- Chimera-users - RBVI Mailing Lists

essential dynamics
by bala 07 Apr '08

07 Apr '08

Hello all, I have done a pca analysis using ptraj program of amber. I want to view the result of the same. Is there any that i can do it with chimera. I am aware that it can be down analyzed vmd. But i am more comfortable with chimera and i would be happy to perform the analysis in chimera if i can. Thanks, Bala

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Re: [Chimera-users] Chimera - Surface Residue Identification
by Elaine Meng 07 Apr '08

07 Apr '08

On Apr 7, 2008, at 9:33 AM, Thiruvarangan Ramaraj wrote: > Thanks for your reply. > I can find out the residues from one chain that are from certain > distances from another chain. But it will give all the residues, > instead I want only the residues that are in the surface of the > chain. Is there any way to do identify the residues that lie on the > surface of a chain. > > I tried to use surfcat, but it is not working, I am sure I am not > doing it correct. > Any help would be greatly appreciated. > Thank You > Sincerely > Thiru Dear Thiru, You can just add another step that says a residue just have a certain amount of surface area. Some new surface-area features were recently added to Chimera, so I recommend getting a daily build. First you would need to use "surfcat" and show the surfaces you want. I don't know what you tried, or what chains are in your structure, so I can't give exact steps. However, here is an example. If you have chains A,B,C and you want one surface around A and another around B,C together, you would use these commands: surfcat group1 :.a surfcat group2 :.b:.c surface group1 surface group2 Then, use Select by Attribute ("Select... by Attribute Value" in the Chimera menu): in that tool, choose attributes of "residues" and in the "Attribute" menu, choose the name of the surface area attribute. The name is areaSAS if you want solvent-accessible surface area, areaSES if you want solvent-excluded surface area. The values in the structure are shown in a histogram, and you would move the vertical bars to enclose the range of values you want the residues to have. Lots of residues have a tiny amount of surface area, so you would probably want to set the minimum at some positive number. Click Apply to select that set of residues. Then you can narrow the set of residues to only those in the zone, for example: select :.a & :.b zr<4.5 & sel (like my previous example plus "& sel" which means "and also already selected"). In the future it should be easier, with a command something like select :.a & :.b zr<4.5 & :/areaSES>50.0 (avoiding the separate "Select by Attribute" step) but currently, there is a bug that prevents using areaSAS and areaSES in the command line. 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

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about problems with windows version
by Ricardo José Soares Torquato 07 Apr '08

07 Apr '08

Dear friends I got chimera program from website, and install on my notebook, and installed the last realese of windows version, my machine has a turion64 as a processor and WinXP pro as OS, but after the installation I try to run it, I got this message: ! Outline highlight not supported by hadware, in small windows. Can you help? thank's Ricardo

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Fitting multiple pdb models
by Pabhashi Fernando 07 Apr '08

07 Apr '08

Hi, I am at the moment trying Chimera, and quite like it! This is to get a clarification: I need to fit 6 independent pdb models that account for different domains of the protein into my EM map. How can I do this? And, is there an evaluation criterion for the fitting? Many thanks. Best wishes, Lasanthi ___________________________________________________________ Yahoo! For Good helps you make a difference http://uk.promotions.yahoo.com/forgood/

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Map image script
by Tom Goddard 07 Apr '08

07 Apr '08

Hi Richard, Here's a Python script that will make 6 thumbnail images of each map in a directory along +/- x, y and z axes. It sets the map contour level to the mean plus two standard deviations. To use it edit the line that sets the directory where the maps reside. Then start Chimera and open the Python file. Make sure not to cover the Chimera window while it is capturing images. The JPEG image file are placed in the same directory and have names matching the map files with suffixes 1,2,3,4,5,6. Tom # ---------------------------------------------------------------------------- # Make 6 views along +/- xyz axes of each map in a directory. # # Sets image size, background color, silhouette edges, and map contour level. # from chimera import runCommand as run run('windowsize 100 100') # Set image size. run('cd /tmp/emdb') # Go to directory containing maps run('set bg_color white') # White background from chimera import viewer viewer.showSilhouette = True # Turn on silhouette edges import os # Get all files that end with ".map" filenames = os.listdir('.') filenames = [f for f in filenames if f.endswith('.map')] # Create images for f in filenames: run('open %s' % f) # Open map # Set contour level to (mean + two standard deviations) from VolumeViewer import active_volume v = active_volume() m = v.matrix() level = m.mean() + 2*m.std() run('volume #0 level %.6g' % level) # Create 6 map images. fprefix = f.rstrip('.map') # Remove ".map" suffix run('copy file %s_1.jpg jpeg' % fprefix) run('turn y 90') run('copy file %s_2.jpg jpeg' % fprefix) run('turn y 90') run('copy file %s_3.jpg jpeg' % fprefix) run('turn y 90') run('copy file %s_4.jpg jpeg' % fprefix) run('turn y 90') run('turn x 90') run('copy file %s_5.jpg jpeg' % fprefix) run('turn x 180') run('copy file %s_6.jpg jpeg' % fprefix) run('close all')

