January 2015 - 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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New molecule from selection?
by Oliver Clarke 03 Apr '15

03 Apr '15

Hi, This may already be implemented, but I couldn’t find it - the nearest equivalent feature I know of is copy/combine, but that only works on whole models, not taking into account selections. I was wondering if it would be possible to implement a feature creating a new model comprised of all atoms in the current selection? This would be particularly helpful when combining many parts of multiple models, or when creating a separate model consisting of a subselection of the current model. This can be done at present using a combination of copy/combine and selecting and deleting those parts of the copied molecules that are not in the selection, but this gets messy for complicated selections. Best, Oliver.

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Using Chimera to measure voxel densities
by Noble, Alex 30 Jan '15

30 Jan '15

Hi all, I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera? Best, -Alex Noble

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Question
by Monete Rajão Gomes 28 Jan '15

28 Jan '15

Hi, I have some problem these days about superimpose templates with matchmaker. I followed this tutorial http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-August/006686.html. There are regions on aminoacids sequences which are identical. So, when I superimpose them, they stay separated. I am sending a screenshot attached. It would be great if you could help me. Best, Monete

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Morph conformations - estimated time to completion in status bar?
by Oliver Clarke 26 Jan '15

26 Jan '15

Hi all - silly little feature suggestion, but I was wondering if it would be possible to add an live-updating “x % complete” or “estimated time to completion” entry in the status bar when running Morph Conformations? When morphing two structures with very large numbers of atoms, morph conformations can take a long time (hours) to complete, and it would be handy to know whether it is nearly done or not (currently it just shows “computing interpolation 1” until it is finished). On a related note, is there any way to speed up morph conformations for large structures? E.g calculating transformations using C-alpha atoms only? Best, Oliver.

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modelling a dimer
by David Norman (Staff) 23 Jan '15

23 Jan '15

I am trying to model a symmetrical dimer using modeller within Chimera. I cannot work out how to present the alignment and pdb. files in oder to do this. Any hints please. Thanks David David Norman Ph.D Nucleic Acids Research Group School of Life Sciences MSI/WTB Complex Dow St. Dundee, DD1 5EH, Scotland, UK. phone +44(0)1382 384798 mobile +44(0)7808572788 E.mail d.g.norman(a)dundee.ac.uk Web site: http://www.lifesci.dundee.ac.uk/people/david-norman The University of Dundee is a Scottish Registered Charity, No. SC015096 The University of Dundee is a registered Scottish Charity, No: SC015096

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how to find non-bonded interactions between a protein and a ligand?
by Sam Paul D. 22 Jan '15

22 Jan '15

Hi, I need to find non-bonded interactions between a protein and a ligand through command line. Could anyone please suggest which chimera command to use with the syntax? With regards, Sam

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Find subsequence programatically
by Thomas Hrabe 22 Jan '15

22 Jan '15

Hi Chimera Team, How can I automate the Sequence View -> Edit -> Find Subsequence Tool programmatically with the Chimera shell or better within python? Thank you, Thomas

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