- Chimera-users - RBVI Mailing Lists

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 09 Mar '18

09 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 22 Feb '18

22 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 15 Feb '18

15 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 14 Feb '18

14 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 14 Feb '18

14 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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Pipes command deletes the previous pipes model
by vamsee 12 Feb '18

12 Feb '18

Hello Elaine, I'm trying to create pipes models with different edge colors for 2 models. I use the following command for the first model (model # - 0.11). *pipes #0.11 helixArrow false helixSplit false helixSplitRatio 7.0 helixEdgeColor blue* Then I try to create the second pipes model using the same command with the model number changed (model number #0.12) *pipes #0.12 helixArrow false helixSplit false helixSplitRatio 7.0 helixEdgeColor red* Basically the difference between the two pipes models is the edge color. But, when I run the second command, it deletes the first pipes model (#0.11). I'm not sure what is going on. I'm attaching the whole code here. Please advise. *open 0 4G80.pdb* *split* *delete #0.1-10* *focus* *color white,r #* *pipes #0.11 helixArrow false helixSplit false helixSplitRatio 7.0 helixEdgeColor blue* *pipes #0.12 helixArrow false helixSplit false helixSplitRatio 7.0 helixEdgeColor blue* Thank you, Vamsee

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"Save Image..." with higher pixel than my screen comes out blank
by Jun Ha Song 12 Feb '18

12 Feb '18

Hello, I have been fan of "Save Image..." when I am making figures. I have been using the function for some time, and last time I used it was Friday (Feb 9th, 2018). I would take images of 5000x3750 with supersample of 4x4 all the time. However, today, I noticed that the function was not working. When I specify pixel that is above the screen resolution (1920x1080), it would just be blank black image with specified image size. However, if I do not change the Chimera resolution and keep it default (ex. 1024x768), it is properly imaged. I have not had any system change in my computer. The only change is that I am currently using my laptop's screen, whereas before I have been using monitor connected to my laptop via HDMI cable. What could be the reason for this sudden malfunction? Best, Junha.

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Error while using minimize
by Andres Benitez 12 Feb '18

12 Feb '18

Hello, I am trying to use minimize to resolve side chain positions which were mutated using pymol. The file is saved as a pdb, but I am getting errors when I try to use the minimize function. I am wondering if the error is because the structure has some loops removed, or if there is something else going on. I've attached the chimera session file and a text file with the errors I am getting. Thanks, Andres Benitez

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Download specific chain only
by Healey, Joe 12 Feb '18

12 Feb '18

Hi again Chimera team, I need to download a chain from an enormous macromolecular complex as it's so large it actually crashes Chimera! Is it possible to do this directly in chimera somehow (downloading just that specific chain or chains? The fetch dialogue doesn't seem to like the typical underscore notation (e.g. 5IV5_BB ) 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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Surface/Cap colouring
by Healey, Joe 11 Feb '18

11 Feb '18

Hi chimera team, Is there an easy way to control the transparency of a surface and its clipping cap separately? I managed to do this in one session where the caps are solid, but the rest of the surface is transparent (e.g. see this link: https://drive.google.com/file/d/1-WQtUdYWbITetPl2RgRtU96eXKUj3_v5/view?usp=… ) [https://lh5.googleusercontent.com/QS16L041E4BqEh_EynLj2msR0gbNQVXbSZ7QexXke…]<https://drive.google.com/file/d/1-WQtUdYWbITetPl2RgRtU96eXKUj3_v5/view?usp=…> 3J9Q_wholetier_sliced_colcap.tif<https://drive.google.com/file/d/1-WQtUdYWbITetPl2RgRtU96eXKUj3_v5/view?usp=…> drive.google.com However in a different session I'm struggling to figure out how I achieved this. If I alter the surface colour in the Inspect dialog, it sets the surface and cap transparency to be the same. If I change the suface cap colour in the Effects > Side View dialogue, it gives the desired differential transparency, but colours ALL the surface endcaps identically which isn't what I want. Help me unpick what I did! 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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Hydrogen bonds for specific residues
by Seera Suryanarayana 10 Feb '18

10 Feb '18

Dear users, I have done simulations for 100ns and I generated clusters. I want know the hydrogen bonding during simulations for specific residues. Kindly let me know how do we select particular residues for hydrogen bonding in chimera. Thanks in advance, Surya Graduate student India.

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regarding getting molecule from the ChEBI ID
by Dilip H N 09 Feb '18

09 Feb '18

Hello, I have got beta-alanine zwitterion from ChEBI webpage and its ChEBI ID is *CHEBI:57966* So how can i get the molecule from its CHEBI id..?? I am able to get it from PubChem Id but, unable to get it from CHEBI id.... How can i solve this issue..?? Thank you. -- With Best Regards, DILIP.H.N Ph.D. Student ‌ <https://mailtrack.io/> Sent with Mailtrack <https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ndnaehg…>

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Regarding getting zwitter-ionic stucture of beta-alanine
by Dilip H N 09 Feb '18

09 Feb '18

Hello, I was able to get the beta-alanine neutral structure in chimera using the PubChem id ie., 239. But i want beta-alanine in its zwitterionic form since in water systems it will be in more stable in zwitterionic and i can run the simulation. So, how do i get it in zwitterionic form..?? Any suggestions are appreciated. -- With Best Regards, DILIP.H.N Ph.D Student <https://mailtrack.io/> Sent with Mailtrack <https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ndnaehg…>

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help require urgently
by Samman Mansoor 07 Feb '18

07 Feb '18

Dear users! anyone please help in saving the multimers generated by unit-cell option by making copies of a protein.... i want to save all the copies in pdb file but i am unable to do this ...i need someone's help urgently. the problem is attached in the screenshot...kindly help me to solve it thanks.

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Calculating distances in and between sheets
by Einav Tayeb-Fligelman 05 Feb '18

05 Feb '18

Dear all, I am trying to calculate distances in a unique structure in which alpha-helices stack into sheets, as in beta-sheets. I wish to calculate the distance between two facing sheets and between helices along each sheet. The structure theoretically contains tens of thousands of helices in each sheet (the content of the asymmetric unit is only one helix and the rest are a result of symmetry operations). I tried creating planes, one for each sheet, and calculate their distances, but I get zero since the planes are not exactly parallel. I also tried calculating centroid to centroid distance (I used 4 helices for each sheet), but there is an angle between the centroids and therefore I get a longer value then expected. Same when calculating axis to axis distance. Is there a good way to calculate such things with chimera? and if so, I would appreciate an explanation for an "alpha-helical sheet" containing structure, as well as for facing beta-sheets containing structure (in case there is a difference in the explanation). Thank you in advance, Einav -- PhD student at the Landau lab Faculty of Biology Technion, Israel Institute of Technology Haifa, Israel E-mail :einavtf@campus.technion.ac.il Tel at the lab:+972-77-8871964 <+972%2077-887-1964>

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Values on electrostatic map at mouse locations (in surface-colour-options)
by Boaz Shaanan 05 Feb '18

05 Feb '18

Hi, I'm seeing some weird values when I use this option, for example high +ve value when touching a very red area or -ve on a very blue area ( I use 3 colours scheme). I'm running linux alpha version v. 1.13 (build 41653) from 5 Jan 2018. The electrostatic potential was calculated in delphi. I have a vague recollection that this feature behaved more reasonably in the past when I used it (I could of course be wrong). Thanks for your help. 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

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Questions regarding Ribbon Structures
by Alex Yorn 05 Feb '18

05 Feb '18

UCSF Chimera, Just discovered your software and it's amazing! Thank you for making it free for academic use! I just have a quick question regarding the possibility of "filling-in" or changing the linewidth of ribbon structures. I would like to have my ribbon structures completely filled in and not hollow, so when I view them with "Side View" opition, I don't see emptiness inside. I've attached two photos. The first is a view of the ribbon structure from the outside. The second is a view of the ribbon structure view from the inside, where you can see that it's hollow. I would like to know what function or command to use to correct this so it's complete solid inside. Sincerely, Alex YornPhD Candidate Department of Molecular BiologyUniversity of Toronoto

2 1

Combining multiple files into one PDB file
by Liyana Binti Azmi 02 Feb '18

02 Feb '18

Hello, I’m Liyana, a PhD student from University of Glasgow. I’m using Chimera to dock my low resolution cryo-EM map to my pdb file, where the EM map represents a helical oligomeric form of the pdb file. So far, I’ve made multiple copies of my pdb and fitted it against my EM map and now I’m trying to save my multiple files as one file. I’ve referred to this message on the Chimera mailing list (www.cgl.ucsf.edu/pipermail/chimera-users/2014-May/009926.html<http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-May/009926.html>) and tried saving my files via ‘Save PDB’ and combining my files to one file. However, I couldn’t upload this on PyMOL or any other programs for subsequent analysis. Is there something wrong with my file? Attached is my file after using instruction A. I’ve also tried combining my files using the ‘combined’ feature but still get the same problem. Attached is my file after using instruction B. Could you have a look at these files, please? Thank you for your time. Best wishes, Liyana

