- Chimera-users - RBVI Mailing Lists

FW: Question about 3D visualization by chimera
by Williams, Joanne 21 Mar '18

21 Mar '18

From: "Ahmet Cenk ANDAC, ISU" <acandac(a)istinye.edu.tr> Date: Monday, March 19, 2018 at 5:28 PM To: "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu> Subject: Question about 3D visualization by chimera Hi! I was wondering if it would be possible to view 3D projections of molecules in chimera using polarized glasses? If not, would the Chimera team consider adding such feature in the next release of chimera? Thanks,, Cenk Andac, M.S., M.S., Ph.D., Head, Chair Asst. Professor of Medicinal Chemistry Head of Pharmaceutical Sciences Division Chair of Medicinal Chemistry Department School of Pharmacy, Istinye University, Zeytinburnu-Istanbul, TURKIYE http://eczacilik.istinye.edu.tr/akademik-kadro/ahmet-cenk-andac.shtml Cell: +90-(536)-4813012 E-Mail: cenk_andac(a)yahoo.com

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Autodock Vina outputs
by Elaine Meng 20 Mar '18

20 Mar '18

Hi Simon, The various output files are described in Chimera’s Autodock Vina documentation. As also mentioned in that page, when the docking results are returned they get opened up automatically: i.e. you do not have to explicitly open any files. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> That link is the copy on our website, but you should see basically the same page if you just click the Help button on the Autodock Vina dialog. If no results appeared automatically, the possibilities include: - job is still running - job failed for some reason, check Reply Log - job finished but zero results possible given the input structures/parameters I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco >> >> From: simon chapman <rowanlodge19(a)gmail.com> >> Subject: Re: [Chimera-users] substituting atoms >> Date: March 20, 2018 at 4:31:04 AM PDT >> To: Eric Pettersen <pett(a)cgl.ucsf.edu> >> >> Many thanks Elaine and Eric, much obliged. Sorry if I got the protocol wrong! >> >> 5 files appear on my desktop after a docking run. One is the conf fie, the others are PDB or PDBQT files for ligand and receptor. >> >> I'll keep battling, but perhaps cc.ing your colleagues will help. I'llet you know if the puzzle is resolved. >> >> Simon >> >> On 19 March 2018 at 17:26, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: >> Hi Simon, >> You should initially send these types of questions to the chimera-users list. I’m one member of a programming team and therefore not the expert on all aspects of Chimera — AutoDock Vina being one of the ones I’m not an expert on. I have cc’ed the team members who are the AutoDock Vina experts on this mail and one of them should be able to help out… >> >> —Eric >> >>> On Mar 19, 2018, at 8:17 AM, simon chapman <rowanlodge19(a)gmail.com> wrote: >>> >>> OK, me again....the Irish troublemaker. >>> >>> I've been tinkering with the AutoDock Vina facility in Chimera Tools. All goes well until a pop-up asks me to specify a file type to open the resulting configuration file. >>> >>> I have no idea what those abbreviations mean. I tried a few, but error messages appear every time. >>> >>> Any thoughts? More beers if you can help. >>> >>> Best wishes Simon >> >> <vina 1.PNG> >> <vina 2.PNG> >> >

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Save Image problem
by James Boyd 20 Mar '18

20 Mar '18

Hi, I am a new Chimera user although I have used other molecular graphics programs from time to time. I like the CHimera feel and the menus are pretty easy to navigate. I am trying to save on screen images as .jpg files. I keep getting an error message that says that the file doesn't exist ( e.g. C:\Users\james\desktop\protein\protein.jpg does not exist.) When I look in the folder an image file by that name has been created but it has no image in it. (see NADPH2 for an example). I was able to get an image saved correctly one time (NADPH.jpg) but not again so things appear to be working, it's just that I am doing something wrong. Any suggestions? Thanks, Jim James G Boyd, PhD HealthTell, Inc. 145 S 79th St Chandler, AZ 85226 james.boyd(a)healthtell.com (cell) 860-941-9566 (off) 925-215-5615 (x1001)

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Metal Geometry
by Pascal Auffinger 16 Mar '18

