- Chimera-users - RBVI Mailing Lists

I Can't Open My ZDOCK Output File Into Chimera
by Nissa Nabila 22 Aug '17

22 Aug '17

Hello and hi! My name is Nissa Nabila and I am a Chimera user. Recently, I did a docking job on ZDOCK server webpage, and already got all the output files. But then, those output files cannot be opened by Chimera even though the output files are all in PDB format. So, can you please help me to solve this problem? Attached is the ZDOCK output file that need to be viewed by Chimera. Have a review. Thank you in advanced!

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Helix voxels labeling
by natan geier 22 Aug '17

22 Aug '17

Hello, I am currently studying the connection between density maps and the secondary structure elements. I have a density map file for a certain protein, giving for each voxel a density value, and what I am missing is a "helix map", giving a binary value for each voxel, representing wether it is a part of a helix or not. In order to build this "helix map", I need to use the .pdb file of that protein, but I am not really sure how to extract an appropriate 3D boolean matrix out of this file. Any suggestions would be greatly appreciated. Thanks

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Regarding generating a .pdb file of peptide (Diglycine)
by Dilip H N 22 Aug '17

22 Aug '17

Hello, I have install chimers in ubuntu 14.04.. I am finding difficult to get the .pdb format for diglyicne peptide... 1] If in Build Structure i select PubChem CID and type 11163 (Diglycine PubChem CID) i am getting error as:- Error fetching 11163:[Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssi.c:590) 2] I even tried through File - Fetch by ID - Pubchem and typed 1163 (Diglycine PubChem CID).. but in vain..i am getting the same error.. So can anybody kindly help....i am a novice here.. Thank you... -- With Best Regards, DILIP.H.N Ph.D Student <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dili…>

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biounit
by Arthur Szabo 18 Aug '17

18 Aug '17

When one fetches structures from the PDB data base what is the difference between fetching using the PDB only selection and the pdb biounit selection? Arthur G. Szabo

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move different map to the same origin of coordinate
by C.J. 18 Aug '17

18 Aug '17

Dear specialists, I open a map(#1) and make icosahedron surface(#1) using Tools-> Higher-Order structure->icosahedron surface. But the model #0 and #1 don't have the same center, how could I center them into the origin of same coordinate? Thanks! -- Best regards! Jianhao

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advanced option for WebGL?
by Albert 17 Aug '17

17 Aug '17

Hello, I noticed that Chimera can export a scene as HTML file which is based on WebGL. However, we can no longer change the displaying styles through this .html file since there is no any menu or option button in the page. Would it be good if Chimera could provide this function? As far as I know, PyMOL has similar function, but the generated .html provide a menu to change the scene styles. see here https://pymolwiki.org/index.php/Pymol2glmol Thank you very much. Albert

2 1

Draw Line
by Catherine Jenifer Rajam Rajendran 17 Aug '17

17 Aug '17

Hi Eric, Can you please tell me what are the ways to draw an axis. I have a directional vector - x, y, z coordinates (e.g., 0.407 -0.747 0.526) and a point (14.395, 37.07, -12.029). How to draw an axis in chimera tool with these two data? Thanks, Catherine

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command line minimization
by Milo Westler 16 Aug '17

16 Aug '17

We are trying to automate the minimization of a series of compounds using the system command line. Since we have quite a few compounds, we are interested in using the Gasteiger method for assigning charges. The command line minimize includes the AM1-BCC method.. Is there a way to run an automatic minimization using the Gasteiger method? Currently we use: chimera --nogui --silent R.mol opt.cmd Where opt.cmd is: minimize write #0 R_min.pdb -- -- Milo =================================================== National Magnetic Resonance Facility at Madison An NIH-Supported Resource Center W. Milo Westler, Ph.D. NMRFAM Director Senior Scientist and Adjunct Professor Department of Biochemistry University of Wisconsin-Madison DeLuca Biochemistry Laboratories 433 Babcock Drive Rm B160D Madison, WI USA 53706-1544 EMAIL: milo(a)nmrfam.wisc.edu PHONE: (608)-263-9599 FAX: (608)-263-1722 ======================================================================= ========

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Match->Align commandline
by sonal rashmi 10 Aug '17

10 Aug '17

sir/mam, i want to use chimera Match->Align feature using the commandline or nogui script (python) to align multiple protein sequences (pdb files) to generate the alignment on MultiAlignViewer and save it as clustal (.aln) file. I tried out the python codes posted on the portals but non of them are giving proper alignment. kindly advice as to what i can do? Is there any commandline available for it? Thanking You Sincere User

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Problem with added ions in Amber
by George Tzotzos 08 Aug '17

