- Chimera-users - RBVI Mailing Lists

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>

3 2

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

1 0

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

17 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

4 4

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

2 2

Chimera Dowload
by Lance Patten 14 Jul '17

14 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.

3 5

http download links are insecure
by Yuri 13 Jul '17

13 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

2 1

rainbow with atom-spec of a portion of a chain
by Cheng, Micah 13 Jul '17

13 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.

2 1

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.

3 3

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

3 2

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.

3 5

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

2 1

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

2 2

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.

2 2

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.

2 1

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

4 5

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

2 2

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

2 5

software for protein 3D structure visualization
by fateme shaki 07 Jul '17

07 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

2 2

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.

3 2

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

3 4

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 .

1 0

Difference between Chimera and ChimeraX
by Bon Ikwuagwu 26 Jun '17

26 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

5 4

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

1 0

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

2 1

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!

2 1

DockPrep sometimes fails with altPos
by Visvaldas Kairys 23 Jun '17

23 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

2 2

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

2 2

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 ================================================= =================================================

2 1

Measuring Distances in the Reciprocal Space Transform
by Martin Lawrence 22 Jun '17

22 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

2 1

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

3 3

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

2 1

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

2 2

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

1 0

Question about Chimera
by Shabnam Nadjafi 16 Jun '17

16 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

2 2

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 > >

2 1

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

3 3

Re: [Chimera-users] Generate the tranfromation or bio matrix from the docking complex using Chimera
by Elaine Meng 14 Jun '17

14 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

2 2

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

2 1

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

3 2

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

3 4

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

2 2

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

2 4

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 > >

1 0

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

3 4

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

2 1

Axis Of Symmetry
by Catherine Jenifer Rajam Rajendran 06 Jun '17

06 Jun '17

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: I am using chimera version 1.11.2. Can you please help me with this? Thanks, Catherine

2 2

measure surface area
by 陈柳青 06 Jun '17

06 Jun '17

Hi! i want measure several selected residues surface area and volume, but in the reply log, it always give the total surface area and volume of the protein, how can i get only the selected residues surface area? because this residues make a cavity , which may binding substrate. in addition, the castP server can't give me the pocket i wanted, because it give a bigger pocket than i wanted. thanks in advance！ liuqing chen -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

2 1

extracting real numerical values for steric energies
by Fenton Heirtzler 05 Jun '17

05 Jun '17

Hello, I'm using Chimera to optimize the structures of several small-molecule transition metal complexes. The goal is to compare the steric energies of different diastereomers. I 've searched the local documentation on version 1.11.2 (Macintosh) for the term "Minimize structure" but found nothing which actually described the meaning,number format, reference points and units which are produced by the "Minimize Structure" command and appear in the "Reply log". For example, the potential energy values which are returned can be either < 0 or > 0 (!!) If a minimization is occurring, then the force field will describe those parameters - but the preceding values make no sense. Some advice and instruction would be appreciated. Thanks *Dr. Fenton Heirtzler* ------------------------------- Phone: +1-301-312-5145 LinkedIn <http://www.linkedin.com/in/fentonhorgchem/>

2 2

Chimera files to be read in Pymol?
by Tuli Mukhopadhyay 05 Jun '17

05 Jun '17

Hello, Is there a (simple) way to read Chimera session in Pymol or vice versa? Tuli -- -- Tuli Mukhopadhyay Department of Biology Indiana University Simon Hall MSBI, Room 220C 212 S. Hawthorne Drive Bloomington, IN 47405-7003 Phone 812.856.3686 Fax 812.856.5710 sumukhop(a)indiana.edu | Tuli Lab Webpage <http://www.bio.indiana.edu/~tulilab/> | @TuliLab <https://twitter.com/TuliLab>

2 1

Re: [Chimera-users] Chimera how to question
by Elaine Meng 05 Jun '17

05 Jun '17

> On Jun 5, 2017, at 5:59 AM, Egor Tchesnokov <tchesnok(a)ualberta.ca> wrote: > > Hello, > Is there a way to delete a set of residues in the beginning of the sequence, so these residues disappear from the sequence in the pdb file? > I am working on the structure-base alignment and the exogneous residues in the protein sequence (eg. affinity-tag) interfere with the nubmering of the endigenous residues. > Thank you > Egor Hi Egor, Of course you can delete atoms. You can select them and then use menu: Actions… Atoms/Bonds… delete, or you can use the “delete” command ...either with selection (delete sel) or with some other kind of specification of what you wanted to delete, e.g. delete :1-20.A ...to delete residues 1-20 of chain A. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html> Maybe in your case it would be easiest to use the sequence window (Favories… Sequence) to select the set of residues you want to delete by dragging a box around them, and then using the menu or command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html> However, this will not change any sequence numbering. Chimera just uses the numbers that are in the input file. Sometimes but not always, affinity-tag residues are given negative residue numbers in the input file. If you want to renumber residues, see menu: Tools.. Structure Editing… Renumber Residues, or the command “resrenumber”: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/renumber.…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/resrenumber.html> Chimera questions should be sent to chimera-users(a)cgl.ucsf.edu (CC’d here) to ensure that they will be answered. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

failure to add-H to quaternary C
by Francesco Pietra 05 Jun '17

05 Jun '17

pdbqt from autodock-vina -> pdb with chimera -> addH with chimera. Chimera fails (systematically) to add one H to a quaternary carbon of the diterpenoid. avogadro (which does not understand pdbqt) does the addH job correctly from chimera-savedpdb. Should Eric be interested, I could send (privately) the file best regards francesco pietra