2 1

Chimera Color Coding Chains that are Interacting
by Andrew Cuyegkeng 01 Feb '18

01 Feb '18

Hello, I am an undergraduate researcher still learning how to use Chimera. Our lab is exploring intramolecular bonds within a complex. I am aware of the FindContact tool but was running into problems when it came to color coding these interactions. I would like to color code the different chains that are involved in these interactions and make everything that's not interacting the color black. What would the best approach to this be? Thanks, Andrew

3 4

Minimizing the structure in Chimera
by Veijola Elias 31 Jan '18

31 Jan '18

Dear Mr. or Mrs. I am trying to minimize a structure of mutated coEnzyme B but the program gives me this error

2 3

Adding Missing residues
by ARMIN HODAEI 31 Jan '18

31 Jan '18

Dear Chimera Users, I am trying to add missing residues to the protein with the ID: 1u54 But unfortunately for chain A, I cannot do the adding. I go to "Tools > Structure Editing > Model/Refine Loops". Then I choose "chain A" and I select "all missing structure" and then "apply". But I got an error. Is there any other way for it? for "chain B" it works. Best Wishes, Armin -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

4 5

launch behavior query
by Oliver Clarke 29 Jan '18

29 Jan '18

Hi, I have Chimera listed as the default app on my Mac to open MRC and PDB files. It used to be that if I double clicked on a pdb, and I had Chimera open, the pdb would open in that instance of chimera. Now, it always spawns a new instance of chimera. Is there any way to revert to the old behavior? Cheers Oli

2 1

Quantification of electron density volume
by Priyamvada Acharya 27 Jan '18

27 Jan '18

Hi everyone, I am wondering if there is a way to extract the values plotted under Tools > Volume Data > Values at Atom Positions? Specifically, I would like to quantify the electron density surrounding a domain and compare it to another domain. This can be easily done if the values in the Histogram plotted under the tool mentioned above can be tabulated on a per-atom basis (perhaps within a PDB file, in the B-factor column). If anyone knows other methods to achieve this goal, that would be helpful as well. Thank you very much in advance for your feedback and suggestions! Best regards, Priyamvada

2 1

Alignment of repeated domains
by Benitez De La Fuente, Francisco 26 Jan '18

26 Jan '18

Hello, I'm using the tool MatchMaker to align different structures. My reference protein has 3 domains very similar and I would like to show an alignment of other 3 proteins with each one of those 3 domains. The problem is that the 3 protein always align to the same domain (one of the 3, instead of each one with a different domain). How can I do so I can exclude the part of the protein already aligned in new alignments? I hope I explained myself and thank you in advance. Francisco Benitez.

2 2

How do i rectify this error
by Niasha Tauro 25 Jan '18

25 Jan '18

Hello Chimera Users Can you please help me rectify the following error showing on chimera (1.11.2 version) during molecular docking: 'C:\molecular' is not recognized as an internal or external command, operable program or batch file. ----- Application stdout ----- [no output] ----- I have installed Autodock Vina and i am using the local executable location: vina.exe your assistance will be greatly appreciated kind regards Nyasha Tauro <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 2

Turning models on/off on a perframe basis
by Esser, Lothar (NIH/NCI) [E] 24 Jan '18

24 Jan '18

Hi, in a short animation I would like to turn on/off a second model that is overlapping with the main model. The idea is to show differences by showing/hiding side chains of the second model. I know I can turn off models with ~modeldisp #1 but I don't know how to do that properly in a perframe statement turn y 2 180 perframe "modeldisp #1 " range 0,1 frames 180 # pseudo code wait clearly range does not quite work and $1 is presumably not setup to be ~ or nothing. I want to turn #1 on/off say every 6 degrees. How can this be done ? Thanks, Lothar

2 2

mouse hovering not working
by Fabian Glaser 23 Jan '18

23 Jan '18

Dear all, The mouse hovering is not working for me, I use a Mac, and tried several version of Chimera, but the residue / atom number automatic labelling does not appear when hovering over. Any suggestion? 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

3 3

chimera website
by 陈柳青 22 Jan '18

22 Jan '18

hi i can not log chimera website . can not download the software. what's problem? sincerely liuqing chen | | 陈柳青邮箱：519198561(a)163.com | 签名由网易邮箱大师定制

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Re: [Chimera-users] question about AutodockVina /CHIMERA
by Elaine Meng 22 Jan '18

22 Jan '18

Hi Osvaldo, Without more information, I have no idea, sorry. If you are sure that the process finished (click the “i” icon near the bottom right corner of the Chimera window to make sure), I can only say to check in the Reply Log (open from Chimera Favorites menu) and see if it says anything else useful. The Autodock Vina process does not run on our system, so there is nothing I can check here; Chimera just has an interface to send and receive results from a web service that is run by another lab, as explained in the help page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> For the future, please send Chimera questions to the chimera-users(a)cgl.ucsf.edu address (CC’d here) to ensure they come to our attention. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 19, 2018, at 4:04 PM, ogs <ogs(a)ibt.unam.mx> wrote: > > to whom it may concern, > > hi! > I am having some problems using AUTODOCK-VINA / CHIMERA. > > I recently docked a linand, but I did not get the name.pdbqt file as result (I only got the name.receptor.pdb and pdbqt and the name.ligand.pdb and pdbqt) > > The software show a message telling me that the process has ended and I need to check the files (but I did not see the name.pdbqt file) > > What is happening? What could I do to solve this problem? > Thanks a lot. > Osvaldo Gómez Secundino

2 3

MD movie residue network analysis
by Neha Gandhi 22 Jan '18

22 Jan '18

Dear List, I am loading gromacs trajectory in Chimera using .tpr and .xtc files. The residue number in gro file starts from 83 and not from 1. When I perform residue network analyis using chimera and cytoscape, the numbering of residues starts from 1. Is there a way to change the residue numbers either in .tpr file or in cytoscape? Changing the residue numbering after the trajectory is loaded doesn't help. Thank you for your attention. Regards, Neha -- Regards, Dr. Neha S. Gandhi, Vice Chancellor's Research Fellow, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000 Australia LinkedIn Research Gate <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 1

Inactive atoms
by Nazahiyah Rodzli 22 Jan '18

22 Jan '18

Dear Chimera Users, My Chimera seems to display atoms and side chains in dimmed dark colour (picture below). I’ve tried to change the colour but they don’t work. I also can’t select any of the atoms/sidechains by mouse click+ctrl unless I pick select all from the select menu. I am using Chimera 1.10 version. Could you help me how I can change the settings perhaps? Best regards, Naza

2 1

Rotate and transform command
by 大帅 22 Jan '18

22 Jan '18

Hi, Therefore, we used UCSF Chimera to have a map's smmetry axes (approximately) parallel to the XYZ axes. The procedure followed by the relion tutorial we used for that was to read in InitialModel/symC1/run_it003_class001.mrc; use the duplicate option under the File menu of the Volume viewer. Then to deactivate map #1 on the Model Panel; rotate map #0 to have it’s symmetry axis more or less parallel to the XYZ axes; and then to use in the Command Line entry field: run_it003_class001.mrc; and save this model in the InitialModel/symC1/ directory with the name inimodel.mrc I have done as the above tutorial in relion, but the saved inimodel.mrc file does not change its position or orientation at all. So, my question is what commend can save a map after rotating or transforming its x,y,z coordinate ? What is the procedures to do so ? Thanks Dashuai

2 1

emails
by Aga Szydlik 20 Jan '18

20 Jan '18

May I please ask to be unsubscribe from all "chimera users questions" emails, thank you Aga Szydlik PhD Candidate, School of Pathology, University of the Witwatersrand National Institute for Communicable Diseases, a Division of the National Health Laboratory Service Centre for HIV & STI's: HIV Virology Section (Morris Laboratory) 1 Modderfontein Road Sandringham, 2131 South Africa email: agas(a)nicd.ac.za<mailto:agas@nicd.ac.za> | www.nicd.ac.za<http://www.nicd.ac.za/> [cid:image003.png@01D2F0EE.60CC2540] Practice Number: 5200296 The views expressed in this email are, unless otherwise stated, those of the author and not those of the National Health Laboratory Service or its management. The information in this e-mail is confidential and is intended solely for the addressee. Access to this e-mail by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken or omitted in reliance on this, is prohibited and may be unlawful. Whilst all reasonable steps are taken to ensure the accuracy and integrity of information and data transmitted electronically and to preserve the confidentiality thereof, no liability or responsibility whatsoever is accepted if information or data is, for whatever reason, corrupted or does not reach its intended destination.

