- Chimera-users - RBVI Mailing Lists

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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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

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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

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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

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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

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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.

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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>

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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

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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

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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

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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>

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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

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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

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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.

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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

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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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