2 1

surfaces
by P. Buscemi 01 Jun '17

01 Jun '17

Elaine, A conceptual question. I'm trying to work with surfaces - large flat surfaces that proteins and polymers might adsorb. Think fibrinogen on medical devices. Chimera does not seem to like large surfaces in box. IF a portion of the surface slips outside the box, it goes to the other ( abnormal side). Constraining a portion of the surface does not help. Constraining all of the surface has not been tried. I'd like to use a box to keep the solvent and protein local. Any suggestions on how to handle this, or point me to a URL ? Can I constrain only in two directions perhaps ? or use a box size 30,30, infinite ? Best Paul Buscemi, Ph.D.

2 5

addaa
by ‪farial tavakoli‬ ‪ 31 May '17

31 May '17

hi I am new chimera user. I wanna add an amino acid before the lys 12 in N-ter of my protein sequence but i dont know how should i type its command. I read the tutorial but just found adding an amino acid in C-ter. is there anyone who ca help me? I would be grateful if anybody helps me in the new residue's conformation ? thanks alotF.T

2 1

membership
by P. Buscemi 31 May '17

31 May '17

Dear Chimera, I had registered as a member, but when I send or even return emails, I get placed on "hold till approved" waiting list. Can this be corrected ? Regards, Paul Buscemi, Ph.D. UMN

2 1

Re: [Chimera-users] Help in docking with Chimera
by Elaine Meng 30 May '17

30 May '17

Hi Zahir, It might just be display (like one bond not shown) without any affect on the calculations because of the format of the file output by Autodock Vina. Autodock Vina is not our program, so we cannot control the output format. However, impossible for us to tell if that is the issue unless you send us an example file or files. You could use menu: Help… Report a Bug and include brief explanation and your email address and attach the example file or session that shows the problem. Keep in mind it might not be a Chimera bug. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On May 25, 2017, at 1:13 PM, Md Zahir Uddin <m_uddin(a)u.pacific.edu> wrote: > > Hi, > We are seeing a new problem in the docking of our peptides. After docking of our peptides using Autodock Vina function in Chimera, we are seeing in the output that the peptides are broken (splitting into two parts) at the protein's binding site. Our peptides are 8 amino acid long (one is 5 amino acid cyclic peptide by disulfide bond) and we prepared the peptides using the Build Structure function in Chimera and then dockprep & minimize structure. > Can you please help me in this? We would really appreciate your help. > Thanks, > Zahir >

1 1

it might be nice to have the code on github
by Francois BERENGER 30 May '17

30 May '17

Hello, Sometimes, I want to dig into the source code of chimera, to know the implementation details of something. For projects hosted on github, this is easy. Also, in my experience, github fosters contributions from users. That being said, I did not use chimera for 2/3 years. I am glad to see that it is even more powerful and easy to use than before. The tutorials are also excellent (like: Preparing Molecules for DOCKing) and the .bild format that chimera can read in is extremely programmer friendly (it is so easy to generate). My love for chimera (over pymol) is renewed. Regards, Francois.

2 1

high resolution animation in chimera
by Gangwar, Shanti P. 26 May '17

26 May '17

Dear Chimera Developing team, I am trying to make an animation using chimera. But it looks like that the animation output is poor quality, seems less dpi. How to get a high resolution animation, say 300 dpi, suing chimera? Thank you very much, Shanti Pal ******************************************** Shanti Pal Gangwar, Ph.D Dept of Pharmacology and Toxicology University of Texas Medical Branch Galveston, Texas-77555 Mobile: +1-409-256-8400 Email: spgangwa(a)utmb.edu

5 8

custom presets not appearing
by Healey, Joe 26 May '17

26 May '17

Hi Chimera Team, I've defined a custom preset (implemented in both python and 'chimera language'), and I've placed in a folder which I have directed the custom preset dialogue to. E.g, in /Users/joehealey/Documents/Warwick/PhD/Structural_Work/Scripts/Presets/ I have the following script (chimera implemented one): # Goodsell.cmd ############################################################# # # # Chimera syntax commands for use as a preset. Sets the # # depiction in the style of David Goodsell. # # (The PDB Molecule-of-the-Month style). # # # ############################################################# # Create lower resolution surface models: sym surfaces all resolution 2 # Hide dashed bonds that may appear though the surface setattr g display false # Apply silhouette edging and colouring set silhouetteWidth 3.5 set silhouetteColor black set silhouette # Set depth cueing depth and colour set dcColor black set dcStart 0.5 set dcEnd 1.5 # Set background transparency set bgTransparency # Set lighting mode for flat rendering lighting mode ambient # Hide ribbons ~ribbon # Set surface colour color red ,s # Make sure molecule is in focus focus However, as per the documentation ( http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets ) the preset doesn't appear in the presets menu. I can execute the script as normal with exec, and it works and has the desired effect, but I'd like it to be in the preset menu if possible? I suspect I'm missing something? Thanks, 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

2 2

Non-canonical H-bonds
by Markus Heller 25 May '17

25 May '17

Hi, Are there any plans to extend the H-bond detection functionality to include non-canonical H-bonds, e.g. C―H...A (A = N, O, S), D―H...π (D = N, O) and C―H...π varieties? Thanks Markus

