December 2014 - Chimera-users - RBVI Mailing Lists

regarding distance measurement
by abhishek jamwal 02 Dec '14

02 Dec '14

Dear All, I have created a stereoview using chimera where I am showing distance between sidechain atoms of a protein. when I save an image of this stereoview (tiff, 600dpi), the connector lines showing the distances are fading, they are not of same quality in the image as in the original view ! Is there a way to save image without disturbing quality of the connector lines showing distances ? thnx abhishek

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How to use a colour-valued attribute?
by Mungo Carstairs 02 Dec '14

02 Dec '14

Hi, This feels like a basic question but it has stumped me for a day now so here we go... I'm exploring ways of programmatically setting colours to find the most efficient method. This is for the 'custom coloured' case (residue-based colour schemes are not a problem). The simple version is to send as many 'color' commands as there are colours in my (Jalview) sequence: color #ffafaf #0:1.B|#0:5.B|#0:7-8.B|....;color #ffff00 #0:39.B|#0:44.B|#0:47.B|#0:77.B; This works, but doesn't seem to scale up well for large/many structures - I start to see Chimera using 100% CPU for minutes at a time. I'm trying instead to see whether setting a colour-value attribute is faster. I can set the attributes ok with commands like setattr r color green #0:1-84.B etc and confirm they are set with list residues spec #0:1-84.B attribute color but I can't figure out how to get Chimera to use the attribute value as the display colour. 'Render by Attribute' only seems to consider numeric (range-valued) attributes, not colour-valued. I thought perhaps 'my' colour was just hidden in the colour hierarchy, but removing other colours doesn't seem to help. What am I missing? Thanks, Mungo Carstairs Division of Computational Biology University of Dundee http://www.jalview.org The University of Dundee is a registered Scottish Charity, No: SC015096

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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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select chain and elements simultaneously
by Jacob Lewis 02 Dec '14

02 Dec '14

Hi all, I am new to chimera is it possible to select chain and element for a structure? for instance select chain A and element carbons so they can be coloured red for example? thanks in advance. Jacob

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Re: [Chimera-users] [Chimera-announce] new Chimera release (v1.10)
by Elaine Meng 01 Dec '14

01 Dec '14

Dear Debasish Banerjee, There may have been changes in the ModBase website, or maybe even the UniProt website -- you would need to ask those developers. The ability of Chimera to show ModBase models did not change. Today looking at the ModBase website, I'm having a problem where it always says there are no models for some sequence, even when I know there are models. I don't know if this is the same problem you were having. I know there are models because I can fetch them using Chimera menu: File…Fetch by ID, choosing database: Modbase and entering a sequence ID (UniProt or other). The same can be done with a command, for example: open modbase:P33533 So maybe you can use that approach instead. Regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 29, 2014, at 2:39 AM, "Debasish Banerjee" <dbanerjee(a)banerjee.net.in> wrote: > To > Elaine Meng, > May be I didn't explain properly. Most UniprotKB database entries have used Modbase in the 3D structure database section. In any entry where Modbase is used, clicking on search button next to the Modbase entry used to open that structure entry page using Chimera. With the current version that doesn't seem to happen (as it was happening with the earlier versions). Please advice. > Thanking You, > Debasish Banerjee > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Wed, 26 Nov 2014 23:02:40 > To: Debasish Banerjee <dbanerjee(a)banerjee.net.in> > Cc: Mailing List <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-announce] new Chimera release (v1.10) > On Nov 25, 2014, at 4:17 PM, Debasish Banerjee <dbanerjee(a)banerjee.net.in> wrote: > > > To, > > Elaine Meng, > > I had downloaded Chimara 1.10 but it doesn't seem to operate on other sites like UniprotKB. Can you please comment. > > Debasish Banerjee > > > Dear Debasish Banerjee, > Not sure I understand your question. UCSF Chimera is a molecular modeling/graphics program that you use on your own computer. > > The only relationship to UniProtKB is that you can fetch sequences and annotations from that site while using Chimera. Maybe you mean you had trouble fetching data from the web (Chimera menu: File… Fetch by ID)? > > We haven’t heard reports of a problem. For example, I can start UCSF Chimera 1.10, use menu: File… Fetch by ID, choose database “UniProt” and then get the sequence for NGF_HUMAN shown in Chimera. Of course, you have to be connected to the internet. Otherwise, if you have some specific problem you can use Chimera menu: Help… Report a Bug and give enough information about the steps you tried so that somebody else could reproduce it. > > Best, > Elaine

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