November 2007 - Chimera-users - RBVI Mailing Lists

Question about the dotted bond
by Hyunmi Sun 13 Nov '07

13 Nov '07

Dear Whom it may concern Hello, I am currently using Chimera to access a pdb file. When I fetch the pdb file, one of the bonds between two ligands is illustrated as a dotted line in the wire representation. Why is this so? Thanks for the help! Sincerely, Hyunmi Sun

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Output of volume rotation angles and shifts in Chimera
by Duncan Sousa 13 Nov '07

13 Nov '07

Hi, I use Chimera to manually align 3D electron microscopy structures. I'm hoping someone knows how to output the angles and shifts of rotated and shifted volumes. Since one can restore sessions, the angles and shifts must be saved somewhere right? Thanks, Duncan __________________________________ Duncan Sousa, Ph. D. Department Physiology & Biophysics Boston University School of Medicine 715 Albany Street Boston, MA 02118

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Calculating the center of mass of a ligand
by Jean-Didier Maréchal 13 Nov '07

13 Nov '07

Hi everyone, I have another question: what would be the easiest way to calculate the center of mass of a given set of atoms? In particular, is there a python module that already has this function implemented? I am interested in particular to find the center of mass of a ligand bound to a protein. Thanks a lot, JD

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IDLE for listing selected residues.
by Jean-Didier Maréchal 13 Nov '07

13 Nov '07

Hi everyone, I'd like to use chimera to generate the list of the oxygen atoms of the water molecules located at less than 5.0 A of a ligand. Selecting the water molecules have been the easiest part... select :HOH & :301.a zr < 5.0 with :301.a my ligand. Then in the IDLE, I tried a series of alternative to generate the list. I use the different tips that were posted in the digest recently and arrived to this: for i in range(1,len(chimera.selection.currentResidues()): print chimera.selection.currentResidues()[i] Right, this gives me the list of residues, unfortunately, that would be a LOOOT better for me is to have the Serial number of the oxygen atoms... currentSerialNum and currentSerialNumber do not see to be a correct selection type. If there is any way that can do this? Thanks a lot JD On Sat, 2007-11-10 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: Z-slice transparency (Tom Goddard) > 2. production release candidate (Eric Pettersen) > 3. pipes and planks (Dougherty, Matthew T.) > 4. Re: pipes and planks (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 09 Nov 2007 12:47:12 -0800 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Z-slice transparency > To: Lu <lugan(a)caltech.edu>, "'Chimera BB'" > <chimera-users(a)cgl.ucsf.edu> > Message-ID: <4734C750.5020803(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Lu, > > I think I know why the volume planes are slightly transparent for > you. You are using Chimera version 1.2422 and I changed the volume > solid rendering transparency behavior in the later Chimera version > 1.2434 (August 3, 2007). You can either get the most recent Chimera > from the daily builds web page: > > http://www.cgl.ucsf.edu/chimera/alpha-downloads.html > > Or in older Chimera versions use volume menu entry Features / Brightness > and Transparency and change transparency to 0. You'll have to type this > in the entry field and press return because the slider does not go all > the way down to zero. This transparency value modulates the > transparencies given by the height of the brightness / transparency > yellow curve on the histogram. Newer Chimera changed the modulation > behavior to keep completely opaque voxels still completely opaque while > older Chimera did not. > > Tom > > > > ------------------------------ > > Message: 2 > Date: Fri, 9 Nov 2007 15:52:29 -0800 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: [Chimera-users] production release candidate > To: chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <7B31B33A-569C-4808-AD94-EBCD134DEC26(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi all, > We have put a production release candidate up for download (http:// > www.cgl.ucsf.edu/chimera/download.html) It would help us out if > people would try it out and see if it all works okay. Major changes > from the 1.2422 release include: incorporation of what were > previously "experimental features", such as morphing between volume > data sets; major revamp of the Volume Viewer interface; display of > dendrograms in Multalign Viewer; use of rotamer libraries in swapping > residue side chains and the ability evaluate possible swaps based on > clashing, fit into density maps, or hydrogen-bond formation. A more > exhaustive list of features is here: http://www.cgl.ucsf.edu/chimera/ > docs/relnotes/snapshot.html > > --Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > >

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RMSD
by Julien Orts 13 Nov '07

