- Chimera-users - RBVI Mailing Lists

export pdb file
by Shuanghong Huo 29 Mar '04

29 Mar '04

Hi, I remember that Midus can export pdb file, but I cannot find this function in Chimera. Thanks, Shuanghong

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question
by Wendy Ochoa 28 Mar '04

28 Mar '04

Could you please tell me how can I define the secondary structure of the protein i am displaying with chimera. I know the secondary structure of my pdb, so I would like to draw a picture of the protein showing the B sheets and alpha helix in different colors. Thansk a lot!!!

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32 bit / 64 bit Linux mixup
by Thomas Goddard 13 Mar '04

13 Mar '04

The 32 bit Linux Chimera 1917 was accidentally replaced with the 64 bit Linux version yesterday (Thursday 11 AM PST, March 11). The 32 bit version has been restored Friday 7 PM PST, March 12. Tom

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Re: [Chimera-users] chimera-1.1917-linux.exe: Exec format error. Wrong Architecture.
by Pattanayek, Sabuj 13 Mar '04

13 Mar '04

[root@eglimp]# uname -iorsp Linux 2.4.22-openmosix2smp athlon i386 GNU/Linux it seems the link to chimera-1.1917-linux.exe on the download page is actually the link to the x86_64 version: [root@eglimp]# head chimera-1.1917-linux.exe ELF> @@@@"@@@@@�@@@@d�d�PP��``P`@@ P�d � � �||Q�/lib64/ld-linux-x86-64.so.2GNU etc.. and [root@eglimp]# head chimera-1.1872-linux.exe ELF44 (#�#��x▒�@ /lib/ld-linux.so.2GNUCVN>LU@SB<5QF/4)1K$.TG!J▒= Can you please put the correct link to the x86_32 linux version on the download page? Thanks, Sabuj Pattanayek Quoting Greg Couch <gregc(a)cgl.ucsf.edu>: > The linux distribution is only for the Intel/AMD x86 architecture. Are > you trying in install on something else? For example, and Alpha or > PowerPC? > > - Greg > > On Fri, 12 Mar 2004, Pattanayek, Sabuj wrote: > > > I'm getting this error when I try to run the installation > > > > -rwx------ 1 root root 26226504 Mar 12 12:02 > chimera-1.1917-linux.exe > > [root@eglimp]# chimera-1.1917-linux.exe > > chimera-1.1917-linux.exe: Exec format error. Wrong Architecture. > > [root@eglimp]# ./chimera-1.1917-linux.exe > > ./chimera-1.1917-linux.exe: Exec format error. Wrong Architecture. > > [root@eglimp]# md5sum chimera-1.1917-linux.exe > > 67e955ce87d000916039d94c7d6d0a56 chimera-1.1917-linux.exe > > [root@eglimp]# uname -rs > > Linux 2.4.22-openmosix2smp > > > > web page: > > > > linux chimera-1.1917-linux.exe > > Size: 26226504 bytes > > MD5: 67e955ce87d000916039d94c7d6d0a56 >

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save session stripping TER statements from PDB's
by Pattanayek, Sabuj 13 Mar '04

13 Mar '04

In version 1.1892 (and older possibly), file > save session seems to be stripping TER statements from PDB files. The TER statement is helpful for specifically telling Chimera and other PDB viewers not to connect consecutive residues in a PDB (for example ATP/water molecules at the end of a PDB that are not part of the main protein chain). Re-inserting TER's manually into the .py file can become cumbersome especially when one PDB insertion in the .py is 27000+ columns long. Would it be possible to fix this in future versions? Thanks in advance, Sabuj Pattanayek

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[Chimera-users] chimera-1.1917-linux.exe: Exec format error. Wrong Architecture.
by Pattanayek, Sabuj 12 Mar '04

12 Mar '04

I'm getting this error when I try to run the installation -rwx------ 1 root root 26226504 Mar 12 12:02 chimera-1.1917-linux.exe [root@eglimp]# chimera-1.1917-linux.exe chimera-1.1917-linux.exe: Exec format error. Wrong Architecture. [root@eglimp]# ./chimera-1.1917-linux.exe ./chimera-1.1917-linux.exe: Exec format error. Wrong Architecture. [root@eglimp]# md5sum chimera-1.1917-linux.exe 67e955ce87d000916039d94c7d6d0a56 chimera-1.1917-linux.exe [root@eglimp]# uname -rs Linux 2.4.22-openmosix2smp web page: linux chimera-1.1917-linux.exe Size: 26226504 bytes MD5: 67e955ce87d000916039d94c7d6d0a56 Thanks in advance Sabuj Pattanayek