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pov-ray problem
by Fabian Gmail 07 Apr '08

07 Apr '08

Dear chimera experts, I have some difficulties creating high-quality pictures with pov-ray I get them very dark, so in pockets for example I can not distinguish colors. How I could make a pov-ray picture less dark? Thanks a lot, Fabian Glaser -- Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL Web: http://bku.technion.ac.il Email: fglaser(a)tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396

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Chimera - Surface Residue Identification
by Thiruvarangan Ramaraj 07 Apr '08

07 Apr '08

Hello, I am new to Chimera, I am trying to identify the residues that lie on the surface of a antigen complex that are within certain distance from the antibody. Any help would be greatly appreciated. Thank You --------------------------------- You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost.

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chimera explodes
by liane saiz 05 Apr '08

05 Apr '08

Hello everybody: I had some problems with chimera. I installed version 2470 but it explodes when I try to select anything with the following error: Segmentation fault (core dumped) I tried also version 1.2422 and I got the same error. All other features of chimera seems to work properly. In both cases the installation process seems normal. I'm running chimera in linux (ubuntu gutsy) with a 2.6.22-14-generic kernel. In other computer in the lab with the same linux distribution and kernel, all features in chimera 1.2470 work fine (including the select menu). Thanks in advance for any help. Liane

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Chimera crashes
by Ben Keshet 04 Apr '08

04 Apr '08

Hi, I have been using Chimera on my desktop successfully - great program. However, when I run Chimera on my laptop, Chimera tends to crash, usually when the screen saver starts. the message I have is: chimera failed abnormally; the exit code was :3. I am not sure how to open the debug mode (I tried to right-click ==> properties and change the target by adding '--debug' but I am getting an error message that the name is not valid. my machine is Dell Vostro 1500 with XP with a GeForce 8400M GS video card. Any suggestion are welcome. Thanks, Ben

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surface color command
by Michael DiMattia 04 Apr '08

04 Apr '08

Hello, Is there a command for "surface color"? The menu window that lets you color a molecule radially. I'm wondering if there is a command-version of this task so that I can put it into a script. I looked up "surface color" in the Chimera help files but I don't see a command. Thanks! Mike

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Re: [Chimera-users] Chimera-users Digest, Vol 60, Issue 4
by Boyle, Joseph J 03 Apr '08

