- Chimera-users - RBVI Mailing Lists

opening huge models
by benoit.zuber＠ana.unibe.ch 17 Mar '16

17 Mar '16

Hello Opening a model of the 80S ribosome takes about 30 minutes on my computer (chimera version 1.10.2 build 40686). Is this normal? Is there any way to speed up this step (for example, could the task be parallelized)? Thanks in advance Ben -- Prof. Benoît Zuber Institute of Anatomy University of Bern Baltzerstrasse 2 Postfach 922 3000 Bern 9 Switzerland benoit.zuber(a)ana.unibe.ch +41 31 631 84 40 http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html

1 0

Computational power requirement
by Pascal Albanese 17 Mar '16

17 Mar '16

Dear staff, we need some advice about the computational power required by the software to perform several operations/processing with big volumes obtained by cryoEM at high resolution. For example the fitting of several pdb crystal structure (n=20-30) into a single volume at high resolution of a protein complex (MW > 1.2 MDa). What kind of graphics power do we'll need to run Chimera properly with this kind of structures? and CPU/RAM performance? If you have any suggestion. Thanks in advance for your help, all the best, Pascal -- Pascal Albanese, *PhD student*, Università di Padova Via Ugo Bassi 58 B, 35121 Padova, Italy e-mail: pascal.albanese(a)studenti.unipd.it *Research assistant*, Politecnico di Torino Dipartimento DISAT, BioSolar Lab Viale Teresa Michel 5, 15121 Alessandria, Italy e-mail: pascal.albanese(a)polito.it Tel: 0131 229301 Fax: 0131 229344

2 1

centre of local mass
by Morris, Kyle 16 Mar '16

16 Mar '16

Dear Chimera dev and community, If I have approximately placed a marker into my volume density, is there a way to recentre this marker according to the centre of mass of the local density rather than the centre of mass of the whole volume? Many thanks for your help! Best wishes, Kyle

2 1

figured somethings out
by A G Szabo 15 Mar '16

15 Mar '16

I sent in some questions yesterday evening. I have figured out how to color the ribbon segment of a residue different from the ball and stick or stick color of the side chain. Still have a question about getting rid of the dashed lines from the Mg atom. Thank you Arthur G. Szabo Emeritus Professor Wilfrid Laurier University.

2 1

Force stick representation of a residue in ribbon display
by Eiros Zamora, Juan 15 Mar '16

15 Mar '16

Dear Chimera experts, Is it possible to show in stick representation the C=O bond of the backbone of a residue while maintaning the ribbon representation of the backbone? I’ve tried setting on the ‘ribbackbone’ command, but that activates all the backbone atoms for other stick-displayed atoms, and I want to avoid that. [cid:2BB6667F-5FB4-4181-9046-58DEC52A2F11@ch.ic.ac.uk][cid:7A0C477F-BD71-4D55-96A5-FFDA096DBD9E@ch.ic.ac.uk] I’m attaching two images to clarify what I mean. Basically, to keep it as image1 but displaying the C=O bond of THR 71, to make the 2.88 Å distance clearer. Any help on this matter will be greatly appreciated. Best, Juan

2 1

question
by A G Szabo 14 Mar '16

14 Mar '16

I have included a part of a structure in this Email. In January Elaine Meng communicated with me about how to color an individual atom in an amino acid that is shown as a ball and stick. So you see I have colored an oxygen atom red in a threonine residue that is part of a peptide that is bound to the protein that is mainly shown as a ribbon structure. Note the Glutamic acid residue shown only as a stick and colored lime green. The peptide backbone of this residue which is in a ribbon representation is also colored lime green So question #1, how can I just color the side chain and not the peptide bond which is in the ribbon. I want to keep the ribbon a continuous blue. Note the Aspartic acid residue that is part of pink ribbon and represented as a ball and stick. So I want to color the side chain the same lime green, I know how to do that, but again the ribbon part of that Asp will also be lime green. Even if all I want is to have one of the oxygen atoms of the side chain colored red, I can do that as well except that the ribbon portion, the peptide bond also is colored red. Question #2: There is a metal ion colored light blue or cyan, How can I get rid of the four short dashed lines that link it to the aforementioned Glu and Asp, as well as another Asp residue? Thank you for your assistance. Arthur G. Szabo Professor Emeritus Wilfrid Laurier University.

1 0

help with antechamber
by Philip Hanley 14 Mar '16

14 Mar '16

To whom it concerns, I’ve been using antechamber as part of a university project. I’m away from the university for the next few weeks and have downloaded chimera on my mac. I was using chimera on linux in the university. Im having the same issue, irregardless of what molecule i have, which is dock prep / add charge. I’m following the same procedure as i did in the university with molecules i know add charge did work for, but am receiving the following error; Charge model: AMBER ff99SB Assigning partial charges to residue TAG (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/4n/vv33g5cj65175vlsgg86_0h00000gn/T/tmpm0Jyho/ante.in.mol2 -fi mol2 -o /var/folders/4n/vv33g5cj65175vlsgg86_0h00000gn/T/tmpm0Jyho/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (TAG) (TAG) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (TAG) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (TAG) Reason: image not found (TAG) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (TAG) (TAG) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (TAG) Total number of electrons: 98; net charge: 0 (TAG) (TAG) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (TAG) 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 Failure running ANTECHAMBER for residue TAG Check reply log for details Is there anything possible wrong with the general settings in the program that have to be changed? i have literally installed chimera, and changed no settings thus far. I have looked up forums relating to similar issues but have no found a solution. Any help would be highly appreciated, thanks in advance, phil

2 1

Use of custom color palettes for Render by attribute?
by Oliver Clarke 14 Mar '16

14 Mar '16

Hi, Render by attribute currently only has five pre-defined palettes (Red-blue, blue-red, cyan-maroon, rainbow, and gray). Often I will use the same color palette repeatedly for the same task in Render by Attribute (e.g. dodger-blue/white/orange red for hydrophobicity). Is it possible to make such custom palettes persist in the drop down menu in Render by attribute? If not would it be possible to add such an option in ChimeraX? Cheers, Oli.

2 1

How to model a loop using a template
by Elisa Pieri 11 Mar '16

11 Mar '16

Dear all, I have installed Chimera on my computer, but I am still new to the program, so forgive me if my question is trivial. I have a nmr structure (completely defined) and a X-ray structure of the same protein, but this last structure has a missing loop. How can I model this missing loop in the x-ray structure using the nmr structure as template (i.e. freezing the x-ray structure and adding only the nmr loop)? I tried opening both structures and using the Tools > Structure Editing > Model/Refine Loop, but if I choose the x-ray structure, then I don't see where to state that I want to use the nmr structure as template. I hope that I explained my problems. Can you help me? Elisa

2 1

[BUG report] in list atoms sel command
by Michał Kadlof 10 Mar '16

10 Mar '16

Hello, I noticed this behaviour: 1. Selecting some atoms with mouse 2. Command: list atoms sel It gives me output: No value provided for keyword 'sel' Is it how it is supposed to work? How can I get list of manually selected atoms? -- Michał

2 1