD Head of the Structural Bioinformatics section Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web http://bku.technion.ac.il/ Tel +972 (0) 4 8293701

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Ligand Center of Mass
by ARMIN HODAEI 11 Jul '17

11 Jul '17

Dear Chimera users, I have been wondering, is there a way to find a ligand Mass weighted center of mass in Chimera? For example in the 1G6N(rcsb ID) protein I want to know the cAMP ligand's COM. Best, -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

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Is it possible to translate single selected marker when many other models are still active, using constrained move function?
by Jun Ha Song 10 Jul '17

10 Jul '17

Hello all, [image: Inline image 2] I am looking at my map, which I have zoned one flat plane of it, not from the top, but at inclined angle of 10˚ from above. My goal is to move markers that are at the far side of this plane from left to right (Red Arrow), without the marker going out of the plane. Because I am looking at my plane not from the top, any movement of my mouse in y-axis of my view, will cause my marker to go outside of the plane. The only way to move the marker, using Movement Mouse mode, is to solely translate my mouse in x-axis using xy-translation (Middle Mouse Button). Because it is impossible to solely move my mouse in x-axis only, I tried to use Constrained Movement tool to limit my translation in one axis only, but I soon discovered that constrained movement is applied to all active models in the session. Is it ever possible to use constrained movement only for the marker that I have selected, which will move due to Movement Mouse mode being set at "Move Selection"? I was actually fortunate enough to find a little utility called "DragLock", which literally locks the axis of drag translation in either x-axis or y-axis, "DragLock" is only functional for Windows, not for Mac. Any method to limit my mouse translation in x-axis only would suffice, and I know constrained movement already provide exactly that; if only I can move one marker of my selection, not entire active models. Any advice would be helpful! Sincerely, Jun Ha Song.

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Is it possible to configure Chimera Tools Window Start-up Position in Dual Monitor?
by Jun Song 10 Jul '17

10 Jul '17

Hello everyone, There are quite a few tools that I always use when I use Chimera, and I really cannot do the work I need to do without having all the tools open in their own separate windows. I find it very convenient to configure those tools to open all together when I start Chimera every single time. I also connect a monitor to my laptop to visualize my map on it, and place all my tool windows on the other screen. I am wondering if there is an option to specify all the tool windows' start-up position and size over dual monitor screens. When I click on the Chimera icon to do some work, all the windows, both main Chimera graphics window and all the tool windows, only open on the main display. I have been reading all the instructions regarding window position for hours, and it appears that the only parameter that I can play with is - Which screen Chimera will open (using *--screen screen_number*) - Graphics window size (using *windowsize [width height]*) - Graphics window position (using *windoworigin [x y]*) and nothing else. Is it ever possible to... Q1. Specify exact position where all of the tool windows will open? and also, can I... Q2. Allow Chimera windows to open over both screens, not only one screen? I know all it takes for me to re-arrange is about 10 seconds of drag, but if there is a way to configure start-up position of all the windows, that would make using Chimera even more enjoyable. Best, Jun Ha Song.

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Problem using Chimera with NLOpredict
by Roger Hawksworth 10 Jul '17

10 Jul '17

Hi, Please see attached Word .docx file which is also contained within the attached .zip file. Today, 08th July 2017, is the first time that I have used Chimera. Perhaps the .cfg file I tried to use is somehow "corrupt"? Best Wishes, Roger H

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Centering Origin Index on Command Line
by Yong Zi Tan 10 Jul '17

10 Jul '17

Hi, Could I check if there is a command line version of the "center" button under Origin Index in the Volume Viewer? Thank you! [cid:image001.png@01D2F697.ECEEC010] Warmest Regards, Yong Zi Tan

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large datasets
by Arthur Szabo 10 Jul '17

