April 2007 - Chimera-users - RBVI Mailing Lists

Ribosomal RNA depiction
by Thomas Goddard 12 Apr '07

12 Apr '07

Hi Jean-Francois, Here are some tips for showing coarse RNA depictions. I too had lots of different colors for the ribosome rna bases using the nucleic acid blobs tool but I changed them. Here was my procedure. 1. open 1s72 2. select chain 0 (menu Select / Chain / 0) 3. invert selection to select all proteins (menu Select / Invert) 4. delete all the proteins (menu Actions / Atoms+Bonds / Delete 5. open reschains.py 6. open multiscale (menu Tools / Higher-order Structure / Multiscale Models) 7. select multiscale multimer type None and press Make models. 8. press multiscale select All button, change resolution to 2, press Resurface 9. ctrl-click on backbone to select it 10. invert selection (menu Select / Invert) 11. click multiscale color button and set color of all bases http://www.cgl.ucsf.edu/home/goddard/temp/1s72-rna.png Nicer simplified depictions can be made using ribbons with a single side chain atom as a sphere. The ribbon style editor (Tools / Depictions / Ribbon Style Editor) can fatten up the ribbon. Or for fancier bases shown as slabs use the Nucleotides tool (Tools / Depiction / Nucleotides), for example, http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/stmvrna/1a34.png Tom jean-francois menetret wrote: > > Hi Tom, > > the new reschains.py works well; but how did you specify the color > scheme in 1s72_rna.png using "multiscalemodel" option ? I am getting so > many different colours (see attached jpeg) > > Jean-François Ménétret, PhD > Boston University School of Medicine

1 1

exporting ".pov" session
by Tom Goddard 12 Apr '07

12 Apr '07

Jean-Francois asks about what is exported to POV-ray. jean-francois menetret wrote: > > Hi Thomas, > > I have a question about saving ".pov" session > > Items of the chimera window that are not shown at the time of the > export command are saved in the povray scene. > Is that normal ? How can I save one object at a time ? > > Jean-Francois

3 3

Suggestion on biological assembly load
by Miguel Ortiz-Lombardia 11 Apr '07

11 Apr '07

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, I have small suggestion to make that I would find helpful if implemented in chimera: I think it would be great if the "biological assembly" could be fetched by ID from the File menu, just as it goes now for the pdb coordinates file from the RCSB site. Such assemblies are kept at the PQS database at the EBI (Cambridge). The links there follow this syntax: http://pqs.ebi.ac.uk/pqs-doc/macmol/<ID>.mmol where <ID> is obviously that of the PDB structure. Despite the extension, it is a plain PDB file. The CRYST1 record (for crystallographic structures) of such coordinates files has been modified to space group P1, since the crystallographic operations of the original structure don't hold. A potential problem if these files is that they don't seem to care about having duplicated atom numbers... These assemblies are most often correct and validated by experiments. However, you might want to add a caveat or, even better, an intermediate window with a link to the place where the PQS explains how that particular oligomer was generated and why it is considered biologically relevant: http://pqs.ebi.ac.uk/pqs-bin/macmol.pl?filename=<ID> Best regards, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork(a)yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFGGL+gF6oOrDvhbQIRAtQ2AKCi9oIpIJffYwshk1PgB2aiG4e9rgCghjzZ Uz0yTug1VXEHXNP2MG2HsmI= =EGzy -----END PGP SIGNATURE-----

4 3

exporting a mineral structure as VRML
by Janet Iwasa 11 Apr '07

11 Apr '07

Hello, I'm trying to use Chimera to export a mineral file ( http://virtual-museum.soils.wisc.edu/soil_smectite/soil_smectite.pdb) as a ball and stick VRML structure, but I'm running into a bit of difficulty since some of the bonds don't get made into sticks -- rather, they appear as purple dotted lines in the viewer. Any suggestions on how to get these bonds to be made into geometry? thanks! Janet Iwasa

