September 2014 - Chimera-users - RBVI Mailing Lists

Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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layering problem
by Joseph Atherton 20 Aug '15

20 Aug '15

Hi! I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this? Cheers, Joe

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Double structure while loading the pdb file
by Sanjeev Sariya 27 Oct '14

27 Oct '14

Hi Members/Developers, I loaded pdb file 1U19- Bovine Rhodopsin. structure is double the length what is to be. On terminal, on doing color red: 113 I see that 2 residues are colored. Why there are 2 molecules in same file? How do I hide one molecule?

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Reg: Peptide Dimer
by Amit Jaiswal 30 Sep '14

30 Sep '14

Hi, I would like to know if is it possible to prepare peptide dimer In Chimera. If yes, how and if no what are the possible ways to prepare it? Thanks in advance. With kind regards, Amit Jaiswal -- *Yours Sincerely,* *~~~~~~~~~~~~~~~~~~~~~~~~**~~~* *Amit Jaiswal,* *A.T. Road, Tarajan,* *Jorhat - 785001,* *Assam.-------------------------------------------* *Centre for Bioinformatics,Pondicherry Central University,* *Pondicherry - 605014,* *Pondicherry. * *~~~~~~~~~~~~~~~~~~~~~~~~**~~~**~*

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Proposal to add ability to load CATH domains in Chimera
by Tony Lewis 30 Sep '14

30 Sep '14

Dear Chimera people, Many thanks to all Chimera contributors. Please may I propose an addition to allow users to access our CATH domains in the same way that they can currently access SCOP domains ( https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/scop.html )? PDBs for CATH domains can be loaded from URI's of the form: http://data.cathdb.info/latest_release/pdb/1cukA01 For information, CATH domain IDs contain 7 digits: - 1-4 : (eg 1cuk ) : PDB code - 5 : (eg A ) : chain code - 6-7 : (eg 01 ) : 2-digit domain number ( '00' for whole chain domains ) We here at CATH would be very happy to provide any other information required to implement this. Many thanks for your help. Kind regards, Tony Dr Tony Lewis Orengo Group UCL

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Regarding organic molecule minimization
by Satheesh G 29 Sep '14

29 Sep '14

Dear Sir, The azo compounds (organic molecule) minimization using Chimera software giving linear form (R-N=N-R to R-N=N-R (180 degrees bong angle between R-N=N instead R-N=N- 120 degrees). Which is not true. I have used the gasteiger and amber ff12sb force field. Please suggest me to solve this problem. Thanking you. Satheesh. [image: Inline image 1]

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Select next residue
by Tom Goddard 29 Sep '14

29 Sep '14

Hi Yanyan, I added three new keyboard shortcuts. “rn” selects the next residue after the currently selected one and the currently selected one gets unselected — basically it just moves the selection down by one residue. This applies even if a several residues are selected, the whole selection just gets moved down the chain by one position. “rp” selects the previous residue, and “ri” selects all residues between two currently selected residues. These should help you move the selection along in a quick way. Chimera keyboard shortcuts are not enabled by default. To enable them use the Chimera command “ac” (stands for accelerators) or use menu entry Tools / General Controls / Keyboard Shortcuts and click “Enable keyboard shortcuts”. If you use that menu entry then it will be remembered and shortcuts will be enabled when you start Chimera the next time. Shortcuts are all 2 letters and you don’t hit return after typing one. To get back to typing a command instead of a shortcut use the shortcut “cl” (command line). Here’s the list of shortcuts from the Chimera documentation. http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/ali… The new ones will be in tomorrow’s daily build (dated Sept 27, 2014). Tom On Sep 26, 2014, at 7:10 AM, Zhao, Yanyan wrote: > Hi, Tom. > > Thank you so much for the chimera lecture yesterday. It is very helpful. > I'm Yanyan from Baylor college of Medicine and is a rotation student in Wah's lab now. I'm using this software now. But I have a problem finding the keyboard shortcuts for selecting residues. I want to select residue one by one along the whole chain. But Ctl+left mouse click is a pain when dealing wit so many residues. Is there any shortcuts that I don't need to click the mouse and still can flow through the chain? > > Thanks. > > Best regards, > Yanyan

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running chimera on FC20
by David Roberts 29 Sep '14

29 Sep '14

Hi all, I just did a clean install of FC20 on an AMD dual core system. I opted for the 32 bit version, as these workstations are used for multiple things (and I find that it’s just easier most of the time, though 64 bit may be where I need to go eventually). I installed Chimera Version 1.9, Build 39798 on Fedora FC20. When running chimera, my computer constantly freezes. Obviously I’m missing something. I’m not doing anything fancy - I use Zalman monitors connected to generic video cards. I can run coot fine - I don’t know about ccp4i (it seems to run, but I haven’t challenged it in any way). As long as Chimera is not running, my computer runs nicely. I have flash/etc… working fine. Any thoughts on where I should start here? This happens on 3 separate systems (that are essentially the same, but not identical clones). I’m assuming I missed something obvious in the install. Thanks Dave

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How to load PDB data inline in Chimera script/command files
by Tony Lewis 29 Sep '14

29 Sep '14

Dear Chimera people, Many thanks to all Chimera contributors. Please can anyone tell me if there's a way to include PDB data *inline* in Chimera script / command / Chimerax files? PyMOL's read_pdbstr() command loads PDB data from an inline string, which means one file can contain both the structural data and the associated commands. That's rather convenient. I would much appreciate any help on how to do the same with Chimera. Apologies if the answer is obvious. Many thanks and kind regards, Tony Dr Tony Lewis Orengo Group UCL

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