2 2

Surface function question
by Frances Shepherd 25 May '17

25 May '17

Hi, I am modeling a rotavirus VP7 protein using Chimera (PDB 3fmg), and I’m having trouble with the surface function. This protein is modeled with a monoclonal antibody conjugated to it, which I am able to hide. But when I show the surface for just the VP7 protein, there are gaps in the surface. The gaps appear to be in the areas where the VP7 protein comes into contact with the antibody. Is there a way to fill in these gaps? I’ve seen other publications that have used this protein (same PDB number), but the surface is complete. If you have any suggestions, I’d appreciate it. Thanks! -Frances

2 1

Input from Avogadro, solvation.
by Paul Buscemi 23 May '17

23 May '17

Dear Chimera, Three basic questions: I’m using Avogadro to construct my models and import as mol2 or pdb types. I often obtain messages as or that the atom is not “listed” . Is there a preparation I can use for transfer of models ? Alternatively do you suggest any other program to construct models ? 2) If I use Tools to solvate a model, should I use the “Start solvate tool” under MD and/or check “Periodic Boundary Conditions. 3) Im considering building a multicore system ( two 16 core Xeon’s) as a 64 bit system would Chimera take advantage of the multi-core system ? Would the upgrade funds be better spent on memory ? Regards, Paul Buscemi, UMN BICB

4 9

ImportError: libGL.so.1: cannot open shared object file: No such file or directory - Error shown when trying to run xdg-setup or chimera (Linus Ubuntu)
by Hannah Goldberg 23 May '17

23 May '17

Hello, I have installed the 32 bit version of Chimera-1.11.2, and I am having difficulty getting the icon on the desktop and launching. I get the following error: ImportError: libGL.so.1: cannot open shared object file: No such file or directory I have tried installing the libgl1-mesa-glx package and have even tried Idconfig. I can't find any errors similar to this anywhere. Please help! I can give more info if needed - I will be at my desk all day trying to install this Icon! -Cheers, Hannah -- *Hannah Goldberg* Case Western Reserve University Class of 2019 Physics B.S. Geological Sciences B.S. Undergraduate Research Assistant- Theoretical Biophysics

2 1

FW: chimera download
by Williams, Joanne 23 May '17

23 May '17

Here is another inquiry for user help. From: bushra TAJ <bushraistaj(a)gmail.com<mailto:bushraistaj@gmail.com>> Date: Thursday, May 18, 2017 at 10:53 PM To: Joanne Williams <Joanne.Williams(a)ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> Subject: Re: chimera download Hello Sir will you please guide me for one more thing, I got pdb of my protein and have Autodock installed in my PC. I have 6 derivatives that I synthesized myself, can I load chemdraw.cdx file in chimera to prepare it for docking and finally safe it in Mol2 format??? What format I can take of my ligand to load in Chimera?? On Fri, May 19, 2017 at 9:50 AM, bushra TAJ <bushraistaj(a)gmail.com<mailto:bushraistaj@gmail.com>> wrote: My full name is Maria Taj Muhammad and I am doing PhD at Karachi University Chemistry department in Karachi city of PAKISTAN. is that OK Regards On Thu, May 18, 2017 at 7:41 PM, Williams, Joanne <Joanne.Williams(a)ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> wrote: Hello, Apologies, I was waiting to hear back from you. Please send me the following information: 1. Full Name: 2. School Name or company name that you are affiliated with: Thank you, JoAnne From: bushra TAJ <bushraistaj(a)gmail.com<mailto:bushraistaj@gmail.com>> Date: Wednesday, May 17, 2017 at 10:35 PM To: "Williams, Joanne" <Joanne.Williams(a)ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> Subject: Re: FW: chimera download Hello Sir I know I am disturbing you, but I asked for Chimera free trial (if possible). waiting for your kind response On Thu, May 11, 2017 at 8:12 PM, Williams, Joanne <Joanne.Williams(a)ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> wrote: Ok, let me know which school you are affiliated with and I will see about getting you access. Thank you, JoAnne From: bushra TAJ <bushraistaj(a)gmail.com<mailto:bushraistaj@gmail.com>> Date: Thursday, May 11, 2017 at 2:28 AM To: "Williams, Joanne" <Joanne.Williams(a)ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> Subject: Re: chimera download I am associated with a school and need for my project (that small work that I am left with. Any chance? On Wed, May 10, 2017 at 8:23 PM, Williams, Joanne <Joanne.Williams(a)ucsf.edu<mailto:Joanne.Williams@ucsf.edu>> wrote: Hello, Thank you for your inquiry. I am sorry, we do not offer a free trial period. Are you affiliated with a school or company? Thank you, JoAnne From: bushra TAJ <bushraistaj(a)gmail.com<mailto:bushraistaj@gmail.com>> Date: Monday, May 8, 2017 at 1:22 AM To: "chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>" <chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>> Subject: chimera download Hello Sir Can I download chimera as free trial on my laptop. windows 7, 500GB, 32bits???

