- Chimera-users - RBVI Mailing Lists

save manipulated electron density maps in spider
by Jan-Christian Schuette 25 Feb '08

25 Feb '08

Dear Chimera Developers, I quite often have to manipulate electron density maps in the spider format. When using chimeras volume eraser function, it doesn't allow me to save the new map back to spider or another easy-to-convert file format (such as brix or ccp4). I would be great if you could add such a feature in the next version of the software. Best regards, Jan-Christian Schuette

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Re: [Chimera-users] distance
by Elaine Meng 22 Feb '08

22 Feb '08

Hi! Eric has kindly provided a python script (attached at the bottom) that will write all the current distance measurements to the Reply Log. Just open the python file with Chimera and it will happen. Alternatively, depending on your situation, you could use "findclash," as discussed in these chimera-users messages a few months ago: http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/ 002061.html http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/ 002069.html http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/ 002070.html 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 Feb 21, 2008, at 5:24 PM, 吴超 wrote: > Thanks, Elaine! > The problem is that I want to automatically calculate a number of > distances in non-gui interface, and sent the date to a file, just > like the logfile. > So is there a chance that I can achieve it using chimera? > > On Fri, Feb 22, 2008 at 1:00 AM, Elaine Meng <meng(a)cgl.ucsf.edu> > wrote: > > The distances are listed in a separate dialog - choose "Tools... > Structure Analysis... Distances" from the menu to open that dialog. > You can adjust the number of decimal places in the measurement, and > there is a "Save" button if you want to save distances or other > measurements to a text file.

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Driving matchAtoms from the IDLE
by Jean-Didier Maréchal 22 Feb '08

22 Feb '08

Hi Guys, I'd like to superpose two inorganic complexes using two differently "ordered" atom sets. My compound has quite similar substructures but I am sure at all what is the best "ordered" selection of atom pairs to align. Therefore, I'd like to make a "extensive" search (with an heuristic approach to define...) passing by the idle. I am unfortunately missing something before getting to this point! Lets say that I just want to align the nitrogen atoms of the my two structures. I have: import chimera import numpy from chimera import match from chimera import runCommand runCommand("select #1@N=") an1=chimera.selection.currentAtoms() runCommand("select #0@N=) an2=chimera.selection.currentAtoms() chimera.match.matchAtoms(an1,an2) And then it's when I am already stuck! the resulting prompt does not provide mistake an gives: chimera.match.matchAtoms(an1,an2) (<_chimera.Xform object at 0x9463ef8>, 0.034256915079603358) But how this results can be send to the graphical window? I guess I have to use the Xform object, but I can not clearly understand how to do this. Thanks for any help! JD On Thu, 2008-02-21 at 12:00 -0800, chimera-users-request(a)cgl.ucsf.edu wrote: > 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: distance (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Feb 2008 09:00:37 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] distance > To: "??" <lynnwuchao(a)gmail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <0E85C396-8C7D-4182-A029-5C0155245C3A(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=UTF-8; delsp=yes; format=flowed > > Hi! > > The distances are listed in a separate dialog - choose "Tools... > Structure Analysis... Distances" from the menu to open that dialog. > You can adjust the number of decimal places in the measurement, and > there is a "Save" button if you want to save distances or other > measurements to a text file. > > 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 Feb 20, 2008, at 11:38 PM, ?? wrote: > > > Hi, folks, > > I select two atoms and measured their distance using the command > > distance and can see the exact distance value in the graphic > > interface, but when I go the log file i can not find it. > > Can anybody give me a hand and tell me why can I find it? Thanks.. > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 58, Issue 24 > *********************************************

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placing a helium atom at a given position.
by Jean-Didier Maréchal 22 Feb '08

