- Chimera-users - RBVI Mailing Lists

show axis ?
by Stefan Bäckström 03 Mar '10

03 Mar '10

Hi. It is possible to show the box of a volume, and I wonder if it is possible to show the X, Y and Z axis as lines ? Best, Stefan Bäckström Medical Biochemistry Göteborg University Sweden

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groups
by Jean-Paul Armache 03 Mar '10

03 Mar '10

Hello, I am often juggling between different sets that are to be turned on/off together. Is there a way of grouping maps/pdbs so that instead of turning 20 pdbs on, i could just click on a group to which they belong ? If there is something like that, could you point me to it ? And if not, would it be possible to have it in the Model Panel? Best regards, Jean-Paul Armache

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chimera-users@cgl.ucsf.edu
by Jozef Lewandowski 03 Mar '10

03 Mar '10

Hi everybody, I am trying to get a list of all hydrogen atoms within certain distance from a specific atom. I found an old thread suggesting using findclash for that. When I use: findclash #0.265:4@c overlap -8 hbond 0 ignoreIntraRes false log true bondSeparation 0 everything works fine and I get the list of all the atoms within the desired distance limits. However, I get all types of atoms. To select only for contacts to hydrogens, I have tried to add the "test" option but when I type: findclash #0.265:4@c overlap -8 hbond 0 ignoreIntraRes false log true bondSeparation 0 test @H the procedure does not report on any contacts. Am I misunderstanding the syntax? What is the way to get only the distances between :4@c and all hydrogens within ~10A? Moreover, I am ultimately interested in the sum of all reported distances (or more specifically sum of (1/r)6 where r is the distance). Is there simple way to get this value calculated in Chimera (e.g. simple script)? Unfortunately, I have no idea about Python coding, so right now I have to import the list to Excel and calculate what I need in there (which is fine for a few atoms but slightly tedious when you have to check several hundred of them...). Any help would be appreciated. Thanks, Józef

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Sum of distances
by Jozef Lewandowski 03 Mar '10

03 Mar '10

Hi everybody, I am trying to get a list of all hydrogen atoms within certain distance from a specific atom. I found an old thread suggesting using findclash for that. When I use: findclash #0.265:4@c overlap -8 hbond 0 ignoreIntraRes false log true bondSeparation 0 everything works fine and I get the list of all the atoms within the desired distance limits. However, I get all types of atoms. To select only for contacts to hydrogens, I have tried to add the "test" option but when I type: findclash #0.265:4@c overlap -8 hbond 0 ignoreIntraRes false log true bondSeparation 0 test @H the procedure does not report on any contacts. Am I misunderstanding the syntax? What is the way to get only the distances between :4@c and all hydrogens within ~10A? Moreover, I am ultimately interested in the sum of all reported distances (or more specifically sum of (1/r)^6 where r is the distance). Is there simple way to get this value calculated in Chimera (e.g. simple script)? Unfortunately, I have no idea about Python coding, so right now I have to import the list to Excel and calculate what I need in there (which is fine for a few atoms but slightly tedious when you have to check several hundred of them...). Any help would be appreciated. Thanks, Józef

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constraints and restraints
by Elaine Meng 02 Mar '10

02 Mar '10

Hello, The Chimera release notes describe what is new or changed in a release: <http://www.cgl.ucsf.edu/chimera/docs/relnotes.html> ... clicking the "1.4" link: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.4.html> The meaning of "constraint" "restraint" and "tether" may change based on which program you are using. Each program should explain it in its own documentation. In programs I've used, "constraints" meant atoms are completely fixed in place (frozen, cannot move) whereas "restraints" use a force constant like a spring, and allowed some movement. I don't have any opinion on the technical definition of "tethering." Again, don't rely on my descriptions as final because different programs may use the words to mean different things. Chimera minimization only allows "fixing" some of the atoms so they can't move at all. It does not allow holding atoms in place with force constants. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.… > I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html > nice to give you a letter! > is there a new one ,really? > what is the new feature in the least software? > > I want constraint ,restraint and tether some atoms and backbone. > how can I do constraiting ,restrainting and tethering in > software.how can i set value for constraiting ,restrainting and > tethering. > what is the difference between them? > > thank you! > >

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NAMD trajectory and AMBER topology
by Francesco Musiani 02 Mar '10

