- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Distance tool: Line thickness of the number (of angstroms) in the picture
by Boaz Shaanan 21 Oct '17

21 Oct '17

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Distance tool: Line thickness of the number (of angstroms) in the picture
by Boaz Shaanan 21 Oct '17

21 Oct '17

Hi, The number that shows up after creating a distance is very thin and can hardly be seen. I couldn't find how to make it thicker (I did change the actual line thickness in the menu). I also tried in the preference menu that you pointed to a user a while ago but it didn't work for me. How can I change it? This is on the Windows 64b nightly build from 17 October. Thanks. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Saturday, October 21, 2017 1:17 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 174, Issue 28 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Trouble with Volume surface and active model not aligned (Elaine Meng) 2. Re: Selecting residues in chains defined by segname (Francesco Pietra) 3. Re: Selecting residues in chains defined by segname (Elaine Meng) 4. Re: Trouble with Volume surface and active model not aligned (Phan Trieu Truong) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Oct 2017 13:41:34 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Phan Trieu Truong <truongp(a)uga.edu> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Trouble with Volume surface and active model not aligned Message-ID: <5596D972-35F9-4643-8CDB-6F7D4DE590FD(a)cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8 Hi Phan, I?m not sure what happened either, since your images show the ?A? (active for motion) boxes in the Model Panel are checked for both the molecule and the orbitals, meaning that using the mouse should move both of them together. You could try command: reset ? to put them back together. If that doesn?t work, you may have to start over by quitting and reopening the files. However, if you didn?t uncheck the ?A? boxes or the ?Active models? boxes below the Command Line, mouse movements should always move them both together. Maybe you accidentally had one of the A(ctive) boxes unchecked and moved the other model. In that case, reset will 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 Oct 20, 2017, at 8:57 AM, Phan Trieu Truong <truongp(a)uga.edu> wrote: > > Hi, > > I have been using Chimera to visualize MO orbital on molecules from ORCA calculations. I have been able to visualize the MO orbitals as a surface volume from cube files. However, I just found out that when I try to reorient the molecule with the surface volume, they are no longer aligned. I don't know what I did to cause this. Any help is much appreciated. > > Attached is the picture of the molecules before and after I tried to reorient the molecule with the surface volume. > > Thank you, > Phan > <Before and after reorientation.jpg.png>_______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ Message: 2 Date: Fri, 20 Oct 2017 23:37:32 +0200 From: Francesco Pietra <chiendarret(a)gmail.com> To: Eric Pettersen <pett(a)cgl.ucsf.edu> Cc: chimera <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Selecting residues in chains defined by segname Message-ID: <CAEv0nmsDA8dd+hQ8H_t9uK8-LntPucKQ7UiiqVybva3XWdBgjA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" A pity, in my view. As more and more complex proteins are being examined (thanks to faster clusters), working without segname would be practically impossible in the frame of today pdb files. For example, how visualizing the trajectory of a particular ligand in a 24-chain protein assembly? I can do that with vmd, but at the price of a less clear-cut trajectory and poorer graphics. But I understand that there may be different viewpoints. Cheers francesco On Fri, Oct 20, 2017 at 8:36 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Realistically no. Too many other priorities. The gap will eventually get > filled in in ChimeraX, but even that will be awhile. > > ?Eric > > On Oct 19, 2017, at 1:24 PM, Francesco Pietra <chiendarret(a)gmail.com> > wrote: > > Hi Eric: > > Any plan to fill this gap? > > thanks > > francesco > > On Thu, Oct 19, 2017 at 7:59 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > >> Hi Francseco, >> Unfortunately, segment IDs are not preserved by the trajectory reader. >> >> ?Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >> On Oct 19, 2017, at 9:53 AM, Francesco Pietra <chiendarret(a)gmail.com> >> wrote: >> >> Hi Elaine: >> While, as I wrote, the commands for segname did work fine with .psf/.pdb >> namd files, >> in contrast, with .psf/.dcd files (movie) >> >> select @/pdbSegment=C1 >> >> selects all chains of the protein assembly, including ligands. The same >> occurs with >> >> select @/pdbSegment=O2C1 >> >> where O2C1 is the segname of the molecule dioxygen associated with chain. >> >> This occurs both on my desktop and on a large-memory nextscale cluster on >> remote visualization (the latter is the actual interest) >> >> Do you know of any remedy? >> >> thanks a lot >> >> francesco >> ---------- Forwarded message ---------- >> From: Francesco Pietra <chiendarret(a)gmail.com> >> Date: Mon, Oct 16, 2017 at 7:12 PM >> Subject: Re: [Chimera-users] Selecting residues in chains defined by >> segname >> To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >> >> >> Hi Elaine: >> >> Great! >> >> thank you >> francesco >> >> On Mon, Oct 16, 2017 at 5:58 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >>> Hi Francesco, >>> The symbol for intersection is ?&? ... in other words, you could use >>> >>> select :17 & @/pdbSegment=A1 >>> >>> Intersection and union symbols are explained here: >>> <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/at >>> om_spec.html#combinations> >>> >>> I hope this helps, >>> Elaine >>> >>> > On Oct 16, 2017, at 12:29 AM, Francesco Pietra <chiendarret(a)gmail.com> >>> wrote: >>> > >>> > Hi Elaine: >>> > That works fine. However, I was unable to extend your suggestions to >>> pick up a specific residue within a specific chain. Neither "select :17 >>> @/pdbSegment=A1" nor "select @/pdbSegment=A1 :17" are valid commands >>> (obviously expected). >>> > >>> > On the other hand, with such complex situations, it is Xplor, with its >>> segname features, that helps. >>> > >>> > Should you need a pdb fine with segname, I could attach a simple one, >>> with a single chain. >>> > >>> > On Sun, Oct 15, 2017 at 8:04 PM, Elaine Meng <meng(a)cgl.ucsf.edu> >>> wrote: >>> > Hi Francesco, >>> > Although I don?t have an example file with segnames to try myself, I?m >>> told you can specify by the atom attribute pdbSegment, e.g. >>> > >>> > select @/pdbSegment=A1 >>> > color red @/pdbSegment=F3 >>> > >>> > I hope this helps, >>> > Elaine >>> > >>> > > On Oct 15, 2017, at 10:40 AM, Francesco Pietra < >>> chiendarret(a)gmail.com> wrote: >>> > > >>> > > Hi Elaine: >>> > > >>> > > I am referring to Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote: >>> > > and your answer: >>> > > >>> > > command: select :45.a-d > or > command: select :45.* > > Or, to >>> select residue 45 in just chains A and D: > > command: select :45.a,45.d >>> > > >>> > > I have a more complex case, where chains are defined by segname, >>> > > for example >>> > > >>> > > A1 A2 A3 A4 A5 etc >>> > > >>> > > while the standard PDB definition is "A" for all them. >>> > > >>> > > The same for standard "B", "C" etc. >>> > > >>> > > As I want to display a movie of ligand pathways, where the ligand >>> > > moves from, say, "A1" to, say, "F3", I want in the first instance >>> > > become able to select particular residues in particular chains, >>> > > as defined by their segname. >>> > > >>> > > Could you imagine a simple way not requiring selection by atom >>> numbers? >>> > > Thanks >>> > > francesco pietra >>> > >>> > >>> > _______________________________________________ >>> > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> > Manage subscription: http://plato.cgl.ucsf.edu/mail >>> man/listinfo/chimera-users >>> >>> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mail >> man/listinfo/chimera-users >> >> >> > >