10 Jul '17

I am trying to work with a data set that has three copies of a protein complex per asymetric unit in the cell. It is a rather large complex. I can delete two of the copies and work with only one complex. There are 9 chains in each complex. 3 oligonucleotide sequences, and 6 proteins of different sizes, the largest having about 1400 residues. The way in which I selected only one complex to visualize was to delete the other 18 chains one at a time. There must be a way of deleting each of the other two copies all at once but I did not try to find it in the Chimera tutorial list. The deletion only eliminates the image of each complex. Both complexes are still there in the total data set. The result is that saving a session takes about three minutes because it saving all the coordinates of the three copies of the complex. How can I make the process more efficient and delete two copies from the coordinate data set. Thank you Arthur G. Szabo

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software for protein 3D structure visualization
by fateme shaki 08 Jul '17

08 Jul '17

Dear Sir/Madam, I am looking for a program which could transform enzyme activity to a 3-dimentional form of the enzyme. I am not sure about such a program and I am not sure whether there is such program or not. I just saw the software for protein 3D structure visualization on your website and I assumed that this program might be useful. Could you please assist me in this case. Thank you in advance. Fateme

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Can I attach images when asking Chimera users mailing list?
by Jun Song 07 Jul '17

07 Jul '17

Hello, I have been looking at the archived discussions, and I have never seen a single discussion that had any images. Is it just archived transaction that is lacking images, or is it not possible to attach images to this email? Best, Jun Ha Song.

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Define Plane
by Catherine Jenifer Rajam Rajendran 01 Jul '17

01 Jul '17

Hi, I am trying to understand how the plane is defined in chimera. Can you please help me with that? "Define a plane for the specified <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> atoms. Eigenvectors/values are calculated from the atomic coordinates after subtracting the position of their non-mass-weighted centroid. The plane is anchored at the centroid and aligned with the first two eigenvectors (the third eigenvector is normal to the plane)." Define a plane for the specified <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> atoms. - specified atoms, i use 'sel protein' Eigenvectors/values are calculated from the atomic coordinates - atomic coordinates, so x,y,z coordinates of all atoms. (Can you please explain a bit more like how and what you read from PDB file to define plane). after subtracting the position of their non-mass-weighted centroid - how is non-mass-weighted centroid is calculated The plane is anchored at the centroid - which centroid is this? Is the protein moved to the origin(0,0,0) position? Thanks, Catherine

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Fwd: pdb-l: EMBL-EBI user survey
by Eric Pettersen 28 Jun '17

28 Jun '17

> Begin forwarded message: > > From: Gerard DVD Kleywegt <gerard(a)xray.bmc.uu.se> > Subject: pdb-l: EMBL-EBI user survey > Date: June 27, 2017 at 3:30:30 AM PDT > To: pdb-l(a)ucsd.edu > Cc: Gerard Kleywegt <gerard(a)xray.bmc.uu.se>, "Gerard Kleywegt \(EBI account\)" <gerard(a)ebi.ac.uk> > > Dear colleagues, > > EMBL-EBI (http://www.ebi.ac.uk/) is running a worldwide survey to understand > usage of its resources (there are several dozen, including UniProt, Ensembl, > ChEMBL, EuropePMC, PDBe, EMDB/EMPIAR and many more). We would like to ask you > to forward this request within your department, company or institution. We are > interested in responses from a wide range of scientists, in particular those > who do not think of themselves as bioinformaticians. The results are extremely > valuable to EBI in helping us to understand our users, and our users' needs. > > Here is the link to the survey: > https://www.surveymonkey.co.uk/r/2017_EBI_survey > > Many thanks! > > --Gerard > > --- > Gerard J. Kleywegt, EMBL-EBI, Hinxton, UK > Head of Molecular and Cellular Structure > gerard(a)ebi.ac.uk pdbe.org emdb-empiar.org > PA: Pauline Haslam pdbe_admin(a)ebi.ac.uk > > TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see > https://lists.sdsc.edu/mailman/listinfo/pdb-l .

