August 2009 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

5 7

Question regarding saving PDB in Chimera
by Pancera, Marie (NIH/VRC) [E] 24 Nov '09

24 Nov '09

Hello, I am using Chimera to fit coordinates into EM density. However I have problems when I save with Chimera as the coordinates that I am saving are not the one I see on the screen. Here is what I do: File Save PDB chose the folder A file name A file type The model that I want to save, i.e the one I see on the screen And then I have to select save relative to model, otherwise I am saving the original molecule, the problem is that I am not sure relative to which model I have to save it. IS there an easier way to just save what I can see on the screen? Thanks, Marie

5 7

Zalman 3D
by Miles Pufall 11 Sep '09

11 Sep '09

Hi Guys - I got a Zalman 3D - it's pretty cool with Coot and Pymol. Your site says the row-interleaved stereo view under camera will work with this monitor, but I wasn't having much success. Do you have some more detailed instructions for this particular monitor? I can drop by and visit with it, or you can come see me if you's like. Thanks! Miles in Yamamoto Lab S574 Genentech Hall

5 4

2D projections
by Ana Luiza 03 Sep '09

03 Sep '09

Hi, Is it possible to build 2D projections from a 3D surface in Chimera? Thanks, Ana Luiza.

3 3

chimera latest build
by Bala subramanian 01 Sep '09

01 Sep '09

Friends, 1) I downloaded the chimera's today's build and tried to change the nucleic acid representation using..Depiction in Tools. I get the following error. Kindly write me what is going wrong ? TclError: unknown option -width TclError: unknown option -width File "CHIMERA/share/CGLtk/OptionMenu.py", line 15, in __init__ See reply log for Python traceback. Thanks, Bala

4 3

substitute single residue
by Andrew P. Hinck 01 Sep '09

01 Sep '09

Dear all, I was hoping to make some single amino acid substitutions in the context of a protein binding interface. I've only briefly poked around, but so far the only way I see to do this is to delete existing atoms/bonds one by one, and then rebuild (the alternate amino acid) atom-by-atom/bond-by-bond. Is there an easier way (like, telling the program to substitute an Asp for a Lys, or something akin to this)? Thanks in advance for any suggestions. Andy Hinck Andrew P. Hinck, Ph.D. Professor, Department of Biochemistry, MC 7760 University of Texas Health Science Center at San Antonio San Antonio, TX 78229-3900 office: 210-567-8780 mobile: 210-725-4438 fax: 210-567-8778 email: hinck(a)uthscsa.edu websites: http://hincklab.uthscsa.edu http://nmr.uthscsa.edu

4 4

Centro-symmetric space groups
by Michael Day 31 Aug '09

31 Aug '09

How do you get Chimera to recognize centrosymmetric space groups. If I include the space group on the CRYST1 card of the PDB file all is well for non-centrosymmetric groups but when a center of symmetry enters the picture all bets are off. I'm using Tool->Higher-Order Structure->Unit cell For example adding the space group in column 56 of the PDB P1 as P 1 - all's good P-1 as P -1 - complete nonsense although it recognizes there are two symmetry elements P2 as P 1 2 1 - all's good P21 as P 1 21 1 - all's good P212121 as P 21 21 21 - no problem But; P21/c as P 1 21/c 1 - no recognized symmetry elements and no unit cell expansion. Cheers, Mike <<< ------------------------------------------------------------------------> >> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday(a)caltech.edu <<< ------------------------------------------------------------------------> >>

3 3

Re: [Chimera-users] Problem building 3D structure from smile text ...(Solved. Thanks)
by Sergio Garay 29 Aug '09

29 Aug '09

Thank tou Alaine. The new chimera version works perfect! On Fri, Aug 28, 2009 at 5:29 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Sergio, > Normally if you want to report an error it is best to use "Help... Report a > Bug" in the Chimera menu since that would automatically include information > about your computer and Chimera version, and let you attach files. > > However, in this case I can immediately see the problem: you need a newer > version of Chimera! > > You would need a version from July 3 or later, for example the August 20 > snapshot: > <http://www.cgl.ucsf.edu/chimera/download.html#snapshots> > > Explanation: The SMILES -> 3D structure conversion is done by a Web server > provided by a group at Indiana University, and a few months ago they changed > how this service is accessed. It was necessary to change Chimera to use the > new, updated service. > > I tested the following command in the snapshot version just now, and it > worked fine: > > open smiles:N[C@@H](C)C(=O)O > > Using this command is the same as entering the SMILES in the Build > Structure dialog. I also checked doing it that way. > > I think you will be pleasantly surprised to see the many improvements we > have made in Build Structure and in other tools, and the many new features > that have been added to Chimera! > > Improvements between 1.3 and the snapshot (and you were using a version > older than 1.3): > <http://www.cgl.ucsf.edu/chimera/1.4_b28596/docs/relnotes/snapshot.html> > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

1 0

movie image resolution
by Anastasia A Aksyuk 28 Aug '09

28 Aug '09

Hi, It is very easy to specify resolution for a saved image, but not for the images used to create a movie. Is there a way to generate a movie or a stack of images with higher resolution then a display screen? I seem to be limited to 1273x870. Thanks a lot, Anastasia

3 2

Problem building 3D structure from smile text ...
by Sergio Garay 28 Aug '09

28 Aug '09

Hi all I'm trying to build a 3D structure from this smile text: N[C@@H](C)C(=O)O But the program stops and doesn't respond to any key. The log window shows the next message: <type 'exceptions.KeyboardInterrupt'> Exception in Tk callback Function: <bound method BuildStructureDialog._placeAtoms of <BuildStructure.gui.BuildStructureDialog instance at 0x31ca3b0>> (type: <type 'instancemethod'>) Args: () Traceback (innermost last): File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ None File "CHIMERA/share/BuildStructure/gui.py", line 632, in _placeAtoms None File "CHIMERA/share/BuildStructure/Smiles.py", line 15, in openSmiles None File "CHIMERA/share/BuildStructure/Smiles.py", line 21, in smiles2mol None File "CHIMERA/share/BuildStructure/SOAPpy/WSDL.py", line 61, in __init__ None File "CHIMERA/lib/python2.5/urllib.py", line 82, in urlopen return opener.open(url) File "CHIMERA/lib/python2.5/urllib.py", line 190, in open return getattr(self, name)(url) File "CHIMERA/lib/python2.5/urllib.py", line 325, in open_http h.endheaders() File "CHIMERA/lib/python2.5/httplib.py", line 860, in endheaders self._send_output() File "CHIMERA/lib/python2.5/httplib.py", line 732, in _send_output self.send(msg) File "CHIMERA/lib/python2.5/httplib.py", line 699, in send self.connect() File "CHIMERA/lib/python2.5/httplib.py", line 673, in connect self.sock.connect(sa) File "<string>", line 1, in connect None <type 'exceptions.KeyboardInterrupt'>: Am I doing something wrong? I am working with this chimera version: alpha version, build 2577, 2008/12/09 -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

2 1