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Trouble with Volume surface and active model not aligned
by Phan Trieu Truong 20 Oct '17

20 Oct '17

Hi, I have been using Chimera to visualize MO orbital on molecules from ORCA calculations. I have been able to visualize the MO orbitals as a surface volume from cube files. However, I just found out that when I try to reorient the molecule with the surface volume, they are no longer aligned. I don't know what I did to cause this. Any help is much appreciated. Attached is the picture of the molecules before and after I tried to reorient the molecule with the surface volume. Thank you, Phan

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Map to CCP4 Style Mask
by Martin Lawrence 20 Oct '17

20 Oct '17

Hi All, Is there a quick and easy way in Chimera to impose a density level cutoff and write out a ccp4 style mask file? Thanks, Martin Martin Lawrence Department of Chemistry and Biochemistry Montana State University Bozeman, MT 59717 USA

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Coloring higher ordered structures
by Frances Shepherd 19 Oct '17

19 Oct '17

Hello, I’m working with a rotavirus capsid structure and I’d like to highlight individual residues on it if possible. I’m using PDB #3IYU which I split into individual chains, and used the multiscale model function to create the capsid structure. I’m able to color different surfaces, but it applies the color to each spot where the chain is on the entire capsid, rather than just one subunit. I’d like to recreate the kind of figure from a paper by Zeller et al (2012), attached below. Additionally, is it possible to color individual residues on a capsid structure? Thanks in advance! -Frances Shepherd

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POV Ray export
by Greg Williams 19 Oct '17

19 Oct '17

I have done an Export Scene command to generate a POV Ray file for external rendering (Chimera 1.11.2 and Mac OS 10.12.6) using the default Chimera settings. If I open the file in POV Ray 3.70, the Render command gives the following error message: Possible Parse Error: Cannot find file 'transforms.inc', even after trying to append file type extension. "/Users/Greg/Dropbox/POV Ray/POV Prac 2.pov" line 7 Parse Error: Cannot open include file transforms.inc. Any suggestions for fixing the file? Thanks, Greg Williams

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Wall eye stereo has no depth in orthographic projection
by Boris Steipe 19 Oct '17

19 Oct '17

Hello - When viewing a molecule in wall-eye stereo and orthographic projection, the scene is "flat", i.e. the L and R images are identical. Perspective projection works as expected. Is there a workaround? Chimera 1.12 (41617) Mac OS X 10.11.16, NVIDIA GeForce GT 750M Thanks! Boris

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2d projection of 3d model
by D.A. Semchonok 18 Oct '17

18 Oct '17

Dear colleagues, I would like to make 2d projection of my 3d model and save it as an image. How can I do that? Thank you! Sincerely, Dmitry

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Need help performing a high throughput screen using Chimera
by NOOR GREWAL 18 Oct '17

18 Oct '17

Hello, I am an undergraduate student at UC Berkeley. I want to use UCSF Chimera as a part of my research project. How can I run multiple (~20,000 ligands) ligand-docking experiments in parallel using Chimera? I have a Mac OSX Sierra and I am trying to use the command line/terminal for this. I am unable to find documentation and tutorials that can help me. I am very new to this. Could you please guide me on how to best navigate this process? Thanks. Best, Noor

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MD Trajectory Error
by Bryan Dunyak 13 Oct '17

13 Oct '17

I'm trying to run a molecular dynamics simulation in Chimera 1.12rc on a small molecule. On the first run, it worked perfectly. On subsequent runs, when it begins the MD simulation it errors with the following message in the reply log: "The existing trajectory output files are not compatible with the current molecular system, and therefore cannot be appended to with additional MD steps. You need to either remove/rename the existing files, or specify different file names for output." I've tried to find the trajectory output files in /tmp, I've tried reinstalling Chimera, I've looked in other directories without any luck. What should I be doing at this step? Where can I find these files? Thanks! Bryan

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Genetare animation from several .cube files
by Henrique C. S. Junior 12 Oct '17

12 Oct '17

Dear list, I'm getting results from an RT-TDDFT calculation that generates several (> 450) .cube files and I'd like to know if we have a nice way to generate an animation. I know that Chimera can generate beautiful images, but can I load each .cube as a frame and animate the result? Thank you so much for any help -- *Henrique C. S. Junior* Industrial Chemist - UFRRJ M. Sc. Inorganic Chemistry - UFRRJ Data Processing Center - PMP Visite o Mundo Químico <http://mundoquimico.com.br>

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Fwd: Re: Chimera Users
by Greg Couch 12 Oct '17