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Difference between Chimera and ChimeraX
by Bon Ikwuagwu 27 Jun '17

27 Jun '17

Hello, I'm a first year graduate student and I am wondering what the differences are between Chimera and ChimeraX? I want to use the tools that are present in Chimera, but I don't know if those tools are also present in ChimeraX. Any feedback would be helpful. Best, Bon Ikwuagwu -- Bon Ikwuagwu PhD Student, Chemical and Biological Engineering Northwestern University

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Libfftw3.so.3
by Robert Waugh 26 Jun '17

26 Jun '17

Hello, I am a Masters Student from Kingston University, I am currently using Chimera as part of a Bioinformatics Project. For this project, I have decided to use IMP to integrate the data I have to make a coarse grained model. Unfortunately, upon using MultiFit I receive the error which I have posted below which states that I cannot open the shared object file libfftw3.so.3. I was wondering if it would be possible if you were to make this file available so that I can complete my Multifit Modelling. https://pastebin.com/kkRW6X3U Thank you, It would be much appreciated, Robert Waugh

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Trying to change dihedrals: ValueError: bond is part of a cycle
by Nikolaos Bismpikos 26 Jun '17

26 Jun '17

Hey, my goal is to change the dihedrals of an already existing pdb template in order to find low-energy protein conformations. The issue I have here is that for some residues the dihedrals phi and psi cannot be changed. That's the error I get: Traceback (most recent call last): File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimeraInit.py", line 683, in init chimera.openModels.open(a, prefixableType=1) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1929, in open models = func(filename, *args, **kw) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1299, in _openPython loadFunc(sandboxName, fileName, f) File "predictor.py", line 40, in <module> es.main_loop(); File "/home/nick/Python/pdb/AbstractOptimizer.py", line 97, in main_loop self.fs, self.evals, self.terminate = self.eval_pop(self.eval_func,self.pop,self.evals,self.eval_budget,self.extra_par) File "/home/nick/Python/pdb/eval_energy.py", line 20, in eval_energy allR[j].phi = pop[i,j]; File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/phipsi.py", line 98, in setPhi _setAngle(bond, phi, getPhi(res, missingIsError=True), "phi", anchorSide) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/phipsi.py", line 147, in _setAngle br = BondRot(bond) ValueError: bond is part of a cycle Is there a way to determine beforehand which bonds are part of circle and hence which residues' dihedral information cannot be changed? Thank you in advanced for your time, Nikolaos Bismpikos

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Chimera to Excel
by Fábio Pereira 24 Jun '17

24 Jun '17

Good Afternoon, I would like to know if i can to export informations opened in View Dock to Microsoft Excel. If this is possible, how can i do ? great!

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DockPrep sometimes fails with altPos
by Visvaldas Kairys 24 Jun '17

24 Jun '17

Dear Chimera users and developers, I’d like to point out I often have a minor inconvenience when dealing with high resolution Xray structures when trying to add hydrogens via DockPrep. If two consecutive residues have both alternative postions A and B, Chimera in the process of hydrogen addition often gets confused and puts “TER” between the residues, also reporting non-integer charges in the log. I think what is happening, the program picks “A” variant for one residue and “B” for the consecutive residue, and apparently this causes bond detection algorithm to ignore the bond between the residues (due to length I guess). I resolve this by manually editing out one of the AltPos (say, “B”) out of the PDB file for the offending residues, but I guess the program should be able to do it automatically. A PDB example where this happens is 2r3i (or 2r3r). Best regards, Vis

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strand inside and edge color
by Kyle Morris 23 Jun '17

23 Jun '17

Dear Chimera dev, Sorry if I missed this in the documentation and online… Is it possible to make the inside and side edges of strands a color independent of the models coloring? Akin to using ribinsidecolor white to color the inside of helices white, I would like to color the inside and side edges of strands white. Thanks for your help as always! Best wishes, Kyle

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suggestion: data mode
by Dougherty, Matthew T 23 Jun '17

23 Jun '17

would be helpful to display data mode (byte, float, etc) on the volume viewer panel, approximately in the same location as origin index, voxel size, etc. For mrc files I can dump the header and pick thru it, for other formats the method is not so clear. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Measuring Distances in the Reciprocal Space Transform
by Martin Lawrence 23 Jun '17

