- Chimera-users - RBVI Mailing Lists

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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