3 4

Re: [Chimera-users] question about report of hydrogen bonds that Chimera produces
by Elaine Meng 22 May '17

22 May '17

> On May 22, 2017, at 2:43 PM, Roberto Garza-Lopez <RAGL4747(a)pomona.edu> wrote: > > Hi Elaine, I saw your name in the chimera group in a conversation on line and I was wondering if I can ask you a very simple question. > > I used FindHBond under Structure Analysis to generate the document with all the hydrogen bonds for protein PDB# 1aac (amicyanin). See attached. > > I noticed that for some H bond distances the report includes both A---B and B---A like in the cases below which of course have the same distance. > > <image001.png> > <image002.png> > > <image003.png> > <image004.png> > > However for other cases like the one below, I do not find the reverse, meaning LEU 80.A O à VAL 43.A N. WHY IS THAT? > > VAL 43.A N LEU 80.A O no hydrogen 2.815 N/A > > Thanks, > Roberto Hi Roberto (CC-ing chimera-users(a)cgl.ucsf.edu , recommended address for Chimera questions) It is because the lines list H-bond donor before H-bond acceptor. Some groups can be both donor and acceptor, but some groups (like carbonyl O) can only be acceptors, and some can only be donors. The results include a title row which explains what the columns mean. For example, opening 1aac and running findhbond gives: #0, chain A: amicyanin 1aac opened Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: #0 1aac H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): ASP 1.A N HOH 297.A O.1 no hydrogen 3.132 N/A ASP 1.A N HOH 297.A O.2 no hydrogen 3.093 N/A ASP 1.A N HOH 297.A O.3 no hydrogen 3.360 N/A LYS 2.A N LEU 62.A O no hydrogen 2.776 N/A [… etc. …] 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

1 0

Some questions about the software
by Lizar wang 22 May '17

22 May '17

Good morning, When I open Chimera11.1.2, it shows that" Chimera existed abnormally; the exit code is 1. Use the -- debug command line option for the full error message." What should I do? I cannot see the interface, just this error window.Thank you. User 发自我的 iPhone

2 1

FW: UCSF CHIMERA
by Williams, Joanne 22 May '17

22 May '17

Hello, I am not sure if you already responded to this email below or if I forwarded it even. Just in case, please read below. Thank you, JoAnne From: Manjunath gl <glmanjunath.iitm(a)gmail.com<mailto:glmanjunath.iitm@gmail.com>> Date: Monday, May 15, 2017 at 11:02 PM To: "chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>" <chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>> Subject: UCSF CHIMERA Hi Please let me know can I use this software for geomaterial modeling? Thanks Dr. Manjunath

3 2

Using vop to cover a whole molecule
by Pradeep Pallan 22 May '17

22 May '17

Hi All, I would like to know how to extend an e-density map in y or z direction. Here is my case: The DNA structure that was refined in shelx. Model #0 is DNA and the e-density map is model #1. When I used vop cover #1 atom #0, the electron density covers the molecule along two axes, and for the third axis it covers partly. How to extend the e-density map in a particular axis? Thank you! -- ------------------------------------------------------------------- Pradeep Pallan

2 3

Open a file with Windows 10 Command Prompt
by Mark F Rosenberg 20 May '17

20 May '17

For Mac in Terminal I can type Chimera and the file name to open a volume etc which is very useful. In Windows 10 for Command Prompt Terminal I cannot seem to achieve this. I thought if I added "open" after the executable I could achieve this but it does not appear to work. Please can you advise? Many thanks. Mark

4 3

Re: [Chimera-users] Help in docking with Chimera
by m_uddin 19 May '17

19 May '17

Hi Dr. Elaine, Got it. It worked. Thanks a lot. Zahir -------- Original message --------From: Elaine Meng <meng(a)cgl.ucsf.edu> Date: 5/19/17 1:01 PM (GMT-08:00) To: Md Zahir Uddin <m_uddin(a)u.pacific.edu> Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Help in docking with Chimera Hi Zahir, Based on the error message, all I can suggest is to make sure that the location for output files is somewhere you have permission to write and read files. I.e in the Autodock Vina dialog, there is an “Output file” box. Next to it is a button “Browse” which you should click and then navigate in the resulting dialog to set the location to some folder in which you are sure that you have permission to read and write files. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.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 > On May 19, 2017, at 11:46 AM, Md Zahir Uddin <m_uddin(a)u.pacific.edu> wrote: > > Hi, > My name is Zahir. I am a Ph.D. student of Pharmaceutics at University of the Pacific. Recently in our lab we were trying to do some docking of our peptide ligands on the human Aminopeptidase N (CD13) receptor using the Autodock vina option in the Chimera. But everytime we are getting an error message and the docking stops. I am attaching the error message here. We did dockprep of the receptor and ligands. And we tried to do the docking with both pdb and mol2 files. > > We would really appreciate your help in this regard. > Thanks, > Md Zahir Uddin

1 0

Help in docking with Chimera
by Md Zahir Uddin 19 May '17

19 May '17

Hi, My name is Zahir. I am a Ph.D. student of Pharmaceutics at University of the Pacific. Recently in our lab we were trying to do some docking of our peptide ligands on the human Aminopeptidase N (CD13) receptor using the Autodock vina option in the Chimera. But everytime we are getting an error message and the docking stops. I am attaching the error message here. We did dockprep of the receptor and ligands. And we tried to do the docking with both pdb and mol2 files. We would really appreciate your help in this regard. Thanks, Md Zahir Uddin <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 1

saving rotated volume
by Reginald McNulty 18 May '17

18 May '17

Dear Users, I have two objects open in Chimera. One is a .bild file that shows axes x,y,z. The other is a volume of a virus with a tail. I used “activate only” to manipulate the volume relative to the axis.bild object. After rotating the virus to align the tail to the Z-axis, I try to save the map but it’s always back in the original position when I re-open it in Chimera. Is there a way to save this transformed map? -Reggie