23 Jun '17

Dear Chimera Users, I would like to measure the reciprocal space distance between features in the fourier transform of my map. Can anyone give me a hint as to the easiest way to do this? Thanks, Martin Martin Lawrence Department of Chemistry and Biochemistry Montana State University Bozeman, MT 59717 USA

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Please Help Me: Vina Tool Error in Chimera:
by Sarah Qassem Azzam 22 Jun '17

22 Jun '17

Dear Chimera help desk, Hope this email finds you well. I am facing a problem with Vina Tool in Chimera, while running molecular docking. I got the following error message: "\Program Files\The Scripps Research Institute\vina.exe"' is not recognized as an internal or external command, operable program or batch file. ---- Application stdout ----- [no output] I did install Vina, and I am trying to run it in Chimera using 'Local' option for executable location. Can you please advise on how to solve this issue? Your time is highly appreciated. Kind regards, Sarah Azzam

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Selecting only protein surfaces programmatically
by Ashton Omdahl 20 Jun '17

20 Jun '17

Chimera friends- I am creating a python script to take the sum of the distance from every atom in a given zone around selected residues to the surface of the protein. As part of this, I would also like to calculate the minimum distance to the surface of any given atom (based on the current surface rolling ball radius algorithm). However, I have been unable to find a command to select only the surface of a protein that works consistently across interfaces. What commands could I do this with both programmatically (in python) and in the GUI command line? Thanks! Ashton

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Installing Chimera and ChimeraX on a CentOS box without root
by Healey, Joe 20 Jun '17

20 Jun '17

Hi Chimera team, I need to install chimera and chimeraX on a server with a GPU which I now have access to assist in visualising larger structures, but I don't have any root privileges. After the first pass installing both, Chimera 1.11 gives me this warning/error when attempting to run: "OpenGL misconfiguration detected. /usr/lib/libGL.so.1 differs from /usr/X11R6/lib/libGL.so.1" And when I close this dialogue box, I get this: "Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 717 Current serial number in output stream: 718 libxcb: WARNING! Program tries to lock an already locked connection, which indicates a programming error. There will be no further warnings about this issue." ----------- And when running ChimeraX for the first time, I get this: " ChimeraX: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ChimeraX) ChimeraX: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cold/chem/msrnbi/bin/chimerax/bin/../lib/libpython3.6m.so.1.0) ChimeraX: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by /cold/chem/msrnbi/bin/chimerax/bin/../lib/libpython3.6m.so.1.0) " Evidently I need 2 different versions of GLIBC for ChimeraX, but assuming I can install these concurrently without root access, how would I go about telling ChimeraX where to look for the libraries? Any advice/documentation you have to get the programs working would be much appreciated. Joe Healey M.Sc. B.Sc. (Hons) MSRB 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> | ORCID: orcid.org/0000-0002-9569-6738

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alter to periodic box
by paul buscemi 17 Jun '17

17 Jun '17

I was experimenting with mixed solvents and found that if you create a box around a molecule say 10A on a side, then de-select "remove solvent" and then create a second box, say 2A on a side, that second box forms around the first. You can then constrain the second box which will for the most part retain the first and the parent molecule during a simulation. This allows visualization of the live trajectory as well. I used MON around water and he process is faster to create than selecting the six outside surfaces of a solvent box. Paul

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Question about Chimera
by Shabnam Nadjafi 17 Jun '17

17 Jun '17

Dear Manager I have a question about "Chimera". Is " "Chimera" free ? Can this program be used without license and complete freely? Thanks, Sincerely Yours, Shabnam Nadjafi

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Re: [Chimera-users] Run procedure
by Elaine Meng 16 Jun '17

