- Chimera-users - RBVI Mailing Lists

2drms
by Bala subramanian 08 Apr '09

08 Apr '09

Friends, Kindly help me with the following queries. 1) How to output the 2drms created for a md. trajectory using MD movie tool. 2) Is there any way to select a square box of a particular length around the molecule and save the image for publication with the desired resolution. I have seen in the chimera archieve that window size can be adjusted. I am not sure if this is the right way to get my job done. Thanks, Bala

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Enhancement request Povray
by Marhoefer, R (Richard) 08 Apr '09

08 Apr '09

Dear Development Team, I would like to generate raytraced images without any shadows. The shininess however should be retained. I experimented with modifying the povray output and added the "no_shadow" keyword to all objects included in the file. This did the job. Could you please add a "no_shadow" option to the povray options panel? It would be very helpful. Kind regards, Richard Dr. Richard Marhoefer Senior Scientist BioChemInformatics Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: richard.marhoefer(a)sp.intervet.com Phone: +49 (6130) 948 204 Fax: +49 (6130) 948 517 Mobile: +49 175 723 081 4 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. --------------------------------------

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python scripts
by christopher lau 07 Apr '09

07 Apr '09

Dear Madam/Sir I am new to Chimera and this forum so I apologize in advance if I my question is inappropriate. I want to start writing python scripts such that I can run the script and the color code, orientation, etc of the molecule opened can be automated. Do you know of any good tutorials that teach what commands are available to use in python for chimera and how to run some basic python scripts in chimera? I have figured out enough to open the Python Shell in Chimera, but that is all. An example python script would be helpful. Thanks everyone, Chris Lau

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chimera help
by Ines COLLINGS 07 Apr '09

07 Apr '09

Dear Madam/Sir, I would like to add the coordinates direction x,y,z in Chimera so that I may know the orientation of the unit cell. Could you let me know how to do this. Thank you very much in advance, Ines Collings

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Re: [Chimera-users] Map Morphing questions
by Thomas Goddard 06 Apr '09

06 Apr '09

Hi Julio, While it is possible to rotate models and use Morph Map at the same time there isn't currently a command to do the morph part. This makes it difficult to record an animation since the morph has to be started by hand from the dialog. The turn command would look like "turn y 3 120" to turn around the y axis in 3 degree steps for 120 steps. Here's the Chimera 1.4 (daily build) "turn" documentation: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html I would like to make a morphmap command so it can be used in animation scripts. Can you explain a bit more your case involving more than 2 maps? Tom Dr .Julio Ortiz wrote: > Hi Tom, > I have been using recently the Morph Map function in Chimera. It is > really helpful! I would like to prepare several movies using this tool. > Three questions: > > 1)Is it possible to combine the morphing with some basic rotations, like > for example around Y axis?. > > 2)I am sure that is doable making some script, but actually..I am so > sorry..I haven't had time to sit down and read carefully how to make > your scripts. > Could you provide me with an initial script to do the rotation of the > morph map which I can start to modify in the future? > > 3) Would it be possible to add more than two maps for the morphing > automatically, and give a sequence of which pairs need to be morphed > instead of make sequential steps? > > Thanks for your help. I hope we can meet again in the near future I > would love to have an update of wht is possible with your wonderful > program. > > Greetings, > Julio >

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Rosetta Academic Training Webinar
by Nir London 06 Apr '09

06 Apr '09

The Rosetta Design Group is proud to present the first webinar in the Rosetta Academic Workshop Series. For the first webinar, we have selected to focus on Protein-Protein Docking based on the answers to the interest poll. We hope this will be the first in a line of helpful and inspiring webinars to kick-off our Rosetta Academic Workshop Series. What: Protein-Protein Docking When: May 4th 2009, 0800-1000 AM EST Where: Your office! Click here for more details and registration (For non html emails: http://rosettadesigngroup.com/RDGLS/index.php?sid=54479&lang=en) Pleas note: This is not a promotional webinar. Rosetta is open-source and freeware for academic and non-profit organizations and can be downloaded here from University of Washington's TechTransfer Digital Ventures. The majority of the webinar is concerned with Rosetta 2.3.0. Rosetta 3.0 is still a beta version. Hope to see you there, Nir London. Rosetta Design Group | http://rosettadesigngroup.com/

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delay in starting the program
by Eaazhisai Kandiah 03 Apr '09