3 4

morphed conformation movie?
by esserlo＠helix.nih.gov 18 May '17

18 May '17

For this one, I found a solution: >Also is there a commandline version to access the conformations and to re-run >kdssp on each interpolated conformation? I read you need the perframe command >for that. Does anyone have a working example ? There is a good example (and several more) in http://www.cgl.ucsf.edu/chimera/animations/animations.html (for instance leucyl-tRNA.cmd ) However, I still don't know how to re-open a morphing menu that disappeared and the per-frame kdssp is not yet clear to me yet. Thanks, Lothar

2 2

morphed conformation movie?
by esserlo＠helix.nih.gov 18 May '17

18 May '17

Hi, I used Tools->Structure Comparison->Morph Conformations and it worked well. However, I somehow lost the menu that opens up after the morph is complete. Well, I cannot find it. How can you re-open it to run through the morphed conformations again ? Also is there a commandline version to access the conformations and to re-run kdssp on each interpolated conformation? I read you need the perframe command for that. Does anyone have a working example ? Thanks, Lothar

2 1

reading in electron density map H32 vs R32
by Christine Gee 17 May '17

17 May '17

Hi, I have a structure in the space group H32. I wrote out a map, which lists it as space group 155. I was wondering if chimera would read that in as space group H32 (R32:h) or as R32 (R32:r). Regards Christine

2 1

Open file interface suggestion
by Dan Kool 15 May '17

15 May '17

Hello, I have been using your software for a while. I love the features and general user interface. There is one thing that drives me nuts, though. The side-by-side list interface when I go to open files.A window-based one would be much easier. Is there an option for that that I am not seeing? If not, I suggest adding the option. Thank you for your software! Best, Dan ---------------------------------------------------- Daniel Kool Graduate Research Assistant, Jernigan Lab Bioinformatics and Computational Biology Iowa State University *kool(a)iastate.edu <kool(a)iastate.edu>*

3 3

error or bug
by Arthur Szabo 15 May '17

15 May '17

Continuing my earlier question. I tried the suggestions sent to me neither split nor surfcat seemed to work. After some attempts I received this window and reported the bug [cid:image001.png@01D2CD74.26A7D780] I then tried to use molmap and I did get a surface and saw how by moving the cursor in the molmap window I could get the surface to progressively disappear leaving the selected domains that were colored previously. The surface was for the entire protein, one of the models #0. I could also change the surface color. Then I went looking at some of the tabs on the molmap window and cannot describe the sequence, but ended up with another window that I eventually found out was for visualizing Cryo EM maps. Now I have a surface that is multicolored and looks like jelly beans. Somehow perhaps by selecting one of the models from the command lines, (#0) I was able to pull out a surface of the entire molecule, rotate it etc, and progressively remove the surface, til the selected domains remained. Stuck!!! This is one model: [cid:image003.png@01D2CD79.3D09E040] [cid:image004.jpg@01D2CD79.3D09E040] HERE IS ANOTHER which is #1 or #2 [cid:image005.jpg@01D2CD79.3D09E040] [cid:image006.png@01D2CD79.3D09E040] Arthur Szabo

2 4

Visualizing specific atoms in autodock-vina output
by Francesco Pietra 15 May '17

15 May '17

I am trying to investigate the protein surrounding a docked (autodock-vina, alpha chimera 1.1 build 40505 linux 64) ligand. I am interested in the environment of specific atoms of the ligand. With command sel #1.1@N z<5 I can investigate the protein at 5A from BOTH nitrogen atoms of model 1.1. How to select one of the two existing N atoms in the ligand? Same questions for other ligand atoms (there are many O-atoms) Is that possible without elaborating the vina output? thanks francesco pietra

4 8

Saving multiscale models only?
by Healey, Joe 12 May '17

12 May '17

Hi Chimera team, Is it possible to save a multiscale model without the atomic coordinates that generated it in the first place? I've seen that the multiscale models can be saved within Scenes, but I'd like to save it as a 'structure' such that I can continue to use it in subsequent sessions. At present, when I close the PDB model that generated the MultiScale map, the map also closes. 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

2 1

surface transparency animation
by esserlo＠helix.nih.gov 12 May '17

12 May '17

Hi, I am trying to animate a transition of a surface from 100% transparent to opaque. In a test (the real case is more complicated) I did this: open 1hen.pdb # Lysozyme test # Chimera shows a blue ribbon model on gray background surface #0 scolor #0 color green # chimera shows a green surface over a (now invisible) blue ribbon model # According to the manual the following (I think) should work: transparency 80,s #0 # I expected to see the green surface to become 80% transparent and the blue ribbon model to shine through. # No luck. What am I missing ? BTW the page https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/transparency… seems to be missing the last example concerning transparency of surface patches. Thanks, Lothar

2 3

scripting & density
by Dougherty, Matthew T 12 May '17

12 May '17

Hi, I have a dataset, its values are 1-255. I would like to modify the density values using a script. Specifically, I would like to set density values 50-74 & 90-110 to the value of zero. Is there a way to do that using scripting, or do I need to do that using python? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

2 3

surfaces
by Arthur Szabo 12 May '17

12 May '17

Working with a structure that has many domains. I would like to show the surface of three of the domains. I have hidden the ribbon residues of all but the ribbons of three domains. I receive the following error message [cid:image001.png@01D2CB26.2CA19B30] The domains are not contiguous in the structure, but even if I try to show the surface of only one domain I get the same message. And going to the Selection inspector is not helpful since it is not obvious as to how that option assists the surface representation. Over to you Thanks Arthur G. Szabo