02 Mar '10

Hi all, I would like to visualize in Chimera a trajectory obtained with the program NAMD, but I have a .prmtop topology file generated using AMBER instead of a .psf topology file. I have these files beacuse in NAMD is possible to use AMBER format topology. Is it possible to implement an additional feature in Chimera which allows to visualize NAMD trajectory using AMBER topology? Thanks in advance, Francesco -- Francesco Musiani -- Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin 40, I-40127 Bologna, Italy Phone: +39-051-2096236 - Fax: +39-051-2096203 E-mail: francesco.musiani(a)unibo.it Web: http://bioinorg.agrsci.unibo.it

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load pdb files from local PDB mirror
by Mark Moll 02 Mar '10

02 Mar '10

I have a local mirror of all PDB structures (as pdb files). It’d be nice if Chimera could use this, but it seems that Chimera expects a “flat” directory structure rather than the hierarchical directory structure of the PDB. For example, on my machine the pdb file for 1ady is stored in ${HOME}/pdb/ad/pdb1ady.ent.gz, but when I fetch by ID, the file will not be found. Instead, Chimera will download the file and save it in ${HOME}/pdb/PDB/1ADY.pdb. Is there some way to handle both cases (flat & hierarchical directory structure)? -- Mark

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multi-threading
by Jean-Paul Armache 02 Mar '10

02 Mar '10

Hello, I know that this topic might've emerged earlier, but I was curious whether there were any plans to implement multi-threading into Chimera ? Best regards, Jean-Paul Armache

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Re: [Chimera-users] How are chains paired in morphing?
by Eric Pettersen 01 Mar '10

01 Mar '10

The sequences are in input order unless you ask for the return value to be a dictionary (with the 'asDict' keyword). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 22, 2010, at 11:25 AM, Conrad Huang wrote: > There's a comment in Segment.py: > > # Get the chains from each model. If they do not have the > # same number of chains, we give up. Otherwise, we assume > # that the chains should be matched in the same order > > It uses molecule.sequences() to get the chains. Eric, does > sequences() return the chains in input order, or is it random (eg > hash order)? > > Conrad > > On 2/22/2010 10:26 AM, Thomas Goddard wrote: >> Bobby Laird showed me a homo-tetramer with chains A, B, C, D that >> when >> morphed between two states with the Chimera morph conformations tool >> swapped two of the monomers. In other words the 4 chains from one >> state >> weren't correctly paired with the 4 chains from the other state so >> two >> monomers exchanged positions during the morph. The tetramers were >> built >> from dimers 1pfk and 2pfk by using the symmetry of the unit cell with >> other software (coot?). >> >> How does morph conformations decide which chains to pair? >> >> >> Tom >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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saving moved maps
by Erika Mancini 26 Feb '10

26 Feb '10

Dear Chimera users, is it possible, after moving maps around, to save them into their new positions? I tried save map from volume viewer, but maps are saved in their original positions. Thanks! erika

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question
by Huang, Xinlei 25 Feb '10

25 Feb '10

Hi, Thank you for inventing the software, it rocks! By the way I have a question about viewing the 3D reconstruction image of a Virus like particle containing small nanoparticle cores. When I tried to increase the electron density in order to see the inside cores there always was a box showed up along with the nanoparticle. I want to know is there a way to remove the outside box? Here I attach an image to explain better what I mean. I appreciate you help. Thanks xinlei

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variable surface visualization
by Zambonelli, Carlo 25 Feb '10

25 Feb '10

Dear All, I am working with a glycoprotein structure and I want to visualize the protein surface as a continuum with the glycans sticking out as sticks. If I visualize the surface of the whole molecule (including sugars), and then I select the sugars only and visualize them as sticks, the surface of the amino acids immediately connected to the sugar (Asn) appear to be clipped. One solution could be to the following: 1. save the model with a different name 2. load the 2 identical structures and align them 3. remove the sugars from one structure only and use it to visualize the protein 4. the second structure is used for visualizing the sugars and not the protein. I used to do something similar with Pymol, and it should work with Chimera as well, but I am sure there is a better/simpler solution. Any suggestion? Thank you for your help. Carlo

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quesitons
by Xinlei Huang 25 Feb '10

25 Feb '10

Hi, Thank you for inventing the software, it rocks! By the way I have a question about viewing the 3D reconstruction image of a Virus like particle containing small nanoparticle cores. When I tried to increase the electron density in order to see the inside cores there always was a box showed up along with the nanoparticle. I want to know is there a way to remove the outside box? Here I attach an image to explain better what I mean. I appreciate you help. Thanks xinlei Chemistry Department Indiana University-Bloomington

