Hi all, i ve just installed the latest daily build version and i´ve noticed that the sequence viewer has a new "look". However, i have difficulties to get used to it... Some examples: -when i want to view the sequence of a pdb file containing seven chains, i get seven different pop-up windows (...) showing the sequences corresponding to the seven different chain ID´s.... -Moreover, it isn´t so "easy" anymore to select aminoacids directly in the sequence viewer (e.g. too many colors) and therefore now i´m selecting residues using only the command line.. My colleagues also prefer the older version.. is there a simple way to install the latest chimera version but keep the old version of the sequence viewer? Thanks! -Christos ------------------------------- Christos Gatsogiannis Insitute of Zoology, Dpt. II cryoEM Lab, AG Markl Joh. v. Müllerweg 6 Johannes Gutenberg University Mainz, Germany +49-6131-3923091 ------------------------------- ________________________________________ Von: chimera-users-bounces@cgl.ucsf.edu [chimera-users-bounces@cgl.ucsf.edu] im Auftrag von chimera-users-request@cgl.ucsf.edu [chimera-users-request@cgl.ucsf.edu] Gesendet: Mittwoch, 17. Dezember 2008 21:00 An: chimera-users@cgl.ucsf.edu Betreff: Chimera-users Digest, Vol 68, Issue 22 Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: (Thermal ellipsoids) anisotropic temperature factor ellipsoids (Eric Pettersen) 2. Re: (Thermal ellipsoids) anisotropic temperature factor ellipsoids (Eric Pettersen) 3. possibilities to save parts of models (selection)? (Sebastian Kruggel) 4. Re: possibilities to save parts of models (selection)? (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Tue, 16 Dec 2008 14:59:34 -0800 From: Eric Pettersen <pett@cgl.ucsf.edu> Subject: Re: [Chimera-users] (Thermal ellipsoids) anisotropic temperature factor ellipsoids To: Tom Goddard <goddard@cgl.ucsf.edu> Cc: 'Chimera BB' <chimera-users@cgl.ucsf.edu> Message-ID: <9A34751B-6356-4AF4-A8C7-31757E5FFBF1@cgl.ucsf.edu> Content-Type: text/plain; charset="us-ascii" On Dec 12, 2008, at 10:40 AM, Tom Goddard wrote:
Hi David,
Ok I see now, it's a matter of choosing the size of each ellipsoid to have a 50% chance of finding the atom in that volume. This shouldn't be too hard but I'll let Eric tackle it if he has time.
Hi David, This is one of those things that I'll endeavor to get into Chimera's production version of thermal ellipsoids, but that I can't spare the time for until then. My guess is that the eigenvectors/values of the U matrix are at the 50% probability level, but verifying that would require some research. If you do look into and find that that's not the case, just change the setting of the 'scale' variable of the start of the script to change the ellipsoid sizes to whatever size encloses 50%. --Eric
Hi Christos, In previous releases, there were two tools that showed sequences: the sequence viewer (single sequences) and Multalign Viewer (sequence alignments). We plan to show additional information with sequences (e.g. UniProt markups) and as a step in that direction we decided to unify our presentation of sequence info by making MAV capable of showing single sequences. That way, the work to show sequence information in the user interface won't have to be duplicated each time we add something. So, rather than restore the old sequence viewer, what I would prefer to do is make the MAV interface better for showing single sequences. Would it help if single sequences were combined in a single dialog, like in the previous sequence viewer? I don't think that's too hard to do. As for color, I think you're right that for a single sequence it makes more sense to show that columns as black, since there is no conservation per se down the column. I can easily change that. You can too, in fact, by choosing Preferences->Analysis in the MAV window and changing "Residue letter coloring" to "black" (the preference will be carried over to future MAV dialogs). So what other changes would make the MAV version of the sequence version more usable? I guess this is actually a general question to everybody... --Eric On Dec 17, 2008, at 5:05 PM, Gatsogiannis, Christos wrote:
Hi all,
i ve just installed the latest daily build version and i´ve noticed that the sequence viewer has a new "look". However, i have difficulties to get used to it... Some examples: -when i want to view the sequence of a pdb file containing seven chains, i get seven different pop-up windows (...) showing the sequences corresponding to the seven different chain ID´s.... -Moreover, it isn´t so "easy" anymore to select aminoacids directly in the sequence viewer (e.g. too many colors) and therefore now i´m selecting residues using only the command line.. My colleagues also prefer the older version.. is there a simple way to install the latest chimera version but keep the old version of the sequence viewer? Thanks!