16 Jun '17

Hi Paul, (1) please send questions to the chimera-users address, CC’d here. Questions sent just to me may fall through the cracks. (2) all I know about the Molecular Dynamics Simulation tool, I have written in its documentation. You can see it by clicking the Help button on the dialog or viewing the copy at our website: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html> See the sentence containing “clicking Run” about 1/3 of the way down and the last sentence in the page starting with "After the completion of any MD run…” I am guessing that you chose the recording option in the MD Movie dialog. If you are not sure which data it is showing, Quit from the MD Movie dialog. Then from the Tools menu, restart MD Movie and specify the specific MMTK input (trajectory) file that you want, like we discussed earlier. Although I said earlier that if you gave the same output name for both equilibration and production, the production might overwrite the equilibration, I’m no longer sure about whether it overwrites or just gets added to the end. However, you should be able to tell by the number of frames in the output trajectory. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 16, 2017, at 12:03 PM, pbuscemi <pbuscemi(a)q.com> wrote: > > Elaine, > > In doing a simulation, does it matter which screen is used to select "RUN" ie, minimize, equilibrium,production, or other. > > i.e If I select equlibrium, is production also run ? When a movie is recorded, is it from equilibrium or production portion ? > > thanks > Paul > >

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structureViz Path problem
by sriram raghavan 16 Jun '17

16 Jun '17

Dear Sir, I find it difficult to troubleshoot the path setting problem, which I am facing while operating with the structureViz plugin. Please kindly help me in installing the app. I have set UCSF chimera path as below but still i am not able to save the setting if default setting is the problem.[image: Inline image 1] I get the following error. [image: Inline image 2] With Regards S.Sriram Ph.D. Research Scholar CAS in Crystallography and Biophysics University Of Madras Mail:hypowergravity@gmail.com

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Re: [Chimera-users] Generate the tranfromation or bio matrix from the docking complex using Chimera
by Elaine Meng 15 Jun '17

15 Jun '17

> On Jun 14, 2017, at 9:35 AM, Elumalai Pavadai <epavadai(a)fiu.edu> wrote: > > Dear Meng, > > I have a cylindrical symmetry protein complex modeled with the protein-protein docking. Since the docking complex is very big in terms of size and number of atoms, I would like to generate the transformation matrix from it. Using the matrix , I can be able to generate the complex with Chimera. So, my question is that how to generate the transformation matrix from the protein complex with Chimera? > > Thank you, and I look forward to hearing from you. > > Kind regards, > Elumalai Dear Elumalai, I’m CC-ing chimera-users(a)cgl.ucsf.edu … it is the recommended address for Chimera questions, to ensure you get a response and allowing others to make suggestions. I’m guessing that you mean your large complex is several copies of the same protein, arranged in some symmetrical way, and instead you would like to have a file with only one copy but also the matrices describing the whole thing. If you had such a file, you could open it in Chimera and then generate the whole thing from the matrices. However, Chimera does not have the tools to go in the opposite direction, to figure out all the matrices from the whole complex. So if I understood your problem correctly, you would need to find some other program to do this. I haven’t done it myself, so I don’t know what you could use. If your protein-protein docking program created this symmetrical structure, maybe it can output the needed matrices. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Smooth "Rocking" Loop Movie
by Andrew Oliver, II 14 Jun '17

14 Jun '17

Dear Chimera, I am trying to create a "rocking" movie of a molecule that will continuously loop. I am using the command: movie record; rock y 10 68; wait; rock y -10 68; wait; movie stop; movie encode However, when I do this, there is always a slight pause at the end of the movie, before it starts the next loop -- which means it doesn't loop smoothly. Is there a way to create the movie so that there will be no pause before each successive loop? Many thanks, Andrew Oliver

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region bounds for pdb
by Edoardo D'Imprima 14 Jun '17

14 Jun '17

Dear Chimera users, I find very handy the function “Region bounds” to cut the EM maps in order to better visualise some part of the volume. I was wondering if there is an equivalent for PDBs. Many thanks in advance, Edoardo --------------------------------------------------- Edoardo D'Imprima PhD Student Max Planck Institute of Biophysics Structural Biology Department Max-von-Laue Straße 3 60438 Frankfurt am Main Germany Tel: +49 (0) 69 6303 3015

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Files generated by UCSF Chimera as .MRC format do not open with AMIRA 5.3.3
by Savriama, Yoland F 13 Jun '17