16 Mar '18

Dear All, Metal Geometry is a great tool. However, it can be tedious to use it when the list of metals is long like in some ribosomes where sometimes over 200 of them are found. Is there a quick way to move from a given metal to the next one without using the pulldown menu ? Thanks a lot, Pascal ----- Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffinger(a)ibmc-cnrs.unistra.fr <mailto:p.auffinger@ibmc-cnrs.unistra.fr> -----

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Topology file creation
by Sankaran SV . 16 Mar '18

16 Mar '18

Hi users, Currently Iam working on protein glycosylation. Can anyone could give me a reference for topology file creation for running the simulation of glycosylated protein. -- Sankaran.s.v bbin

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Permission to use Chimera for non-academic purposes
by Helander, Jon 16 Mar '18

16 Mar '18

Hello, I'm a computational biologist at Wash U. in Saint Louis and have been using Chimera for some years now. I also do some stock market research in biotech and write informative articles about some companies that do small-molecule research. To aid in this, I would like to include some Chimera-generated images. Would this be alright and can I obtain some written confirmation if so? Thanks Jon Helander

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Surface picking
by Priit Eek 15 Mar '18

15 Mar '18

Hi, I am trying to visualize some specific inner cavities in a structure. I can display the MSMS surface and split it into pieces (accelerator Sc), but then I need to select the extra surfaces to hide/delete them (starting with the main outer surface). For some reason surface picking with mouse (Ctrl + left click) doesn’t work. I checked the surface attributes and ‘selectable with mouse’ was true. I recall that this used to work some years ago, but not anymore. I am using the latest daily build (v1.13 build 41684) on macOS v10.12.6. Is this a bug or have some settings changed? I couldn’t find anything referring to this in the docs. Best regards, Priit

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Animation
by David Bhella 14 Mar '18

14 Mar '18

Dear All, I have noticed that the animation tool appears to begin encoding movies before the final frame settings are set, consequently all my movies are missing the last frame. I can see a way to fix this but, it would be better if it didn’t happen. Has anyone else noticed this? D. Dr David Bhella Director - Scottish Centre for Macromolecular Imaging MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch [University of Glasgow: The Times Scottish University of the Year 2018]

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Re: [Chimera-users] ellipsoids
by Tom Goddard 12 Mar '18

12 Mar '18

Hi Carlos, The fix is in tonight’s daily build, the one that will be compiled in about 14 hours (2 AM Pacific time). It is not available yet. Chimera does not handle small molecule crystals. It is for protein and nucleic acid structures. So it does not handle the small molecule cif format which has extra symmetries that occur only in small-molecule crystals — you will need other software for that. Tom > On Mar 12, 2018, at 12:04 PM, Carlos Romero wrote: > > Hello Tom, > > thank you for your quick answer. I just installed the daily build however the problem persist. Any suggestion? > Moreover i have a new problem, a cif file that contain totally symmetric molcule, Chimera only represent half! while other softwares confirm that the cif file is correct. An expert in crystallography said that it might because a special inversion center and that " the program should apply the symmetry to complete the molecule" could you help me with this too? i thank you very much for your valuable help > > Carlos > > On Mon, Mar 12, 2018 at 7:06 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Carlos, > > The Chimera unit cell tool was not copying the anisotropic b-factor information. I fixed that in tonight’s daily build. > > Tom > > > > On Mar 12, 2018, at 6:16 AM, Carlos Romero wrote: > > > > First of all congratulations for the your software Chimera, it renders really beautiful images and helps attracting the interest of students for science! > > > > I have a question. I am representing an X-ray structure from cif file. I am able to build up the unit cell, but i would like all the atoms to be represented with the thermal ellipsoids. However, i can only apply the ellipsoids to one molecule of the unit cell. Would it be possible to display all molecules with the ellipsoids and not only one? i was unable to find a solution. > > > > Thanks a lot in advance for any help > > > > kind regards > > > > Carlos > > _______________________________________________ > > 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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ellipsoids
by Carlos Romero 12 Mar '18