2 1

Adding Menu items to Python Shell
by Batra, Vinod (NIH/NIEHS) [C] 16 Jan '18

16 Jan '18

Hi How to add menu items to IDLE-> Python Shell opened with Chimera 1:1x running on OS X. Vinod Batra NIEHS

2 1

Command line selection in Chimera
by Jerry Honts 16 Jan '18

16 Jan '18

Is there any easy way to select *a range of chains* in complex models like the ribosome in Chimera at the command line? I haven't been able to work out the syntax for this type of complex selection at the command line. For example, what is the syntax of the command to select chains 1G through 1Z and chains 10 through 19 in PDB file 5DOY [without explicitly listing them one by one]? I may be missing something simple, and I have not been able to get it to work or find an example in documentation. I have been able to do this in Chimera X but not the current version of Chimera. Thanks, Jerry E. Honts -- Jerry E. Honts, Ph. D. Associate Professor of Biology Drake University 2507 University Avenue Des Moines, IA 50311-4505 Science Connector Building 210 (faculty office)

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Re: [Chimera-users] Pseudobonds in mmCIF
by Elaine Meng 16 Jan '18

16 Jan '18

Just for the benefit of the list, the problem with spurious bonds between residues in Chimera was solved by adding sequence information to the input mmCIF file. Elaine > > On Jan 11, 2018, at 1:35 PM, Henry Nguyen <nguyen.henry.c(a)gmail.com> wrote: > > > > Thanks everyone for all the help. My problem is fixed by running mmtbx.prepare_pdb_deposition with the sequence information. The new cif file is displaying pseudobonds correctly and can be toggled on/off. > > > > Thanks again! > > Henry > > > > On Thu, Jan 11, 2018 at 11:43 AM, Greg Couch <gregc(a)cgl.ucsf.edu> wrote: > > Hi Henry, > > > > Sorry about the problems with mmCIF in Chimera. Those problems are a major reason why we wrote ChimeraX. So please check out ChimeraX, http://www.rbvi.ucsf.edu/chimerax/. The mmCIF reader is several orders of magnitude faster than Chimera's and presents the author numbering to identify residues instead of the internal mmCIF numbering. The graphics in ChimeraX are better too. If there is some feature in Chimera that isn't in ChimeraX yet that you need, please let us know. ChimeraX also works with VR headsets. > > And while ChimeraX shows your structure "correctly". It could do a much better job if the missing sequence information were in the mmCIF file. In Phenix, that is done by running the mmtbx.prepare_pdb_deposition program, i.e, by preparing the mmCIF file so that is suitable for submission to the PDB. That would probably help Chimera too. > > > > HTH, > > Greg

1 0

Does Chimera support stereo with a Nvidia Quadro M4000 graphics card?
by xzhang1999＠zju.edu.cn 13 Jan '18

13 Jan '18

Hi, Does Chimera support stereo on the Nvidia Quadro M4000 graphics card? I have a workstation with a Nvidia Quadro M4000 graphcs card (64bit, win10&ubantu), but cannot successfully have Chimera displaying sequential stereo? Any suggestion would be greatly appreciated. Thanks a lot. Best regards, Xing

2 2

Output of distance measurements
by Marco Sette 13 Jan '18

13 Jan '18

Dear all, I have a very primitive script to measure distances, like distance :1.a@ha :5.b@ha distance :1.a@ha :4.b@ha distance .... etc. I run the script in File --> Open and get the distances in the Structure Measurements panel and then Save. The output file list all the distances but, for my analysis, it would be better to keep the lines separated by a blank line, or something like this. Maybe this is possible by some change in my primtive script but I have no idea... Thanks for your help, Marco

3 3

Pseudobonds in mmCIF
by Henry Nguyen 10 Jan '18

10 Jan '18

Hi, I am trying to disable all pseudobonds between gaps in my structure in an mmCIF file. I've tried: In the Pseudobond Panel, there is only one group (distance monitor) and it has 0 pseudobonds in the group. Hiding that group doesn't change anything. I also tried disabling them using setattrr ("setattr p display false"/ "setattr p display false") but neither didn't change anything. If I select a psuedobond and examine it using the Selection Inspector, the Pseudobond tab is unselectable under Inspect. Only if I go to the Bond tab can I hide it. I have to use mmCIF format as I have too many chains for a pdb. Thanks, Henry

2 1

Re: [Chimera-users] importing chimera module question
by Mysteray Rice 10 Jan '18

10 Jan '18

Get organized with Yahoo Mail

1 0

write prmtop, source leaprc.ff14SB
by stu118506 08 Jan '18

08 Jan '18

Dear Chimera users, I'd like to save a prmtop file of my protein after preparation for molecular dynamics simulation. I tried to do it by using Tools - Amber - write Prmtop . I get this reply log entry: _command: ['/gpfs/fs5/home-sh/sumbi463/.local/UCSF-Chimera64-2017-12-05/bin/amber16/bin/sleap', '-f', '/scratch/tmpOlw0GO/solvate.cmd']_ _Running sleap command: /gpfs/fs5/home-sh/sumbi463/.local/UCSF-Chimera64-2017-12-05/bin/amber16/bin/sleap -f /scratch/tmpOlw0GO/solvate.cmd_ _(writeprmtop) [gtkleap]$ source leaprc.ff14SB_ _(writeprmtop) Error: can not find file leaprc.ff14SB in all the search path._ _Failure running sleap_ I guess that it should source oldff/leaprc.ff14SB because the file seems to be in the directory oldff. But I don't know if that is right and were I have to change the path. Additionally, addions works perfectly although leaprc.ff14SB is also needed. So there the path seems to be set correctly. Is there anything I can do about it? Thank you Freia Krause Christian-Albrechts Universität zu Kiel,Germany

2 1

Inquiry about hydrogen bond analysis- important
by Mohamed S. Nafie 08 Jan '18

08 Jan '18

Chimera team. I made the hydrogen bond analysis for the co-crystallized ligand for 1DB1 receptor. it makes on the PDB 6 hydrogen bonds through both oxygen and hydrogen of the hydroxyl group (three of both) with the amino acids residues in the binding site, Also chimera forms 6 but through oxygen of hydroxyl group only. This my first question why? The second question is the structure of the Co crystallized Ligand is not correct, when I adjust the bond order of it by Maestro and save it as pdb and reopen it by Chimera, it forms only two hydrogen binds why? Please try to help me in this question, because I need it necessary Thanks Mohamed S. Nafie Assistant lecturer Chemistry Department, Faculty of Science, Suez Canal University Ismailia, P.O(41522), Egypt Mobile: +201065072524

2 1

regarding opening mouth or poc file on chimera
by Ming 05 Jan '18

05 Jan '18

Hi Chimera team, I have a quick question regarding opening CASTp file on Chimera. I downloaded the pdb file together with mouth and poc file and saved them in the same folder. I also made sure the names are consistent among these files. However, I am still getting error messages as following. Error reading 3mbg.poc: ValueError: Mouth info header missing or IDs not consecutive File "/home/ming/.local/UCSF-Chimera64-1.11.2/share/CASTp/__init__.py", line 88, in processInfoFile " IDs not consecutive" % label.capitalize()) See reply log for Python traceback. I looked up the Chimera manual online and it looks pretty straight forward to open either the mouth or poc file but I am not sure why I keep getting the error messages. Any help will be appreciated. Thanks, Ming

2 1

How to set volume view step size in "vop morph" command
by Zheng Liu 04 Jan '18

04 Jan '18

I want create a morph volume between 2 maps (#0, and #1), as a command I wrote:vop morph #0,1 step 1 playStep 0.04 frames 200 step 1 However, the new model #4 morph was display in step "8", not step "1" in the volume view window. How to set the step size in the vop morph command? Thanks!