I have to agree that I much prefer the old sequence viewer. - Miriam ---- Original message ----
Date: Thu, 18 Dec 2008 10:20:07 -0800 From: Eric Pettersen <pett@cgl.ucsf.edu> Subject: Re: [Chimera-users] sequence viewer To: "Gatsogiannis, Christos" <gatsogia@uni-mainz.de> Cc: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu>
Hi Christos, In previous releases, there were two tools that showed sequences: the sequence viewer (single sequences) and Multalign Viewer (sequence alignments). We plan to show additional information with sequences (e.g. UniProt markups) and as a step in that direction we decided to unify our presentation of sequence info by making MAV capable of showing single sequences. That way, the work to show sequence information in the user interface won't have to be duplicated each time we add something. So, rather than restore the old sequence viewer, what I would prefer to do is make the MAV interface better for showing single sequences. Would it help if single sequences were combined in a single dialog, like in the previous sequence viewer? I don't think that's too hard to do. As for color, I think you're right that for a single sequence it makes more sense to show that columns as black, since there is no conservation per se down the column. I can easily change that. You can too, in fact, by choosing Preferences->Analysis in the MAV window and changing "Residue letter coloring" to "black" (the preference will be carried over to future MAV dialogs). So what other changes would make the MAV version of the sequence version more usable? I guess this is actually a general question to everybody...
--Eric
On Dec 17, 2008, at 5:05 PM, Gatsogiannis, Christos wrote:
Hi all,
i ve just installed the latest daily build version and i´ve noticed that the sequence viewer has a new "look". However, i have difficulties to get used to it... Some examples: -when i want to view the sequence of a pdb file containing seven chains, i get seven different pop-up windows (...) showing the sequences corresponding to the seven different chain ID´s.... -Moreover, it isn´t so "easy" anymore to select aminoacids directly in the sequence viewer (e.g. too many colors) and therefore now i´m selecting residues using only the command line.. My colleagues also prefer the older version.. is there a simple way to install the latest chimera version but keep the old version of the sequence viewer? Thanks!
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi all, I have made my intended improvements to the single-sequence viewer now and the new version is in the daily build (which you can get by going to www.cgl.ucsf.edu/chimera and following the "Daily Builds" link). I encourage people who use the sequence viewer a lot to fetch the new version and let me know what you like and what you don't. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Dec 18, 2008, at 10:20 AM, Eric Pettersen wrote:
Hi Christos, In previous releases, there were two tools that showed sequences: the sequence viewer (single sequences) and Multalign Viewer (sequence alignments). We plan to show additional information with sequences (e.g. UniProt markups) and as a step in that direction we decided to unify our presentation of sequence info by making MAV capable of showing single sequences. That way, the work to show sequence information in the user interface won't have to be duplicated each time we add something. So, rather than restore the old sequence viewer, what I would prefer to do is make the MAV interface better for showing single sequences. Would it help if single sequences were combined in a single dialog, like in the previous sequence viewer? I don't think that's too hard to do. As for color, I think you're right that for a single sequence it makes more sense to show that columns as black, since there is no conservation per se down the column. I can easily change that. You can too, in fact, by choosing Preferences->Analysis in the MAV window and changing "Residue letter coloring" to "black" (the preference will be carried over to future MAV dialogs). So what other changes would make the MAV version of the sequence version more usable? I guess this is actually a general question to everybody...
--Eric
On Dec 17, 2008, at 5:05 PM, Gatsogiannis, Christos wrote:
Hi all,
i ve just installed the latest daily build version and i´ve noticed that the sequence viewer has a new "look". However, i have difficulties to get used to it... Some examples: -when i want to view the sequence of a pdb file containing seven chains, i get seven different pop-up windows (...) showing the sequences corresponding to the seven different chain ID´s.... -Moreover, it isn´t so "easy" anymore to select aminoacids directly in the sequence viewer (e.g. too many colors) and therefore now i´m selecting residues using only the command line.. My colleagues also prefer the older version.. is there a simple way to install the latest chimera version but keep the old version of the sequence viewer? Thanks!
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Just to chime in on Eric's announcement -- he didn't mention that the sequence window preferences have also been expanded and reorganized, so that you can save separate "Appearance" preferences for single sequences and multiple alignments. I thought that was important because if you *do* want to adjust the spacing or wrapping or font, etc. of the single sequence view, this can be saved as a preference and it won't affect the appearance of your sequence alignments. We just adjusted the default spacing of single sequences, so you might want to wait one more day to get the daily build to see what we chose for defaults. Otherwise, the many improvements mentioned by Eric are in there already. 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 http://www.cgl.ucsf.edu/home/meng/index.html On Jul 13, 2009, at 4:43 PM, Eric Pettersen wrote:
Hi all, I have made my intended improvements to the single-sequence viewer now and the new version is in the daily build (which you can get by going to www.cgl.ucsf.edu/chimera and following the "Daily Builds" link). I encourage people who use the sequence viewer a lot to fetch the new version and let me know what you like and what you don't.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (4)
-
Elaine Meng -
Eric Pettersen -
Gatsogiannis, Christos -
mgochin＠touro.edu