03 Apr '08

Hello, Is it possible to use Chimera to dock a small ligand into a binding pocket pdb - and if so how is the ligand imported into the protein pdb file ? Yours Sincerely, Joseph Boyle ________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu on behalf of chimera-users-request(a)cgl.ucsf.edu Sent: Thu 03/04/2008 8:41 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 60, Issue 4 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: Smooth Trajectory in MD Movie Tool (Eric Pettersen) 2. Re: Smooth Trajectory in MD Movie Tool (Yan Liang) 3. chimera manual (bala) ---------------------------------------------------------------------- Message: 1 Date: Wed, 2 Apr 2008 16:37:42 -0700 From: Eric Pettersen <pett(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Smooth Trajectory in MD Movie Tool To: Yan Liang <liangyan(a)cems.umn.edu> Cc: Chimera forum <chimera-users(a)cgl.ucsf.edu> Message-ID: <7524F1C4-94F1-487C-A67F-FA6A5B4778DB(a)cgl.ucsf.edu> Content-Type: text/plain; charset="utf-8" Hi Yan, You _could_ write a script to do the averaging, but you would pretty much have to be an expert on how Chimera handles trajectory data to be able to write it in any reasonable amount of time. Since I am such an expert, I've written the script for you and attached it to this message. To do the averaging, simply have your trajectory open and then open the script (either with the File...Open menu or with the "open" command). Note that the script rewrites the coordinates of the trajectory. The only way to restore the trajectory to the "unaveraged" state is by reopening the original files. The main parameter in the script you might want to change is the "window" variable, which controls how many adjacent frames contribute to the averaging. The value in the script right now is 2, which means that the two frames to each side of a frame contribute to the average (with further-away frames contributing less). --Eric ? On Apr 2, 2008, at 2:36 PM, Yan Liang wrote: > Thank you very much Eric. I have tried "Hold selection steady" > function, and it helps a lot to reduce the overall movement of the > large molecule. But as for the residuals, they are still very shaky. > > I am thinking about writing a script to average the movement of > each atom, but I have no experience in Chimera scripting. Do you > think it is possible to write such scripts in Chimera? Thanks. > > Sincerely, > > Yan Liang > Graduate Student > Department of Chemical Engineering and Materials Science > University of Minnesota > > > > On Apr 2, 2008, at 1:42 PM, Eric Pettersen wrote: >> Hi Yan, >> Chimera doesn't yet support smoothing per se. What you can do is >> use "Hold selection steady" in MD Movie's Actions menu to hold one >> or more atoms (possibly all atoms) as steady as possible across >> the trajectory -- which will mostly eliminate the translational >> component of the "shakiness". This "holding steady" is most >> useful for small-molecule trajectories and replica-exchange >> trajectories. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/> >> >> >> On Apr 2, 2008, at 10:44 AM, Yan Liang wrote: >>> Hi >>> >>> I am using Chimera to make a MD movie. The problem is the movie >>> is too >>> shaky. Is it possible to smooth the trajectory by writing a Per- >>> Frame >>> script in MD Movie tool? >>> >>> Thanks, >>> >>> Yan Liang >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >

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chimera manual
by bala 03 Apr '08

03 Apr '08

Hello all, I want to have the pdf version of chimera manual/user guide. I am not finding it anywhere ?. Where can i find it. The only pdf i see is the chimera quick reference guide. Thanks, Bala

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Re: [Chimera-users] Smooth Trajectory in MD Movie Tool
by Eric Pettersen 02 Apr '08

02 Apr '08

Hi Yan, You _could_ write a script to do the averaging, but you would pretty much have to be an expert on how Chimera handles trajectory data to be able to write it in any reasonable amount of time. Since I am such an expert, I've written the script for you and attached it to this message. To do the averaging, simply have your trajectory open and then open the script (either with the File...Open menu or with the "open" command). Note that the script rewrites the coordinates of the trajectory. The only way to restore the trajectory to the "unaveraged" state is by reopening the original files. The main parameter in the script you might want to change is the "window" variable, which controls how many adjacent frames contribute to the averaging. The value in the script right now is 2, which means that the two frames to each side of a frame contribute to the average (with further-away frames contributing less). --Eric On Apr 2, 2008, at 2:36 PM, Yan Liang wrote: > Thank you very much Eric. I have tried "Hold selection steady" > function, and it helps a lot to reduce the overall movement of the > large molecule. But as for the residuals, they are still very shaky. > > I am thinking about writing a script to average the movement of > each atom, but I have no experience in Chimera scripting. Do you > think it is possible to write such scripts in Chimera? Thanks. > > Sincerely, > > Yan Liang > Graduate Student > Department of Chemical Engineering and Materials Science > University of Minnesota > > > > On Apr 2, 2008, at 1:42 PM, Eric Pettersen wrote: >> Hi Yan, >> Chimera doesn't yet support smoothing per se. What you can do is >> use "Hold selection steady" in MD Movie's Actions menu to hold one >> or more atoms (possibly all atoms) as steady as possible across >> the trajectory -- which will mostly eliminate the translational >> component of the "shakiness". This "holding steady" is most >> useful for small-molecule trajectories and replica-exchange >> trajectories. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >> On Apr 2, 2008, at 10:44 AM, Yan Liang wrote: >>> Hi >>> >>> I am using Chimera to make a MD movie. The problem is the movie >>> is too >>> shaky. Is it possible to smooth the trajectory by writing a Per- >>> Frame >>> script in MD Movie tool? >>> >>> Thanks, >>> >>> Yan Liang >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >

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Smooth Trajectory in MD Movie Tool
by Yan Liang 02 Apr '08

02 Apr '08

Hi I am using Chimera to make a MD movie. The problem is the movie is too shaky. Is it possible to smooth the trajectory by writing a Per-Frame script in MD Movie tool? Thanks, Yan Liang

