- Chimera-users - RBVI Mailing Lists

chimera startup problem
by Chen Xu 23 Jan '07

23 Jan '07

Dear List, after upgrading to 1.2304 (1.2303 freeze the computer after several minute loaded with a volume pdb file) , I have problem to start it up on (RedHat): agnieszka@raptor ~]$ chimera Error starting chimera: ValueError: attempt to create string with null pointer (see reply log for Python traceback info) Traceback (most recent call last): File "/sware/chimera/chimera-1.2304/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 255, in init tkgui.initializeGUI(exitonquit) File "CHIMERA/share/chimera/tkgui.py", line 2407, in initializeGUI File "CHIMERA/share/chimera/tkgui.py", line 2368, in createApp File "CHIMERA/share/chimera/tkgui.py", line 1784, in __init__ File "CHIMERA/share/chimera/tkgui.py", line 1811, in makeGraphicsWindow ValueError: attempt to create string with null pointer any help? -- Chen Xu Brandeis University Rosenstiel Center, MS029 Waltham, MA 02454 phone: +1 781 736 2469 fax: +1 781 736 2419

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defining rotation of a chimera markers file
by Jeff 22 Jan '07

22 Jan '07

hello, is there a way to rotate a chimera markers file in a defined way, for instance by providing a sequence of euler angles? The context is in the case of defining a marker set in a a particular volume map, say volume A, and then doing additional processing of volume A outside of chimera, perhaps just a simple series of rotations, creating volume B. now, I would like to use the same marker set in a precise way on volume B (without just visually rotating it into place by hand). is there a way to apply the same rotations to the marker set? thanks, -Jeff

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Experimental features
by Edmond Alexander 22 Jan '07

22 Jan '07

Good Morning, I have attempted to load some of the Chimera "Experimental Features" following the installation instructions: > On Macintosh computers put it in > > Chimera.app/Contents/Resources/share > > > On the Mac you will need to use Finder menu entry Go / Go to Folder... > to see inside the Chimera.app folder. > > When Chimera.app/Contents/Resources/share is typed into the Go To Folder I get a message that the "Folder can not be found". Subsequent searches show only the Chimera application. I am running a Mac G4 running Mac OS 10.3.9 and iMac (Mac Intel) running Mac OS 10.4.8 My Chimera version is 1.2303 Am I missing something? Your help will be greatly appreciated. Thanks in Advance, Edmond Alexander Alexander & Turner Medical Illustration Studio

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hbonds and addh geometry
by Jim Procter 22 Jan '07

22 Jan '07

Hi all. Has anyone noticed and/or fixed the slight problem with applying the hbonds command (without 'sloppy' bond geometry allowed) after adding hydrogens to a structure with addh ? The identified hbonds are marked between donor and acceptor, but the donor's proton seems often seems to lie some way off the hbond vector by a seemingly consistent amount, suggesting a systematic error in the addh protonation geometry. As an aside to this, it would be very nice to be able to re-connect the detected hydrogen bonds so that the bond vector lies between the proton and the acceptor, rather than between the heavy atoms. Does anyone have a script to do this ? thanks in advance! Jim Procter -- ------------------------------------------------------------------- J. B. Procter (VAMSAS Project) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk

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Using 3dconnexion 6DOF controller with Chimera
by Shi Jiye (ROC) 22 Jan '07

22 Jan '07

Hello, Does Chimera support 6DOF controllers such as SpaceExplorer from 3dconnexion? It would be nice to have this feature. Thanks, Jiye Shi **************************************************************************** Legal Notice: This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. UCB screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. UCB accepts no liability for any damage caused by any virus transmitted by this electronic mail.

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AA and DNA base-pair substitutions
by David Segal 22 Jan '07

22 Jan '07

Dear Chimera-users, I would often like to take a pdb of a protein-DNA complex and just change one aa or one base pair. Can Chimera do this? If not, does anyone know of free software that can (for example, Swiss-PDB Viewer can mutate an aa, but not a base). Thanks in advance. - Dave Segal -------- David J. Segal, Ph.D. University of California, Davis Genome Center/Pharmacology 4513 GBSF 451 E. Health Sciences Dr. Davis, CA 95616 Tel: 530-754-9134 Fax: 530-754-9658 Email: djsegal(a)ucdavis.edu Web: www.genomecenter.ucdavis.edu/segal/ NOTICE: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message

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save mol2 command
by Huang, Shengyou 22 Jan '07

22 Jan '07

Hi, Does anybody know a COMMAND which can save a mol2 format file in Chimera? Thanks! Shengyou Huang

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yet another chimera question...
by Jeff 19 Jan '07

19 Jan '07

good morning Tom, there isn't by chance a way to output the orientation/location of a given model (or, likewise, its corresponding per-model clipping plane) so that I can write down particular views that are useful, without having to re-save chimera sessions with unique IDs (my kludge as of right now). and a related follow-up - if so, how do I re-input the orientations by command line in chimera (if possible?) thanks, -jeff

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clarification regarding the application of chimera...
by harini senthil 19 Jan '07

19 Jan '07

I am a final year b.tech industrial biotech student working on docking studies between a polymer and membrane proteins of e.coli. I would like to know whether chimera can be utilised for performing polymer protein docking studies. Thanking you --------------------------------- Heres a new way to find what you're looking for - Yahoo! Answers

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Re: [Chimera-users] chimera to rebuild crystal
by Elaine Meng 18 Jan '07

18 Jan '07

Maybe a more integrated solution would be to put the additional option(s) in Unit Cell - easy for me to say, however! 8-) Elaine On Jan 12, 2007, at 2:15 PM, Thomas Goddard wrote: > Hi Elaine, > > Brady Bernard wanted to output multiple unit cells, more than 3x3x3 > in > fact (which is what multiscale can do). The script lets you set the > number > of unit cells along each axis. That isn't supported in Unit Cell. > > Sorry the Brady email wasn't posted to chimera-users. Nag Eric about > that since the original email went directly to him. Of course, I too > now > have personal email messages from Brady that should have gone to > chimera-users. > I am still figuring out how to forward the mail and have the original > sender's name appear in the chimera-users archive summary. > > Tom

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