- Chimera-users - RBVI Mailing Lists

НА: Re: problem in coloring a selected region
by Sp 12 Sep '11

12 Sep '11

Отправлено с моего коммуникатора HTC

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chimera rotation mode
by Jean-Francois Menetret 12 Sep '11

12 Sep '11

Hello, for some reason, the default rotation option in the viewing window always comes back to "independent" when I restore a session; how could I change the default to be "center of models" for example ? Jean-Francois

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atom order in RMSD calculations
by Elaine Meng 10 Sep '11

10 Sep '11

Hi Kristen, I'm CCing chimera-users since this is more of a user question than developer/programmer (chimera-dev) issue. The serial number is not the main factor in pairing the atoms. As mentioned in the "rmsd" documentation, <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> "If atom order is not specified... the atoms within a residue are ordered first by name, and where these are identical, by alternate location identifier, and where these are also identical, by serial number." As for residues, if your models have multiple residues I believe they are compared in order. However, if your structures have exactly the same atom names and in the same order, I believe the rules above would pair the atoms in the epected order. The only other issue I can think of is that chemically symmetrical pairings are not tried, for example, if you had two phenyl rings or two carboxylates that exactly match in space but the atom names are in "flipped" positions, you would still get a higher RMSD. If it seems Chimera is not pairing the atoms as advertised, please use "Help... Report a Bug" in the Chimera menu and attach a session file with the two models, and give a short description and an email address if you'd like to hear back. There are a couple of ways to explicitly give the atom order, but if your structures have many atoms, they would be difficult/tedious: (a) interactively pick the atoms one by one from the graphics display in the correct order and then use the word "sel" to specify them in the command, as described in more detail in the documentation (link above) (b) specify all the atom names in order in the command I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 10, 2011, at 11:44 AM, Kristen Eisenberg wrote: > [chimera-dev] Calculating RMSD > > Hi, > I want to calculate the RMSD between two mol2 structures in place. The two > structures are different forms of the same structure. I haver modified the > mol2 so that the two of them have the same serialNumber in their respective > atoms. The problem is that when I use the command rmsd #model1 #model2, it > return an incorrect value of the rmsd, as the value showed is too high, > about 5, when it should be about 1 (the two structures are very similar). Is > there any way to calculate the RMSD value in place correctly or I am doing > anything wrong? > > Thanks for your help. > Kristen Eisenberg

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structure editing query
by Bala subramanian 10 Sep '11

10 Sep '11

Friends, I am trying to modify the sugar of a nucleotide. I am interested in making a linkage of two carbons in the sugar as in the attached pdb. I tried to use the Build structure -> modify structure option but it does not work in the sense that when i select carbon atom (c2') and tried to connect it to an oxygen, chimera says that it is already bonded and hence some bonds to create a new one. Is there any way to make such linkages as in the pdb ? Thanks, Bala

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path to an object displayed in a chimera session
by Jean-Francois Menetret 09 Sep '11

09 Sep '11

Hello, how can one find out the path to an object displayed in a chimera session ? Best wishes Jean-Francois

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structure analysis -> axes/planes/centroids
by Keren Lasker 08 Sep '11

08 Sep '11

Dear Chimera group: I have a quick question regarding low resolution representation of secondary structures. In the structure analysis -> axes/planes/centeroids tool there is an option of representing each helix as a axis. Is there a similar option for representing strands? thanks, Keren.

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help! questions about Join Models
by Joyce Yang 08 Sep '11

08 Sep '11

Hi, I am trying to understand what would exactly happen when join two peptide fragment together. My question is how Chimera manage to avoid any collision of atoms from two fragments. Is there any automatic minimization going on while using this Join Models function? Or it is actually possible to see overlapped coordinates of atoms in space after joining two fragments. Thank you very much. Joyce Yang

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color surface based on NMR Order parameters
by lalit.deshmukh＠huskymail.uconn.edu 08 Sep '11

08 Sep '11

Hello, I like the 'surface color ' feature in Chimera. I think, right now, the surface can be colored by radius, height, volume data and so on.. Is it also possible to color the surface based upon the NMR order parameters or intensity ratios (it will be an Excel file containing just two columns: residue numbers and the respective parameter values)? Or this can be done in some other way? Thanks in advance, Regards, Lalit Deshmukh, University of Connecticut Storrs, CT 06269

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Chimera daily-builds: session support for Animate extension
by Darren Weber 07 Sep '11

07 Sep '11

Hi, There is a recent addition to daily-builds to create a scene called 'session'. It can be seen in the Utilities > Animation dialog. The purpose of this scene is to enable easy, quick return to the saved session state after making a few changes, without reloading the session again. There are two potential problems with this new addition: 1. Some of the saved session data or properties may not be supported by the scene facility, yet. Elaine recently sent me an example session that is not yet supported by the scene facility; it contains a 'selection set' that raises an exception in the scene code. Similar problems may arise with other data models or properties. 2. Assuming everything in a session is supported by the scene facility, the 'session' scene should work. That is, it will work only while all the data that it refers to (e.g., models) are present. If changes result in removing any model data that is within the 'session' scene, the scene will contain 'orphaned' references and it will work only on the remaining model data (if any). When data is removed (closed), the scene facility will issue a prompt (warning) about how it will impact the functionality of the scene(s). This new feature to save/restore sessions is experimental in the daily-builds. For anyone using a daily-build for any mission-critical work, it may be handy to have a work around for the above problems. Try making the following changes to $CHIMERA_INSTALL_PATH/share/Animate/Session.py: 1. Comment out line 51 ("Animate.scenes.append('session')") and type 'pass' beneath it (using the same tabbed indentation). This will only disable the creation of a 'session' scene after restoring any session. All other session support remains enabled for scenes. 2. To completely disable all session support in the Animate extension, comment out all the statements that start with "chimera.triggers.addHandler". 3. If you have no need for anything in the Animate extension, completely remove it by deleting all of the content in $CHIMERA_INSTALL_PATH/share/Animate -- Darren -- Darren L. Weber, Ph.D. Programmer/Analyst on Chimera Development Team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco Mission Bay Campus (MC 2240), Genentech Hall (Room N453) 600 16th Street, San Francisco, CA 94158-2517 dweber[at]cgl.ucsf.edu, (415) 488-5439 (google voice) http://www.cgl.ucsf.edu/chimera/

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Re: [Chimera-users] inter-atomic distances do not show in session after daily build upgrade
by Elaine Meng 07 Sep '11

07 Sep '11

Hi Boaz, Generally it is better to use "Help... Report a Bug" and attach the session so that we have the data, but in this case you don't need to do it -- I just reproduced the problem in my own little test session with one distance. I will report the bug and put you on the CC list. I almost always use daily builds too, but since they aren't tested, occasionally some bug will prevent you from doing what you want or need to do. Sometimes I save more than one daily build. Otherwise, I'm hoping you will be able to use the production release (version 1.5.3) until this is sorted out. If you saved the session in a newer version, however, I understand that may not work. I will put the bug at a high priority. Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 3, 2011, at 11:53 AM, Boaz Shaanan wrote: > Hi, > I upgraded to the latest daily build and restored a session that had quite a few distances drawn. The dashed lines don't show while the table of distances is still there. Before the upgrade the session was restored several times and always showed the distances fine. Is there a way to resuscitate the display of distances? I sure hope so. > Cheers, > Boaz

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