2 1

Chimera software error
by محمد عوض على خالد 02 Jan '18

02 Jan '18

Hello everyone. I am interested in using the builtin vina docking tool in Chimera. I get stuck several times at the following Error: ( Running AutoDock Vina for 5x5d failed; see Reply Log for more information: Application stderr ----- 'C:\Program' is not recognized as an internal or external command, operable program or batch file. ----- Application stdout) I check for several tutorials but got the same error, the version I used is Chimera 1.12 and Ulpha version 1.13 in windows 10 platform (64bit) Thank you? Mohammed Khalid Department of Chemistry University of Taif Saudi Arabia ' ________________________________ هذه الرسالة ومرفقاتها (ان وجدت) تمثل وثيقة سرية قد تحتوي على معلومات تتمتع بحماية وحصانة قانونية, ان لم تكن الشخص المعني بهذه الرسالة يجب عليك تنبيه المرسل بخطأ وصولها إليك وحذف الرسالة ومرفقاتها (إن وجدت) من الحاسب الالي الخاص بك ولايجوز لك نسخ هذه الرسالة او مرفقاتها (إن وجدت) أو اي جزء منها أو البوح بمحتوياتها لأي شخص أو استعمالها لأي غرض علما بأن الإفادات والاراء التي تحتويها هذه الرسالة تعبر فقط عن رأي المرسل وليس بالضرورة رأي جامعة الطائف ولا تتحمل جامعة الطائف أي مسئولية عن الأضرار الناتجة عن أي فايروسات قد يحملها هذا البريد . The information in this email and in any files transmitted with it is intended only for the addressee and may contain confidential and/or privileged material. Access to this email by anyone else is unauthorized. If you receive this in error, please contact the sender immediately and delete the material from any computer. If you are not the intended recipient, any disclosure, copying, distribution or any action taken or omitted to be taken in reliance on it, is strictly prohibited. Statement and opinions expressed in this e-mail are those of the sender, and do not necessarily reflect those of the Taif University. '. If the disclaimer can't be applied, attach the message to a new disclaimer message. ' ________________________________ هذه الرسالة ومرفقاتها (ان وجدت) تمثل وثيقة سرية قد تحتوي على معلومات تتمتع بحماية وحصانة قانونية, ان لم تكن الشخص المعني بهذه الرسالة يجب عليك تنبيه المرسل بخطأ وصولها إليك وحذف الرسالة ومرفقاتها (إن وجدت) من الحاسب الالي الخاص بك ولايجوز لك نسخ هذه الرسالة او مرفقاتها (إن وجدت) أو اي جزء منها أو البوح بمحتوياتها لأي شخص أو استعمالها لأي غرض علما بأن الإفادات والاراء التي تحتويها هذه الرسالة تعبر فقط عن رأي المرسل وليس بالضرورة رأي جامعة الطائف ولا تتحمل جامعة الطائف أي مسئولية عن الأضرار الناتجة عن أي فايروسات قد يحملها هذا البريد . The information in this email and in any files transmitted with it is intended only for the addressee and may contain confidential and/or privileged material. Access to this email by anyone else is unauthorized. If you receive this in error, please contact the sender immediately and delete the material from any computer. If you are not the intended recipient, any disclosure, copying, distribution or any action taken or omitted to be taken in reliance on it, is strictly prohibited. Statement and opinions expressed in this e-mail are those of the sender, and do not necessarily reflect those of the Taif University. '. If the disclaimer can't be applied, attach the message to a new disclaimer message.

2 1

Coloring specific amino acid residues in Chimera
by Mariano Carossino 27 Dec '17

27 Dec '17

Hi, I have two trimer structures for the VP7 protein of two different rotavirus strains and I would like to highlight specific amino acid changes between these two. Could you please indicate me how can I color the amino acid residues that differ between these two structures using Chimera? Thank you, MC

2 1

B-factor values
by ARMIN HODAEI 25 Dec '17

25 Dec '17

Dear Chimera Users, I am trying to define new attributes in Chimera, and I have written a new set of scores for every residue (for b-values) but after adding I get this error message. It seems that I have to change the numbering of the residues on the PDB, to get correct colors. Sincerely, -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

2 1

Electrostatic Potential
by chemocev marker 21 Dec '17

21 Dec '17

Hi I am just calculating the Electrostatic Potential, and I wanted to know your opinion which force field is better for metallo proteins.And what is criteria to choose and not to choose the pKA... As I am doing the reaction at different pH and what I see in the PDB the proteins are crystallized at different pH then the reaction conditions. Structures are solved at low pH but the reactions are done at high pH. best Jiri

3 5

box cut out is not a cube!
by Dieter Blaas 20 Dec '17

20 Dec '17

Dear all and Elaine, I have an mrc volume of 450 x 450 x 450 px, put a marker at a particular location and cut out a box with 'Box around selected atoms with padding 60'. However, Chimera shows me the boxed volume as 124 x 123 x 124. I understand that the higher value must result from the voxel size being 0.97 A/px, so the dimensions would be 123.71 x 123.71 x 123.71 or anything similarly rounded. BUT why are the dimensions in x,y,z different and the box not exactly cubic? I noticed that it might have to do with centering but I do not understand how I can cut out a 'really' cubic box! Thanks 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 ------------------------------------------------------------------------

2 5

Question about docking in Chimera
by Ulrich, Rebecca 20 Dec '17

20 Dec '17

Hello, I am trying to do some docking studies in chimera and I have been following a protocol given to me in a drug discovery class that walks me through the dock prep and autodock vina options in chimera. I have tried to run some docking and it will tell me "execution complete- check outputs to verify successful execution" but I don't get any popups with any information about the docking. Is there a way to get the docking values to show? I have done this assignment before and didn't have issues, but now as I am redoing it to prep for some other docking studies, I can't get it to work. Thanks, Rebecca

2 1

Re: [Chimera-users] [Chimera] Failure preparing structure for Autodock Vina
by Elaine Meng 20 Dec '17

20 Dec '17

Dear Jutapat, The chimera-users address (CC’d here) is recommended for questions, for your future reference. Email to me only might fall through the cracks. It is hard to tell what the problem is without having your data, but the message says it cannot figure out the atom type of some atom Ha, so maybe the hydrogen atoms in your input structure have weird names or the names are in the wrong columns of the file. You might try deleting all hydrogens (e.g. command: delete H) before running the tool. However, if that doesn’t work you probably need to correct some error in your input file (the file format or atom names in the file). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 20, 2017, at 1:30 AM, Jutapat Romsuk <jutapat_rom(a)bio.eng.osaka-u.ac.jp> wrote: > > My problem is show below > Wrote prteinA.receptor.pdb > Traceback (most recent call last): > File "/Applications/Chimera.app/Contents/Resources/share/vina/ws.py", line 393, in prepareReceptor > execfile(scriptPath, d) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/Utilities24/prepare_receptor4.py", line 172, in <module> > delete_single_nonstd_residues=delete_single_nonstd_residues) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 533, in __init__ > version=version, delete_single_nonstd_residues=delete_single_nonstd_residues) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 140, in __init__ > self.addCharges(mol, charges_to_add) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 226, in addCharges > chargeCalculator.addCharges(mol.allAtoms) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/MolKit/chargeCalculator.py", line 80, in addCharges > babel.assignHybridization(atoms) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py", line 127, in assignHybridization > a.babel_atomic_number = self.get_atomic_number(a.babel_type) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py", line 103, in get_atomic_number > (name,_name) ) > ValueError: Could not find atomic number for Ha Ha > Receptor preparation for AutoDock Vina failed; please look inReply Log to see error messages. > cannot prepare receptor for AutoDock Vina; please look in Reply Log and/or run Chimera with --debug flag to see errors. > > I would like to know how to fix this problem. Help me please. > > --------------------------------------------------------------------------------------- > Jutapat ROMSUK > Biotechnology Global Human Resource Development Program > > Cell Technology Laboratory > Department of Biotechnology, Graduate School of Engineering, Osaka University > C2-111, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan > Laboratory phone: +81-6-6879-7423 >

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[MGMS-DS]: Molecular Modelling Workshop March 12-14, 2018 in Erlangen, Germany
by Harald Lanig 14 Dec '17