03 Apr '09

Hi Chimera-Developers, Recently, my work-computer was upgraded from MaC-OS 10.4 to 10.5. I installed the Chimera X-windows version for 10.5. Apparently, while starting the program, it takes almost 2min for the program to get activated. While checking the activity monitor, chimera tries to use 'OSASCRIPT' which together with Chimera, showed as 'not-responding'. I couldn't troubleshoot the reason for this huge delay in start and hence rectify it. Any help would be appreciated. Thank you, Eaazhisai Kandiah Laboratory of Structural Biology NIAMS, National Institutes of Health, Room 1511,Bldg 50 9000 Rockville Pike, Bethesda, MD-20892 kandiahe(a)mail.nih.gov Off: 301 451 2281 Fax: 301 480 7629

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calculating centroid of atoms
by Bala subramanian 02 Apr '09

02 Apr '09

Friends, I want to choose certains atoms and get the x,y,z coordinates of the center. Kindly write me how to do it in chimera. Bala

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chimera help
by Terrance Chiang 02 Apr '09

02 Apr '09

Hi, I am trying to show a structural change between two proteins that differ by one amino acid, is this possible with chimera? I was unable to display the transformation I desired, so I looked into other ways to show changes between two overall similar molecules. I found that it is possible to show a change in the surface between two similar molecules, but I am unable to utilize the function because it requires a different file format. I would like to do both... that is, to show the conformational change from one protein to another, as well as show the change in surface from one protein to another, but I keep hitting these road blocks. Any help would be highly appreciated! Thanks, Terrance Chiang

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save reply log via command line?
by Sebastian Kruggel 01 Apr '09

01 Apr '09

dear chimera team / users, i was looking for a way to save the content of the reply log to a text file via command line, because i wanted to embed and process some results given in the reply log in a small cmd/py-script without. thanks in advance, sebastian -- Sebastian Kruggel Institut für Pharmazie Bundesstr. 45 | Raum 112 (406) D 20146 Hamburg Tel +49 (0)40 42838-3626 (-3484) kruggel(a)chemie.uni-hamburg.de

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Re: [Chimera-users] write selected command
by Elaine Meng 01 Apr '09

01 Apr '09

Hi Ed, Are there conformational changes in this process, or do chains simply move as rigid bodies? I had thought there were conformational changes within chains, but now looking at your movie again, I'm not sure. If each rigid body is a separate model, you would simply save the different configurations of the entire set as named positions with the command "savepos". Then you can reset to successive named over a specified number of frames with "reset" or smoothly interpolate over multiple saved positions with "fly". There have been recent improvements including addition of "fly" so I'd recommend a recent daily build if it sounds like this approach is doable. The process would then be scripted in a Chimera command file rather than appearing as playback in MD Movie. Once the command file generates the desired movie content, you could put a "movie record" command at the top and "movie stop" and "movie encode" commands at the bottom. example command files: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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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write selected command
by Edward Brignole 01 Apr '09

01 Apr '09

Elaine and co, I have a mess of models that I'm opening, repositioning a ligand using match to various positions in each model. No problem there. For each model and ligand position I select the correct chains from that model with the repositioned ligand models but can't manage to save coordinates. Obviously there's the save pdb dialog but for all these models and ligands this will be more convenient scripted into chimera commands. I've got it all working except this: select #6:.a-p #8 #9 write selected relative 0 #6,8,9 /path/to/file.pdb ~select The part it doesn't like is the model_numbers and I've tried various permutations without success. The only way I can get it to work is if I only specify one model number. Can you please help me figure out how to phrase this command correctly? An example or two on that commands page might make the syntax easier to decipher. Thank you for your excellent program and support. Ed ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Edward Brignole NIH Kirschstein Postdoctoral Fellow Francisco Asturias Lab, CB227 Center for Integrative Molecular Biosciences The Scripps Research Institute www.scripps.edu/~brignole brignole(a)scripps.edu 443-653-2070 (cell) 858-784-8598 (lab)

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find h bonds
by ROSETTA FORESTIERO 31 Mar '09

31 Mar '09

Hi I have a receptor and more ligands, I want find h-bond between receptor and each ligand using a scripts shell but i have some problem. Can you help me?