12 Mar '18

First of all congratulations for the your software Chimera, it renders really beautiful images and helps attracting the interest of students for science! I have a question. I am representing an X-ray structure from cif file. I am able to build up the unit cell, but i would like all the atoms to be represented with the thermal ellipsoids. However, i can only apply the ellipsoids to one molecule of the unit cell. Would it be possible to display all molecules with the ellipsoids and not only one? i was unable to find a solution. Thanks a lot in advance for any help kind regards Carlos

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Looking for help on starting of Chimera 1.11 on win32
by 杨超 10 Mar '18

10 Mar '18

Hi Chimera users, I am Ph.D. student who foucing on genetic study of skin disease from Anhui Medical University, Hefei, China. Recently, I want to used Chimera to draw a protein structure. But after I installed Chimera 1.11 on my win 7(win32 system), I can't open it. It showed such error when I started the --debug command. Could anyone give me a hand? Thank you so much. Chao Yang Anhui Medical University Hefei, China

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Cannot save PDB as multiple chains of a single model.
by Matthews-Palmer, Teige Rowan Seal 09 Mar '18

09 Mar '18

Dear Chimera-users, I have a PDB file containing a single chain, that I have copied and applied turns about a symmetry axis. So now I have several models with transformed positions. When I save PDB>save multiple models in a single file, my output PDB does not seem to handle CHAINID properly. If my input PDB has CHAINID A and ends with TER, then my output PDB has everything as CHAINID A, no TER, and instead separates the models by MODEL 1 […] ENDMDL MODEL 2 [...etcetera] I would like to save a PDB with these symmetrical copies as different chains A,B,C… (and not different models). Can anyone suggest a way to do this? Help greatly appreciated. Teige

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Density map segments and segment associated sequence extraction
by Ahmad Abdelzaher 26 Feb '18

26 Feb '18

Hello, I have a density map that i'm trying to segment. I want to fit in my structure in the segmented map, and save each segment of the map as an independent mrc map, and each corresponding segment of the sequence as a fasta file. How can I do that? Kind regards

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'Automatically' annotate multiple structures
by Healey, Joe 26 Feb '18

26 Feb '18

Hi again Chimera team, I'm looking for a fairly quick and dirty way to apply some annotations using 2D labels to a bunch of open structures. Basically, I have ~16 structures open on screen, which I then tile to compare. I'd like the model name to be displayed just below each model so that its easy to track. I've found this thread (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-July/004081.html) which appears to be attempting a similar thing (though I'd like to use the model.name not serial number), but the approach doesn't seem to work (no labels appear and there is no information in the reply log or IDLE to give me any clues). Any suggestions/alternatives appreciated! 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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Query
by priyanka bose 23 Feb '18

23 Feb '18

Respected Sir/Madam, I am a former research fellow and trying to use chimera for different view purpose. I tried for the mouse movement option but it is not working. Only some commands work in the downloaded software. Want to know, for the tools to be active is there any need of further license for the tools or any thing else. If yes is there any academic license facility and if no how could I rectify this problem. It will be helpful if I get to know where the problem is. Looking for your reply. Thanking you. -- Yours Sincerely, Priyanka Bose *Project fellow* *Dept. of Chemistry, BHU, Varanasi, UP* *M.Pharm* *Dept. of Pharmaceutical Sciences, Dr. H. S. Gour Central University, Sagar, MP* *Email: meow.bose(a)gmail.com <meow.bose(a)gmail.com>* *phone no: 8335828828*

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query regarding docking by chimera
by Juweria Shahrukh Effendi 21 Feb '18

21 Feb '18

Dear Daron I am new to chimera, I want to check the conserved water molecules in my protein pdb and its reported co-crystalized ligand as i do the dock prep complete adding hydrogen, applying charge, and i complete the whole steps the chimera isnt able to execute attaching the pic of both windows can you please have a look on it and guide me thanks With Regards Dr Juweria Shahrukh Effendi M.B:B.S, M.Phil Biochemistry, PhD Scholar (Computational Drug Design unit)Molecular Medicine Dr Panjwani Center for Molecular Medicine and Drug Research International Center for Chemical and Biological Sciences (ICCBS). Karachi Email i.d: javelightens@yahoo.com.http://sites.google.com/site/zaheerqasmi/groupmemberjavelightens83@gmail.com juweria.shahrukh(a)iccs.edu