4 3

Extra Chimera marker attributes
by Tom Goddard 10 Apr '07

10 Apr '07

Hi Jeff, The Chimera path tracer markers accommodate extra attributes that are read and written to the XML marker files. There is no user interface to define new marker attributes in Chimera. A user interface to define new marker attributes does not seem hard. You could specify an attribute name and value in a command or dialog that assigns that attribute for all selected markers. For these new attributes to be of any use within Chimera more capabilities would be needed. For example some command or dialog that would allow you to select all markers with a certain attribute and value (e.g. is_filament = true). These kinds of capabilities already exist for attributes of atoms of molecules. For example, see the "setattr" and "defattr" commands, and "Render/Select by Attribute" tool, and atom specifiers that can test for specific attribute values. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/defattr.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descri… These will work with path tracer markers since markers are implemented as atoms. But there are problems. For example "defattr" uses names of atoms and the names of the path tracer atoms are not meaningful. Probably "setattr" is more useful and you can set an attribute for all currently selected atoms. The main weakness is that these atom attributes will not be saved in marker XML files. That is probably easy to fix but I would need to investigate how atom attributes are implemented. For markers the attributes are kept in a Python dictionary marker.extra_attributes. I do not know if atom attributes on markers will be saved in Chimera session files. Would have to test that. Tom Jeff wrote: > Tom, > > how hard would it be to add other attribute(s) to the markers > generated with the volume path tracer tool, aside from > marker-to-marker connectivity? Such as the ability to enumerate > individual filaments/objects within a single marker set, or a flag > that would tell whether a set/group is composed of filaments, or > surfaces, or just a point cloud? Either of of these (enumeration, or > object type) could be stored as an integer. > > -Jeff

1 2

transparency factor
by jean-francois menetret 09 Apr '07

09 Apr '07

Is it possible to change the transparency factor of a volume at the command line ? Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

3 3

Fetch EMDB map by id
by Thomas Goddard 09 Apr '07

09 Apr '07

Hi Cathy, It is a good idea to allow fetching EMDB maps by id in the current File / Fetch by ID dialog. Their are two issues related to the large size of some maps that I would like to solve to make that work well. First I would like Chimera not to freeze while the fetching is done. That is what currently happens when fetching files. Instead it could show a progress dialog with a cancel button (like a web browser) and open the map when it finally arrives. Second I would like the map to be saved on your local machine so that you don't have to fetch the same large file more than once. Perhaps the way that would work is the the first time you fetch any file it asks you where to save this and future fetched files, and there will be an option not to save them. This would be remembered in your Chimera preferences file. When you subsequently used the fetch dialog it could first look in the directory where you save fetched files and use the copy there if available. Thanks for the suggestion. It is on my requested features list. Tom

2 1

Re: [Chimera-users] hkcage command
by Thomas Goddard 09 Apr '07

09 Apr '07

Hi Padma, The code for the hkcage command had to be changed for Chimera version 1.2348 and newer because we switched from using the Numeric Python array package to its not completely compatible successor called NumPy. The new code for the hkcage command is on the experimental features web page http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Use that new code with Chimera 1.2363. I have not had time to try flattening an icosahedral map. I made a small step toward another request of yours, plotting radial density. I tried a Python 2-d plotting library called matplotlib that could be used for making radial density plots. It is a pretty big package so we have not decided whether to include it in Chimera. Tom

1 0

GIF animations in Chimera
by Tom Goddard 09 Apr '07

09 Apr '07

Anyone interested in GIF animation output from Chimera? Their main appeal is that they play directly in most web browsers (like banner ads). It was easy to add to the Chimera movie recorder using ffmpeg which is included in the Chimera distribution. But ffmpeg uses a fixed color palette causing severe color banding and does not offer LZW compression resulting in large file sizes. That option looks unusable. I tried another approach using a separate program called "gifsicle". That gave decent coloring and compression but it would require adding gifsicle to the Chimera distribution. I am reluctant to do that (entails future maintenance) unless there is strong interest in making GIF animations. Tom

2 1

[Fwd: Re: GIF animations in Chimera]
by Thomas Goddard 09 Apr '07

09 Apr '07

Miguel uses ImageMagick to make GIF animations from Chimera movie frames. Tom -------- Original Message -------- Subject: Re: [Chimera-users] GIF animations in Chimera Date: Sat, 07 Apr 2007 09:09:43 +0200 From: Miguel Ortiz-Lombardia To: Tom Goddard Hi Tom, I make animated GIFs with Chimera by simply saving the frames and using convert (from ImageMagick). I run an extremely simple script to do so and the results are up to my needs. Cheers, Miguel En/na Tom Goddard ha escrit: > Anyone interested in GIF animation output from Chimera? Their main > appeal is that they play directly in most web browsers (like banner ads). > > It was easy to add to the Chimera movie recorder using ffmpeg which is > included in the Chimera distribution. But ffmpeg uses a fixed color > palette causing severe color banding and does not offer LZW compression > resulting in large file sizes. That option looks unusable. I tried > another approach using a separate program called "gifsicle". That gave > decent coloring and compression but it would require adding gifsicle to > the Chimera distribution. I am reluctant to do that (entails future > maintenance) unless there is strong interest in making GIF animations. > > Tom > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

1 0

Chimera-users April 2007