13 Nov '07

Dear all, First thanks a lot for the great software you provide us!!! I would like to compare structures after an MD simulation. There is a function called match which can be used to calculate the RMSD between selected atoms. The protocol is the following; I select atoms within 5 Angstrom to a reference atom in the structure 1: 300 atoms selected. I do the same for the structure 2 (reference atom is the same): 311 atoms selected The problem is then I can not use the match function since the atom number is different. I selected then residues (the one which are 5A away from the reference atom) instead of atoms but it is a bit fastidious plus it is not the same as a "zone selection" (some atoms are coming even if they are at 5.6A) I print out (from a pdb) the number of desired proton but the command sel @123 do not work because atom selection is done by name and not by number (if it is really the case then it would be nice to have this possibility as well ;-) The last solution would be really easy and quick to do if the selection on atoms can also be done by number. Is there any way to solve this? I need to use all the atoms, so the matchMaker give me an RMSD but it does not use all of the atoms in the calculation of the RMSD. Basically I need the intersection of the two sets (two structures) of selected atoms. In reality I have much more than 2 structures so the protocol should also be scriptable, but I guess everything is scriptable in Chimera (right?) thank in advance many greetings Julien

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pipes and planks
by Dougherty, Matthew T. 10 Nov '07

10 Nov '07

I have about 80 pdb datasets, each corresponding to a single helix. I know I can do one at a time using the gui. What is the method for scripting? thanks, Matt Matthew Dougherty 713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine/Houston Texas USA ========================================================================= =========================================================================

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production release candidate
by Eric Pettersen 09 Nov '07

09 Nov '07

Hi all, We have put a production release candidate up for download (http:// www.cgl.ucsf.edu/chimera/download.html) It would help us out if people would try it out and see if it all works okay. Major changes from the 1.2422 release include: incorporation of what were previously "experimental features", such as morphing between volume data sets; major revamp of the Volume Viewer interface; display of dendrograms in Multalign Viewer; use of rotamer libraries in swapping residue side chains and the ability evaluate possible swaps based on clashing, fit into density maps, or hydrogen-bond formation. A more exhaustive list of features is here: http://www.cgl.ucsf.edu/chimera/ docs/relnotes/snapshot.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] Z-slice transparency
by Tom Goddard 09 Nov '07

09 Nov '07

Hi Lu, I think I know why the volume planes are slightly transparent for you. You are using Chimera version 1.2422 and I changed the volume solid rendering transparency behavior in the later Chimera version 1.2434 (August 3, 2007). You can either get the most recent Chimera from the daily builds web page: http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Or in older Chimera versions use volume menu entry Features / Brightness and Transparency and change transparency to 0. You'll have to type this in the entry field and press return because the slider does not go all the way down to zero. This transparency value modulates the transparencies given by the height of the brightness / transparency yellow curve on the histogram. Newer Chimera changed the modulation behavior to keep completely opaque voxels still completely opaque while older Chimera did not. Tom

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(no subject)
by Ryan 08 Nov '07

08 Nov '07

I am trying to import Chimera in a python script but get the following error message: Traceback (most recent call last): File "./chimera_import.py", line 16, in <module> import chimera File "/usr/local/chimera/share/chimera/__init__.py", line 15, in <module> from _chimera import * ImportError: /usr/local/chimera/lib/_chimera.so: wrong ELF class: ELFCLASS32 Does anyone know what the problem is here? I can run Chimera without a problem in the GUI -- so i would assume that means the chimera class is being properly loaded in that instance. I have the 32 bit Linux version installed on my AMD64 system running SUSE. Thanks for your help, ryan

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Fe in chimera antechamber
by snoze pa 07 Nov '07

07 Nov '07

Hi, I am new in this mailing list but found chimera more useful than any other software. I was building a protein that contain HEME. When I was calculating the charge using chimera interface, then it is asking for HEM[FE] and HEM[nonFE] formal charge. I know chimera is using MMTK and AMBER forcefield. If I will give the default value then it is assigning +2 charge to Fe, which is not a match based on AMBER forcefield. Meanwhile I try to change the Formal charge manually, but still it gives the same +2 for Fe. Anybody used chimera to prepare a protein having heme for dock or geometry build. My another question is: Is it possible in chimera to merge nonpolar hydrogen charges on the heavy atoms, the technique used in autodock. I will highly appreciate your help and suggestions in this matter. thanks in advance. s

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