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chimera
by somnath Dutta 02 Apr '08

02 Apr '08

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chimera segmentation fault
by Selami ERCAN 01 Apr '08

01 Apr '08

hi. i'm using chimera-1.2470-linux_x86_64.exe on suse 10.3. in addition to this my graphic card is nvidia geforce 8600m gt 512 mb and also i have installed mesa and xorg softwares. and here is problem: using 1EP4.pdb from rcsb.org causes problem.whenever i select structure-->main, then action-->surface-->show it crashes. and it gives the report shown below. Copyright M.F. Sanner (March 2000) Compilation flags WARNING: class_arete2: warning hole in a reentrant face 17081 WARNING: class_arete2: warning hole in a reentrant face 22603 WARNING: classe_aretes1: No cycle in face 25771 (nba=-4) WARNING: classe_aretes1: No cycle in face 25772 (nba=-1) WARNING: classe_aretes1: No cycle in face 25774 (nba=-1) WARNING: classe_aretes1: No cycle in face 25776 (nba=-3) WARNING: classe_aretes1: No cycle in face 25779 (nba=-1) WARNING: classe_aretes1: No cycle in face 25781 (nba=-1) WARNING: classe_aretes1: No cycle in face 25783 (nba=-1) WARNING: classe_aretes1: No cycle in face 25785 (nba=-1) WARNING: classe_aretes1: No cycle in face 25787 (nba=-1) WARNING: classe_aretes1: No cycle in face 25789 (nba=-1) RESTART FROM SES: 1 radius of atom 2855 goes from 1.760000 to 1.860000 radius of atom 2857 goes from 1.640000 to 1.740000 radius of atom 2858 goes from 1.760000 to 1.860000 radius of atom 2871 goes from 1.880000 to 1.980000 radius of atom 6942 goes from 1.880000 to 1.980000 radius of atom 6945 goes from 1.760000 to 1.860000 radius of atom 6946 goes from 1.760000 to 1.860000 radius of atom 6947 goes from 1.760000 to 1.860000 radius of atom 6948 goes from 1.760000 to 1.860000 radius of atom 6987 goes from 1.460000 to 1.560000 radius of atom 6988 goes from 1.760000 to 1.860000 Partial mode Segmentation fault

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Eliminate density with small volume
by Bui Khanh Huy 01 Apr '08

01 Apr '08

Hi all, I have an EM density map. Because it's quite noisy, when displayed as a surface rendering in Chimera, there are a lot of blobs surrounding my interested surface (not touching). Is there anyway that I can get rid of those blobs by allowing to display only the blobs with volume bigger than a certain threshold? Thanks, Huy

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Re: [Chimera-users] copy cmd in nogui script
by Eric Pettersen 01 Apr '08

01 Apr '08

On Mar 28, 2008, at 2:50 PM, Ryan Pavlovicz wrote: > Hi Eric, > > I saw your response on the Chimera user group to a question about > saving images in nogui mode. > You mentioned: > > With POVray in the latest snapshot, you can now use the "raytrace" > > > keyword of the copy command to get a ray-traced image in nogui mode. > > > > --Eric > > > Could you explain how to implement this? I could not figure it > out. Thanks, > > ryan Well you probably had trouble because, unbeknownst to me, what I wrote wasn't actually true. Currently, the geometry generation code of Chimera is intimately tied up with the OpenGL code, so Chimera still needs an OpenGL context even in nogui mode in order to generate the geometry to send to POVray. Rather than engage in an extensive rewrite of the Chimera internals, what we are doing for now is making builds that include the OS (off screen) Mesa libraries. We are making such builds for 32 and 64 bit Linux platforms, but only the 64- bit version is building right now. We expect to get the 32-bit version working as time allows in the next few weeks. You can get the 64-bit version by following the "Daily Builds" link off the Chimera home page. We aren't planning to make OS Mesa builds for the other platforms, but if there were enough demand we could change our minds. I've attached an image generated by the following set of commands: windowsize 640 480 open 3fx2 preset apply int 3 turn y 180 focus ligand copy file 3fx2 png raytrace

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list of atoms attributes
by Jean-Didier Maréchal 01 Apr '08