08 Aug '17

In MD movie I loaded complex.prmtop and complex.inpcrd files In Tools/Amber/Add ions I selected Ion types Na+ to neutralise complex.inpcrd using AMBER ff14SB for standard residues and AM1-BCC for other residues (I’m attaching a snapshot showing the Na+ ions in red). I then proceeded to solvate the complex using TIP3PBOX and Box size: 9 NOTE: I unticked the Removed existing ions/solvent box I obtained the following Warning “Could not determine charges for pre-existing solvent/ions from added solvent/ions for: NA NA I generated complex_solv.prmtop and complex_solv.inpcrd files When I checked the complex_solv.prmtop file in cpptraj, I did not see any of the Na+ions (see below). > resinfo #Res Name First Last Natom #Orig #Mol 1 ASP 1 14 14 1 1 2 THR 15 28 14 2 1 ——————— 250 LEU 3988 4006 19 250 3 251 VAL 4007 4023 17 251 3 252 KBR 4024 4062 39 252 4 253 WAT 4063 4065 3 253 5 ———— 10272 WAT 34084 34086 3 10272 10024 10273 WAT 34087 34089 3 10273 10025 Is this what should be expected? Should I consider the solvated complex charge neutralised? Antechamber generated exactly the corresponding complex_solv.prmtop file with Na+ ions Thank you in advance for any suggestions.

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chimera batch process
by y.turgay＠bioc.uzh.ch 08 Aug '17

08 Aug '17

Dear chimera users, I was wondering if you could help me automate the following procedure in order to batch process all my tomograms. What I want to do is to open a segmented tomogram, apply parameters like surface, the step size (1 of 8) to increase the connectivity of what has been segmented, to hide the dust (size: 50) and to threshold the tomogram to 0.5. Afterwards I would select all remaining objects and open a script to invert the surface and execute "mask #0 sel invert true" using the command line in chimera to substract the background from the tomogram. Finally I would save this as new map. Can anyone help me with the commands I have to write in the Terminal to iterate through 200 tomogram folder and automate and batch process this. Best Yagmur Turgay

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looking for help in UCSF Chimera
by Ch Bilal 07 Aug '17

07 Aug '17

Respected Sir/Madam. Its Bilal here and i m doing research on a protein "rstA". I am UCSF Chimera user and i am facing an error while energy minimization i got a pop up windows with this error "No MMKT name of atom "HN1" in standard residue "LYS", please help me out i am attaching my complexes with this mail as well please find the attachment. Thank you!

2 1

Automatically changing rotamers
by Ali Malay 07 Aug '17

07 Aug '17

Dear all, I have a large, capsid-sized structure. Is there an easy way (e.g. using a script) to automatically change all of the rotamers of a particular residue type? For example, I would like to modify all cysteine residues such that they all correspond to the Dunbrack rotamer with Chi1= -61; could this be done using the swapaa command? Thank you in advance! Ali

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surface calculation failed on new laptop
by Paul van Erp 03 Aug '17

03 Aug '17

Dear chimera users and developers, Recently I purchased a new laptop. One of the primary uses of this laptop is rendering structures using chimera and running VR simulations of these structures. I've used the new ChimeraX successfully for this. However I also use the old version of chimera for structure visualization, coloring according to attribute lists and I create morph models between structures. The new laptop is unable to calculate virtually any surface. I've gone through the various troubleshooting pages and tried many things. None seem to be effective. Is it possible that the surface calculation would be more successful on a different computer? Also would this depend on the hardware? or might a similar computer from a different brand suffice? Any help you could offer would be greatly appreciated. Thanks in advance, Regards, Paul van Erp

3 2

Volume transparancy
by Matzov Donna 02 Aug '17

02 Aug '17

Hello, I'm trying to make a movie such that a ribbon model would appear while its maps (represented as surface) is already shown and is partially transparent. For that I wanted to set the ribbon transparency to 100 and then use the following command: transparency 0,r frames 100 The problem is that when when the ribbon in 100% transparent, the shape is still apparent in the partially transparent map. the ribbon shapes are not seen only when the map is not transparent at all. Is there a way to fix that? Thanks, Donna

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put outline box at the center of a marker
by Dieter Blaas 01 Aug '17

01 Aug '17

Hi, I'd like to put an outline box with, say 100 x 100 x 100 px around the position of a marker so as to have the marker exactly in the center of the box. Is this possible? Thanks a lot for help, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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QUESTION
by Arthur Szabo 31 Jul '17

31 Jul '17

I am working with a stretch of dna oligos bound to proteins. I selected all the nucleotides on one strand, showed the atoms as sticks. Then I realized I had wiped out the original colors of the atoms, oxygen, red and nitrogen, blue. How can I restore the atom colors by selecting those nucleotides, and changing the atoms back to their typical colors - as a group. I know how to change the colors of the atoms by first showing them as balls and sticks and then selecting the atoms I want to color. But with 10 nucleotides that is a bit of a pain, selecting them on the screen image. I seem to recall that there is a way to do color all the same atoms at once, but forget how. If I hide the nucleotide side chains, then show them again, I get back to the view where the atoms are not selectively colored. Thanks Arthur G. Szabo

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Re: [Chimera-users] QUESTION
by Rebecca Swett 31 Jul '17

