- Chimera-users - RBVI Mailing Lists

file format conversion using chimera
by snoze pa 12 Mar '10

12 Mar '10

Dear Chimera Users, I want to save/convert a pdb file into .mrc or .ccp4 format using chimera I think I did it before using chimera but don't remember exactly how! I will highly appreciate your help. Thank you S

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Re: [Chimera-users] Chimera: Display map around atoms
by Elaine Meng 12 Mar '10

12 Mar '10

Hi Greg, That "bv" shortcut creates a new, larger map (periodically extended as needed to cover the atoms), which sounds like the opposite of what you want. You can limit the density display to a zone around selected atoms. Choose "Zone" from the "Features" menu in the Volume Viewer dialog to add the relevant controls to the dialog. The zone feature is described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum… > For future questions, it's better to send Chimera questions to the chimera-users(a)cgl.ucsf.edu list rather than to me directly. That way it won't fall through the cracks if I'm on vacation, or sick, or don't know the answer. I hope this helps, ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 12, 2010, at 1:24 PM, Greg Friedland wrote: > Hi Elaine, > Thanks for your earlier help with Chimera. I'm currently have > difficulty displaying a density map. I'd like to only display the > density around protein atoms, not the full symmetry density. I tried > the shortcut 'bv' according to http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/003002.html > but the new map still contains lots of the symmetric molecule > density. Is there another way? > Thanks, > Greg > > Greg Friedland > Postdoc > Sandia National Lab > Joint BioEnergy Institute

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Recording trajectory
by Francesco Pietra 11 Mar '10

11 Mar '10

Hi: I am interested in following the pathway of a ligand forced to leave a protein. I can follow that path with the movie (NAMD format) but I would be interested to also have a trace of the pathway recorded. I would like to show around the protein the various traces for different pathways of exit of the same ligand. thanks francesco pietra

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Re: [Chimera-users] Recording trajectory
by Eric Pettersen 09 Mar '10

09 Mar '10

On Mar 9, 2010, at 2:17 PM, Francesco Pietra wrote: > Hello Eric: > I have seen your later correction mail. > > I had a bad day, that is little time for chimera and with little > success. Please try to guess were I was faulty. > > francesco@tya64:~$ chimera --version > chimera alpha version 1.5 (build 30193) 2010-03-06 09:27:34 GMT > francesco@tya64:~$ > This is amd64, at the moment I have no 32bit computer. > > <select ligand> selects too much. > > <select :residue.number> > <select :residue.name> > do select exactly what I want (which is a small ligand of HEME ligand > of the protein. > > The problem was with <define> command > > MD-movie...Per-Frame "define centroid :residue.number" ... Apply > > then activating the movie gave the same view as not going through the > Per_Frame, i.e., the small ligand does not leave any sphere on the > path. I did not investigate if the sphere are too small to be seen at > the magnification I used, ore have the same color as the background > (black). Very likely, I did some other major mistake. Not sure what to say. Works for me. I've appended an image of centroids tracing the motion of a small ligand in an RNA binding site. I used a step size of 10 and this 'define' command: define centroid raiseTool false radius 1.0 color goldenrod sel "raiseTool false" prevents 'define' from trying to bring up the Axes/ Planes/Centroids tool (and update that tool's table) for every centroid created. The other options control the size and color of the centroid. I had the small ligand selected so 'sel' is my atom spec. I tried it a second time with ":35" (which also selects the small ligand) and that worked too. FYI, "~define" will get rid of all the centroids. I hope this helps somehow. Are you sure you had the "Interpret script as" part of the per-frame dialog set to "Chimera commands"? I can't imagine that you didn't, since you would have gotten some kind of error if it had been interpreted as Python. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] Scripting to write / save multiple models into single pdf file
by Elaine Meng 08 Mar '10

08 Mar '10

On Mar 7, 2010, at 5:12 AM, Sumitro Harjanto wrote: > Hi Meng, > I would like to use chimera to help me with a process of combining > receptors and ligands that were modelled separately (in separate > files) > > So here is my intended framework: > > For each iteration: > • open “template.pdb” template file (which contains the receptor/ > ligand complex) I used to model the receptor and ligand > • open the receptor_model.pdb > • open the ligand_model.pdb > • match receptor to template > • match ligand to template > • close template.pdb > • save the models in their current position into a single new pdb > file. > > I was exploring the feasibility of using the command “write” but I > am not too sure if it will allow me to save the complex as a single > pdb file..? > > On a side note, if it’s possible, any suggestion on how to optimise > the run time since I might be running this for a large number of > iterations ..? I read somewhere about switching off the GUI to save > time, does it help..? > > Thanks! > Cheers, > Sumitro Hi Sumitro, You can't save multiple models in one file with the "write" command, but you can use "write" multiple times, one for each model you want to save. If you make sure to save each model "relative" to the same model, they will be in the correct positions with respect to each other when you reopen the files. See the "relative" keyword: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> Or, if you really need to have them in a single file, you can use the "combine" command to create a new single model from multiple models. You would do that after the matching, but before saving the PDB file. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> I can't answer about how to script for multiple models, or how much faster it might be to use noGUI, so I'm sending this to the chimera- users list. In the future, please send Chimera questions to the chimera-users(a)cgl.ucsf.edu list, because I might be away from work or (like now) others may be better able to answer the question. I hope this helps, ----- 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

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Problem with energy minimization
by Bill McIntire 05 Mar '10

05 Mar '10

I used Dock Prep for my modeled structure, and get no error comments. However, when I try to energy-minimize, I get the following message: No MMTK name for atom "HN1" in standard residue "PRO" PRO is at the N-terminus. I cannot find any help in manual. Please help with this problem. Thanks Bill McIntire

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cap color from command line
by Jean-Paul Armache 05 Mar '10

05 Mar '10

Hello, Thank you for all your previous answers. I would like to ask you whether there is a way to change the cap color not only from the Surface capping tool, but the command line as well and declare it maybe in a script (like for example coloring of the maps and models). Thanks, Jean-Paul

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make one chain from two chains ID in PDB
by Dong, Jianbo 04 Mar '10

04 Mar '10

Hello, I'm working with a PDB file, in this file, one protein peptide was recognized as two chains (B and C), I want to make it as one chain, so it will be easier to do some interface analysis and modeling. I guess I can open the file as WORD file and change all the C to B one by one, but it's too much work to edit it that way. May I get some help for this? Is there a easier way to do this? Many thanks, Jianbo

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positive and negative overlaps
by Kshatresh Dutta Dubey 03 Mar '10

03 Mar '10

Dear all, Can anyone tell me the significance of positive and negative overlaps results in structure analysis module of chimera, as i got 140 contacts that contains both positive and negative overlap values? Any help is appreciated. Thanks in advance Kshatresh Dutta Dubey

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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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