- Chimera-users - RBVI Mailing Lists

Icosahedral model
by 李智海 20 Jun '14

20 Jun '14

Hi， I have a density map of an icosahedral capsid, and now i want to make a icosahedral model to represent the capsid. In this model, every corner represent a capsomere. what can i do to display this in Chimera ? Do I require any plug-in? Thank you！ Best wishes! Zhihai Li School of Life Sciences, Xiamen University. Xiang'an Road(South), Xiang'an District, Xiamen City, Fujian Province, China.

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Fwd: CCL: Coordinate system rotation
by Elaine Meng 19 Jun '14

19 Jun '14

On Jun 19, 2014, at 8:33 AM, "Radoslaw Kaminski rkaminski.rk,+,gmail.com" <owner-chemistry(a)ccl.net> wrote: > Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]=[gmail.com] > Dear All, > > A trivial question. I have a XYZ file with a molecule in some coordinate > system. I would like to have a Z axis be in a certain direction along A...B > atoms. Is there any program that can easily change my coordinate system by > choosing some 3 atoms? I can of course do all transformations by hand (for > example in Excel) but its tedious. I know that ADF is capable of transforming > the coordinates to some specified coordination system (Prof. Baerends' CCL post > from several years ago), but is there any other program that can just make such > transformations quickly? > > Thanks in advance, > Radek From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: Re: CCL: Coordinate system rotation Date: June 19, 2014 9:57:00 AM PDT Hi Radek, With Chimera you could align 2 atoms front->back and then save a PDB file with the transformed coordinates. Not sure if that is exactly what you needed, or whether it is quick enough, but you could automate looping through multiple files with a little bit of Python. (1) open XYZ file (e.g. menu File…Open, choose file.xyz, or command "open file.xyz") <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/xyz.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html> That will automatically assign unique atom names by element and order in file, for example the first C will be C1, the first N will be N1. (2) use "align" command to put atoms A,B in center of view along the line of sight (laboratory Z axis) with A in front and B in back (e.g.: align @c1@o1) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/align.html> (3) save PDB with transformed coordinates (e.g. menu File…Save PDB, un-check "use untransformed coordinates" or command something like "write #0 file.pdb") <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> (4) close structure (e.g. command "close #0" or "close all") … if multiple structures to process, loop back to step 1. See here for writing looping scripts for Chimera: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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split
by John Mercer 19 Jun '14

19 Jun '14

Hi All, I understand the use of split as outlined in the tutorial describing how to find the contact region between two chains. file:///Applications/Bioinformatics/Chimera.app/Contents/Resources/share/chimera/helpdir/UsersGuide/frametut.html I don’t know the proper syntax for models with more than two chains, e. g. A, B, C, D, and E where you might like to split the model either as: A, B, D, and E in one group C in the other or A, B, and D in one group and C and E in the other. I would be grateful for a recommendation for the correct syntax to use in the argument list to form two groups to identify the contact surface after further processing (in the same manner as the tutorial). Thanks, -John

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STL Resolution Issues
by Eric Bell 19 Jun '14

19 Jun '14

Hello, I am trying to change the resolution of the atoms for a large molecule packing, but no matter how I change the zoom or the subdivisions property in the viewing effects, it seems to always produce the same filesize (~900 MB, not something our software can handle). Is this a bug or is it something that I'm doing incorrectly? I'm running on a mac, and I have tested this both with a .mol2 and .pdb file. Thanks, Eric

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how to tranfer a .mrc file to .mtz file
by #ZHANG HAIPING# 18 Jun '14

18 Jun '14

Dear chimera user: I have a .mrc file generated by chimera, now I want to convert it to .mtz formate, so I can load to coot, and examine the structure in details. Can anyone tell me how to convert .mrc to .mtz? Best regards, Haiping

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rename a residue?
by Julian Tirado-Rives 18 Jun '14

