Timeline



Oct 6, 2016:

3:14 PM 2016-10-06 created by Conrad Huang
3:10 PM DeveloperMeetings edited by Conrad Huang
(diff)

Oct 5, 2016:

4:33 PM Ticket #443 (mmaker error: KeyError: ('<', 'M')) closed by pett
fixed: The domain-restricted sequence that was constructed wasn't having its …
3:58 PM Ticket #443 (mmaker error: KeyError: ('<', 'M')) created by Tom Goddard
open 3iko del ~/C open ScNup84_7-488_506-726_new.pdb mmaker #1 to …
1:53 PM Ticket #442 (Deleting atoms of 3jro causes crash) closed by pett
fixed: Fixed. The translation of a min() func from Chimera 1 in its …
12:35 PM Ticket #442 (Deleting atoms of 3jro causes crash) created by Tom Goddard
open 3jro del /a:1100-2000 del :100-200 crashes in …

Oct 4, 2016:

11:25 AM Ticket #441 (cartoon helix tubes choke on 1zik) created by Elaine Meng
Although I can show tube helices for several other models without this …
10:49 AM Ticket #440 (Dual view windows to compare structures) created by mheller@…
Begin forwarded message: From: Markus Heller Subject: [Chimera-users] …

Sep 30, 2016:

2:16 PM Ticket #439 (Signing windows ChimeraX fails) created by Tom Goddard
Successful compile (128.672 sec). Resulting Setup program filename is: …

Sep 29, 2016:

3:20 PM 2016-09-29 edited by Conrad Huang
(diff)
3:20 PM 2016-09-29 edited by Conrad Huang
(diff)
3:16 PM DeveloperMeetings edited by Conrad Huang
(diff)
3:15 PM 2016-09-29 created by Conrad Huang

Sep 28, 2016:

2:31 PM Ticket #438 (PDBFixer doesn't add correct atoms) created by Tom Goddard
PDBFixer on 5jqf incorrectly adds a fourth hydrogen H to the first …
1:24 PM Ticket #437 (OpenMM hangs and uses all system memory, tug atom mouse mode) created by Tom Goddard
Using the tug mouse mode on Mac OS 10.11 and 10.12 frequently at the …

Sep 26, 2016:

11:41 AM Ticket #434 ("ts refresh" gives traceback mentioning ihm) closed by Greg Couch
fixed: This error actually comes from better error checking of the bundle API …

Sep 23, 2016:

4:46 PM Ticket #436 (Tool setup.py cannot register multiple extensions for file format) created by pett
FASTA and several other sequence formats have no "standard" file …

Sep 22, 2016:

4:47 PM Ticket #435 (strand command-line selector broken) closed by pett
fixed: Fixed. Conrad missed the 'strand' and 'coil' selectors when he …
4:40 PM Ticket #435 (strand command-line selector broken) created by Elaine Meng
trying to use atomspec "strand" gives error (e.g. "sel strand") …
4:32 PM 2016-09-22 edited by Elaine Meng
(diff)
4:30 PM DeveloperMeetings edited by Conrad Huang
(diff)
4:09 PM 2016-09-22 created by Conrad Huang

Sep 20, 2016:

2:52 PM Ticket #434 ("ts refresh" gives traceback mentioning ihm) created by Elaine Meng
UCSF ChimeraX version: 0.1 (2016-09-16) toolshed refresh Traceback …
2:35 PM Ticket #432 (capping residue ACE considered ligand, not surfaced) closed by pett
fixed: Capping groups now included in polymer chain.
10:23 AM Ticket #433 (consider PISA fetch for assemblies and/or interface statistics) created by Elaine Meng
Forming URLs to retrieve data from PDBePISA: …

Sep 19, 2016:

4:16 PM 2016-08-29 edited by Tom Ferrin
(diff)
3:32 PM Ticket #432 (capping residue ACE considered ligand, not surfaced) created by Elaine Meng
Example is both chains in 1hzx. Probably the same issue with NME …
2:54 PM 2016-09-19 created by Tom Ferrin
1:56 PM DeveloperMeetings edited by Tom Ferrin
(diff)

Sep 16, 2016:

12:48 PM Ticket #431 (Error opening PDB with blank chain id) closed by pett
fixed
12:32 PM Ticket #431 (Error opening PDB with blank chain id) created by Tom Goddard
open input_nowater.pdb Summary of problems opening input_nowater.pdb: …
11:54 AM Ticket #425 (saving session changes ACE residue from chain A to chain B) closed by pett
fixed: The multi-atom deletion code wasn't updating chains as residues got deleted