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mac version of 1.1917 snapshot
by Eric Pettersen 11 Mar '04

11 Mar '04

Hi again, If you downloaded the Mac version of 1.1917 before about 5pm PST today, you should download it again because we updated it to fix a bug. The non-Mac versions are fine. The Mac version was not displaying atoms in stick, ball-and-stick, or sphere modes (wireframe mode was okay). Sorry for the possible inconvenience! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu

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new snapshot release (1.1917)
by Eric Pettersen 10 Mar '04

10 Mar '04

Hi, We've just put a new snapshot release of Chimera up for download on the web site (http://www.cgl.ucsf.edu/chimera) Here are the highlights of the changes between this snapshot (1.1917) and the previous one (1.1892): tools: Match -> Align can create sequence alignments for multiple matched structures (not just pairs) Multalign Viewer can show/edit sequence annotations for relevant formats (RSF, Stockholm) SimpleSession -- saves label font/size and secondary structure assignments -- compiles to .pyc file: 50% less memory use, 15% less time to restore added Export Surfaces as VRML (in Utilities category) -- save surfaces made by Multiscale Models and Volume Viewer as VRML files added Browser Configuration (also in Utilities) -- configure browsers to send certain file types to Chimera (see also new Web Data preferences) FindHBond and PBReader allow line width to be set Movie has preliminary support for reading GROMOS trajectories newly available commands: bondcolor -- color bonds independent of flanking atoms bonddisplay -- set how bond display depends on flanking atom display bondrepr -- set bond representation to be wire or stick (independent of atoms) hbonds -- command equivalent of FindHBond tool rlabel -- whether residue name/number is included in the first atom label per residue Model Panel new 'render attrs...' button allows coloring by model/residue/atom attributes (e.g. B-factor) The 'render attrs...' interface is in preliminary form and will be changing. It also isn't documented yet but is pretty easy to use. Just pick an attribute of interest and a histogram of values will be displayed. By default there will be three color bars on the histogram that you can grab and move around with the mouse, or add or remove with control-click. You can use the 'Color' color well to set the color of the last bar you picked. The 'No value' color well is used in the rare case of the attribute being missing (or set to None) in the atom/residue/model. Click Apply or OK to make the coloring happen. Several parts of the interface are grayed out since they haven't been implemented yet. In the future you will be able to select by attribute value, and change atom radii or ribbon widths based on attribute values. If you are using the last production release (1.1872) instead of the previous snapshot, then you will also be getting these features when you go to 1.1917: general: additional file formats for saved images (PS, EPS) different lighting scheme in graphics window (over-the-shoulder instead of headlight) tools: added Shininess Control (in Viewing Parameters) -- adjust shininess, brightness, and the color used for shiny highlights Collaboratory section in Preferences allows designation of port number and IP address (for firewalls/NAT) Movie -- allows definition of scripts to be run at each time step -- looping can be turned off Multalign Viewer allows structure selection by arbitrary % residue conservation Volume Viewer options added to subdivide and smooth isosurfaces commands: copy command now offers supersampling and PS/EPS formats new ribbackbone command controls whether ribbon and backbone atoms are shown simultaneously Enjoy! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Use of Chimera for Trends Plant Sci March 2004...
by John F. Allen 24 Feb '04

24 Feb '04

....for article and issue cover illustration. Final proofs attached. Acknowledged. Great program. Will send reprint(s) and final pdf on request. Many thanks John F. Allen Professor of Plant Cell Biology Plant Biochemistry Center for Chemistry and Chemical Engineering Lund University Box 124 SE-221 00 Lund Sweden Tel: +46 46 222 7788 (Office); +46 46 222 4073 (Laboratory) Fax: +46 46 222 4009 (Direct); +46 46 222 4116 (Departmental) E-mail: john.allen(a)plantbio.lu.se Plant Cell Biology: http://plantcell.lu.se Publications: http://plantcell.lu.se:591/john/

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CHIMERA help - coloring density maps
by Padmaja Natarajan 02 Feb '04

02 Feb '04

Hi, I have just started using CHIMERA to look at volume files in the CCP4 format for virus particles. I would like to color the density as a color ramp continuously changing between ANY two specified colors depending on the radial distance from the center of the virus particle (as shown in the attached figure). How do I achieve this with CHIMERA? thank you very much for your help in advance. -Padma

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