18 Jun '14

Dear Chimera team, thanks for all the work you put in into a very, very, useful program. I just have a question that I am hoping is just my inability to find the proper command ... is there a way to rename a residue before writing a PDB? I often use chimera as pre-preparation step before getting into some particular calculation packages, which often require different names for residues to indicate tautomers, protonation, etc. and it would be nice to do it from chimera rather than take the PDB's through a rather annoying set of scripts, sed's, or even text editors! Thanks in advance, - Julian - -- ----------------------------------------------------------------- | Julian Tirado-Rives | | | Department of Chemistry | Phone: (203)432-3356 | | Yale University | Fax: (203)432-6144 | | P. O. Box 208107 | email: Julian.Tirado-Rives(a)yale.edu | | New Haven, CT 06520-8107 | | -----------------------------------------------------------------

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Attaching a Probe to Modify an Existing Amino Acid
by Shana Burstein 18 Jun '14

18 Jun '14

Hello, I am an undergraduate student at Haverford College and I am attempting to attach thiocyanate probes onto different sites along a protein by first replacing the existing amino acid with a cysteine and then by adding a C and N onto the S- of the Cys residue. I know it is possible to carry this out manually using Tools>Structure Editing>Modify Structure, but I am hoping to automate this process by calling an external .py script that will primarily contain a list of preexisting Chimera commands. I have been successful at converting the targeted amino acid to Cys using "swapaa," building a CN residue called MSCN (using the createMolecule.py as a guide), combining the two models into one ("combine selected close True") and forming a bond between the Cys S and CN C atoms ("bond"). At this point, I am seeking help in automating the renaming of the modified residue to MSCN. Currently, Chimera sees this residue as two different separate residues called CYS and MSCN. Is there a way to combine these two structures so that the label corresponds to MSCN and the residue number corresponds to CYS? Sincerely, Shana Burstein Haverford College '15

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delete atoms based on their coordinates
by Aranha, Michelle 18 Jun '14

18 Jun '14

Hi , I wanted to know if there is a way in chimera to select and delete atom/atoms based on their position/coordinates in the simulation box. For example delete water 150 at (x, y, z). I tried zone sel, but I couldnt get it to work. Regards, Michelle ?

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com files & animation
by Dougherty, Matthew T 16 Jun '14

16 Jun '14

When executing a com file for animation production, I would like to see the line that is being executed display in the reply log. Is there a way to do that? I would prefer not using echo commands because of the large number of lines in the file being executed. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Chimera Plugins
by Eric Bell 16 Jun '14

16 Jun '14

Hello, Does a list exist somewhere of plugins developed for Chimera, or would we need to find them posted separately on a host site? Also, I found recently a software that gives preset .stl mesh resolutions for all atoms of the same element so that when they are 3d-printed, the atoms can all be distinguished from one another: http://cad4.cpac.washington.edu/WinXMorphHome/Cif2VRMLHome/Cif2VRML.htm However, the rest of the software seems lacking in reference to chimera's capabilities, is there any way that Chimera could have a similar feature? Ideally it would allow the "subdivisions" property of the viewing effects apply to every element, similar to how radius applies to all atoms of the same element. Thanks, Eric

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Adding residue to two sides of DNA
by Mehdi Bagherpour 16 Jun '14

16 Jun '14

Dear Chimera Users, I want to add 3 base-pairs to two side of DNA. I tried more about that but I couldn't. Could some one any idea about doing that in chimera or another programs. Best Regards, Mahdi

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QUESTION
by Eifler, Jay Q. (UMKC-Student) 16 Jun '14

16 Jun '14

Wanting to know if we can use charges assigned by define attribute in a file for the purpose of adding ions. Seems like the Add Ions feature will not do this and will only use the built in methods Gasteigter, etc. I have a HYP residue that the Add Charge feature won't do.

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About direct fetching biological assemblies into Chimera
by Boaz Shaanan 16 Jun '14