12 Oct '17

Forgot to cc the list. -------- Forwarded Message -------- Subject: Re: [Chimera-users] Chimera Users Date: Wed, 11 Oct 2017 23:44:53 +0000 From: gregc(a)cgl.ucsf.edu To: Abhiram Chintangal <achintangal(a)berkeley.edu> AFAIK, Chimera works well with the current NVIDIA drivers. However, it often doesn't work remotely unless you have the same driver on both systems. Is that your use case? Please send me the output of the glxinfo command. glxinfo is in the gxl-utils package. With that information, I might be able to tell what's going on. -- Greg October 11, 2017 3:27 PM, "Abhiram Chintangal" <achintangal(a)berkeley.edu <mailto:%22Abhiram%20Chintangal%22%20%3Cachintangal@berkeley.edu%3E>> wrote: Hello, I am trying to run Chimera on Linux system and I keep running into OpenGL errors after launching it. Here is what I see on my end: X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 155 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 722 Current serial number in output stream: 723 The system where I am trying to run this has a nivdia 750ti and is running Centos7. I have installed nvidia-drivers using binaries downloaded from nvidia.com <http://nvidia.com> Looking forward to his response, Thanks! -- Abhiram Chintangal QB3 Nogales Lab Bioinformatics Specialist @ Howard Hughes Medical Institute University of California Berkeley 708D Stanley Hall, Berkeley, CA 94720

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Chimera Users
by Abhiram Chintangal 11 Oct '17

11 Oct '17

Hello, I am trying to run Chimera on Linux system and I keep running into OpenGL errors after launching it. Here is what I see on my end: X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 155 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 722 Current serial number in output stream: 723 The system where I am trying to run this has a nivdia 750ti and is running Centos7. I have installed nvidia-drivers using binaries downloaded from nvidia.com Looking forward to his response, Thanks! -- Abhiram Chintangal QB3 Nogales Lab Bioinformatics Specialist @ Howard Hughes Medical Institute University of California Berkeley 708D Stanley Hall, Berkeley, CA 94720

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Automate Segmetation
by Soumya Govinda Remesh 10 Oct '17

10 Oct '17

Hello Chimera Developers, There is this repeated procedure that I have to do to get a Segmented map from my soft x-ray tomography maps. Here is what I want do: 1. open *mrc put the map to Level 0.011 2. *vop gaussian #0 sd 0.005* put Gaussian to 0.011 3. Go to: Tools --> Volume Data --> Segment Map Segment the gaussian map Smoothing step: 1 Step size: 500 voxels Keep only regions at lease: 100 voxels Save segments as an .mrc file Go to: File (Segment Map) --> Save all regions to .mrc Set Segment map to 0.011 4. Type: *vop subtract #3 #0* #3 Corresponds with ID# of the segmented .mrc file #0 Corresponds with ID# of the original file 5. *sop split #0 * #0 Corresponds with ID# of the original file - Splits surface into disconnected parts The steps in *bold *are in command line. Is there anyway to have everything in a script format? Setting the levels, opening segmentation and setting values to specific Voxel values every time is quite time consuming. I would appreciate your help. Thanks Best, Soumya Govinda Remesh, Ph.D. Postdoctoral Fellow at Advanced Light Source SIBYLS group: http://sibyls.als.lbl.gov/ Lawrence Berkeley National Laboratory 1 Cyclotron Road MS 6R2100 Berkeley, CA 94720 (phone) 510-495-8179 (cell) 804-402-8730 sgremesh(a)lbl.gov

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B-value coloring
by ARMIN HODAEI 10 Oct '17

10 Oct '17

Dear Chimera users, I would like to change the b-values of a Protein and color the residues in the ranking that I want. I have a sequence of residues from the most functionally important sites to less functionally important. I wanna define them to look red and blue respectively due to the new ranking. Sincerely, -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

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crop a map via commandline
by Edoardo D'Imprima 09 Oct '17

09 Oct '17

Dear Chimera users, is there an equivalent of Volume viewer/Features/Region bounds from the GUI to precisely crop several maps via command line? I tried a combination of volume region and vop zone subregion but it doesn’t really do what I would like to obtain. Many thanks in advance, Edoardo --------------------------------------------------- Edoardo D'Imprima PhD Student Max Planck Institute of Biophysics Structural Biology Department Max-von-Laue Straße 3 60438 Frankfurt am Main Germany Tel: +49 (0) 69 6303 3015

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Chimera for MOFs
by Minoofar, Payam N 06 Oct '17