14 Dec '17

Dear list subscribers, we are very happy to announce next year’s “32nd Molecular Modelling Workshop (MMWS)” (http://mmws2018.mgms-ds.de) that takes place on March, Monday 12th to Wednesday 14th, 2018, at the Friedrich-Alexander-University in Erlangen. The MMWS has a long history of giving young scientists (especially graduate students) the opportunity to present their work and dive into discussions with each other and the “older experts” of the field to gain valuable feedback from academic as well as industrial colleagues. Oral and poster contributions are welcome from all areas of molecular modelling – from the life sciences, computational biology and chemistry, cheminformatics, to materials sciences. Starting with the scientific program on Monday after lunch should allow to avoid travelling on weekend keeping the expenses at a minimum. A hearty workshop dinner and a traditional joint evening in Erlangen’s Steinbach-Bräu brewery complement the scientific program. The workshop is organised by the German Section of the Molecular Graphics and Modelling Society (MGMS-DS e.V.). ####### Pre-conference workshop ####### For the first time at our Molecular Modeling Workshop, Schrödinger is offering a pre-conference workshop entiteled "Structure-based Drug Design using the Schrödinger Suite". If you are interested in participating at the software session, please checkmark the corresponding field upon filling the registration form. ####### Plenary Speakers ####### We are very happy to announce that four outstanding researchers accepted our invitation to present a plenary lecture at the workshop: Bernd Engels (Institute of Physical and Theoretical Chemistry, University of Würzburg) "Towards the Rational Design of Covalent Inhibitors" Pavel Hobza (Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague) "Protein-Ligand Interactions and Drug Design" Gerhard Wolber (Institute of Pharmacy, Free University of Berlin) "Exploring Protein - Ligand Binding Using 3D Pharmacophore Patterns" Marc Hamm (Henkel AG & Co. KGaA) "Facets of Materials Modelling at Henkel" ####### Poster and Lecture Awards ####### As in the past years, there will be two poster awards of EUR 100 each and three lecture awards for the best contributed oral presentations: 1st winner: Travel bursary to attend the Young Modeller's Forum in London, UK, plus a speaker slot option at YMF (travel expenses are reimbursed up to EUR 500) 2nd winner: EUR 200 travel expenses reimbursement 3rd winner: EUR 100 travel expenses reimbursement Only undergraduate and graduate research students qualify for the poster and lecture awards. ####### Registration and poster/talk submission ####### Submit talks and/or poster titles via the registration form accessible on the workshop website https://mmws2018.mgms-ds.de/index.php?m=register The deadline for all submissions is February 16th, 2018. ####### General information ####### Website http://mmws2018.mgms-ds.de will provide all necessary information about the meeting. We are looking forward to meeting you in Erlangen! - Achim Zielesny, Scientific Committee Workshop Organisation 2018 - Harald Lanig, Chairman of the MGMS-DS e.V. (http://www.mgms-ds.org) -- ------------------------------------------------------------------------ PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg Zentralinstitut fuer Scientific Computing (ZISC) Geschaeftsfuehrer Martensstrasse 5a, 91058 Erlangen Fon +49 9131-85 20781 harald.lanig(a)fau.de Fax +49 9131-85 20785 http://www.zisc.uni-erlangen.de ------------------------------------------------------------------------

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Edition of the pdb/trajectories via Chimera
by James Starlight 04 Dec '17

04 Dec '17

Dear Chimera Users! I have a pdb file for the 16 monomers of the coarse-grained GPCRs and its corresponded trajectory in dcd. In both files all the monomers are defined as the same letter of the chain (X). My question: are there an easy way to assign a unique letter to each of the monomers in the both files via Chimera to facilitate the further analysis ? Thanks so much! James

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fail to install chimera 1.12
by Haoming Zhang 01 Dec '17

01 Dec '17

Hello, I would appreciate your help for some problems with installation of chimera 1.12 in rhel 7.4 linux. Although we have installed chimera in rhel 5.4 before, this time we upgraded OS to rhel 7.4 and run into the problem. Basically I downloaded the binary file from your website and run the bin file in the Download directory. But the process failed. I have included the error message in the attachment and would appreciate your help. Sincrely, Haoming Zhang PhD Research Assistant Professor The University of Michigan Ann Arbor, MI PS. I have troubled attaching the file. SO I paste it below: root@boxx Downloads]# ./chimera-1.12-linux_x86_64.bin UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Original path: '/root/Downloads' inflating: chimera_install_aelQQu/installer inflating: chimera_install_aelQQu/chimera.bin Enter install location: /opt/UCSF/Chimera64-1.12 Extracting files. This may take a few minutes. Executing command: './chimera.bin -q -d /opt/UCSF/Chimera64-1.12' UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://www.info-zip.org) Install desktop menu (icon has to be done by user)? yes Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.12/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/opt/UCSF/Chimera64-1.12/share/chimeraInit.py", line 628, in init import chimera File "/opt/UCSF/Chimera64-1.12/share/chimera/__init__.py", line 2758, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/opt/UCSF/Chimera64-1.12/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/opt/UCSF/Chimera64-1.12/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/opt/UCSF/Chimera64-1.12/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/opt/UCSF/Chimera64-1.12/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: libXss.so.1: cannot open shared object file: No such file or directory ERROR in chimera_final_install: unable to install desktop icon: result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_aelQQu' Installation is done; press return. When I run chimera in the installed directory, I got this error. root@boxx bin]# ./chimera Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.12/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/opt/UCSF/Chimera64-1.12/share/chimeraInit.py", line 628, in init import chimera File "/opt/UCSF/Chimera64-1.12/share/chimera/__init__.py", line 2758, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/opt/UCSF/Chimera64-1.12/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/opt/UCSF/Chimera64-1.12/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/opt/UCSF/Chimera64-1.12/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/opt/UCSF/Chimera64-1.12/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: libXss.so.1: cannot open shared object file: No such file or directory

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question on visualization
by C.J. 01 Dec '17

01 Dec '17

Hi specialists, I have a problem when adjusting the level of a map. If the level > 0, it seemed OK, but when it is less than 0, it showed a solid box. This is different from EMAN2. In EMAN2, the threshold less than 0 also works. I'm not sure whether the defining of level is the same as the threshold in EMAN2. Or is there any other way to show the density of a map as in EMAN2 with threshold less than 0? Some snapshots of the visualization in both programs are attached to the post. Thank you! regards, Jianhao

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Mutating to Lysine neutral
by Alireza Shaneh 30 Nov '17

30 Nov '17

Hello, I wanted to know if there would be a way to mutate the positively charged Lysine to Lysine neutral in Chimera. Thanks in advance, Alireza

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hiding the structure elements
by chemocev marker 26 Nov '17

26 Nov '17

Hi Is there is way to hide all those structure elements which are not selected in chimera. best Jiri

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Analysis of the protein-protein binding interphaces in MARTINI models
by James Starlight 26 Nov '17

26 Nov '17

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

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Coulombic (Mailing list question)
by RYDER WHITTAKER HAWKINS 22 Nov '17

22 Nov '17

My Question of the Day: - I am running an MD movie in Chimera - I want to display the solvent excluded surface colored by coulombic potential. - I would like to implement this command as a script at each frame. What is the command? I am getting error after error... >coulombic -10 red 10 blue How could I put this in a Per-Frame analysis? Thanks for any suggestions. The documentation is not so clear for this coulombic function. Ryder Whittaker Hawkins MSc Candidate PI: Dr. Luc Vallières ryder.whittaker(a)crchudequebec.ulaval.ca ca.linkedin.com/in/ryderwh Work: (418) 525-4444 Cell: (613) 979-7729 Dept. of Molecular Medicine Université Laval (CHUL) 2705 Laurier Blvd Québec, QC G1V 4G2

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Axes/Planes/Centroids for the OPM membrane visualization
by James Starlight 22 Nov '17

22 Nov '17

Dear Chimera Users, I have a question regarding Axes/Planes/Centroids for the visualization of the membrane plane predicted by OPM. Firstly, I have uploaded my structure with DUM atoms. Than, I selected the DUM atoms in both layers and try to show the membrane plane via defining of a plane for it. As the result, a cylindrical surface oriented perpendicular to the imaginative membrane has been emerged. What should I change in options to obtain it aligned along the membrane normal in a correct way? Is it possible to make more flexible selection of the DUM atoms only in the selected layer? Thank you for the help! Gleb

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TERs in PDB ?
by Marek Maly 21 Nov '17