31 Jul '17

Hi Arthur, Select your nucleotides and then you can either use the command line with : color byhet selected Or go to Actions > Color > by heteroatom. Cheers, Rebecca From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu<mailto:chimera-users-bounces@cgl.ucsf.edu>> on behalf of Arthur Szabo <agszabo(a)outlook.com<mailto:agszabo@outlook.com>> Date: Monday, July 31, 2017 at 11:53 AM To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] QUESTION I am working with a stretch of dna oligos bound to proteins. I selected all the nucleotides on one strand, showed the atoms as sticks. Then I realized I had wiped out the original colors of the atoms, oxygen, red and nitrogen, blue. How can I restore the atom colors by selecting those nucleotides, and changing the atoms back to their typical colors – as a group. I know how to change the colors of the atoms by first showing them as balls and sticks and then selecting the atoms I want to color. But with 10 nucleotides that is a bit of a pain, selecting them on the screen image. I seem to recall that there is a way to do color all the same atoms at once, but forget how. If I hide the nucleotide side chains, then show them again, I get back to the view where the atoms are not selectively colored. Thanks Arthur G. Szabo This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

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figured it out from the tutorial pages
by Arthur Szabo 31 Jul '17

31 Jul '17

Disregard my earlier message. Arthur G Szabo

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Help
by Marcus Mendes 28 Jul '17

28 Jul '17

Hi All, First of all I want to thanks for the great software. I'm having a problem with the surface calculation. My molecules have 384 aa, with a mutation in 9 positions between them (always in the Chain C). In some molecules there is a hole in the middle of surface (I'm using the Headless chimera). I already tried to customizing some options like probeRadius and Density, but I still have some molecules with a hole. There's anything that I can do to fix this? Best regards Marcus Mendes

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

28 Jul '17

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

2 1

Incomplete Surface Model
by Bosung Kim 25 Jul '17

25 Jul '17

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

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

21 Jul '17

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

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morph interpolation
by Souroprobho Chowdhury 20 Jul '17

20 Jul '17

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

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

18 Jul '17

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

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PROBLEM ABOUT BLAST PROTEIN
by Rosie Spera 18 Jul '17

18 Jul '17

Dear support, I am trying to open Chimera's Blast Protein, but everytime I receive this error: Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.11.2\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.11.2\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 92, in download fp = self.options.transport.open(Request(url)) File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\https.py", line 62, in open return HttpTransport.open(self, request) File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 69, in open raise TransportError(str(e), e.code, e.fp) TransportError: HTTP Error 407: Proxy Authentication Required Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from Blastp request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.11.2\share\blastpdb\ParserBlastP.py", line 361, in _initBlast self.opal = OpalService(self.ServiceName) File "C:\Program Files\Chimera 1.11.2\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Blast web service appears to be down. See Reply Log for more details. I have configured Chimera to use the proxy server and I have saved the setting. I hope any help. Best wishes Inviato da Outlook<http://aka.ms/weboutlook>

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

18 Jul '17

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

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

18 Jul '17

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

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

17 Jul '17

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

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Chimera Dowload
by Lance Patten 15 Jul '17

15 Jul '17

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

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http download links are insecure
by Yuri 14 Jul '17

14 Jul '17

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

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rainbow with atom-spec of a portion of a chain
by Cheng, Micah 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.

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Nvidia Quadro P5000
by Josep TRIVIÑO VALLS 13 Jul '17

13 Jul '17

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

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

13 Jul '17

Hi Chimera Team, I've been following this great tutorial: https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html#case1 To render a structure by conservation. I'd like to run this non-interactively for a number of proteins though. Could you tell me what the python or 'chimera code' equivalents would be? For instance, I would provide a structure (or structures in a session) and MSA in fasta format already, so without interactive menus I'd like to: 1. Open the structure(s) and MSA 2. get the conservation from MultAlign (the actual conservation metric doesn't particularly matter to me at the moment) 3. Render any open models by conservation, say using the cyan-maroon colour scale 4. Additionall depict as smooth worms with defined min and max radii If this is possible! Thanks! Joe Joe Healey M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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

11 Jul '17

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

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change model ID
by Fabian Glaser 11 Jul '17

11 Jul '17

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

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Ligand Center of Mass
by ARMIN HODAEI 11 Jul '17

11 Jul '17

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

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

10 Jul '17

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

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

10 Jul '17

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

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

10 Jul '17

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

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

10 Jul '17

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

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large datasets
by Arthur Szabo 10 Jul '17

10 Jul '17

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

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

08 Jul '17

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

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

07 Jul '17

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

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Define Plane
by Catherine Jenifer Rajam Rajendran 01 Jul '17

01 Jul '17

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

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

28 Jun '17

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

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Difference between Chimera and ChimeraX
by Bon Ikwuagwu 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

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

26 Jun '17

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

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

26 Jun '17

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

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Chimera to Excel
by Fábio Pereira 24 Jun '17

24 Jun '17

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

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