December 2011 - Chimera-users - RBVI Mailing Lists

mmView - a tool for mmCIF exploration
by Daniel Svozil 06 Dec '11

06 Dec '11

Dear colleagues, We would like to announce the availability of mmView - the web-based application which allows to comfortably explore the structural data of biomacromolecules stored in the mmCIF (macromolecular Crystallographic Information File) format. The mmView software system is primarily intended for educational purposes but it can also serve as an auxiliary tool for working with biomolecular structures. The mmView application is offered in two flavors: as a publicly available web server http://ich.vscht.cz/projects/mmview/, and as an open-source stand-alone application (available from http://sourceforge.net/projects/mmview) that can be installed on the user’s computer. Petr Cech and Daniel Svozil -- Daniel Svozil, PhD Head of Laboratory of Informatics and Chemistry Institute of Chemical Technology Czech Republic phone: +420 220 444 391 http://ich.vscht.cz/~svozil

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Re: [Chimera-users] MD plots
by George Tzotzos 05 Dec '11

05 Dec '11

Apologies for repeating this. Here are the snapshots On Dec 5, 2011, at 9:58 PM, turk(a)lmb.uni-muenchen.de wrote: > have you tried: > >> distance model_number:residue_A@atom model_number:residue_B@atom > > > George Tzotzos <gtzotzos(a)me.com> wrote : > >> I'm trying to plot the distance between two atoms is a MD trajectory. >> >> I use the command line to select, for example :124@H :121@O >> >> The window in MD Plots fails to show my selection. >> >> Is there something I get wrong? Your help will be much appreciated >> >> Regards >> >> George >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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Re: [Chimera-users] MD plots
by George Tzotzos 05 Dec '11

05 Dec '11

Thanks for this. I tried, still the result is the same. I'm attaching two snapshots in case it helps with the diagnostics. All the best George On Dec 5, 2011, at 9:58 PM, turk(a)lmb.uni-muenchen.de wrote: > have you tried: > >> distance model_number:residue_A@atom model_number:residue_B@atom > > > George Tzotzos <gtzotzos(a)me.com> wrote : > >> I'm trying to plot the distance between two atoms is a MD trajectory. >> >> I use the command line to select, for example :124@H :121@O >> >> The window in MD Plots fails to show my selection. >> >> Is there something I get wrong? Your help will be much appreciated >> >> Regards >> >> George >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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MD plots
by George Tzotzos 05 Dec '11

05 Dec '11

I'm trying to plot the distance between two atoms is a MD trajectory. I use the command line to select, for example :124@H :121@O The window in MD Plots fails to show my selection. Is there something I get wrong? Your help will be much appreciated Regards George

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add custom residues to rotamer library or for swapaa command
by Sabuj Pattanayek 05 Dec '11

05 Dec '11

Hi, How do I add custom residues so that they're usable with swapaa or the rotamer tool? Thanks, Sabuj

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CASTp unable to recognise pdb format
by George Tzotzos 03 Dec '11

03 Dec '11

Hi everybody, I used Modeller to generate a structure which I then saved using Chimera. The CASTp server complains that the structure is not in pdb format. I'm attaching the pdb file to help with the diagnostics. Good weekend to all George

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Cando
by poorvi garg 02 Dec '11

02 Dec '11

Hii.., I have generated the json files by sending it to cando . The files we have generated is opened in UCSF Chimera but I am not able to perform any options or operations of the tool . Could you tell me how to perform operations on bld files of the json file obtained. thanks Regards, Poorvi Garg

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volume calculation
by sdimicco 02 Dec '11

02 Dec '11

Dear Chimera developers, is it possible to calculate the volume of the binding site by the softwere? How can I do it? Thank you in advance. Simone

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Multi-align: retract
by George Tzotzos 01 Dec '11

01 Dec '11

I'd like to retract the previous message. I found a way to edit the protein names. It's a bit roundabout but it works. I saved the alignment in Clustal, opened with an text editor, edited the names and saved. Then I opened the file in Chimera. Regards George

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Multi-align
by George Tzotzos 01 Dec '11

01 Dec '11

Hi everybody, I'm wondering if there's a way to edit the protein names in Multi-align. It seems that protein names are generated automatically. An example is attached. The problem is that in scalable eps, sometimes the names overlap with the line numbers. Reducing the ellipsis in Multi-align preferences truncates the names. Thanks for any suggestions George

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