06 Oct '17

Greetings and Salutations, I recently started using Chimera to view .cif files for metal organic framework (MOF) unit cells, and I get the impression that Chimera is not quite rendering them correctly. I thought I'd ask the community if visualizing MOFs is a priority for Chimera before I start whinging. (No, I'm not British.) If it is a priority, to whom can I mail the cif files in order to determine whether the problem lies with Chimera or with the file? Many thanks, Payam ------------------------------------------- Payam Minoofar, Ph. D. | Research Scientist | Teledyne Scientific & Imaging | 1049 Camino Dos Rios | Thousand Oaks, CA 91360 | 805.373.4514 voice | 805.373.4105 fax | Payam.minoofar(a)teledyne.com<mailto:Payam.minoofar@teledyne.com> | -------------------------------------------

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help please!
by Nathan Goldfarb 05 Oct '17

05 Oct '17

Hello: I am trying to prep my ligand which is a tripeptide ending with a boronic acid. Chimera will not let me assign charges to it. It does not like the boron and says there is no Sybyl equivalent in the error message. Do you know how to get around this problem? Thanks! -- Nathan E. Goldfarb, M.S., Ph.D. Assistant Professor of Biochemistry 904-716-7339 [image: LinkedIn] <http://www.linkedin.com/in/nathangoldfarb>

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Re: [Chimera-users] High Sierra fix
by VAZQUEZ SENTIS MARCO EUGENIO 05 Oct '17

05 Oct '17

Hey there, Thanks for the information. However, the representation of atoms is still wrong in with High Sierra. I’m attaching an image of what I see. Have you received reports like this?. Is there any fix for that? thanks!! [cid:C21A9AF2-1CF2-4300-9F85-A65D871E91E9@mundo-R.com]

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Chimera help for tomography data!
by Swetha Vijayakrishnan 05 Oct '17

05 Oct '17

Dear All, I am new to using chimera for EM tomography data. Essentially I am trying to create a movie with tomography and subtomogram data within a single movie. However, i am having trouble making and rendering the movie. I can open the tomogram tilt series (created in IMOD) and manually move it along using the planes option along the axis of interest. However i was trying to see if the Volume series option helps play it automatically but it doesn’t seem to do so. Is this the right way to do it? Any help on how i can play through the tomogram through the various planes back and forth and how i can create a movie will be greatly appreciated. Thanks and best wishes, Swetha Dr Swetha Vijayakrishnan MRC-University of Glasgow Centre for Virus Research (CVR) University of Glasgow, Sir Michael Stoker Building, 464 Bearsden Road, Garscube campus Glasgow G61 1QH UK Email: Swetha.Vijayakrishnan(a)glasgow.ac.uk<mailto:Swetha.Vijayakrishnan@glasgow.ac.uk> Phone: +44 (0) 141 330 4025 http://www.gla.ac.uk/colleges/mvls/supportforresearch/nerd/

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Create oxime functional group
by Wikel, Jim 04 Oct '17

04 Oct '17

Hello, I recently had difficulties with creating a particular structure in Chimera. The SMILES is depicted below. The problem is I have not been able to represent the oxime portion of the molecule. I have tried to reset atomtypes, redrawing the structure, adding and deleting the atoms, passing it through other drawing programs, reformatting the file to other formats, but to no resolution. Chimera insists on adding a hydrogen to the oxime nitrogen prior to minimization. I am puzzled and suspect I may be doing fundamentally wrong. Any advice would be helpful. CC1CC(C)CN(C1)S(=O)(=O)C1=CC=C2C(=C1)C(=NO)C1=CC(=CC=C1C2=NO)S(=O)(=O)N1CC(C)CC(C)C1? Thanks you. jim

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unit for the diameter of the erase sphere
by Dieter Blaas 02 Oct '17

02 Oct '17

Hi, what is the unit of the diameter of the erase sphere Angstrom or pixels? Thank you very much, regards, 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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Re: [Chimera-users] Query (how to find H-bonds)
by Gurudeeban Selvaraj 01 Oct '17