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areaSAS calculation intuition detail
by Daniel Ziemianowicz 21 Feb '18

21 Feb '18

Hello, I have read as much as I can about SASA calculations but I'm still missing something. I've been enlightened on the difference between solvent-excluded surface (SES) and solvent-accessible (SAS) - particularly from this post: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-September/005532.html >From my understanding, the SES is calculated via the 'rolling sphere' method, where the radius of the probe contacts the VDW surface of individual atoms. This used to be my understanding of SAS, as other descriptions have explained it this way, but I now realize this is incorrect. The SES is also what is shown when one enables the surface representation. Now, I read the description of how SAS is calculated at: https://www.cgl.ucsf.edu/chimera/data/sasa-nov2013/sasa.html which more or less makes sense to me. Basically, the radius of the probe is the 'limit of what is seen' from the perspective of the probe center when it overlaps with the VDW of molecule atoms. In this regard, is it true that the SAS probe 'penetrates' the SES surface representation, so greater probe radii observe a greater SAS, with respect to residues. Conversely, larger probe radii observe a reduced SES, with respect to residues. This is my understanding based on my calculations in Chimera. The missing intuition is that I do not understand what the 'limit of penetration', so to speak, is for the SAS probe. E.g. given a protein and its surface, is the probe center limited by the surface but it's radius penetrates/overlaps the surface and the residues within? There must be some sort of limit for the probe center, I imagine, otherwise it would penetrate within the protein molecule and 'see' everything. I hope my question and explanations are clear. It's rather difficult to describe without a visual aid. Regards, Dan Z P.S. these sort of calculations are a dream with Chimera!

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Blast web service appears to be down
by Anitha 16 Feb '18

16 Feb '18

Hi Blast web services and modeller web services are down for the past week. I was able to rectify modeller by opting to run locally Is there any similar options for Blast services? Regards Anitha.S

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Surface selections
by Healey, Joe 16 Feb '18

16 Feb '18

Hi Chimera team, A quick and easy question I hope, is there a shorthand command I can use to select all surfaces? I've tried: sel surf all sel surf sel ,s and some other variations. If this is possible, I'm sure it's simple but I'm just not quite getting there? 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

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Chimera user advice
by Wil Ratzan 16 Feb '18

16 Feb '18

Hello, I truly appreciate the development and distribution of software such as Chimera to the scientific community, but alas I am not 'computer-savvy.' I would like to map highly conserved residues of a protein onto its crystal structure (PDB 3V0I). I can view the PDB file of the crystal structure using Chimera, but I am having a hard time figuring out how to highlight residues. Could you please give me some advice about how to identify and mark particular residues using this file? I apologize if this request seems trivial, and I appreciate any advice. Thanks, -Wil Ratzan Dept. of Cell Biology and Neuroscience Montana State University Bozeman, MT 59717

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Re: [Chimera-users] Analysis of the protein-protein binding interphaces in MARTINI models
by James Starlight 15 Feb '18

