October 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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Display atoms after multiscale model
by vamsee 02 Dec '14

02 Dec '14

Hello, I am working on a virus capsid and trying to figure out the buried surface area between subunits (similar to what ViperDB has. I have to do this for a few capsids and I am trying to automate this to the maximum possible extent. I have been able to follow the steps in this link Buried surface area calculation <http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-December/001131.html> and manually calculate the information. Are there commands available to do the same? Also, what is the difference between the surfaces created using a multiscale model and surfaces computed from the atom-spec? Would this difference in the surface affect the calculation of the buried surface area? And if it does affect it which one be a more accurate representation? Thank you Vamsee

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Visualizing MDFF Runs in Chimera
by Joshua Carter 05 Nov '14

05 Nov '14

Hello, I am currently working on some MDFF simulations and have been visualizing them in chimera. I am trying to color the proteins by rmsd over the course of the simulation. I was thinking that there may be a way to do this using the attribute calculator tool between the first and last frames of the simulation. Does anyone know if this is possible or if there is a better way to do it? Josh

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A question about MD movie
by Sherry Wang 02 Nov '14

02 Nov '14

Hi, Is it possible to to record a MD movie that combines several dcd files playing simultaneously, not sequentially? Thanks. Sherry Wang ******************************************************** Shu-Ying Sherry Wang, Associate Professor Department of Microbiology and Immunology National Cheng Kung University 1 University Road Tainan, Taiwan 701 Tel: 886-6-2353535 ext.5634 Fax: 886-6-2082705

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Selection Mode via command line?
by Korbin West 31 Oct '14

31 Oct '14

Hi, I was wondering if there was a way to switch selection modes via the command line. I've been looking through the select command page on the user guide and can't figure a way to change the mode this way. Can anyone give me a tip? Thanks so much, Korbin West

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Color-picker/eye-dropper tool?
by Oliver Clarke 30 Oct '14

30 Oct '14

Greetings, Just a request for the wish-list - is there any prospect of implementing a color-picker (eye-dropper) in chimera at some point? This would be particularly handy for matching colors between figures, or to figures made in another program. At the moment I use an external mac app, Sip, to do do the same thing, but an integrated tool would be nice to have. Best, Oliver.

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change segmented object colour
by Deran Reddy 29 Oct '14

29 Oct '14

Dear Sir/Madam Please could you provide instructions on how to change the color of a segmented object created by using (segger) segment map function. I cant find a color editor to change this color, such as that for the volume viewer. Any help would be greatly appreciated. Kind Regards Deran Reddy <table width="100%" border="0" cellspacing="0" cellpadding="0" style="width:100%;"> <tr> <td align="left" style="text-align:justify;"><font face="arial,sans-serif" size="1" color="#999999"><span style="font-size:11px;">This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. </span></font></td> </tr> </table>

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DLP-link for 3D sequential stereo viewing
by David Bhella 29 Oct '14

29 Oct '14

Dear colleagues, I am having some difficulty configuring a 3D projector for use with chimera, so I am hoping that someone may be able to offer some advice. Briefly we have a Projection Design F35 DLP projector that uses DLP-link to synchronise the shutter glasses. I have a Windows 7 PC with an nVidia K-series video card to run the projector (I have to use Windows - please don’t say use linux!). Through the nVidia GUI I set the driver to DLP, but in chimera the image does not seem to be flickering and there is no 3D image, even though the glasses are shuttering. The image is distorted in a similar way to that seen with shutter glasses but it is static. The only way I can get chimera to give a flickering image is when I set it to use the DIN socket, but of course the image is not synched to the glasses. I would be grateful for any advice on system settings I may need to make to get this working. Thanks, D. Dr David Bhella MRC-University of Glasgow Centre for Virus Research Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch

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Chimera-users October 2014