21 Nov '17

Hello, is it possible to save the given molecular model (which is open in Chimera) in PDB format but with the TER string between consequent residues ? example: --------------------------- ATOM 1 Si1 CEN A 1 56.395 15.633 50.147 1.00 0.00 Si TER ATOM 2 C1 RE1 A 2 54.892 16.772 50.453 1.00 0.00 C ATOM 3 H1 RE1 A 2 54.289 16.821 49.538 1.00 0.00 H ATOM 4 H2 RE1 A 2 54.219 16.552 51.290 1.00 0.00 H ATOM 5 C2 RE1 A 2 55.394 18.185 50.780 1.00 0.00 C ATOM 6 H3 RE1 A 2 55.896 18.665 49.932 1.00 0.00 H ATOM 7 H4 RE1 A 2 56.038 18.053 51.659 1.00 0.00 H ATOM 8 C3 RE1 A 2 54.181 19.075 51.202 1.00 0.00 C ATOM 9 H6 RE1 A 2 53.674 18.496 51.984 1.00 0.00 H ATOM 10 H5 RE1 A 2 53.589 19.325 50.313 1.00 0.00 H ATOM 11 Si3 RE1 A 2 54.714 20.646 51.949 1.00 0.00 Si ATOM 12 C4 RE1 A 2 53.140 21.420 52.746 1.00 0.00 C ATOM 13 H8 RE1 A 2 53.430 22.271 53.376 1.00 0.00 H ATOM 14 H7 RE1 A 2 52.690 20.675 53.413 1.00 0.00 H ATOM 15 H9 RE1 A 2 52.466 21.649 51.911 1.00 0.00 H ATOM 16 C5 RE1 A 2 55.491 21.841 50.620 1.00 0.00 C ATOM 17 H12 RE1 A 2 56.423 21.426 50.217 1.00 0.00 H ATOM 18 H10 RE1 A 2 55.768 22.733 51.196 1.00 0.00 H ATOM 19 H11 RE1 A 2 54.875 22.300 49.836 1.00 0.00 H TER ATOM 20 C1 RE1 A 3 57.436 16.272 48.673 1.00 0.00 C ATOM 21 H1 RE1 A 3 58.039 17.117 49.028 1.00 0.00 H ATOM 22 H2 RE1 A 3 58.209 15.633 48.228 1.00 0.00 H ATOM 23 C2 RE1 A 3 56.488 16.820 47.464 1.00 0.00 C ATOM 24 H3 RE1 A 3 55.675 17.467 47.819 1.00 0.00 H ATOM 25 H4 RE1 A 3 55.960 16.034 46.910 1.00 0.00 H ATOM 26 C3 RE1 A 3 57.354 17.603 46.475 1.00 0.00 C ATOM 27 H6 RE1 A 3 58.241 17.015 46.210 1.00 0.00 H ATOM 28 H5 RE1 A 3 57.812 18.464 46.978 1.00 0.00 H ATOM 29 Si3 RE1 A 3 56.645 18.300 44.851 1.00 0.00 Si ATOM 30 C4 RE1 A 3 55.474 17.030 44.146 1.00 0.00 C ATOM 31 H8 RE1 A 3 54.666 17.578 43.646 1.00 0.00 H ATOM 32 H7 RE1 A 3 54.864 16.542 44.918 1.00 0.00 H ATOM 33 H9 RE1 A 3 55.893 16.349 43.396 1.00 0.00 H ATOM 34 C5 RE1 A 3 58.034 18.987 43.812 1.00 0.00 C ATOM 35 H12 RE1 A 3 59.000 18.584 44.141 1.00 0.00 H ATOM 36 H10 RE1 A 3 58.180 20.062 43.974 1.00 0.00 H ATOM 37 H11 RE1 A 3 58.009 18.601 42.786 1.00 0.00 H TER ATOM 38 C1 RE1 A 4 57.426 15.522 51.783 1.00 0.00 C ATOM 39 H1 RE1 A 4 58.370 14.991 51.606 1.00 0.00 H ATOM 40 H2 RE1 A 4 57.769 16.539 52.007 1.00 0.00 H ATOM 41 C2 RE1 A 4 56.787 14.966 52.995 1.00 0.00 C ATOM 42 H3 RE1 A 4 57.587 14.881 53.741 1.00 0.00 H ATOM 43 H4 RE1 A 4 56.321 13.982 52.869 1.00 0.00 H ATOM 44 C3 RE1 A 4 55.776 15.938 53.682 1.00 0.00 C ATOM 45 H6 RE1 A 4 54.722 15.759 53.439 1.00 0.00 H ATOM 46 H5 RE1 A 4 55.920 17.004 53.467 1.00 0.00 H ATOM 47 Si3 RE1 A 4 55.756 16.172 55.603 1.00 0.00 Si ATOM 48 C4 RE1 A 4 57.359 16.942 56.191 1.00 0.00 C ATOM 49 H8 RE1 A 4 57.601 17.853 55.629 1.00 0.00 H ATOM 50 H7 RE1 A 4 58.242 16.306 56.061 1.00 0.00 H ATOM 51 H9 RE1 A 4 57.248 17.148 57.263 1.00 0.00 H ATOM 52 C5 RE1 A 4 55.827 14.369 56.251 1.00 0.00 C ATOM 53 H12 RE1 A 4 56.581 13.702 55.818 1.00 0.00 H ATOM 54 H10 RE1 A 4 54.854 13.866 56.186 1.00 0.00 H ATOM 55 H11 RE1 A 4 56.205 14.393 57.280 1.00 0.00 H TER . . . --------------------------- If yes, how to do it ? Thank you in advance for your advice. Best wishes, Marek -- Vytvořeno poštovní aplikací Opery: http://www.opera.com/mail/

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Re: [Chimera-users] will chimeraX support the BILD file format?
by Francois BERENGER 21 Nov '17

21 Nov '17

On 11/17/2017 09:53 AM, Greg Couch wrote: > We've been debating that. The bild format has many commands. Which ones > do you use? I ask because I have code that implements the transforms, > color, and shape commands, but not any of the line drawing, polygon or > marker commands. Does that work for you? I use most of the drawing commands, to create graphical annotations (arrows, boxes, spheres). And I love the fact that they can be colored and made transparent. The whole format is potentially useful to me. This is a big advantage of Chimera over pymol for example. Don't loose that. Pymol is a mess for that and it forces you to go down to Python. Going through a simple specialized text format like BILD is a huge win. The BILD file format is trivial to generate by hands (for quick test) and via any programming language (when in production). Regards, F. > -- Greg > > On 11/16/2017 04:35 PM, Francois BERENGER wrote: >> Hello, >> >> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html >> >> I am a huge fan of this chimera feature, so I hope it will >> not disappear (trivial to create graphical annotations by hand >> or via a program). >> >> Regards, >> F. >> _______________________________________________ >> 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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Fwd: Does volume outline is bigger than actual volume?
by Elaine Meng 21 Nov '17

21 Nov '17

> > From: Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> > Subject: Does volume outline is bigger than actual volume? > Date: November 21, 2017 at 6:00:17 AM PST > > Hello, > > I need to understand precisely what Chimera do. Please look at the attached screen shoot. The arrows are anchored in point (0,0,0), and they are point in direction [(1,0,0),(0,1,0),(0,0,1)] red, yellow and blue respectively. > > I set my volume to minimum (grey cube), I checked "Show outline box using color", and I noticed it does not cover the shape of my volume. > > There are "margins" in the top, and the bottom visible in the image and much smaller on the sides. > > Why they are there? What is its exact size? Where does volume actually begins in the (0,0,0), or slightly below that point? > > -- > best wishes, > Michał Kadlof <m.kadlof(a)cent.uw.edu.pl <mailto:m.kadlof@cent.uw.edu.pl>>

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Match command question
by Yann STERCKX 21 Nov '17

21 Nov '17

Dear Chimera users, I've been struggling with the match command and was hoping you could help me out. I'm working a tetrameric enzyme. When the enzyme binds ligands, its domains rotate over a pivot point in the monomer. What I would like to do is superpose different liganded structures of the enzyme on the four monomer pivot points. Here's what I've done so far: * Each liganded state of the tetrameric enzyme is a single model * I use the match command to superpose the structures on the monomer pivot points (residues 430-433 in the structure). I used the following command match #model1:430-433 #model2:430-433 What is strange is that I obtain exactly what I want for 2 out of 4 models. Using this command I get an rmsd of 0.77A. But for the other 2 models, match does not seem to work as I obtain an RMSD of 27A and the superposition is clearly off. Including the iterate option does not alleviate the problem. I don't want to use matchmaker because this feature will, at least in my understanding, try to optimally fit two chains (or selections within two chains) on top of each other. If I do that, I do not get to see how the enzyme rotates around the monomer pivot points. How come match works really well for 2 out of 4 structures, but fails to perform the same task for the rest? Any pointers on what I might be doing wrong? Many thanks and kind regards, Yann PS: I've browsed through the archive, but could not really find a thread related to this problem (unless I overlooked it).

