March 2016 - Chimera-users - RBVI Mailing Lists

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

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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.

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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

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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.

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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

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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.

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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

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[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

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Re: [Chimera-users] importing xyz file
by Eric Pettersen 10 Mar '16

10 Mar '16

Okay, you can do that by “fixing up” your original file (tmp.pdb) after opening it. So open your original file and then get rid of the “missing structure” pseudobonds by going to “Tools->General Controls->Pseudobond Panel” and choosing the “missing structure” group in the table and clicking the “close” button on the right (not the bottom! Afterward you can dismiss the panel with the bottom Close button). Then you can force chimera to show the suppressed “long” covalent bonds with this command: “setattr b display 2”. That will result in Chimera treating those bonds normally (i.e. shown if both endpoint atoms are shown) instead of as chain breaks. —Eric > On Mar 10, 2016, at 12:11 AM, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> wrote: > > Thank you for your fast and detailed answer. Is it the only solution? I would like not to loose the possibility of rendering it in rainbow or ribbon style. > > ----- Oryginalna wiadomość ----- > Od: "Eric Pettersen" <pett(a)cgl.ucsf.edu> > Do: "Michał Kadlof" <m.kadlof(a)cent.uw.edu.pl> > DW: "chimera List" <chimera-users(a)cgl.ucsf.edu> > Wysłane: czwartek, 10 marzec 2016 0:31:58 > Temat: Re: [Chimera-users] importing xyz file > > > Hi Michał, > When Chimera reads a PDB file, it adheres to the implied conventions of the PDB — which is what is tripping you up here. The two conventions that are getting you are: (1) consecutive residues in ATOM records with no intervening TER card are connected, and (2) jumps in the residue numbering of consecutive residues along with separation in 3D space imply missing intervening structure. (1) will add extra bonds you didn’t explicitly put in your CONECT records. (2) will change some inter-residue bonds into “missing structure” pseudobonds. > So if we fix your PDB file, Chimera will like it better. :-) The changes are: > > > — Change ATOM records to HETATM records > — Put all the atoms into a single residue > — Change the residue name from GLY to UNK > — Give the atoms unique names (I used C0 through C69) > > > I have attached the edited version of your file. > > > —Eric > > > > > > > Eric Pettersen > UCSF Computer Graphics Lab > > > > > > > > > > > > > On Mar 9, 2016, at 1:48 PM, Michał Kadlof < m.kadlof(a)cent.uw.edu.pl > wrote: > > > > Thank you for your advice. I decided to translate my XYZ structure into PDB file with CONNECT records but I observe strange behaviour. Chimera seems not rendering all of bonds. Some of them in dense place, are render as pseudobonds. Is it how it supposed to work? bond command tells me: Attempt to form duplicate covalent bond. > > I'm including screenshot, and my structure. It's obviously not a protein, but I would like to use some tools from chimera to work with it. > > Can you help me? > > -- > Michał Kadlof > > > ----- Oryginalna wiadomość ----- > Od: "Eric Pettersen" < pett(a)cgl.ucsf.edu > > Do: " chimera-users(a)cgl.ucsf.edu BB" < chimera-users(a)cgl.ucsf.edu > > DW: "Michał Kadlof" < m.kadlof(a)cent.uw.edu.pl > > Wysłane: środa, 13 styczeń 2016 19:03:32 > Temat: Re: [Chimera-users] importing xyz file > > > > > > > On Jan 13, 2016, at 9:58 AM, Elaine Meng < meng(a)cgl.ucsf.edu > wrote: > > (1) after reading in the XYZ file, add bonds manually yourself, for example, select two “atoms” (Ctrl-click, Shift-Ctrl-click) and then use command “bond sel”. Repeat. This could be tedious if you have a lot of bonds to add. You could also use atom names instead of selecting, for example “bond @c1,c2”. Although the XYZ file doesn’t contain atom names, “atoms” of the same “element” will be named in Chimera according to element with a sequential number appended (the first C is named C1, the second C is named C2, etc.). > < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/xyz.html > > > > And the above could be combined into a script, e.g.: > > > open myfile.xyz > bond @c1,c2 > bond @c1,c7 > … > > > > > That script file could then be opening with a single command in Chimera: “open myscript.cmd”. > > > —Eric > > > > > Eric Pettersen > UCSF Computer Graphics Lab > > > > <Screenshot_2016-03-09_22-47-44.png> <tmp.pdb> _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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importing xyz file
by Michał Kadlof 09 Mar '16

09 Mar '16

Hello, I would like to visualize in chimera objects (not exactly atoms) from my XYZ file. I can import them ans see as scattered balls but I would like to see them connected to each other in order that they are appear in file. The distances are much larger than usual inter atoms interactions. Is it possible? -- best Michał Kadlof

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Chimera-users March 2016