- Chimera-users - RBVI Mailing Lists

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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