16 Jun '14

Hi Tom, This is a nice addition but can you ALSO give the option of fetching just one of the biological assemblies? It is my experience that biological assemblies for a particular pdb entry consist of one correct assembly, in the sense of biological function corresponding to the description given by the depositors and other assemblies. I usually flip between the assemblies on the RCSB website before deciding which one to fetch. With your new addition this of course can all be done now in Chimera but if possible, I'd rather not waste time and disk space with meaningless assemblies. What do you think? Cheers, Boaz Message: 6 Date: Mon, 2 Jun 2014 16:53:06 -0700 From: Tom Goddard <goddard(a)sonic.net> To: "Hurt, Darrell (NIH/NIAID) [E]" <darrellh(a)niaid.nih.gov> Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Fetch biological unit? Message-ID: <0086EC78-81D4-4892-9A22-A4177426F74D(a)sonic.net> Content-Type: text/plain; charset=windows-1252 Hi Darrell, I added a Chimera Fetch dialog entry ?PDB biounit? that will fetch all the biological assembly files for a pdb id ? there can be more than one. Also they can be fetched using the Chimera command: open pdbbuID:2bbv Will be in tonight?s daily build. Tom Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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Color by RMSD for multi-chain structure?
by Oliver Clarke 13 Jun '14

13 Jun '14

Hi all, Is there an easy way to color two superimposed structures by RMSD (per C-alpha pair)? I had a quick look through the manual and the mailing list and I couldn’t find any easy way to do so for a structure that consists of more than one chain. I think this would be a very useful addition to either render by attribute or the calculation of a morph (because presumably the paired CA-CA distances are already calculated in the process of generating the morph). I have aligned based on one chain in a complex, and would like to color the entire complex by RMSD (to highlight the parts that move the most between two states of the same complex). I can calculate the per CA RMSD using “rmsd #1 #2”, but I can’t see any obvious way to assign that to a residue attribute using the attribute calculator or setattr etc. Many thanks, Oliver.

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easy way to make alignments in chimera
by Michał Kadlof 13 Jun '14

13 Jun '14

Hello, I would like to ask if there is any quick way to make aligment (with secondary structure score included) beetwen two homologous protein structures, and save them in Stockholm format (information about missing residues is needed). I have houndreds of such pairs, and it would be very helpfull to do it by script for headless Chimera. -- yours sincerely Michael Kadlof University of Warsaw

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Subclass chimera.Molecule
by Jaime Rodríguez-Guerra 13 Jun '14

13 Jun '14

Hello, I am trying to extend the chimera.Molecule class() to add a few methods and attributes, but the followin error arises: TypeError: Error when calling the metaclass bases type '_molecule.Molecule' is not an acceptable base type File "/home/jr/x/gaudi/gaudi/molecule.py", line 51, in <module> class Compound(chimera.Molecule): Is there any workaround? I want my Compound objects to behave like standard chimera Molecules (with all their attributes and stuff), and also be able to call custom methods on that Molecule. Thanks in advance, Jaime.

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how can i register to use chimera
by carlos martinez 12 Jun '14

12 Jun '14

how can i register to use chimera program

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python printing in x3d2collada.py
by Dougherty, Matthew T 11 Jun '14

11 Jun '14

I was delving into the chimera code and wanted to print some variables to better understand how the code works. When I use a print statement I do not see anything in the reply log or the IDLE window. here is an example for filename in args: print filename print >> sys.stdout, "FN: %s" % filename Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Re: [Chimera-users] "ligand" category for selection
by Hurt, Darrell (NIH/NIAID) [E] 10 Jun '14

10 Jun '14

I guess one way to do it might be to use a different specifier for ligands, like maybe: :/numAtoms<100 -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: <Hurt>, Darrell Hurt <darrellh(a)niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Date: Thursday, June 5, 2014 12:41 PM To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] "ligand" category for selection Hi Chimera friends, I'm trying to use the attached MOL file (dopamine) in Chimera and I want to run a Python script on it. My script does some things to the molecule using selection categories. I'm trying to select this molecule as "ligand", but I get a "No atoms specified" error. Alternatively, is there a way in Python to ignore the error if I get it and keep processing the rest of the script? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Fwd: STL Output
by Tom Goddard 10 Jun '14