13 Jun '17

Greetings, I am a researcher working at the University of Helsinki (Finland) and I have used the software UCSF Chimera to process 3D CT-Scans data. I saved the process files as a single .MRC file. When I tried to open it with Amira 5.3.3 it displays the following error message: "No valid licence found for extension Amira Microscopy Option 5.3 Please contact us". The console also says "Access denied for 'readMRCFileStack'" I thought that Amira could read these standard .MRC files? Could it be there was an issue during the file export with Chimera? Best wishes, Yoland Savriama, PhD P/O Jernvall Institute of Biotechnology P.O. Box 56 (Viikinkaari 5) FIN-00014 FINLAND

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Helix represented as sheet, dispite best efforts
by Matthias Vorländer 13 Jun '17

13 Jun '17

Hi everyone, for some reason, chimera displays one helix in a structure as a messed up beta sheet. I am attaching the PDB file and an image (same structure as backbone and ribbon representation). I have tried adding HELIX records manually, ksdssp or the setattr command, but the result is always the same. I would be very grateful for suggestions what could be causing this problem, as I will have to remake all my figures in pymol otherwise (which displays the helix correctly). Many thanks Matthias Vorländer PhD student EMBL Heidelberg - Müller Lab Meyerhofstraße 1, 69126 Heidelberg

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sphere transparency
by Thomas Pochapsky 12 Jun '17

12 Jun '17

Is there any command corresponding to surft (surface transparency) that will modulate the visibility of a sphere representation of a ligand? I want to change it in the course of a morph between substrate-bound and substrate free forms of the same enzyme. I will probably have other questions, but this seems like a good place to start... Thanks, Tom Pochapsky

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Re: [Chimera-users] Axis Of Symmetry
by Elaine Meng 09 Jun '17

09 Jun '17

Hi Catherine, Please send Chimera questions to chimera-users(a)cgl.ucsf (CC’d here) to ensure a response. This "measure rotation” command does not use any atoms, it merely reports how a model is currently rotated and translated relative to the another model. The rotating/translating is done by the matching command before that measurement. From our previous emails I see you were using the “matchmaker” command (same as “mmaker”) which, as described in the manual, uses only CA atoms: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html> If you want to use other atoms in the fitting, you have to instead use the “match” command with the specific atoms given in the command. See the manual: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html> See also the page on “Superimposing Structures” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> and for a specific example, the “Matching” section in the Glycoside Hydrolases tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 9, 2017, at 12:02 PM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu> wrote: > > Hi Elaine, > > Can you tell me how Axis is configured? after using the command measure rotation, it gives me the reply log with information like axis, axis point, rotation angle etc., But I want to know specifically if Axis is calculated by just using the CA atoms of the chains or All atoms? Is there a way to find axis only using CA/All atoms. > > Thanks, > Catherine > > On Tue, Jun 6, 2017 at 4:33 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Catherine, > (Cc’ing chimera-users(a)cgl.ucsf.edu which is the recommended address for Chimera questions) > > As the message suggests, your models #0 and #1 are not rotated from each other. I’m guessing that you opened the same dimer structure twice and then matched it to itself. For example, if your structure contains chains A and B, it sounds like A was matched to A and B to B, so there was no rotation (zero degrees). You have to make sure that the matching is A to B and B to A. To do this with the “mm” command, for example, you would have to specify the chains AND use the “pair ss” option. > > There is a specific example of commands for structure 5hvp in this previous post. > <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-April/013290.html> > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > On Jun 6, 2017, at 1:22 PM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu> wrote: > > > > Hi Eric, > > I am trying to find Axis of Symmetry in Dimers. I executed mm command, and then tried to execute measure rotation #0 #1 command. It throws me an error: > > > > <image.png> > > > > I am using chimera version 1.11.2. Can you please help me with this? > > Thanks, > > Catherine > >

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model recordings
by P. Buscemi Ph.D. 08 Jun '17