22 Feb '08

Hi again, that follows an e-mail exchange with Eric a while ago. I am trying to place a given atom (for the moment, helium is fine) to given x,y,z coordinates. You told me that the new BuildStructure module could do that, unfortunately after having imported the module import BuildStructure when I do BuildStructure.placeHelium(res,model=0,position=13.2909,75.4474,25.4248) I have SyntaxError: non-keyword arg after keyword arg I tried different argumentations of this but I can't have it working, if you can tell me how to do this, that would be perfect. All the best, JD some time ago Eric On Thu, 2008-02-21 at 12:00 -0800, chimera-users-request(a)cgl.ucsf.edu wrote: > 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: distance (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Feb 2008 09:00:37 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] distance > To: "??" <lynnwuchao(a)gmail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <0E85C396-8C7D-4182-A029-5C0155245C3A(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=UTF-8; delsp=yes; format=flowed > > Hi! > > The distances are listed in a separate dialog - choose "Tools... > Structure Analysis... Distances" from the menu to open that dialog. > You can adjust the number of decimal places in the measurement, and > there is a "Save" button if you want to save distances or other > measurements to a text file. > > 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 Feb 20, 2008, at 11:38 PM, ?? wrote: > > > Hi, folks, > > I select two atoms and measured their distance using the command > > distance and can see the exact distance value in the graphic > > interface, but when I go the log file i can not find it. > > Can anybody give me a hand and tell me why can I find it? Thanks.. > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 58, Issue 24 > *********************************************

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managing bond order
by Victor Kenyon 21 Feb '08

21 Feb '08

hi all, typically when i import a paired back active site of a protein, chimera wants to connect atoms that should not be connected. is there a way to select bonds that violate a certain bond length so i can remove them? or a possible work around? thanks for your help. victor Victor A. Kenyon kenyon(a)chemistry.ucsc.edu 831.252.7667.

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distance
by 吴超 21 Feb '08

21 Feb '08

Hi, folks, I select two atoms and measured their distance using the command distance and can see the exact distance value in the graphic interface, but when I go the log file i can not find it. Can anybody give me a hand and tell me why can I find it? Thanks..

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modifying presets
by glenn millhauser 20 Feb '08

20 Feb '08

Hi Folks, Is there a way to edit the Presets to include additional protein features? Specifically, I work with quite a few disulfide rich proteins and it would be great to select the Preset Interactive 1 and have it automatically draw Cys side chains with disulfide links. Many thanks, glenn Glenn L. Millhauser Department of Chemistry & Biochemistry UC Santa Cruz Santa Cruz, CA 95064 831 459 2176 voice 831 566 3337 cell 831 459 2935 fax http://chemistry.ucsc.edu/~glennm http://www.chemistry.ucsc.edu/faculty/millhauser.html

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Re: [Chimera-users] [chimera-dev] change hand ?
by Tom Goddard 20 Feb '08

20 Feb '08

Hi Stefan, You can flip the hand of the map by making the grid spacing negative along one axis. Chimera wasn't intended to do this so I'm not sure everything will work correctly. To make this change use the volume dialog Coordinates panel and change voxel size from (for example) 0.37 to 0.37 0.37 -0.37. The three numbers are grid plane spacing along the x, y, z axes. If they are all the same Chimera just shows one number. In Chimera 1.2470 the volume surface will become dark. To remedy this use the volume dialog Surface and Mesh options panel and turn off "two-sided surface lighting". A current Chimera daily build will not have that problem. Chimera won't correctly save the flipped map. So this is not an ideal way to proceed. I don't know of software that will write out the flipped map though it must exist. Tom Stefan Backstrom wrote: > Hi. > > Is it possible to flip the hand of a cryo-EM map in chimera ? > > Best wishes, > > Stefan Bäckström > Medical Biochemistry and Biophysics > Umeå University > Sweden > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev >

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volume rendering depth issue with multiple volumes (segmented layers)
by William Jeffrey Triffo 19 Feb '08

19 Feb '08

hello, I remember past posts mentioning depth issues when rendering multiple volumes. I have several layers (6) that I have segmented out individually. Last night, they appeared to render 'in order' (the layers are parallel, and up to 6 thus overlap if rotated into the correct view). this morning, though, I notice that 'volume 2' is rendering 'on top' of everything else. is there a way I can trick this to work, or is there something I may be missing / clicked wrong? thanks, -Jeff -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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menssage error
by DRT/BA - Elias Silva dos Santos 19 Feb '08

19 Feb '08

Hi!! I am preparing a molecule for docking that he has two centers of iron sulphur [ 4FE-4S]+2 and one molecule of FAD. When trying to place loads I am recebeno error messages (DOCK Prep). As I must proceed to decide the problem Elias

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