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Re: [Chimera-users] Web Access Data
by Elaine Meng 31 Mar '09

31 Mar '09

Hi Thiru, The easy way to tell if a chimerax file is OK is to just try opening it in Chimera with File... Open (file type could be "all (guess type)" or "Chimera web data"). The format is described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.h… > The "name" is the name to use for the local copy of the file from the web, and "loc" is where it is on the web. So "name" is not that important except that it should be the right type (if the file is python, the name should end in .py). As far as I can tell, your chimerax file looks OK. If opening the chimerax file directly in Chimera works OK, but clicking the link on your web page doesn't, your webmaster may need to change a server setting: the MIME type application/x-chimerax should be mapped to the extension .chimerax in the server configuration file. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 31, 2009, at 11:47 AM, Thiruvarangan Ramaraj wrote: > Hi Elaine, > > Thanks for your help. I know it is a delayed response, I did not get > a chance to have a look at it. I am trying to spend some time now on > web access data. > > So, following your instructions, I created a session in chimera and > saved it as a python session, 1A14AgSurface.py > > I was looking at the chimerax file, it had > > <file name="session.py" format="text" loc="http://sfld.rbvi.ucsf.edu/data/site_sessions/1yey.py > "/> > > it has two .py files, I am little confused about session.py and > 1yey.py > > Here is the 1A14Ag.chimerax file that I have > > <?xml version="1.0"?> > <ChimeraPuppet type="std_webdata"> > <web_files> > <file name="1A14AgSurface.py" format="text" loc="http://www.cs.montana.edu/~tramaraj/Research/1A14AgSurface.py > "/> > </web_files> > </ChimeraPuppet> > > I am not sure if I have the file tag written correctly. > > In my website, I would have something like the following > <a href="1A14Ag.chimerax"> <img src="1A14AgSurface.png"> </a> > > Any help would be greatly appreciated. > > Thank you for your > time and help > > Sincerely > > Thiru R > > > > > > > --- On Tue, 3/3/09, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Web Access Data > To: thiruvaranganr(a)yahoo.com > Cc: chimera-users(a)cgl.ucsf.edu > Date: Tuesday, March 3, 2009, 10:10 AM > > Hi Thiru, > The session file is python (*.py) ... you cannot just rename it as > *.chimerax. > Instead you would make a chimerax file that gives the names/ > locations of any > files you want to open in Chimera, such as the python session file, > and can > include various Chimera commands. If all you want to do is open the > session, > the chimerax file will be very simple. > > For example, these 6 lines of text are a chimerax file from the > Structure-Function Linkage Database > (SFLD): > > <?xml version="1.0"?> > <ChimeraPuppet type="std_webdata"> > <web_files> > <file name="session.py" format="text" > loc="http://sfld.rbvi.ucsf.edu/data/site_sessions/1yey.py"/> > </web_files> > </ChimeraPuppet> > > Your web page would link to the chimerax file. Then when the > chimerax file is > opened by Chimera, Chimera will get the session file named inside. > > The page at the SFLD that has this link is > <http://sfld.rbvi.ucsf.edu/cgi-bin/SFLDvm.py?view=family&id=111> > The chimerax file is linked to the large "Active Site" image. > > You can test your chimerax file without using the web just by > opening it in > Chimera. Then if it works, you can link it to a web page, but there > is one more > step: > > If you are using a cgi-bin script to create the chimerax files on > the fly, the > cgi-bin script must specify the Content-type header as application/x- > chimerax. > > If you just have pre-made chimerax files, your webmaster needs to > change the web > server settings so that it sends this information along with the file. > > The chimerax format is described here: > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.h… > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > > > On Mar 2, 2009, at 6:46 PM, Thiruvarangan Ramaraj wrote: > > > Hello All, > > > > I created a session and saved it under .chimerax extension. I have > a link > > to this session on a web page. When I click on this link I wanted > the > > session to open directly using the chimera program. > > > > > > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.ht… > > > > I tried to follow the instructions given in the above link, still > I am > unsuccessful in figuring it out. > > > > Any suggestions/ideas would be greatly appreciated. > > > > Thank You > > > > Thiru > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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distance measurements
by Jean-Paul Armache 31 Mar '09

31 Mar '09

hello, i would like to ask whether there is a way of automatically measuring the distance from all residues in a chain to residue X in the same chain? best regards, jean-paul armache

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benchmark results page blocked by apache authentication
by Sabuj Pattanayek 30 Mar '09

30 Mar '09

Hi, The Chimera wiki page for benchmarks https://socrates2.cgl.ucsf.edu/trac/chimera/wiki/benchmarks has been blocked from being accessed by apache authentication. Thanks, Sabuj

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Fwd: accessible surface area for electron density maps
by David Chenoweth 27 Mar '09