2 1

vop scale and vop morph (maybe chimeraX?)
by Oliver Clarke 11 May '17

11 May '17

Hi, When I morph two maps, if they have different mean/sd, I always have to scale the mean and sd of the second map to that of the first, otherwise the morph looks very non-linear - nothing happens until fraction 0.9, and then the morphing happens increasingly fast (so not ideal for visualization). If I normalize one map to the other I get a beautiful, smooth, linear morph. Would it be possible in either chimera or chimeraX to automate this? Either to add an option to vop scale to scale one map directly to the parameters of another (rather than having to use vop measure mapstats) or to have an option for vop morph to put both maps on the same scale? Cheers Oli

2 1

suggestion: if clip planes cross, swap them?
by Oliver Clarke 11 May '17

11 May '17

Hi, Quite often, in aliases and scripts where I am adjusting the clip planes, I get the error “far clip plane placed in front of near clip plane”, or words to that effect. I’ve tried various ways to remedy this but it has to be done on a case by case basis and sometimes I just can’t figure it out. Would there be any possibility for Chimera to rather than triggering an error in such a case, just swap the clip planes when this happens, so the near plane becomes the far plane, and vice-versa? Or is there some other foolproof way to avoid this? I get this error when I want to adjust the hither and yon planes successively - would it be possible to add a command that adjusts them both at the same time, like `section` but with simultaneous independent control over both clip planes? Cheers Oli

2 1

morph map fails with solid representation
by Oliver Clarke 10 May '17

10 May '17

Hi, When I create (using the latest nightly build) a morph between two maps using the “Morph map” GUI, and then I change the representation of the resultant volume to solid, the morph no longer runs, or rather, it appears to run, but the solid volume does not update. This used to work - I used it to create quite a few movies - so I guess it is a bug? Cheers Oli

2 1

symmetrical fit of maps
by Oleksiy Kovtun 10 May '17

10 May '17

Hi all, is there is a way to do symmetrical fit and add symmetrical copies for map to map fitting? The standard symmetrical fitting protocol (measure symmetry. #0...; sym #1 group #0 update true; fitmap...) only works for molecule to map fit. Thank you, Oleksiy Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun(a)mrc-lmb.cam.ac.uk

2 1

translation and rotation in MATLAB using transformation matrices from chimera
by Oleksiy Kovtun 10 May '17

10 May '17

Dear all, I need to merge two maps in MATLAB using alignment data from chimera. Inputs: two maps of the same box size, origin. I use matrixget - to report translation and rotation matrices for the aligned map . Translation operation works well when transferred into MATLAB (briefly, translation matrix gets converted in eulers and pased on to tom_rotate command in MATLAB, TOM package). However the x y z translation coordinates (the fourth column top to bottom in matrixget - output) are way off the real translation when using tom_shift command in MATLAB, TOM. I found out that if I open the rotated map and fit it again, it gives close to correct translation matrix. What's going wrong here? Does anyone have a solution how to overlay 3D arrays in MATLAB using chimera-reported transformation matrices? Many thanks, Oleksiy Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun(a)mrc-lmb.cam.ac.uk Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun(a)mrc-lmb.cam.ac.uk

3 4

Multiple fitting of structures in to EM densities
by Healey, Joe 10 May '17

10 May '17

Dear chimera team, I have a large EM density I would like to fully populate with a number of copies of a protein. To be more specific, the EM density is of 2 concentric protein rings (EMDB-6720), and each concentric ring is stacked 3 or 4 times. Each ring is a hexamer, so I would like to populate every single ring with 6 copies of each protein (but the inner and outer rings are 2 different proteins). What would be the best mechanism to iteratively import a protein, populate an EM density space, then move on to the next one? Currently, I think if I was to simply open several copies of the protein, they would probably all try to fit within the same EM density position, leaving the rest of the structure empty? My apologies if this isn't totally clear, I've tried to explain it as best as I think I can. I'm happy to accept solutions in 'chimera language', python (or I also have Jaime's Pychimera installed). Many thanks 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

2 3

Re: [Chimera-users] Wire thickness
by Oliver Clarke 10 May '17

10 May '17

Hi Hernando, I used the ca_and_sidechains alias in this script (you should be able to get the individual commands from that). https://github.com/olibclarke/chimera-trimmings/blob/master/chimera_aliases… Cheers Oli > Dear Chimera > How do you set the thickness of the backbone and side chains independently to produce figures like the ones below (sorry I hijacked the picture used in blurred-display discussion). > > Thanks > > H.