10 Jun '14

Begin forwarded message: > From: Tom Goddard > Subject: Re: [Chimera-users] STL Output > Date: June 10, 2014 at 2:02:27 PM PDT > To: Eric Bell <Eric.Bell(a)oberlin.edu> > > Hi Eric, > > Chimera doesn’t represent molecules as polyhedrons. Are the orange octahedrons each representing one molecule? And what are the red spheres at the corners, with some red spheres out in space? And what are the little attached pink spheres? This kind of display would require a new Chimera plug-in. The graphics would be easy to do in Chimera. I don’t think such a model would hold together very well when printed in 3d. > > The Crystal Contacts tool in Chimera is remotely related, showing contacts between asymmetric units in a crystal > > https://www.cgl.ucsf.edu/chimera/experimental/crystal_contacts/clashes.html > > Tom > > > On Jun 10, 2014, at 1:50 PM, Eric Bell wrote: > >> Dear Tom, >> >> The polyhedral models look something like the attached image. Does chimera do anything like this or would I have to code a separate plugin? >> >> Thanks, >> Eric<polyhedra.jpg> >> On Jun 10, 2014, at 2:15 PM, Tom Goddard wrote: >> >>> Hi Eric, >>> >>> Not sure what kind of CrystalMaker polyhedral models you were thinking about printing. Chimera can show crystal unit cells. Here are 4 unit cells each containing 8 copies of a small protein (1a0m) shown with the Chimera Unit Cell tool (menu Tools / Higher Order Structure / Unit Cell) with the proteins shown as solvent excluded surfaces (menu Actions / Surface) and each unit cell colored differently (selected by hand with a mouse drag, then used menu Actions / Color). >>> >>> Tom >>> >>> <1a0m_2x2_unitcells.jpg> >>> >>> >>> On Jun 8, 2014, at 7:47 PM, Eric Bell wrote: >>> >>>> Dear Chimera Developers, >>>> >>>> My name is Eric Bell, and I am a student at Oberlin College. I have been using Chimera for 3d printing of molecular models because of its ability to handle many of the processes needed for atom editing as well as its ability to export in an .stl format. However, an issue I've run into is that the resolution of those .stl meshes is rather high, and there does not exist an option, to my knowledge, to alter the amount of vertices on the spheres. This causes an issue when we want to print spacefill models of large molecules, because Chimera will output such large files that our software isn't able to properly process the file without serious resource consumption. Is there anything that I as a user can alter to change the resolution of these spheres, or is it a setting that has been compiled so that I can't edit it without recompiling? I am familiar with python so navigating code would not be an issue for me if necessary. Thank you! >>>> >>>> Sincerely, >>>> Eric Bell >>>> >>>> P.S. Another thing we were looking for that has yet to be done is to print polyhedral models like those in programs such as CrystalMaker. As far as I know Chimera doesn't have this functionality but a programming environment called Bsoft is using the native save file format of chimera to do it because of its similarity to XML. >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users(a)cgl.ucsf.edu >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >

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Fwd: STL Output
by Tom Goddard 10 Jun '14

10 Jun '14

> From: Eric Bell > Subject: Re: [Chimera-users] STL Output > Date: June 10, 2014 at 1:50:49 PM PDT > To: Tom Goddard > > Dear Tom, > > The polyhedral models look something like the attached image. Does chimera do anything like this or would I have to code a separate plugin? > > Thanks, > Eric > On Jun 10, 2014, at 2:15 PM, Tom Goddard wrote: > >> Hi Eric, >> >> Not sure what kind of CrystalMaker polyhedral models you were thinking about printing. Chimera can show crystal unit cells. Here are 4 unit cells each containing 8 copies of a small protein (1a0m) shown with the Chimera Unit Cell tool (menu Tools / Higher Order Structure / Unit Cell) with the proteins shown as solvent excluded surfaces (menu Actions / Surface) and each unit cell colored differently (selected by hand with a mouse drag, then used menu Actions / Color). >> >> Tom >> >> <1a0m_2x2_unitcells.jpg> >> >> >> On Jun 8, 2014, at 7:47 PM, Eric Bell wrote: >> >>> Dear Chimera Developers, >>> >>> My name is Eric Bell, and I am a student at Oberlin College. I have been using Chimera for 3d printing of molecular models because of its ability to handle many of the processes needed for atom editing as well as its ability to export in an .stl format. However, an issue I've run into is that the resolution of those .stl meshes is rather high, and there does not exist an option, to my knowledge, to alter the amount of vertices on the spheres. This causes an issue when we want to print spacefill models of large molecules, because Chimera will output such large files that our software isn't able to properly process the file without serious resource consumption. Is there anything that I as a user can alter to change the resolution of these spheres, or is it a setting that has been compiled so that I can't edit it without recompiling? I am familiar with python so navigating code would not be an issue for me if necessary. Thank you! >>> >>> Sincerely, >>> Eric Bell >>> >>> P.S. Another thing we were looking for that has yet to be done is to print polyhedral models like those in programs such as CrystalMaker. As far as I know Chimera doesn't have this functionality but a programming environment called Bsoft is using the native save file format of chimera to do it because of its similarity to XML. >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> >

