- Chimera-users - RBVI Mailing Lists

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

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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

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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

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