have Blast Protein report resolution

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-5.4.13-201.fc31.x86_64-x86_64-with-fedora-31-Thirty_One
ChimeraX Version: 0.92 (2020-02-15)
Description
Suggestion: I think it would be really useful if the Blast Protein tool reported the resolution of each hit in its output table. That's of almost equal importance to the alignment score and E-value in determining how useful a given structure is likely to be for comparative modelling. In many cases it's preferable to use a model with a slighly lower score if the resolution is substantially better.

Log:
UCSF ChimeraX version: 0.92 (2020-02-15)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open closed_PHX_RFM_M_0_0001.pdb

Summary of feedback from opening closed_PHX_RFM_M_0_0001.pdb  
---  
warnings | Ignored bad PDB record found on line 108  
LINKR G a 130 A a 141 gap  
  
Ignored bad PDB record found on line 109  
LINKR G a 225 U a 287 gap  
  
Ignored bad PDB record found on line 110  
LINKR C a 323 G a 329 gap  
  
Ignored bad PDB record found on line 111  
LINKR G a 697 C a 729 gap  
  
Ignored bad PDB record found on line 112  
LINKR C a 736 U a 743 gap  
  
11 messages similar to the above omitted  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
Duplicate atom serial number found: 6  
9819 messages similar to the above omitted  
  
closed_PHX_RFM_M_0_0001.pdb title:  
\--- [more info...]  
  
Chain information for closed_PHX_RFM_M_0_0001.pdb #1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
  
Non-standard residues in closed_PHX_RFM_M_0_0001.pdb #1  
---  
MG — (MG)  
ZN — (ZN)  
  

> open post_autoB_closed_masked.mrc

Opened post_autoB_closed_masked.mrc, grid size 400,400,400, pixel 1.06, shown
at level 0.0176, step 2, values float32  

> open unsharpened_closed.mrc

Opened unsharpened_closed.mrc, grid size 400,400,400, pixel 1.06, shown at
level 0.0132, step 2, values float32  

> clipper associate #2 toModel #1

closed_PHX_RFM_M_0_0001.pdb title:  
\--- [more info...]  
  
Chain information for closed_PHX_RFM_M_0_0001.pdb  
---  
Chain | Description  
1.1/1 | No description available  
1.1/2 | No description available  
1.1/3 | No description available  
1.1/4 | No description available  
1.1/5 | No description available  
1.1/6 | No description available  
1.1/7 | No description available  
1.1/8 | No description available  
1.1/9 | No description available  
1.1/A | No description available  
1.1/B | No description available  
1.1/C | No description available  
1.1/D | No description available  
1.1/E | No description available  
1.1/F | No description available  
1.1/G | No description available  
1.1/H | No description available  
1.1/I | No description available  
1.1/J | No description available  
1.1/K | No description available  
1.1/L | No description available  
1.1/M | No description available  
1.1/N | No description available  
1.1/O | No description available  
1.1/P | No description available  
1.1/Q | No description available  
1.1/R | No description available  
1.1/S | No description available  
1.1/T | No description available  
1.1/U | No description available  
1.1/V | No description available  
1.1/W | No description available  
1.1/X | No description available  
1.1/Y | No description available  
1.1/Z | No description available  
1.1/a | No description available  
1.1/a | No description available  
1.1/b | No description available  
1.1/c | No description available  
1.1/d | No description available  
1.1/e | No description available  
1.1/f | No description available  
1.1/g | No description available  
1.1/h | No description available  
  
Non-standard residues in closed_PHX_RFM_M_0_0001.pdb #1.1  
---  
MG — (MG)  
ZN — (ZN)  
  

> clipper associate #3 toModel #1

> select /1

4372 atoms, 4454 bonds, 1 model selected  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> hide #1.3 models

