March 2009 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Question regarding saving PDB in Chimera
by Pancera, Marie (NIH/VRC) [E] 24 Nov '09

24 Nov '09

Hello, I am using Chimera to fit coordinates into EM density. However I have problems when I save with Chimera as the coordinates that I am saving are not the one I see on the screen. Here is what I do: File Save PDB chose the folder A file name A file type The model that I want to save, i.e the one I see on the screen And then I have to select save relative to model, otherwise I am saving the original molecule, the problem is that I am not sure relative to which model I have to save it. IS there an easier way to just save what I can see on the screen? Thanks, Marie

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color scale bar
by Yao Cong 17 Jul '09

17 Jul '09

Hello Chimera developer, I am rendering a PDB file colored according to B-factor value by "render by attribute" tool. How can I generate a color scale bar besides the structure labeling the color scale used? Many thanks, Yao Cong

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sequence viewer
by Gatsogiannis, Christos 13 Jul '09

13 Jul '09

Hi all, i ve just installed the latest daily build version and i´ve noticed that the sequence viewer has a new "look". However, i have difficulties to get used to it... Some examples: -when i want to view the sequence of a pdb file containing seven chains, i get seven different pop-up windows (...) showing the sequences corresponding to the seven different chain ID´s.... -Moreover, it isn´t so "easy" anymore to select aminoacids directly in the sequence viewer (e.g. too many colors) and therefore now i´m selecting residues using only the command line.. My colleagues also prefer the older version.. is there a simple way to install the latest chimera version but keep the old version of the sequence viewer? Thanks! -Christos ------------------------------- Christos Gatsogiannis Insitute of Zoology, Dpt. II cryoEM Lab, AG Markl Joh. v. Müllerweg 6 Johannes Gutenberg University Mainz, Germany +49-6131-3923091 ------------------------------- ________________________________________ Von: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] im Auftrag von chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Gesendet: Mittwoch, 17. Dezember 2008 21:00 An: chimera-users(a)cgl.ucsf.edu Betreff: Chimera-users Digest, Vol 68, Issue 22 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: (Thermal ellipsoids) anisotropic temperature factor ellipsoids (Eric Pettersen) 2. Re: (Thermal ellipsoids) anisotropic temperature factor ellipsoids (Eric Pettersen) 3. possibilities to save parts of models (selection)? (Sebastian Kruggel) 4. Re: possibilities to save parts of models (selection)? (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Tue, 16 Dec 2008 14:59:34 -0800 From: Eric Pettersen <pett(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] (Thermal ellipsoids) anisotropic temperature factor ellipsoids To: Tom Goddard <goddard(a)cgl.ucsf.edu> Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> Message-ID: <9A34751B-6356-4AF4-A8C7-31757E5FFBF1(a)cgl.ucsf.edu> Content-Type: text/plain; charset="us-ascii" On Dec 12, 2008, at 10:40 AM, Tom Goddard wrote: > Hi David, > > Ok I see now, it's a matter of choosing the size of each ellipsoid to > have a 50% chance of finding the atom in that volume. This > shouldn't be > too hard but I'll let Eric tackle it if he has time. Hi David, This is one of those things that I'll endeavor to get into Chimera's production version of thermal ellipsoids, but that I can't spare the time for until then. My guess is that the eigenvectors/values of the U matrix are at the 50% probability level, but verifying that would require some research. If you do look into and find that that's not the case, just change the setting of the 'scale' variable of the start of the script to change the ellipsoid sizes to whatever size encloses 50%. --Eric

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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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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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