27 Mar '09

Begin forwarded message: > From: David Chenoweth <dchen(a)caltech.edu> > Date: March 27, 2009 8:58:31 AM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] accessible surface area for electron > density maps > > Hi Elaine and Murali, > > I have a similar problem that I've been trying to resolve. > Calculating the accessible surface or solvent accessible surface is > also something I've been interested in doing with Chimera but I > don't think the area of the molecular surface is the same as the > solvent accessible surface area. I believe that accessible surface > comes from the locus of the center of a spherical probe as it rolls > over the Van der Waals surface of a molecule. The molecular surface > uses the locus of the inward facing spherical probe. They both > depend on the spherical probe size which is set to the appropriate > solvent molecule. Can you tell me which of these two methods Chimera > is using when it calculates the area (if either)? Is there a way to > calculate the solvent accessible surface area of a molecule with > Chimera or some way to manipulate the current area calculator to > give this value? I also think that depending on the quality of the > electron density map one could get very different results for this > calculation (especially if there is missing electron density or at > different map contour values). If anyone has any advice for the best > way to calculate solvent accessible surface area I would really > appreciate the help. > > Thanks, > Dave Chenoweth > > ********************************************** > David M. Chenoweth > California Institute of Technology > Division of Chemistry and Chemical Engineering > Mail Code: 164-30 > 1200 California Boulevard, 91125 Pasadena > California, USA > > Phone: 626-395-6074 > Email: dchen(a)caltech.edu > ********************************************** > > On Mar 27, 2009, at 8:14 AM, Elaine Meng wrote: > >> Hi Murali, >> If I understand correctly, you want to get the area of a contour >> surface of the density shown using the Volume Viewer tool. If you >> want the total surface area, even of multiple separate blobs, use >> "Measure Volume and Area." If you want to measure the area of >> different blobs individually, use "Measure and Color Blobs." >> >> These can be started from the Tools menu of the Volume Viewer dialog, >> and also from the main Chimera Tools menu (Tools... Volume Data... >> [name of tool]). >> >> For more details on how to use a tool, press the Help button on the >> dialog. That opens the documentation included with your download. >> Our web site also has copies of the documentation: >> <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/measurevol… >>> >> <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/pickblobs/… >>> >> >> 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 >> >> On Mar 27, 2009, at 7:42 AM, Murali Ayaluru wrote: >> >>> Dear Chimera users, >>> I want to calculate the accessible surface area for an electron >>> density map (mrc format) that I am working on. Can anyone, who >>> knows how to do this, tell me how to do this? >>> Thanks in advance for your reply, >>> Regards, >>> Murali >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > >

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Re: [Chimera-users] accessible surface area for electron density maps
by Elaine Meng 27 Mar '09

27 Mar '09

Hi David, As soon as you show a molecular surface, both the total solvent- excluded (molecular surface by Richards definition) and solvent- accessible areas are reported in the Reply Log. It has been like that since before the July 2008 release. The surface that is actually displayed is the solvent-excluded surface. You can adjust parameters that affect the results such as probe radius and atomic radii, but the defaults are reasonable. The area values are also assigned as per-atom and per-residue attributes named areaSES and areaSAS, so you can use Attribute Calculator to get sums over subparts of the surface. For details, see this page and links therein: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ representation.html#surfaces> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 27, 2009, at 8:58 AM, David Chenoweth wrote: > Hi Elaine and Murali, > > I have a similar problem that I've been trying to resolve. > Calculating the accessible surface or solvent accessible surface is > also something I've been interested in doing with Chimera but I > don't think the area of the molecular surface is the same as the > solvent accessible surface area. I believe that accessible surface > comes from the locus of the center of a spherical probe as it rolls > over the Van der Waals surface of a molecule. The molecular surface > uses the locus of the inward facing spherical probe. They both > depend on the spherical probe size which is set to the appropriate > solvent molecule. Can you tell me which of these two methods > Chimera is using when it calculates the area (if either)? Is there > a way to calculate the solvent accessible surface area of a > molecule with Chimera or some way to manipulate the current area > calculator to give this value? I also think that depending on the > quality of the electron density map one could get very different > results for this calculation (especially if there is missing > electron density or at different map contour values). If anyone has > any advice for the best way to calculate solvent accessible surface > area I would really appreciate the help. > > Thanks, > Dave Chenoweth

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Re: [Chimera-users] accessible surface area for electron density maps
by Elaine Meng 27 Mar '09

