- Chimera-users - RBVI Mailing Lists

Joining models question
by Kyle J. Lauersen 29 Jan '16

29 Jan '16

Hello, I am trying to join the two models attached to this sequence. I have used the sequence selection code in atom specifier: #1:559.a@C #0:2.a@N Where model #0 is YFP and #1 is PcPs. When I go to join models, the Apply button is not accessible. Can you indicate if I am doing something incorrect in the selection of the C and N atoms? Thank you for your time. Kyle Dr. Kyle J. Lauersen Algae Biotechnology & Bioenergy Center for Biotechnology Bielefeld University p: +49 (0) 521 106 12289 e: kyle.lauersen(a)uni-bielefeld.de <mailto:kyle.lauersen@uni-bielefeld.de>

2 3

Question from PhD student
by T-I 28 Jan '16

28 Jan '16

Dear Chimera, I would like to know exactly how to enclose my EM density map within a cube of specified size (where x, y and z have equal dimensions, i.e x,y,z = 150 pixels). It seems that when I place a marker (from volume tracer) on my map and then specify the padding number a rectangular cube is produced instead. I there a simple command to do this or can it be done from the GUI? Many thanks T.I PhD student, London

2 1

Tool:Structure Editing:Model:Refine loops
by Jingchuan Sun 26 Jan '16

26 Jan '16

Hello, When I tried MODEL plugin to model loop, the changes in result model is not just the selected loop to be modelled. It renumbered residues. There are several missing residues outside the selected loop in my old model. They become connected (in not accepting way) in returned models. Could I disable this "over-reach"? I only need to model the selected loop, no change to other places or renumbering. Best, Jingchuan

2 1

rendering of custom annotation
by Helge 26 Jan '16

26 Jan '16

Dear Chimera users, I have some data, which contains numbers of hits for each given residue of a chain (in my case the 25S rRNA). The data consists of a table with two columns: residues and corresponding hits. I would now like to color each residue in Chimera, relative to the amount of hits, with the highest number always getting a defined color. Is this possible? best regards, Helge

2 2

Add Charges failure (libquadmath)
by Lluis Blancafort 25 Jan '16

25 Jan '16

Hi, I’m running Chimera alpha version 1.11 on Mac OSX El Capitan 10.11.2 The Add Charges tool does not work for non-standard residues with AM1-BCC. The Reply Log reports a problem with libquadmath and later with sqm utility (see below). I don’t have libquadmath.0.dylib installed. Can anybody help? Thanks! Lluís Blancafort Institut de Química Computacional i Catàlisi Universitat de Girona 17071 Girona Spain (1) Charge model: AMBER ff14SB Assigning partial charges to residue SGA (net charge -1) with am1-bcc method Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/6j/nf071g8n2b5csd0rdcm8n5sc0000gn/T/tmpKi57P0/ante.in.mol2 -fi mol2 -o /var/folders/6j/nf071g8n2b5csd0rdcm8n5sc0000gn/T/tmpKi57P0/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 (SGA) (SGA) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (SGA) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (SGA) Reason: image not found SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (SGA) (SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (SGA) Total number of electrons: 136; net charge: -1 (SGA) (SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (SGA) Error: cannot run "/Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit

2 1

my question
by Yanli Li 25 Jan '16

25 Jan '16

Dear sirs/madams, I am a PhD student in Universitat Autònoma de Barcelona. I am working on the Porcine Reproductive and Respiratory Syndrome Virus (PRRSV). I have got differences of cytokine profiles and phenotype regulation of antigen presenting cells by different isolates through the lab work. Now I intend to predict the structure of the whole or some parts of the viral particle with UCSF CHIMERA. However, there are only three relevant structures(nucleocapsid, nsp1, nsp4) that have been published. Is it possible to realize it? If yes, can you tell me the method in brief? Thanks a lot! Waiting for your reply. Best wishes, Yanli LI

3 2

the fastest way to convert a pdb to density map
by 李智海 22 Jan '16

22 Jan '16

Hi, Here I want to calculate a model-to-map FSC curve. If I am not wrong, firstly I am supposed to convert the pdb file to a density map. So I was just wondering in Chimera, how to use command molmap to generated a map with the same pixel size and dimensions as the corresponding map? Any help will be high appreciated. Best, Zhihai Li

2 2

Select residues with missing atoms?
by Oliver Clarke 19 Jan '16

19 Jan '16

Hello, Is there any way to select/color all protein residues with incomplete sidechains? This would be very helpful when looking at a structure and deciding whether it is necessary to run dock prep to fill them in prior to performing other calculations (e.g. sometimes I am only concerned with what is going on around a ligand binding site). Cheers, Oliver.

2 2

question
by A G Szabo 15 Jan '16

15 Jan '16

I have to admit that my understanding of the various commands to use for very specific functions in Chimera is difficult for me to find the correct command. I know how to color a specific residue using the sequence table and the color chart. So how do I color a specific atom in a residue. For example I am interested in coloring the nitrogen of the Asn amide side chain say color red. How can I do this? When I highlight a residue and visualize it as a ball and stick, then color it different from the color of the helix, the color of that part of the helix changes to the color of the ball and stick, different from the color of the rest of the helix. How can I reset the color of the helix location of that residue, leaving the ball and stick as another color. Thank you Arthur Szabo Professor Emeritus Chemistry and Biochemistry Wilfrid Laurier University Waterloo Canada.

2 5

Geometric Center
by tobias.eilert＠uni-ulm.de 15 Jan '16

15 Jan '16

Hello, I want to translocate a protein such that its geometric center is the origin. Finally I want to save this new configuration in a pdb-file, so it is conserved like this. Do you have any suggestions? With kind regards Tobias Eilert

2 1