15 Feb '18

Thank you so much for the suggestions, Elaine! Indeed, I have turned off the both flags but the intra-models contacts are still recognized. it seems that in order to determine carefully the per-residual contacts between monomers, I should to make a backmapping of the CG models to AA. James 2017-11-27 9:23 GMT+01:00 <sdimicco(a)unisa.it>: > Grazie mille > > > Il 2017-11-23 04:47 James Starlight ha scritto: > > Thank you for the suggestions, Elaine ! > > I have already tried "Find Clashes/Contacts" plugin. In generally, it > works good, however its application on more complex oligomeric > patterns (e.g if I deal with 10-20 GPCRs in one system) is a bit > complicated. Briefly, if I select only one monomer and than try to > find its contacts with the rest of the atoms ( I have changed the > contact threshold to -1.2 for the MARTINI) - it works fine. However, > If I selected all of the atoms (even excluding inter-residue and > inter-molecular contacts) and changing the search criterium "against > themselves" - it found alot of contacts within the monomers. Does > anybody use any tricks for the MARTINI models to fascilitate the > contact searching? > > > James > > 2017-11-22 17:52 GMT+01:00 Elaine Meng <meng(a)cgl.ucsf.edu>: > > Dear James / Gleb, > This question seems too broad, perhaps. I don't know that much about > MARTINI, so I'm guessing instead of atoms you just have a bunch of points > that each represent multiple atoms. In that case you could probably use any > analysis that does not directly use exact atomic locations, atomic radii, or > atomic point charges. Analyses that DO use those things include > surface-area calculations, Find Clashes/Contacts, FindHBond. > > Maybe you should just first think about what Chimera analysis you want to > use, then just try it on your GC model and see if it works rather than > trying to get some exhaustive list of what might work. > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Nov 22, 2017, at 2:23 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: > > Dear Chimera users! > > I would like to make some analysis of the protein-protein binding > established in coarse-grained MARTINI simulations. Briefly Chimera has > recognized a coarse-grained pdb file of 16 martini models of GPCRs. > What Chimera tools (e.g. contact maps, clustering of interphaces) > should work with CG models? What tricks should be used to make this > analysis easier? Because I am working with several proteins in one > system, I would like to work with its CG models without the conversion > to all atomistic representations. > > I thank you so much for the help! > James > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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Video issues
by Mark Warren 15 Feb '18

15 Feb '18

Hi, Running win10 and using Chimera 1.12. Upon startup I'm getting the splash logo, then the rapid access screen. All OK so far. However I load any protein and the dialog along the bottom status bar confirms its loaded but the screen still shows the rapid access screen. I can toggle the lightning button in the bottom right as much as I like but it remains on the rapid access screen. Any ideas what to check? Thanks The Medicines Discovery Catapult is one of a network of elite technology and innovation centres established by Innovate UK as a long-term investment in the UK's economic capability. Applying business-led research, Catapults help businesses transform great ideas into valuable products and services to compete in the global markets of tomorrow. Medicines Discovery Catapult is a company limited by guarantee, registered in England and Wales with company number 09928547. Our registered office is at Medicines Discovery Catapult, Mereside, Alderley Park, Alderley Edge, Cheshire, SK10 4TG. This email and any attachments may contain confidential information and is intended solely for the addressee. If you have received it in error, please send it back to us and immediately and permanently destroy all copies. Do not use, copy or disclose the information contained in this message or in any attachment.

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Feature to remove default bond between hydrogen atoms of water while loading MD trajectory
by NARINDER Kaur Harika 13 Feb '18

13 Feb '18

Dear Sir/Ma'am, I hope you are doing good. I am interested in making MD movie from AMBER trajectory in chimera 1.12 version. Unfortunately when I load prmtop and mdcrd files in MD movie, it shows default bond between hydrogens of water molecule. I dont want to show this bond while presenting my research at meetings so I would be really grateful if I can get any help regarding removing this unwanted bond in water molecules. For further clarity I have attached avi movie file of small section of my trajectory. Thank you very much for your help and support. With Regards, Narinder Kaur Harika Georgia state university

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TM tendency hydrophobicity scale
by Shyam Saladi 13 Feb '18

13 Feb '18

Hi all -- I have put together a Chimera attribute definitions to color residues according to the TM tendency hydrophobicity scale: Zhao and London, Protein Sci 15:8 (2006), doi: 10.1110/ps.062286306 An amino acid "transmembrane tendency" scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: relationship to biological hydrophobicity In case it's helpful to others, it's attached to this message. Perhaps the Chimera team would also be interested in including it with the other scales <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html> online as well. Thanks, Shyam -- Shyam Saladi <http://shyam.saladi.org> NSF Graduate Research Fellow Biochemistry and Molecular Biophysics California Institute of Technology

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Errno 13
by Dustin Park 13 Feb '18

13 Feb '18

Hello, After using docking preparation and run, I set the executable location to vina and clicked ok. However, the result is that there is a chimera error ([errno 13] Permission denied. Can you explain to me how to get past the docking preparation step and why this error is coming up? Not sure how else to do this step. Thank you.

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