- Chimera-users - RBVI Mailing Lists

resolution distribution on density maps
by onetwo 24 Mar '16

24 Mar '16

Hi All, I have seen images in several papers, where the authors present resolution distribution for the density maps obtained by cryo-EM. I wanted to know to how to make these images for a low resolution cryo-EM map in Chimera. Thanks and Regards Shivushiv

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Fwd: Center of model/volume shifts
by Elaine Meng 23 Mar '16

23 Mar '16

Hi Preeti, It might not be a bug if the models were somehow moved separately. Similar to my previous response on chimera-users to a slightly different question, it may be possible to bring them back into register by by (A) copying the transformation of the original map to the filtered map, e.g. command: matrixcopy #N #M … where N is the model number of the original map and M is the model number of the filtered map (see model numbers by showing the Model Panel from the Favorites menu). or (B) by resetting all model positions, e.g. command: reset If neither of those work, it would be helpful if you would report (to the chimera-bugs email address) which version of Chimera you are using (e.g. from the “version” command) and what series of steps can be used to reproduce the problem. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > Begin forwarded message: > > From: Preeti Gipson <gipsonpreeti(a)gmail.com> > Subject: Center of model/volume shifts > Date: March 22, 2016 at 5:39:36 PM PDT > To: chimera-bugs(a)cgl.ucsf.edu > > Hi, > I notice an error in recalling the position/center of the volume map (please see image). > > If I apply a low pass filter/mask etc and open the volume it does not overlay the current map. I never came across this issue with the same operations. I have tried restarting session, chimera & even updating. > > It will be great to have your suggestions to fix this issue, as you can imagine. It basically means redoing an entire session, especially if pdb structures have been fit in the model. > > Thanks, look forward to possible solutions. > > Thanks, > Preeti > -- > ------------------------------------------------------- > Preeti Gipson > Postdoctoral Associate > Howard Hughes Medical Institute > Dept. of Molecular and Cellular Physiology > Stanford University, CA > >

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maintain .seg alignment to .mrc between sessions
by Amy Jobe 23 Mar '16

23 Mar '16

Hello, When I segment an 80S ribosome into individual ribosomal proteins and rRNAs, it takes some time and I often need to close and reopen my session. Whenever I reopen my session, though, my .seg file is no longer aligned to my .mrc map, and I have to spend time manually (and probably slightly inaccurately) re-aligning them. I've tried using the Associate Selected option in the daily build, although I'm not sure if it's meant to maintain alignment, and it hasn't fixed the problem. Can anyone help me with this? I'm using the daily build and the most recent stable version on Mac. Thanks, Amy Jobe -- PhD candidate, Joachim Frank group Department of Biological Sciences Columbia University 2-221 P & S Black Building 650 W. 168th St. New York, NY 10032 Telephone: (315) 879-8192 E-mail: abj2111(a)columbia.edu Lab website: http://franklab.cpmc.columbia.edu/franklab/

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using fitmap with per-frame analysis.
by Bala subramanian 22 Mar '16

22 Mar '16

Friends, I have a task which is as follows; I have done the simulation of a protein, whose EM map is already available. I want to fit the MD snapshots on to the map and to filter out some best frames based on the overlap statistics. I am aware that chimera does only rigid body fitting. I would like to know, for instance, if I can open the EM-map and the MD traj in Chimera and use per-frame analysis to achieve my goal. Also, i need some way to output/write the fitting statistics (eg. overlap value) to a file so that i can later filter out the best frames based on the statistics. Thank you, Bala C. Balasubramanian

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representative fits in chimera fitmap search
by Jan Kosinski 18 Mar '16

18 Mar '16

Hi, In the fitmap command global search, how the unique fit is selected from the cluster of similar fits? Ideally, from each cluster, I would like to obtain the fit the gave the best cross-correlation. But, I think, based on the fit_search code in FitMap/search.py, what is happening is that the first unique fit ever encountered is added to the fit list: close = b.close_transforms(ptf) if len(close) == 0: transforms = [M.multiply_matrices(ptf, mtv) for mtv in mtv_list] stats['hits'] = 1 f = Fit(models, transforms, volume, stats) f.ptf = ptf flist.append(f) b.add_transform(ptf) fo[id(ptf)] = f else: s = fo[id(close[0])].stats s['hits'] += 1 and any subsequent fit that is close to the first, would be discarded, even if it gives better cross-correlation. Do I understand correctly that the unique fit is not necessarily the best scoring fit from the cluster? Thanks in advance for clarification, Jan

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reset positions
by Dougherty, Matthew T 18 Mar '16

18 Mar '16

I have two positions set, p1 & p3. When I do "reset p1; reset p3 100" I have a trajectory problem with the camera crashing through a structure in between p1 & p3. I would like to create a new position p2 to avoid the crash, going from p1 to p2 to p3. I can get close to the crash by a freeze command. How can I determine the frame number being executed by the reset command when I freeze? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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opening large 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 it normal? Is there any way to speed up this step (for example, can 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

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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

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Computational power requirement
by Pascal Albanese 16 Mar '16

16 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

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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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Generating small planes inside inorganic bridges
by Henrique C. S. Junior 08 Mar '16

08 Mar '16

Dear Chimera list, As a inorganic chemist sometimes I have to deal with a variety of bridges (see image attached for an example) and it'd be very useful and didactic if I could create a little plane (like a distorted square) inside this bridges to mark different properties. Is this possible in Chimera? Thank you in advance. -- *Henrique C. S. Junior* Químico Industrial - UFRRJ Mestrando em Química Inorgânica - UFRRJ Centro de Processamento de Dados - PMP

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default position in space
by Jakob Suckale 07 Mar '16

07 Mar '16

Dear Chimera team, What determines the position of objects in space? I have done some testing with tubulin (1TUB), hemoglobin (1HHO), and collagen (1BKV). They all end up in very different and seemingly random position in print space after STL export (see screenshot). Is there a way to predict how items will appear to allow one to adjust the position beforehand with move commands? This is secondary for in silico simulations within Chimera but crucial for printing of real models. If they are cut by the plane everything below will not be printed, i.e. tubulin in my example would not be printed at all without adjustments and the others would be cut. All the best, Jakob

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color surface by volume data - thickness
by R.I.Koning＠lumc.nl 04 Mar '16

04 Mar '16

Dear all, Is it possible, while coloring the surface of a sphere using volume data value, to increase the thickness of the volume that is used to color that surface? I guess now just a 1 pixel thick intersection of the sphere with the volume is used, but I would like to vary the width of this intersection. Roman Koning

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Calculate distances between ligand atoms to select the most distant pair
by Felipe Vasquez 04 Mar '16

04 Mar '16

Hi, I am interested in select those two atoms more distant into a ligand. However, how could I estimate this so I have not to calculate the distance manually for all possible pairs one by one? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Profesional - Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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Hiding Chains
by Adith Arun 04 Mar '16

04 Mar '16

Hello, I have three chains in the protein, and I want to only view one of the chains. How do I hide the other two chains, so that the only chain that is seen on the Chimera viewer is the one I want to manipulate? Thanks!

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Selection of a CASTp/Surfnet cavity from command line
by Felipe Vasquez 04 Mar '16

04 Mar '16

Hi, I was trying to automatize the selection of those residues members of a certain cavity predicted by CASTp, starting from the opening of the file to the writing of the residues list (all from command line). However, I do not know how to select a cavity with an specific ID so I have not to do it manually. There is a strategy to achieve this goal from the command line? How could I do the same for Surfnet cavities? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Profesional - Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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