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Coordinates of atoms and volumes
by Michał Kadlof 20 Nov '17

20 Nov '17

Hi, 1. is there any way to get the exact Cartesian coordinates of any atom directly in Chimera? 2. Is there any way to get exact value from exact place inside density volumetric data? -- best wishes Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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PipesAndPlanks coloring not accurate
by Andrew Hagen 17 Nov '17

17 Nov '17

Hello, I have a protein model that I colored according to region: N-terminal domain (green), a domain that I inserted (gray), and the flanking (GGS)2 linkers (tan). When I apply PipesAndPlanks, the tan regions are changed to either green or gray, which is not desired (and apparently, the PipesAndPlanks' color cannot be changed once rendered). Is this a bug or am I doing something wrong? To add a little more detail, I manually Frankensteined this model together. At the genetic level, it's just a domain insertion, flanked by linkers, but in Chimera I did this by: Opening my wt protein model (green), splitting the chain into two models at an internal site, generating GGSGGS linkers de novo in Chimera and joining these to the new models, and then finally joining those two fragments through a "bridge" of another model. There was lots of manual torsioning and minimizing using FoldIt in this process. I can imagine a work around is just to overlay two PipesAndPlanks renders and masking different regions, but this seems inelegant. Any assistance/advice is appreciated! --Andrew

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Re: [Chimera-users] visualisation of volumes
by Elaine Meng 16 Nov '17

16 Nov '17

Hello Michał, The answer is actually shown in the command line of your screenshot image! You would use the “volume” command to set levels and colors. Instead of a color name you could give r,g,b,a values (red, green, blue, alpha=opacity, each on a scale 0-1). Just like you can say “level” multiple times in the same command, you can also give “color” multiple times. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general> 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 16, 2017, at 6:22 AM, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> wrote: > > Hello, > > how can I achieve the effect visible in attached image from command line? > > I need to add several semi transparent isosurfaces for a single volume. > > <Zaznaczenie_139.png>

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Command line for labelling specific residues in a zone
by Mark Rosenberg 16 Nov '17

16 Nov '17

I am not sure if this request was missed. I am having difficulty finding the syntax to write a line command in Chimera to label the non-polar or polar residues in say a 5 Angstroms zone. I would be grateful if you could advise me how to code the command line for labelling these residues with a 1-letter code please ? Once I see the format then I can readily adapt this to other situations. Thank you in advance. Mark

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Chimera/Modeller to add missing residues
by Daipayan Sarkar 16 Nov '17

16 Nov '17

Hello Elaine, I am using Chmiera-Modeller GUI to add the missing residues for my PDB file: (https://files.rcsb.org/view/1YPH.pdb) >From the mailing list, I am following the procedure listed in: http://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009174.html However, once the missing residues for chains A and B are included, I save the new PDB file using File > Save PDB... > under save models selection "selected all three files" and clicked OK. The resulting PDB file includes the original header with additional 'MODEL 1', 'MODEL 2' and 'MODEL 3'. How to save the atom coordinates as a single PDB file after adding the missing residues? Any comments/suggestions is appreciated. Regards, Daipayan

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Chimera comands
by Michał Kadlof 16 Nov '17

16 Nov '17

Hello, I have some troubles with finding in documentation suitable commands. How do I should write script which: - open a trajectory in saved PDB or PSF/DCD in MD movie tool. - read pseudobonds from file, and change the color of all of them at once - change origin, voxel size and rotation angle of opened volumetric data Can you help me? -- best wishes, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl <mailto:m.kadlof@cent.uw.edu.pl>>

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scripting: howto add IDATM labels
by Wiktor Pronobis 15 Nov '17

15 Nov '17

Hi all, I have a python script and want to know, how do I 1. add IDATM labels to the atoms 2. add a label in the upper right/left corner 3. make image nicer 4. save image as png I use the command "from chimera import runCommand as rc" and then "rc(COMMAND)" What should COMMAND be for my questions 1. - 4.? Thanks in advance, wpron

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Re: [Chimera-users] the matrix reported in 'fit in map'
by Tom Goddard 14 Nov '17

14 Nov '17

Hi Qiang, Glad you figured this out. Chimera uses whatever map origin is specified in the map file, and this may not follow the EMAN2 convention of putting the origin at the center of the map. You can change the map origin in Chimera using Volume Viewer panel menu entry Features / Coordinates, and you could save a new map with that origin with Volume Viewer menu File / Save Map As…. Tom > On Nov 13, 2017, at 8:10 PM, 周强 wrote: > > Hi Tom, > Thank you very much for your kind reply. > I have tested the Chimera matrix in EMAN2 Transform class as you described. The rotation part is consistent between Chimera and EMAN2. The translation part is also consistent if the origin index is set to the center of the map. ( For even images, the center is at (nx/2,ny/2) where the first pixel is at (0,0). For odd sized images, the center is at ((nx-1)/2,(ny-1)/2). The same concept extends to 3-D. http://blake.bcm.edu/emanwikiEman2TransformInPython ). > > Qiang > > >> -----原始邮件----- >> 发件人: "Tom Goddard" <goddard(a)sonic.net> >> 发送时间: 2017-11-14 02:13:27 (星期二) >> 收件人: "周强" <zhouq2015(a)mail.tsinghua.edu.cn> >> 抄送: >> 主题: Re: [Chimera-users] the matrix reported in 'fit in map' >> >> Hi Qiang, >> >> The 3x4 matrix reported by Chimera has the 3x3 rotation in the first 3 columns and the translation in the last column. I do not know EMAN2 conventions. Chimera does not use or convert to Euler angles. Keep in mind that the rotation is about the origin of the map coordinates which is set by the “Origin index” value (shown with Chimera Volume Viewer menu entry Features / Coordinates). If you rotate your map about a different origin, then that becomes a non-zero translation and a rotation about the map origin. >> >> Tom >> >> >>> On Nov 10, 2017, at 8:36 PM, 周强 <zhouq2015(a)mail.tsinghua.edu.cn> wrote: >>> >>> Dear Chimera developer group, >>> I am Dr. Qiang Zhou from Tsinghua university in Beijing China. Recently I'm going to calculate relative position between two maps with 'fit in map' in chimera. The 'fit in map' feature reported a matrix of 3 x 4. Can I convert this matrix to Euler angle with transform class of EMAN2 directly? Is the matrix of chimera same to that of EMAN2? BTW, The translation column in chimera matrix maybe contains a bug. I just manually rotated a map and then fit it into the original map. The matrix reported by Chimera should contain zero translation column. However, it reported a non-zero value (about 6-7 pixel) in translation column. >>> Thank you very much. >>> Qiang >>> _______________________________________________ >>> 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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Help using Chimera with SFLD - I cannot 'view in chimera'
by Anne-Frances Miller 14 Nov '17

14 Nov '17

Dear Elaine, or other Chimera Guru, I would like to start using the wonderful tools in SFLD, and watched the tutorials, however when I try to do any of the things that is supposed to send something to Chimera, it crashes. I cannot open enzyme active sites in Chimera, or HMM alignments. I have updated by chimera. I am running Mac OS X 10.10.5, and firefox 56.0.2 Anne-Frances Miller Professor of Chemistry University of Kentucky

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cap clipping plane
by René Frank 13 Nov '17

13 Nov '17

Hi, I have a problem that the cap of my clipping plane is capping only some of the electron density. See screenshot attached. Any tips on how to ensure all electron densities, including smaller structures, are capped would be gratefully received. Many thanks, René ============================= Dr R. Frank, PhD MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH United Kingdom Lab: +44 1223 267487 Mobile: +44 7870 208280 ============================

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question
by 等儿会儿 13 Nov '17

13 Nov '17

dear editor： i am a noob with using Chimera. Now, i want to find and select all amino acid surrounding my ligand within a particular range（eg. 10Å）,how should i do? thanks for your help ! from a user

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the matrix reported in 'fit in map'
by 周强 13 Nov '17

13 Nov '17

Dear Chimera developer group, I am Dr. Qiang Zhou from Tsinghua university in Beijing China. Recently I'm going to calculate relative position between two maps with 'fit in map' in chimera. The 'fit in map' feature reported a matrix of 3 x 4. Can I convert this matrix to Euler angle with transform class of EMAN2 directly? Is the matrix of chimera same to that of EMAN2? BTW, The translation column in chimera matrix maybe contains a bug. I just manually rotated a map and then fit it into the original map. The matrix reported by Chimera should contain zero translation column. However, it reported a non-zero value (about 6-7 pixel) in translation column. Thank you very much. Qiang

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working with PDB files from XplorNIH
by Miriam Gochin 13 Nov '17

13 Nov '17

I am wondering if it is possible in Chimera to select between different chains in a multimer that are defined by the SEGID parameter in XPLOR. This appears on columns 77-80 of the PDB file, e.g. in this homotrimer: ATOM 1 N GLN 1 -2.276 -27.488 29.307 1.00 0.00 A ... ATOM 684 N GLY 1 4.365 -26.465 20.200 1.00 0.00 C --- ATOM 1357 N GLN 1 13.798 -26.207 29.441 1.00 0.00 E ... Atom selection results in picking up 3 atoms instead of 1, since Chimera expects the chain designation after the residue name. The XPLOR output is therefore not compatible with Chimera input requirements and I am wondering if there is a workaround. Many thanks for any suggestions. --------------------------------- Miriam Gochin Touro University California miriam.gochin(a)tu.edu 707-638-5463

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help！
by 余汉文 12 Nov '17

12 Nov '17

Good afternoon! Can you give me a favor? I have a serious problem in the process of studying application cytoscape. I can't open protein structure formate file in cytoscape via RINalyzer. However UCSF Chimera does not start. SO I check the path to UCSF Chimera. The Chimera is installed at D:\Chimera. Finally, i open the dialog Cytoscape Preferences Editor to modify the path "D:\Chimera\bin". But i can't open the protein structure formate file in cytoscape via RINalyzer as same as early. I Heartfelt thank you to help me solve this problem. From the student in china