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STL Output
by Eric Bell 10 Jun '14

10 Jun '14

Dear Chimera Developers, My name is Eric Bell, and I am a student at Oberlin College. I have been using Chimera for 3d printing of molecular models because of its ability to handle many of the processes needed for atom editing as well as its ability to export in an .stl format. However, an issue I've run into is that the resolution of those .stl meshes is rather high, and there does not exist an option, to my knowledge, to alter the amount of vertices on the spheres. This causes an issue when we want to print spacefill models of large molecules, because Chimera will output such large files that our software isn't able to properly process the file without serious resource consumption. Is there anything that I as a user can alter to change the resolution of these spheres, or is it a setting that has been compiled so that I can't edit it without recompiling? I am familiar with python so navigating code would not be an issue for me if necessary. Thank you! Sincerely, Eric Bell P.S. Another thing we were looking for that has yet to be done is to print polyhedral models like those in programs such as CrystalMaker. As far as I know Chimera doesn't have this functionality but a programming environment called Bsoft is using the native save file format of chimera to do it because of its similarity to XML.

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CASTp data
by Felipe Vasquez 09 Jun '14

09 Jun '14

Hi, I am currently trying to identify certain features from a particular binding cavity, and I decided to use CASTp plugin from Chimera. However, I realized that the data obtained directly from CASTp online server are not the same that those obtained by CASTp from Chimera. Examples include not only the number of pockets, but also the volume and surface area of them. What is the meaning of this confusing results? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* 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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electrostatic potential based on Swiss-Model
by Jingga Inlora 06 Jun '14

06 Jun '14

Hello, I am a graduate student at the University of Michigan and I am currently trying to obtain images of my proteins with electrostatic potentials for my manuscript. For one of my proteins, there is no solved protein structure (by X-ray crystallography or NMR) and I had to use SWISS-MODEL to predict the structure. I did electrostatic potential calculation using DelPhi but when I visualized it using Chimera, the electrostatic distribution is not what I expected. I did notice the electrostatic potential calculations for other previously solved protein structures took much longer and resulted in bigger files, whereas the SWISS-MODEL-predicted protein contains much smaller .phi file size. I was wondering if you have any idea how accurate it is to calculate the electrostatic potential based on a SWISS-MODEL predicted protein structure, and if there are ways to improve the reliability of the calculated electrostatic potentials for that protein? Thank you very much for your help! Sincerely, Jingga Inlora

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undo
by Antón Vila Sanjurjo 06 Jun '14

06 Jun '14

Hello, I am working with chimera sessions involving a large numer of 70S ribosomes. I keep modifying the sessions over and over, so I save new sessions every day. Much of what I do is labeling interesting residues, measuring distances, coloring these residues, etc. Sometimes I make a mistake, like accidentally selecting and modifying a large portion of the model, and I loose an important amount of information. In these cases, I find that there is no way to go back to the previous state of the system, other than clossing the session and re-opening the latest saved one. Unfortunately, this means loosing a lot of unsaved work. While there is an "undo" option under the "select" tab, it does not really allow one to return to the previous state of the system. In fact, I'm not even sure of what it does. My question is, is there a way to return Chimera to the state ocurring immediately before the last action? In case this does not exist, can it be implemented? best, Antón -- Antón Vila-Sanjurjo, PhD Marie Curie fellow Grupo QOSBIOS, Dept. Química Fundamental Facultade de Ciencias Universidade de A Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain). tlf: (34) 981-167000 ext:2659 e-mail: antonvila.s(a)gmail.com

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