- Chimera-users - RBVI Mailing Lists

cannot interpolate models: underlying C++ Atom object is missing
by Frembgen Kesner, Tamara A 01 Oct '08

01 Oct '08

Hello, Does anyone know what the error message cannot interpolate models: underlying C++ Atom object is missing means? (And what I can do about it?) I am getting this message when I attempt to create a morph between two .pdb files using minimize. Thank you.

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Re: [Chimera-users] 1HLA- how to make ribbon image?
by Elaine Meng 30 Sep '08

30 Sep '08

Hi David, To summarize for the chimera-users list: 1HLA is an alpha-carbon-only structure, which cannot be shown as a ribbon in Chimera. However, there are many other structures of this protein, several at higher resolution and including all backbone atoms, allowing them to be displayed as ribbons. This Uniprot page has a long list of structures (about 80% of the way down is a "3d structure databases" section): http://www.uniprot.org/uniprot/P01892 The best resolution looks like 1.4 Angstroms, structures 1i4f and 1oga. Both match up with the CA-trace in 1hla quite well. Since they include all backbone atoms, they can be displayed as ribbons. I suggest using 1i4f. 1oga is just as good but has two copies. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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1HLA- how to make ribbon image?
by Edelshtein, David 30 Sep '08

30 Sep '08

Hello, I am an ITL researcher, I use chimera for making a ribbon image of 1HLA molecule, and I need to mark specific residues, (by the number/position). So far, I am unsuccessful in converting wire style to the ribbon style. Please let me know if you can help, advice or direct me to required info. David, Edelshtein SRA II UCSF ITL

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COLOURING A SUBUNIT
by Tom Goddard 30 Sep '08

30 Sep '08

skmolugu(a)miners.utep.edu wrote: > Hi, > thank you very much for your reply, > I have another question, is there a way to colour a symmetric map which has 4 subunits in to four different colours? > thank you for your time, > regards, > sudheer. > Hi Sudheer, If you have 4 monomer PDB models fit into the map, color them differently (e.g. command "rainbow chain"), then use the Color Zone tool to color the map to match the monomers. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#colorz… The Chimera volume guide may help with future questions: http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html Tom

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Re: [Chimera-users] SEPARATING A SUBUNIT
by skmolugu＠miners.utep.edu 29 Sep '08

29 Sep '08

Hi, I have a CryoEM density map with 14 subunits with seven fold symmetry. Is there a way in chimera to separate only one subunit from the entire map. thanks, sudheer

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Calculating RMSD for ligand
by 吴超 27 Sep '08

27 Sep '08

Hi, dear folks, I want to evaluate the docking performance by calculating the RMSD of heavy atoms between ligand crystal conformation and docked conformation. I use the following command: rmsd #0:1.het & ~element.H #1:1.het & ~element.H But Chimera seems to forget the correct order and give a pairwise alignment not the way I want . I wonder if there is a way that I can get the correct selection order so as to calculate RMSD. Best -- Chao Wu Currently: National Institute of Biological Sciences, Beijing Huang Niu's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206

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calculating symmetry for a dimer structure
by Katryna Cisek 26 Sep '08

26 Sep '08

Hi, Is there a way of calculating symmetry for a dimer structure in chimera, e.g. axis of symmetry? Thanks, Katryna

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calculating symmetry for a dimer structure
by Katryna Cisek 26 Sep '08

26 Sep '08

Hi, Is there a way of calculating symmetry for a dimer structure in chimera, e.g. axis of symmetry? Thanks, Katryna

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error in vista
by Mugnaioli, Enrico 25 Sep '08

25 Sep '08

Dear Chimera Users, I installed Chimera in my new PC, working under Vista. Apparently, the installation was fine, but when I started the program I got this error. What can I do? Best regards, Enrico Mugnaioli

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adding H
by Barbara Truitt 25 Sep '08

25 Sep '08

I have a compound which has an imidazole ring. When I Add Hydrogens, no hydrogens are added to the nitrogen atoms when I use the build from 9/21/08. The build from 9/4/08 adds the hydrogens, but some of the charge assignments in the resulting mol2 file don't make sense. Barb Truitt

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