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Help with chimera / sfld compatibility
by Anne-Frances Miller 11 Nov '17

11 Nov '17

Hello experts, I have tried reloading many things and switched browsers. When I am in SFLD and want to view my aligned sequences of the subgroup identified by my enzyme, in chimera, I get the error message: Error while processing /Users/afm/Desktop/sfld-3.chimerax: '/var/folders/zg/vzx644v88xl59y001s75rw2h0000gp/T/hmmer_align_fsgWHiJp.sto' is not a Stockholm file Also Any ideas? IOError at /ajax/download_temp/hmmer_align_mZdHMnpU.sto/ [Errno 2] No such file or directory: u'/tmp/sfld/hmmer_align_mZdHMnpU.sto' Request Method: GET Request URL: http://sfld.rbvi.ucsf.edu/django/ajax/download_temp/hmmer_align_mZdHMnpU.st… Django Version: 1.6.8 Exception Type: IOError Exception Value: [Errno 2] No such file or directory: u'/tmp/sfld/hmmer_align_mZdHMnpU.sto' Exception Location: /usr/local/projects/sfld/production/www/sflddjango/apache/../../sflddjango/sfldajax/views.py in download_tempfile, line 61 Python Executable: /usr/bin/python Python Version: 2.7.5 Python Path: ['/usr/local/projects/netgen/production/lib/python/netgen/interface', '/usr/local/projects/sfld/production/lib/python/sqlparse-0.1.13-py2.7.egg', '/usr/local/projects/sfld/production/lib/python/MySQL_python-1.2.3-py2.7-linux-x86_64.egg', '/usr/local/projects/sfld/production/lib/python/django_debug_toolbar-1.2.2-py2.7.egg', '/usr/local/projects/sfld/production/lib/python/pycharm-debug.egg', '/usr/local/projects/sfld/production/lib/python/Sphinx-1.0.7-py2.7.egg', '/usr/local/projects/sfld/production/www/sflddjango/apache/../../../lib/python', '/usr/local/projects/sfld/production/www/sflddjango/apache/../..', '/usr/lib/python2.7/site-packages/PEAK_Rules-0.5a1.dev_r2713-py2.7.egg', '/usr/lib/python2.7/site-packages/Extremes-1.1.1-py2.7.egg', '/usr/lib/python2.7/site-packages/AddOns-0.7-py2.7.egg', '/usr/lib/python2.7/site-packages/DecoratorTools-1.8-py2.7.egg', '/usr/lib/python2.7/site-packages/BytecodeAssembler-0.6-py2.7.egg', '/usr/lib/python2.7/site-packages/SymbolType-1.0-py2.7.egg', '/usr/lib/python2.7/site-packages/PrivateWikis-1.0.0-py2.7.egg', '/usr/lib64/python27.zip', '/usr/lib64/python2.7', '/usr/lib64/python2.7/plat-linux2', '/usr/lib64/python2.7/lib-tk', '/usr/lib64/python2.7/lib-old', '/usr/lib64/python2.7/lib-dynload', '/usr/lib64/python2.7/site-packages', '/usr/local/lib64/python2.7/site-packages', '/usr/lib64/python2.7/site-packages/gtk-2.0', '/usr/lib/python2.7/site-packages', '/usr/local/lib/python2.7/site-packages', '/usr/local/projects/netgen/production/lib/python'] Server time: Sat, 11 Nov 2017 08:54:00 -0800 Anne-Frances Miller Professor of Chemistry University of Kentucky

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labels turned white
by Oleksiy Kovtun 09 Nov '17

09 Nov '17

Dear community, I encountered a problem with 2D labels turning white disregards what colour presets I give. The script reads title presets from a file (2dlabel path) and then display the title with these commnads: 2dlabels change * bgColor 1,1,1,0.75; 2dlabels change title visibility show The 'title' label should appear as opaque black font as defined in the label file: Label title (x,y): (0.18,0.5) text: u'Title' shown: False font size(s): 40 font style(s): bold font typeface(s): sans serif color(s): (0, 0, 0, 1) But it appears in white. Bizarrely all other presets in the label file translate into the title appearance as they should except for the colour. I run Chimera 1.11.12 (build 41280) on Unix. Script and label file are attached. Thank you. Oleksiy Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun(a)mrc-lmb.cam.ac.uk

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All PDB ca atom pairwise distance
by Kyle Morris 03 Nov '17

03 Nov '17

Dear chimera dev and users, Is there a way to calculate (using the GUI, commands or using a python script) the pairwise distances for every single c-alpha atom in a set of loaded PDB coordinates and spit this out to a file for further analysis? There are 142,800 atoms in the current loaded assembly. Thanks! Kyle

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rmsd graph
by SEFA ÇELİK 02 Nov '17

02 Nov '17

Dear Dr. I am using Chimera software(windows platform). I tried to get rmsd graph. And I got the result. But, graph's x-axis "*frame*" and y-axis "*rmsd*" value. I want the x axis to be the "*time*". Briefly, I want to see how the value of rmsd changes with time. Can you help with this? Could you explain in detail? Best regard Dr. Sefa Celik

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error during MPEGM enconding
by Edoardo D'Imprima 02 Nov '17

02 Nov '17

Dear Chimera team, I ma trying to record a simple movie using the following command #!/bin/csh -f # # windowsize 900 1094 movie record supersample 4 volume #0 style solid; wait volume #0 planes z,0,0; wait volume #0 planes z,0,115; wait movie stop ###bitrate 5000 movie encode output my_movie.mp4 quality highest framerate 25 mformat mp4 however I keep on getting this error message: /Applications/Chimera/Chimera.app/Contents/Resources/bin/ffmpeg -r 25.0 -i /var/folders/2h/r_flycl50hj8klh8w4t1xmw400030f/T/chimovie_Vcz6-%05d.ppm -vf crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -f mp4 -pix_fmt yuv420p -qscale 1 /Users/user/Desktop/folder/my_movie.mp4 An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: libavutil 52. 48.100 / 52. 48.100 libavcodec 55. 39.100 / 55. 39.100 libavformat 55. 19.104 / 55. 19.104 libavdevice 55. 5.100 / 55. 5.100 libavfilter 3. 90.100 / 3. 90.100 libswscale 2. 5.101 / 2. 5.101 libswresample 0. 17.104 / 0. 17.104 libpostproc 52. 3.100 / 52. 3.100 [image2 @ 0x7fac00802000] Could find no file with path '/var/folders/2h/r_flycl50hj8klh8w4t1xmw400030f/T/chimovie_Vcz6-%05d.ppm' and index in the range 0-4 /var/folders/2h/r_flycl50hj8klh8w4t1xmw400030f/T/chimovie_Vcz6-%05d.ppm: No such file or directory Could you please let me know what am I doing wrong? I tried both on my laptop (MacBook Pro (Retina, 13-inch, Early 2015) with OS version 10.11.6 (15G1004)) and our linux terminals (Linux sbterm 3.10.0-514.16.1.el7.x86_64 GNU/Linux) It happens on both Chimera 1.12 and Chimera 1.11 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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ChimeraX x Chimera feature comparison?
by Gustavo Seabra 02 Nov '17

02 Nov '17

Hi guys, I wonder if there is a ChimeraX x Chimera feature comparison anywhere. I’m aware of the “ChimeraX Advantages” page (http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html) However, I’m actually looking for a comparison that can tell what features are currently on Chimera that are *not* in ChimeraX, to consider if there is any reason to keep both in the computer. Thanks, -- Gustavo Seabra Adjunct Professor Federal University in Pernambuco Recife - PE - Brazil +55-81-2126-7450 x5023 (goo.gl/ktsXSc)

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problem with showing broken peptide after residues with alternative conformation
by Wangshu Jiang 01 Nov '17

01 Nov '17

Dear Chimera Support, I am using Chimera to performing structural analysis for a manuscript. I have been struggling to show the protein structure with PDB entry 3LR2, the peptide bond between residue with alternative conformations and the next residue was shown broken, both in backbone and in ribbon presentation. I am not sure what went wrong here, I compared the PDB text file to other PDB entries with alternative conformations and I did not find obvious differences. It would be nice to show all the rotamers in the PDB instead of manually deleting by coot just from ‘eyeballing'. Could you please help me to solve this issue? Any suggestion is deeply appreciated! I attached an image illustrating the problem I described. I hope to hear from you soon! Best Regards, Wangshu Jiang PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden [cid:0D42E809-5937-4AC1-83FB-07A00C355333] Wangshu Jiang PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden

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