01 Oct '17

Dear Dr. Elaine Thanks! But I want to see protein and ligand (peptide) structure. I could not see ligand, the display shows only protein structure. The file I enclosed is docked result. Instead of ligand there is a dotted line in between the protein.....I could not see this before. The attachment file has (2 to 195 protein) and (1-7 peptide). I can see the individual structure in separate file but I could not see in same pdb file (docked result). The tutorial is not helping to fix the issue Please make me clear! ------------------ Sincerely Dr. Gurudeeban Selvaraj, Ph.D. Postdoctoral Researcher Center for Food Science and Technology School of Chemical Engineering and Environment Henan University of Technology, Zhengzhou, China Mobile: +86 1883 800 2927; +91 84890 55578 ORCID:http://orcid.org/0000-0002-7223-3853 Residence: Room No. 503, Foreign Teacher's Apartment, University Garden, Lianhua Street No. 50, Hi-Tech development Zone, Zhengzhou, 450001, China ------------------ Original ------------------ From: "meng";<meng(a)cgl.ucsf.edu>; Send time: Sunday, Oct 1, 2017 1:28 AM To: "Gurudeeban Selvaraj"<gurudeeb99(a)qq.com>; Cc: "UCSF Chimera Mailing List"<chimera-users(a)cgl.ucsf.edu>; Subject: Re: [Chimera-users] Query (how to find H-bonds) Dear Dr. Selvaraj, Probably you just need to display the atoms, command “display” or menu: Actions… Atoms/Bonds… show. This is just a general part of using Chimera. I recommend going through the “Getting Started” tutorial to become more familiar with the program: <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> Good luck, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 30, 2017, at 4:57 AM, Gurudeeban Selvaraj <gurudeeb99(a)qq.com> wrote: > > Dear Dr.Elaine, > > Thanks for the information. It is working now but some of them I could not see hydrogen bonds (Intra). Now I could not see the ligand structure of the docked result in Chimera. > > I have enclosed file and snap shot of my issue. Let me know, what will do? > > <3_8_sol_3.ref.pdb><image.jpg>

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Re: [Chimera-users] Query (how to find H-bonds)
by Gurudeeban Selvaraj 30 Sep '17

30 Sep '17

Dear Dr.Elaine, Thanks for the information. It is working now but some of them I could not see hydrogen bonds (Intra). Now I could not see the ligand structure of the docked result in Chimera. I have enclosed file and snap shot of my issue. Let me know, what will do? ------------------ Sincerely Dr. Gurudeeban Selvaraj, Ph.D. Postdoctoral Researcher Center for Food Science and Technology School of Chemical Engineering and Environment Henan University of Technology, Zhengzhou, China Mobile: +86 1883 800 2927; +91 84890 55578 ORCID:http://orcid.org/0000-0002-7223-3853 Residence: Room No. 503, Foreign Teacher's Apartment, University Garden, Lianhua Street No. 50, Hi-Tech development Zone, Zhengzhou, 450001, China ------------------ Original ------------------ From: "Elaine Meng";<meng(a)cgl.ucsf.edu>; Send time: Friday, Sep 29, 2017 5:06 AM To: "Gurudeeban Selvaraj"<gurudeeb99(a)qq.com>; Cc: "UCSF Chimera Mailing List"<chimera-users(a)cgl.ucsf.edu>; Subject: Re: [Chimera-users] Query (how to find H-bonds) > On Sep 28, 2017, at 1:54 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Many orange lines are drawn on the structure to show the H-bonds. One minor correction: for you, the lines will be whatever color is shown in the square color well near the top of the H-bond dialog… the default is a bright blue color similar to cyan. Elaine

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Query
by Gurudeeban Selvaraj 28 Sep '17

28 Sep '17

Dear Support Team, Thanks for the academic free of Chimera. I have a doubt, how can I visualize H-bonding interactions of docked structure of protein-protein interaction. I used FireDock for docking studies. While running on FindHbond on structure/binding tool it says no H-bonds, but i click both shows something.....How can i see protein-protein interacting HBond and label it? For the reference, I enclosed two files. Thanks in advance! ------------------ Sincerely Dr. Gurudeeban Selvaraj, Ph.D. Postdoctoral Researcher Center for Food Science and Technology School of Chemical Engineering and Environment Henan University of Technology, Zhengzhou, China Mobile: +86 1883 800 2927; +91 84890 55578 ORCID:http://orcid.org/0000-0002-7223-3853 Residence: Room No. 503, Foreign Teacher's Apartment, University Garden, Lianhua Street No. 50, Hi-Tech development Zone, Zhengzhou, 450001, China

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