3 2

Wire thickness
by Hernando J Sosa 10 May '17

10 May '17

Dear Chimera How do you set the thickness of the backbone and side chains independently to produce figures like the ones below (sorry I hijacked the picture used in blurred-display discussion). Thanks H. [cid:image001.jpg@01D2C8F6.BEA06B60][cid:image002.jpg@01D2C8F6.BEA06B60]

1 0

Re: [Chimera-users] Gaussian blur depth cueing? (ChimeraX)
by Tom Goddard 09 May '17

09 May '17

Before/after pair - at large size, I think the blur is helpful, but YMMV > On May 9, 2017, at 12:09 PM, Oliver Clarke <olibclarke(a)gmail.com <mailto:olibclarke@gmail.com>> wrote: > > Perhaps a better example: > > <brightness_blur.jpg> >> On May 8, 2017, at 10:07 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Oliver, >> >> The depth of field blur images I have seen of maps and molecules have all struck me as cool looking and less useful then conventional brightness based depth cuing. Brightness depth cue allows you to include more of the structure in back while reducing the obscuring effect it has on stuff in front. Blurring depth cue interferes much more with the stuff you want to be in focus. Your image minimizes the badness by not having any blurring in the central region of the image, but the periphery where there is blurring may be artistically nice, but I hope you are not looking at the structure there. >> >> That said the technique could be done using the depth buffer that assigns depth to each pixel — it can’t be done really well that way because that depth only gives the front-most object and if transparency is present the pixel shows multiple objects at different depths. I think it would require a compelling mock-up image to make it worth spending effort on this effect. It is relatively easy to make a mock-up image by using clip planes to save several images representing slabs at different depths, then blur each slab image differently depending on depth in a photo editor and composite. >> >> Tom >> >> >>> On May 5, 2017, at 6:42 AM, Oliver Clarke <olibclarke(a)gmail.com <mailto:olibclarke@gmail.com>> wrote: >>> >>> Hi, >>> >>> I was wondering if you have thought about implementing depth-dependent gaussian blur as a depth cueing mechanism in ChimeraX? >>> >>> The idea would be to blur the image in a manner dependent on the distance from the plane intersecting with the center of rotation, to mimick depth of field in a camera. >>> >>> Mocked up in the attached using a tilt/shift effect, but without access to real depth information - I wonder if it might better convey depth information than distance-dependent changes in brightness/contrast under some circumstances? >>> >>> Cheers >>> Oli >>> >>> <test_image_tilt_shift.png> >>> _______________________________________________ >>> 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> >> >

2 1

Gaussian blur depth cueing? (ChimeraX)
by Oliver Clarke 09 May '17

09 May '17

Hi, I was wondering if you have thought about implementing depth-dependent gaussian blur as a depth cueing mechanism in ChimeraX? The idea would be to blur the image in a manner dependent on the distance from the plane intersecting with the center of rotation, to mimick depth of field in a camera. Mocked up in the attached using a tilt/shift effect, but without access to real depth information - I wonder if it might better convey depth information than distance-dependent changes in brightness/contrast under some circumstances? Cheers Oli

2 4

Re: [Chimera-users] Query regarding chimera tool
by Elaine Meng 09 May '17

09 May '17

On May 8, 2017, at 10:54 PM, bushra TAJ <bushraistaj(a)gmail.com> wrote: > Hello Sir > I want to do some docking studies of my own synthesized compounds. I found them very active in some anti-cancer assays. > I will use AUTODOCK for this purpose. I have got the Pdb file of my target protein from PDB database. > My problem is how to make pdb of my molecule (input file for autodock) can I use chimera for that?? > I have chem-draw file format of my molecules will that open in chimera to make their pdb format. > Regards > In the menu under Tools….. Surface/Binding Analysis: There is a “Dock Prep” tool for preparing PDB files. There is also an “Autodock Vina” tool that will make prepared files in pdbqt format, but it will also run Autodock Vina docking (in other words, the prepared pdbqt files are a by-product but you could also use them as input to something else). You should look at the manual pages for more information. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> Also in the future please send Chimera questions to chimera-users(a)cgl.ucsf.edu and include a useful subject line like “preparing molecules for docking.” Messages to my individual email address may not get answered. 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

1 0

All-by-all distances
by Elaine Meng 09 May '17

09 May '17

> From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: Chimera Question > Date: May 8, 2017 at 6:03:55 PM PDT > > Hi Shawn, > I’m out sick… please send Chimera questions to chimera-users(a)cgl.ucsf.edu list. On second thought, I think I can answer quickly. However, for future reference please use the user list for Chimera questions and include a informative “subject” line to make it easier for others to find … thanks! Command: findclash :lys@n test self overlap -99999 log true … will put all the Lys N -> Lys N distances (within about 1000 A … just use a larger-magnitude negative overlap if you think there are longer distances) in the Log. It won’t be a table, though, just a list of distances that you would have to process yourself. Or instead of “log true” (or in addition to it) you could use the “saveFile” option to specify putting the same output into a text file. Command and options described here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>> Output is like the following example for PDB 2gbp, with distances in the last column: 464 contacts atom1 atom2 overlap distance LYS 191.A N LYS 189.A N -1.010 4.290 LYS 223.A N LYS 227.A N -1.505 4.785 LYS 246.A N LYS 300.A N -3.378 6.658 […etc…] However I suspect maybe you meant NZ (the end of the sidechain) instead of the backbone N, in which case the command would be something like findclash :lys@nz test self overlap -99999 log true … with output like: 465 contacts atom1 atom2 overlap distance LYS 270.A NZ LYS 276.A NZ -1.932 5.212 LYS 308.A NZ LYS 246.A NZ -2.262 5.542 […etc…] Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > >> On May 8, 2017, at 4:14 PM, Shawn Sternisha <ssternisha(a)chem.fsu.edu> wrote: >> >> Hello Dr. Meng, >> >> Sorry to bother you but I have a question about Chimera that I have not been able to find an answer to, despite intensive web searches. I have seen your name on a lot of useful posts and answers so I figured I would give emailing you a shot. I have been searching for a method to measure all possible distance between Lys residues in a protein in a high-throughput manner. >> >> For example, if my protein has 17 Lys residues, is it possible to generate a table that has distance measurements between the N atoms of all of them. I believe that would be 231 possible distances. Any advice you could provide would be greatly appreciated. Thank you for your time in advance. >> >> Best, >> Shawn Sternisha >> PhD Candidate, Miller Laboratory >> Dept. of Chemistry and Biochemistry >> Florida State University > >