01 Apr '08

Hi again, When using the python shell, I am often struggling to find the attribute for the atoms I work on. for at my list with the selected atoms, I caught that at[i].name gives the atom name of the entry at[i], at[i].residue provides with the name residue.chain, etc. Where can I find in the programmer's guide the full list of available attributes? What would be the way to ask for the serialNumber from the IDLE? Thanks lot 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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vdw define
by Marta Rossini 01 Apr '08

01 Apr '08

Hi all, I know in Chimera the existence of the command vdwdefine to set your desider vdw radius for a selection. My question is: it is possible to save this changes in a file (i.e. obtain a new file in any format convertible to pdb with the modified values)? or it's only a matter of visualization? thanks _________________________________________________________________ Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx…

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Criteras about hydrogen bonds in chimera
by zhaojunwei 31 Mar '08

31 Mar '08

Hi, all I have a question about the hbond. What is the definition about hydrogen bond in chimera? As we know, there're different criterias among softwares, I'm wondering the distence between donor atom and acceptor atom, and the angle of donor-hydrogen-acceptor in chimera. Any reply will be deeply appreciated! It'll be kind if you can send the reply to my address, cause I'm not in the mailing list. Junwei Zhao

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trajectory analysis
by bala 31 Mar '08

31 Mar '08

Dear Chimerians, I have an amber trajectory. I want to use gromacs to do some analysis. Is it possible in chimera to i) convert amber traj to gromacs traj format ii) convert amber topo file to gromacs topo format Thanks, Bala

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selecting one water molecule
by hjoseph＠brandeis.edu 31 Mar '08

31 Mar '08

Hi Everyone, I want to select one water molecule but every time I try to do that, all the molecules get selected. Could some one tell me the command line instruction for selecting water 241. Thanks, Helen Josephine

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Re: [Chimera-users] [chimera-dev] Wrapping Chimera in a Java program
by Tom Goddard 31 Mar '08

31 Mar '08

Hi Fabrice, I do not think Chimera could run using Jython because Chimera uses dozens of compiled C/Python modules. You can communicate with Chimera via a pipe. One approach is to start Chimera with a popen() system call and send commands to Chimera's stdin using the ReadStdin capability: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/readstdin/readstdi… It is also possible to talk to an already running instance of Chimera using the "chimera --send <file>" shell command. This is used to have a web browser helper application directly send files to Chimera. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.ht… The implementation uses a socket that Chimera is listening on but it is somewhat tricky to find the right port number. It is saved on the local machine in a file as a security measure to prevent network connections. The details of that implementation are in your Chimera distribution chimera/share/send_to_chimera.py Scooter Morris in our lab has written code to communicate with Chimera from a Java application called Cytoscape. He might be able to provide more advice. Tom Fabrice Jossinet wrote: > Dear developers, > > I would like to launch Chimera from my Java program. I would like to > send messages to Chimera to highlight in its own display selections I > do in my Java program's display. I already did that with PyMOL using a > pipe communication. > > So, several questions: > - is it possible to start Chimera from a classical python distribution > (not the embedded python of Chimera)? One of my ideas is to start > Chimera from Jython, a Java implementation of Python > - is it possible to communicate with Chimera using a pipe ? > - and the most general question: is it possible to communicate with > Chimera from the outside? > > Thank you for your answers > > Fabrice > >

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origin of volume data
by Greg Pintilie 27 Mar '08

27 Mar '08

A question about data origin in densiy maps... I open a map using the python script (in IDLE): >>> import VolumeData >>> gd = VolumeData.mrc.open ( "MRC map file" )[0] looking at the origin of this map: >>> gd.origin (-135.679992676, -135.679992676, -135.679992676) It is different than the origin reported if I open the same map file in Volume Viewer; pasted from the Volume Viewer dialog: -136.75 -136.75 -136.75 Why the difference? As to why I care, it's because if I open the map as in the python script above and then subsequently use it to compute average density values for certain structures, they are different than the average density values reported in the 'Fit Model in Map' dialog. It would give me more peace of mind if they matched... Now to start speculating on why the difference, I've seen that, internally, MRC maps define the origin in terms of a grid value, for example -64,-64,-64 in a 128x128x128 map. So the first value for the origin, as in the script method above, is calculated as if the origin is at the _center_ of the first grid point: origin[0] = -64 * step + step/2 (where step is 2.13669279804), while the second value (showing up in Volume Viewer) is simply calculated right on the grid point: origin[0] = -64 * step What's the right way to think about this? In the worst case, it's really a pretty small offset so not a big deal. Greg

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