08 Jun '17

Dear Users groups. I've been struggling with this issue for some weeks. I will describe the problem and then as what information I should supply to help me solve the issue. It's a prototype adsorption experiment. Water onto polyethylene oxide. Each component, when run individually in a simulation will complete in a normal fashion with a good recorded video. All simulations were run with live presentation. However when the two models are run together, the story is different. The sequence below represents 1) the two loaded files ( water and PEO) 2) the PEO selected for later constraint ( control drag) 3) moving the water into positon. At this state the " live" simulation aappears normal. The peo does not move, and the water more or less jiggles into position on the PEO. However, in running the movie, molecules of the PEO are disrupted (4) and occupy the space in fragments originally occupied by the water molecules when it was first loaded. The same phenomenon occurs with a PE surface and with models of EtOH. The temperature is set to 0->100K, Hydrogents added Gasteiger charge calculation, 0 charge total, no periodic box. Again, I do not expect any suggestions ( although none would be refused !) only to ask the proper channels and information needed to approach the issue. Regards Paul Buscemi cid:image002.jpg@01D2DED8.C01C06501 cid:image001.jpg@01D2DED8.C01C06502 cid:image002.jpg@01D2DED8.64FCD8803 cid:image003.jpg@01D2DED8.64FCD8804

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PDB file opens from chimera GUI but not from python script ( )
by Nikolaos Bismpikos 07 Jun '17

07 Jun '17

Hello, I am having a problem with trying to open a .pdb file using a python script. The file opens and the protein structure is displayed properly when I open the file using the Chimera GUI. However, when I try to run the code from a python script, using the demo script for looping through .pdb files I get the following error: ---------------------------------------------------------------------- File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 251, in _compile raise error, v # invalid expression ---------------------------------------------------------------------- This is the code I am trying to run: ---------------------------------------------------------------------- import sys import os from chimera import runCommand as rc # use 'rc' as shorthand for runCommand from chimera import replyobj # for emitting status messages # change to folder with data files os.chdir("/home/nick/Python/pdb") print >> sys.stdout, retval # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # loop through the files, opening, processing, and closing each in turn for fn in file_names: replyobj.status("Processing " + fn) # show what file we're working on rc("open " + fn) replyobj.status("Opened " + fn) # show what file we're working on rc("align ligand ~ligand") # put ligand in front of remainder of molecule rc("focus ligand") # center/zoom ligand rc("surf") # surface receptor rc("preset apply publication 1") # make everything look nice rc("surftransp 15") # make the surface a little bit see-through # save image to a file that ends in .png rather than .pdb png_name = fn[:-3] + "png" rc("copy file " + png_name + " supersample 3") rc("close all") ---------------------------------------------------------------------- The error in more detail, including the traceback from the terminal is the following: ---------------------------------------------------------------------- Processing prediction[NoEnergy-K:0-BS:0.00]-21(20.310186).pdb Traceback (most recent call last): File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimeraInit.py", line 683, in init chimera.openModels.open(a, prefixableType=1) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1929, in open models = func(filename, *args, **kw) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1299, in _openPython loadFunc(sandboxName, fileName, f) File "test1.py", line 23, in <module> rc("open " + fn) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 2747, in runCommand makeCommand(*args, **kw) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py", line 1552, in doOpen paths = testPath(text, wildcarding) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py", line 1538, in testPath return glob(expanded) File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py", line 27, in glob return list(iglob(pathname)) File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py", line 49, in iglob for name in glob1(os.curdir, basename): File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py", line 83, in glob1 return fnmatch.filter(names, pattern) File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/fnmatch.py", line 56, in filter _cache[pat] = re_pat = re.compile(res) File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 194, in compile return _compile(pattern, flags) File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 251, in _compile raise error, v # invalid expression error: bad character range Error while processing test1.py: error: bad character range File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 251, in _compile raise error, v # invalid expression See reply log for Python traceback. ---------------------------------------------------------------------- The error obviously appears at the 2nd line of the for loop ( rc("open " + fn) ) Any tips on why this might happen? I am using Ubuntu 14.04 LTS and the Chimera version I installed is chimera-1.11.2-linux_x86_64.bin

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