27 Mar '09

Hi Murali, As far as I know, there is no definition of accessible surface area for an electron density map (and thus no way to calculate it in Chimera), only for atomic structures. I'll describe how to get it for atomic structures in my next message, replying to David. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 27, 2009, at 8:18 AM, Murali Ayaluru wrote: > Hi Elaine, > > Thanks for the quick reply. I am aware of calculating the total > surface area of the density maps using Chimera and has been using > it for a long time. Now I am interested in the surface area that a > solvent can access (in otherwords called - (solvent) accessible > surface area). This is a part of the total surface area. Please > mail me if this tool is available in Chimera. > > Regards, > Murali

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accessible surface area for electron density maps
by Murali Ayaluru 27 Mar '09

27 Mar '09

Dear Chimera users, I want to calculate the accessible surface area for an electron density map (mrc format) that I am working on. Can anyone, who knows how to do this, tell me how to do this? Thanks in advance for your reply, Regards, Murali

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Bonds vs. Pseudobonds
by Dipl.-Ing. Thomas Mitterfellner 24 Mar '09

24 Mar '09

Hello again! I have a structure containing Germanium bonded to three oxygens and one methyl group. By default, all of the bonds between Germanium and its valences are considered as pseudobonds and hence drawn as such. In the manual, I read that Chimera uses an algorithm that considers atoms classically bonded if the distance is below the sum of their VDW radii (plus a margin of 0.4 A). However, no matter what I set the radius of the Ge atom to (setattr a radius xy Ge), I can't get Chimera to display a regular bond between Ge and its valences. Can you give me a hint how to set a rule when a normal bond is drawn, or how I can draw one manually? Thank you very much, Thomas

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Using per-frame scripts with color by attribute/bfactor
by Andrew M. Simms 24 Mar '09

24 Mar '09

I am making some MD movies using the multiple-pdb file format. I am using coloring by attribute, in this case overriding the "bfactor" attribute for my own purposes. The nature of my analysis is such that the bfactor can change from frame to frame. I use this command in the per-frame script: rangecolor bfactor,a min white max green However, when I try to make a movie, it appears that the bfactor attribute changes are not reflected in the animation. If I look at generated structures individually they are fine. Is there something special I need to specify in per-frame script? Thanks! --Andrew

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Split colors from Volume Viewer
by Damien Larivière 23 Mar '09

23 Mar '09

Dear Chimera team and users, When opening a map (EMD 1126 for example), the structure is displayed in grey. From the menu Volume and Surface colors, it is then possible to color the structure. I would like to export in the OBJ format the colored structure but this one still appears in grey when I display it in a modeler such as 3DSMax. And effectively, the MTL file created by the exporter only contains one color although the structure displayed in Chimera was multicolored. I look at a tutorial explaining that it is possible to Split map from the menu Volume/color zone. It seemed to me that it is a way to get a multicolored structure in the OBJ format. However, when I want to "split map", a message says "no atom selected". May you tell me how to get a multicolored structure (initially opened from a map) in the .obj format ? All the best Damien

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amd64 installation
by Francesco Pietra 23 Mar '09

23 Mar '09

To deal with very large data files i tried to install chimera-1.3.2577-linux_x86_64.exe in /usr/local/chimera. Mainboard Tyan S2895 dual-opterons; OS Debian amd64 lenny; nvidia chipset 6600, nvidia-glx driver To simplify i made the chimera directory to belong to me as user. The installation from my home succeeded, though chimera did not launch. It appears in part for a moment as if there were no opengl support: francesco@tya64:/usr/local/chimera/bin$ ./chimera X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 3 (X_GetWindowAttributes) Resource id in failed request: 0xffffffff Serial number of failed request: 626 Current serial number in output stream: 627 I installed libmotif3. Same issue. Once the problem of running chimera is solved, I plan a reinstall in /usr/local/chimera root root. Should I run the installation from my home as superuser? thanks francesco pietra (I run successfully the 32 bit version of chimera on an old Athlon with libmotif3 support)

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addna?
by julien(GWDG) 23 Mar '09

23 Mar '09

Dear all, I would like to know if there is a way in chimera to add nucleic acid to an existing RNA. Something like addna instead of addaa. many thanks Julien -- European Molecular Biology Laboratory Structural and Computational Biology Unit Meyerhofstraße 1 D-69117 Heidelberg Max-Planck-Institute for Biophysical Chemistry NMR based Structural Biology Am Fassberg 11 D-37077 Göttingen

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