2 1

calculate FSC curve between experimental cryo EM map and model
by #AHMED TOFAYEL# 08 May '17

08 May '17

Dear all, If I want to calculate FSC curve between experimental cryo EM map and model, what is the correct procedure to do so? I will explain what I have tried so far. Although I have variable local resolution in my map, according to FSC=0.143 criterion I have a 4 Ang map (say 1.mrc), I have used 'molmap' command in Chimera to generate a simulated map at 4 Ang. Then I used "vop resample" to take care of the pixel and box values ( then saved as 2.mrc). Thereafter, I have used "e2proc3d.py 1.mrc fsc.txt --calcfsc=2.mrc and plotted the fsc.txt file to get the curve. I am not sure if I am on the right track. My pixel size is 1.28. Best regards, Tofayel

3 3

MD file naming
by P. Buscemi Ph.D. 08 May '17

08 May '17

Please,,,, How does one specify the output file name and location for molecular dynamics output ? regards Paul Buscemi, Ph.D.

3 2

Distance measurement file
by Marco Sette 08 May '17

08 May '17

Dear all, I have to measure the same interatomic distances in different molecules: it is possible to create a file like distance ... distance ... distance ... and use as input, just to avoid typing the same command many times? Thanks for your help, Marco

2 1

hbonds and distances movie script questions
by mfellner＠msu.edu 05 May '17

05 May '17

Good day I am making a movie by writing a chimera command script and I searched through existing chimera topics but I could not find a solution for these issues: Is there a command to display hbonds, I have made a script now to select residues and find the hbonds, even color + line width them and then I get rid of them later by ~hbonds. What I would prefer is to have them premade (so I dont need to select residues during the movie) but not displayed, later I then displayed and undisplayed them with a scipt command. Also I could not get the lineType command to work inside the hbond script (lineWidth worked fine), I had to use the setattribute command in a second script line, so for a splitsecond I have a different linetype displayed. The second question is about distance labelling. I can set the options in the gui and then distances are displaed by a script with the distance in Angstrom shown. Is there a way to undisplay the distance label later but keep the dashed line, so change the gui option with a script? Also I assume this is not possible, is there a script to change where the label will show up next to the line? I have not looked into displaying and undisplaying 2D labels with scripts, maybe that is a possibility? Lastly which is not that important, is there any way to trim the corners easily? I think I am recording a lot of white space to the left and right throughout the movie, if I resize the window the molecule gets focused, so its no longer exactly where I had it related to the corners and I think I would have to adjust the script. Thank you so much, I hope I made my questions clear, chimera is an awesome program, movie is 21 minutes at the moment. Best wishes Matthias Fellner Michigan State University

2 3

Sub-region selection
by Soumya Govinda Remesh 05 May '17

05 May '17

Hello, I am analyzing some tomography data. I am working with multiple maps - one which defines several cells and another that defines their inner organelles. I want to be able to select and save the map for individual cells and their corresponding map for the organelles. In addition to using the sub-region selection in Volume-viewer is there another way to select the cells? Thanks Best, Soumya Govinda Remesh, Ph.D. Postdoctoral Fellow at Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Road MS 6R2100 Berkeley, CA 94720 (phone) 510-495-8179 (cell) 804-402-8730 sgremesh(a)lbl.gov

2 2

Contact Maps (RRdistance Maps) questions:
by Nicole Persky 03 May '17

03 May '17

Hi All, I've just found the RRdistance Map function on Chimera and would like to compare between structures. I would like to: 1- make contact map of protein 1 to protein 1 with a cutoff of about 6 angstroms 2- make a contact map of protein 2 to protein 2 with a cutoff of about 6 angstroms 3- compare these two contact maps using the colors available for the whole contact map. I can only seem to compare the ENTIRE contact map of protein 1 to the ENTIRE map of protein 2, whereas I'd like to mask any contacts over 6 angstroms. Alternatively, if anyone knows of a way to export residue lists of contacts from the contact map site I could just compare them that way. ALSO: Anyone know of a way to map defined attributes onto a contact map? Thanks so much! Sincerely, Nicky

2 6

Working with Electron density map
by MOHD HOMAIDUR RAHMAN 03 May '17

03 May '17

Dear Chimera user's I am trying to super impose molecular dynamics calculated density on cryo EM density and then slice densities to visualize each in different colors. I fitted density successfully now during slicing their X Y Z co-ordinate is not matching. The similar analysis were publish in Marzinek et al., 2016, Structure 24, 1–11 August 2, 2016 http://dx.doi.org/10.1016/j.str.2016.05.014 Please see figure 3 for more details and image attached here. Thank Regards Rahman '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' *M*d* H*omaidur* R**ahman *( Research Scholar ) Lab No. 510, Computational Biophysics Lab. Department of Biotechnology Indian Institute of Technology-Madras Chennai-600 036, India *Mobile No = +91- 7845991785 <078459%2091785>* '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''

2 1