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Re: [Chimera-users] [chimera-dev] run chimera's IDLE in terminal on mac os x
by Eric Pettersen 24 Feb '10

24 Feb '10

On Feb 24, 2010, at 5:34 PM, Yang wrote: > Hi Eric > > I want to manipulate with electron density maps, and just use > chimera functions for reading pdb files and density maps. However, > for high-resolution maps, it takes too long to run the my program on > my mac book. So I want to remotely use the server of our department, > which has much larger memory, to complete this task by typing > commands in terminal. Before that, I had everything done in > chimera's IDLE. So I prefer using chimera functions somehow in > terminal assuming chimera is installed first. > > Thanks for your advice. I think you just want to take whatever commands you were using in IDLE and put them in a Python script (file ending: .py). You can then execute them with "chimera --nogui myscript.py". If you need to supply arguments to the script then instead run it like this: "chimera --nogui --script myscript.py -- arg1 arg2 ...". This is described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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version 1.3
by n.prahl＠freenet.de 24 Feb '10

24 Feb '10

Hi everybody, I don`t find a link on your homepage to download the chimera version 1.3. I only find version before or after chimera 1.3. How can I download the version 1.3? I need this version for my studies. Thank you, Nicole Heute schon ge"freeMail"t? Jetzt kostenlose E-Mail-Adresse sichern! http://email.freenet.de/dienste/emailoffice/produktuebersicht/basic/mail/in…

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Re: [Chimera-users] [chimera-dev] run chimera in terminal on mac os x
by Elaine Meng 24 Feb '10

24 Feb '10

On Feb 24, 2010, at 11:45 AM, ylei(a)ecs.umass.edu wrote: > Dear all > Could somebody tell me how to run Chimera in terminal on the system > of mac? > Thanks. > Yang Hi Yang, It is described in the User's Guide page on Chimera startup: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecore.html> See the part about Mac OS X. To summarize, if Chimera is installed as /Applications/Chimera , to start it from Terminal you would type: /Applications/Chimera.app/Contents/MacOS/chimera (or if it is in a different place or you gave it a different name, substitute those instead). Since that is kind of a long thing to type, you may want to make an alias. My aliases are in the file named .tcshrc in my home directory on the mac, but the filename could be different depending on what shell you are using (maybe .bashrc or .cshrc or something like that). 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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Chemical groups
by Mauro Truglio 23 Feb '10

23 Feb '10

Hi, I'm a newbie, and I'd like to use Chimera to recognize functional groups on a structure or a ligand, and I need it to write a file with the atoms involved. Now, if I do Select>Chemistry>functional group , search for one, and export the results through "write list", it exports a raw list of atoms without any specification of which atom is involved in which f.g.. It could be useful to add some sort of identifier, like: FG1: atom atom atom FG2: atom atom atom How can I do that? Already tried to modify __init__.py in ChemGroups, but all I obtain is a list of physical addresses of atoms, e.g.: Group number 1 : [<_chimera.Atom object at 0xa455db8>, <_chimera.Atom object at 0xa455dd0>, <_chimera.Atom object at 0xa455de8>, <_chimera.Atom object at 0xa455e00>, <_chimera.Atom object at 0xa455e18>] Group number 2 : [<_chimera.Atom object at 0xa455e30>, <_chimera.Atom object at 0xa455e48>, <_chimera.Atom object at 0xa455e60>, <_chimera.Atom object at 0xa455e78>, <_chimera.Atom object at 0xa455e90>] Thank you Mauro Truglio (Bioinformatics Lab - University of Rome Tor Vergata)

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Rendering a vector/axis
by Richard Stanton 23 Feb '10

23 Feb '10

Hi, Is there a way to render a vector after defining it as an axis in the "Axes/Planes" tab under "Structure Measurements"? I am able to define an axis using the selected atoms in my structure but I am not sure how to visually render and alter its appearance, as there is no visual representation on the graphics screen. I was hoping that after using my selected atoms to define the axis I would then have an arrow or line showing me the axis/vector and I could then create different vectors/axis and view them simultaneously to show the difference between their angles. Is there a way to do this? Thanks in advance for the help! Thanks, Rich

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Chemical groups
by Mauro Truglio 23 Feb '10

