- Chimera-users - RBVI Mailing Lists

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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