January 2007 - Chimera-users - RBVI Mailing Lists

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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Re: [Chimera-users] Export idatmType
by Eric Pettersen 18 Jan '07

18 Jan '07

On Jan 17, 2007, at 10:47 PM, Brady Bernard wrote: > is there a way to do this with --nogui so that i can automate it in > a script? > > thanks, > brady It's pretty easy to make a Python script that opens a file, loops through open molecules and then their atoms, and prints our the atom identifier and IDATM type to that file. Here's an example: import chimera f = open("types.txt", "w") for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for a in m.atoms: print>>f, a, a.idatmType f.close() If you save the above into a file with a ".py" suffix (e.g. types.py), then you could save all the types of 1gcn with "chimera -- nogui pdb:1gcn types.py", which would create a file named "types.txt" (in the same folder as types.py) with the types listed. BTW, you need to preserve the indentation of the Python code above -- it matters to Python. If you're automating this in a shell script, it may be simpler to just print the info to standard output and redirect that into a file, rather than open the file in the Python script. The command would then be "chimera --nogui --nostatus pdb:1gcn types.py > 1gcn_types.txt" (note the "--nostatus" flag so that status messages don't get mixed into the output). The Python script becomes: import chimera for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for a in m.atoms: print a, a.idatmType --Eric > ----- Original Message ----- > From: Eric Pettersen > To: Brady Bernard > Cc: Thomas Goddard ; Elaine Meng > Sent: Tuesday, January 16, 2007 4:40 PM > Subject: Re: Export idatmType > > Hi Brady, > Tom forwarded your mail to me. There almost is a way. In the > 1.2318 snapshot, the Render By Attribute tool allows you to save > attribute values to a file using that tool's "File->Save > Attributes..." menu item (saved in the format that Define Attribute > accepts). So, why "almost"? The idatmType attribute is screened > out of the list of available attributes since it can be expensive > to compute the values -- and since you could already select by > IDATM type using the regular selection menu. But now that save > exists I will have to improve Render By Attribute so that it can > know that idatmType values are strings ahead of time (so it doesn't > have to ask for any values to figure that out). > Anyway, for your purposes it is not too hard to force Render By > Attribute to show you idatmType. First, get the 1.2318 release. > Then edit the file <your Chimera>/share/ShowAttr/__init__.py (on a > Mac: Chimera.app/Contents/Resources/share/ShowAttr/__init__.py) > and edit line 24. It will look like this: > > 'name': False, 'idatmType': False, 'idatmIsExplicit': False, > > change it to: > > 'name': False, 'idatmIsExplicit': False, > > Save the file and thereafter Render By Attribute should show you > the idatmType attribute. > > --Eric > >> hi tom - is there a quick way to save the atom types from >> idatmType to a text/log file along with the atom name or number? > >

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Re: [Chimera-users] Movie resolution
by Zoghbi, Maria 18 Jan '07

18 Jan '07

Now it works perfectly! Thanks Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu -----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Wednesday, January 17, 2007 5:04 PM To: Zoghbi, Maria Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Movie resolution Hi Maria, Sorry the code I suggested was not correct. The new lines should have images = ... instead of image = ... Otherwise your change looks correct. Tom

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For Chimera mac users
by Eduardo Sanz-Garcia 17 Jan '07

17 Jan '07

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Chimera-users January 2007