23 Feb '10

Hi, I'm a newbie, and I'd like to use Chimera to recognize functional groups on a structure or a ligand, and I need it to write a file with the atoms involved. Now, if I do Select>Chemistry>functional group , search for one, and export the results through "write list", it exports a raw list of atoms without any specification of which atom is involved in which f.g.. It could be useful to add some sort of identifier, like: FG1: atom atom atom FG2: atom atom atom How can I do that? Already tried to modify __init__.py in ChemGroups, but all I obtain is a list of physical addresses of atoms, e.g.: Group number 1 : [<_chimera.Atom object at 0xa455db8>, <_chimera.Atom object at 0xa455dd0>, <_chimera.Atom object at 0xa455de8>, <_chimera.Atom object at 0xa455e00>, <_chimera.Atom object at 0xa455e18>] Group number 2 : [<_chimera.Atom object at 0xa455e30>, <_chimera.Atom object at 0xa455e48>, <_chimera.Atom object at 0xa455e60>, <_chimera.Atom object at 0xa455e78>, <_chimera.Atom object at 0xa455e90>] Thank you Mauro Truglio (Bioinformatics Lab - University of Rome Tor Vergata)

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Defining planes & Thermal ellipsoids
by David Chenoweth 22 Feb '10

22 Feb '10

Hi! Thanks so much for adding the define plane and define centroid features. Is there any way to add the option of defining the border of the plane as a polygon where the selected atoms define the polygon vertices? This would allow a plane in the shape of a hexagon or any other heterocycle to be inset inside of an aromatic ring for example without the edges of the plane being visible outside the bond enclosed area. Also, the thermal ellipsoid feature looks fantastic, however the probability setting doesn't seem to be functioning. Thanks again for adding all these features, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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How are chains paired in morphing?
by Thomas Goddard 22 Feb '10

22 Feb '10

Bobby Laird showed me a homo-tetramer with chains A, B, C, D that when morphed between two states with the Chimera morph conformations tool swapped two of the monomers. In other words the 4 chains from one state weren't correctly paired with the 4 chains from the other state so two monomers exchanged positions during the morph. The tetramers were built from dimers 1pfk and 2pfk by using the symmetry of the unit cell with other software (coot?). How does morph conformations decide which chains to pair? Tom

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Which Mac daily build to use
by Thomas Goddard 21 Feb '10

21 Feb '10

> on another note: which of the daily builds should I be using? aqua, > aqua-intel, intel-cocoa, intel-cocoa-64. > > not sure on the + & -'s > > do not mind taking some crash risks to push sw dev objectives and reporting. > > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine/Houston Texas USA Hi Matt, The Mac Chimera builds are far too numerous now. I recommend the 64-bit Cocoa build. That is what I use. It has one very serious issue right now that pressing Option-e or Option plus many other other characters will immediately crash Chimera. It is a Tk Cocoa bug that I reported but I need to put a fix into Chimera while I wait for the Tk developers to fix it. If that sounds too dangerous use the Chimera Aqua build (32-bit only). That uses the Mac Carbon API which is the older Mac API that Apple says they will not provide 64-bit support for. So we will replace that with Cocoa in the Chimera 1.5 release in a few months. My least favorite choice is Mac X11 which is not the native Mac windowing system and is the least well supported. That Chimera version will also be eliminated in the future. For the 32-bit versus 64-bit Chimera Cocoa you should use 64-bit if you have Mac OS 10.6 (Snow Leopard) or 32-bit for older Mac OS versions. We don't offer 64-bit Mac Chimera on Mac OS 10.5 or older Mac OS versions. Mac OS 10.6 is the first version of Mac OS that uses 64-bit by default. I've measured performance of 64-bit Mac Cocoa Chimera and it is as good as 32-bit. For the Chimera 1.5 release we hope to only be offering two production Mac Chimera versions 32-bit and 64-bit Cocoa. The X11 version will be in the unsupported category and the Aqua (= Carbon) will be gone. Tom

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centroid measurements typo
by David Chenoweth 20 Feb '10

20 Feb '10

Hi, Sorry there was a typo in the last message! The centroid feature is great, but I would like to select two centroids or a centroid and an atom and then measure the distance between them. When I try this I get the Error Message: "Exactly two atoms must be selected in the graphics window". Is there anyway to add the ability to make these measurements. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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Centroid measurements
by David Chenoweth 20 Feb '10

20 Feb '10

Hi, The centroid feature is great, but I would like to select two centroids of a centroid and an atom and then measure the distance between them. When I try this I get the Error Message: "Exactly two atoms must be selected in the graphics window". Is there anyway to add the ability to make these measurements. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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command line writing PDB files
by Matthew Dougherty 19 Feb '10

19 Feb '10

Is there a command line string for writing out selected atoms as a PDB file? thanks, matt Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================== ==================================

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