Sep 15, 2016:

5:33 PM Ticket #430 (buriedarea and sasa should exclude ions, solvent, ligands) created by Tom Goddard
Should the buriedarea and sasa (solvent accessible surface area) …
5:24 PM Ticket #429 (matchmaker doesn't recognize tRNA as Nucleic?) closed by pett
fixed: Fixed. The wrapping for the C++ function that converts 3-character …
5:23 PM Ticket #428 (buriedarea "select" should clear previous selection) closed by Tom Goddard
fixed: Ok, I made the buriedarea command "select" option replace the selection.
4:07 PM 2016-09-15 created by Conrad Huang
2:09 PM FAI edited by Conrad Huang
(diff)
2:07 PM DeveloperMeetings edited by Conrad Huang
(diff)
12:43 PM Ticket #429 (matchmaker doesn't recognize tRNA as Nucleic?) created by Elaine Meng
open 2tra open 4tra mm #1 to #2 matrix Nucleic ... gives error …
12:16 PM Ticket #428 (buriedarea "select" should clear previous selection) created by Elaine Meng
Using the "select" option of "buriedarea" with gradually increasing …

Sep 13, 2016:

12:26 AM Ticket #426 (Drag selection is selecting more than atoms in rectangle) closed by Tom Goddard
fixed: Fixed. Planar bounds of selection frustum were assuming perspective …

Sep 12, 2016:

2:03 PM Ticket #422 (Fails to start on Mac with spaces in install path) closed by Conrad Huang
wontfix: It's actually the comma that causes this error. Whitespace in the …
1:16 PM Ticket #427 (Add multitouch trackpad rotation and translation) created by olibclarke@…
Begin forwarded message: From: Oliver Clarke Subject: Re: show/hide …
1:14 PM Ticket #426 (Drag selection is selecting more than atoms in rectangle) created by olibclarke@…
This may be only on retina display. Begin forwarded message: From: …

Sep 10, 2016:

7:40 AM Ticket #425 (saving session changes ACE residue from chain A to chain B) created by Elaine Meng
I opened 1hzx, deleted chain B, focused on :ace. Mousing over it …

Sep 9, 2016:

1:45 PM Ticket #424 (mmCIF chain names) created by pett
Need the pdbx_poly_seq_scheme records extruded into the structure …
11:17 AM Ticket #423 (Shell error messages at startup) created by Tom Goddard
Starting Sept 9, 2016 ChimeraX daily build from a terminal spews …
10:59 AM Ticket #422 (Fails to start on Mac with spaces in install path) created by Tom Goddard
If there is a space in the path to the ChimeraX install location or in …

Sep 8, 2016:

5:17 PM Ticket #421 (align not producing same result as Chimera 1) closed by Tom Goddard
worksforme: Eric reports that the problem is that the mmcif and pdb format …
5:01 PM Ticket #421 (align not producing same result as Chimera 1) created by pett
If you open 1b17 and 1ben (in that order) and then use this command: …
4:30 PM Ticket #396 (cannot show Side View) closed by Greg Couch
fixed: Sideview has been ported to Qt, so it is effectively bug-for-bug …
3:01 PM Ticket #184 (seg vault deleting atoms) closed by Greg Couch
worksforme: Lost test program :-( But haven't had any problems recently.
2:57 PM Ticket #109 (Wx defects on Linux) closed by Greg Couch
wontfix: We're not using wx anymore.
2:56 PM Ticket #366 (incomplete logging from multi-command cxcmd links) closed by Greg Couch
fixed: Not sure when this was fixed, but it works now.
10:40 AM Ticket #420 (Human readable atom specifiers) created by tic20@…
Tristan suggests allowing human-readable atom specifiers. The user …

Sep 6, 2016:

2:24 PM Ticket #419 (Read MTZ files, compute and display real-space density) created by ajm201@…
Begin forwarded message: From: Airlie McCoy <> Subject: Re: …
11:53 AM Ticket #418 (problems with help command new-viewer option) created by Elaine Meng
Would be better to change the “help” option “new_viewer” to avoid …
11:38 AM Ticket #417 (Help viewer suggestions) created by Elaine Meng
In addition to bugs #370 and #374, here are some things that could …
11:30 AM Ticket #416 (Interactively extend xray maps to zone around atom.) created by ajm201@…
Begin forwarded message: From: Airlie McCoy Subject: [chimera-dev] …
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