> hide #!1.2 models

> style sphere

Changed 109780 atom styles  

> color #1.1 grey

> color bychain

> color byhetero

> style stick

Changed 109780 atom styles  

> show #1.3 models

> show #!1.2 models

> addh

Summary of feedback from adding hydrogens to closed_PHX_RFM_M_0_0001.pdb #1.1  
---  
warnings | Not adding hydrogens to /B THR 114 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /1 VAL 281 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /2 ARG 622 CB because it is missing heavy-atom bond
partners  
notes | No usable SEQRES records for closed_PHX_RFM_M_0_0001.pdb (#1.1) chain
1; guessing termini instead  
No usable SEQRES records for closed_PHX_RFM_M_0_0001.pdb (#1.1) chain 2;
guessing termini instead  
No usable SEQRES records for closed_PHX_RFM_M_0_0001.pdb (#1.1) chain 3;
guessing termini instead  
No usable SEQRES records for closed_PHX_RFM_M_0_0001.pdb (#1.1) chain 4;
guessing termini instead  
No usable SEQRES records for closed_PHX_RFM_M_0_0001.pdb (#1.1) chain 5;
guessing termini instead  
39 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /1 ALA 3, /2 GLU 323, /3 TYR
4, /4 PHE 106, /5 GLY 29, /6 ALA 2, /7 GLN 181, /8 PHE 6, /9 SER 172, /A U
357, /B SER 2, /C VAL 21, /D LYS 58, /E MET 1, /F ALA 2, /G THR 14, /H MET 1,
/I ALA 6, /J GLY 2, /K PRO 2, /L MET 1, /M ASP 3, /N VAL 14, /O GLY 2, /P SER
16, /Q PHE 12, /R GLY 5, /S GLY 2, /T SER 2, /U GLY 3, /V HIS 18, /W MET 1, /X
VAL 2, /Y GLY 2, /Z THR 4, /a ARG 41, /a U 1, /b THR 2, /c PRO 2, /d GLN 7, /e
GLY 2, /f HIS 76, /g LYS 83, /h GLU 3  
Chain-initial residues that are not actual N termini: /2 THR 496, /9 GLY 361,
/9 THR 398, /I LYS 113, /M LYS 32, /a A 141, /a U 287, /a G 329, /a C 729, /a
U 743, /a U 749, /a G 788, /a G 841, /a C 1423, /a A 1438, /a G 1771  
Chain-final residues that are actual C termini: /4 LEU 377, /5 ASN 352, /A C
695, /F GLY 263, /G ARG 204, /P LEU 151, /R ARG 146, /X PHE 130, /a A 1869, /c
HIS 84, /e ASP 56, /f SER 132  
Chain-final residues that are not actual C termini: /1 VAL 536, /2 GLU 871, /2
ALA 493, /3 ILE 422, /6 SER 216, /7 GLU 552, /8 SER 370, /9 THR 536, /9 ILE
355, /9 GLY 393, /B ALA 218, /C GLY 233, /D THR 278, /E GLY 228, /H LEU 237,
/I LEU 194, /I SER 108, /J GLY 207, /K GLY 186, /L ARG 96, /M LYS 153, /M VAL
23, /N CYS 130, /O VAL 150, /Q VAL 126, /S GLY 133, /T THR 145, /U LYS 143, /V
ALA 117, /W PHE 83, /Y ARG 142, /Z ALA 127, /a GLY 115, /a G 130, /a G 225, /a
C 323, /a G 697, /a C 736, /a C 745, /a C 756, /a C 834, /a C 1417, /a U 1432,
/a U 1761, /b ARG 102, /d LEU 68, /g PHE 150, /h ILE 314  
9529 hydrogen bonds  
Adding 'H' to /2 THR 496  
Adding 'H' to /9 GLY 361  
Adding 'H' to /9 THR 398  
Adding 'H' to /I LYS 113  
Adding 'H' to /M LYS 32  
/1 VAL 536 is not terminus, removing H atom from 'C'  
/2 GLU 871 is not terminus, removing H atom from 'C'  
/2 ALA 493 is not terminus, removing H atom from 'C'  
/3 ILE 422 is not terminus, removing H atom from 'C'  
/6 SER 216 is not terminus, removing H atom from 'C'  
32 messages similar to the above omitted  
90141 hydrogens added  
  

> hide HC

> set bgColor white

> delete nucleic&@H

> isolde restrain ligands #1

> select #1

199909 atoms, 206222 bonds, 32 pseudobonds, 18 models selected  

> select clear

> select clear

> toolshed show "Blast Protein"

> blastprotein /7 database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service1584520645637-1264004637  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1584520645637-1264004637  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  

> open pdb:5A5T

Summary of feedback from opening 5A5T fetched from pdb  
---  
note | Fetching compressed mmCIF 5a5t from
http://files.rcsb.org/download/5a5t.cif  
  
5a5t title:  
Structure of mammalian eIF3 in the context of the 43S preinitiation complex
[more info...]  
  
Chain information for 5a5t #2  
---  
Chain | Description  
A | eukaryotic translation initiation factor 3 subunit A  
C | eukaryotic translation initiation factor 3 subunit C  
E | eukaryotic translation initiation factor 3 subunit E  
F | eukaryotic translation initiation factor 3 subunit F  
H | eukaryotic translation initiation factor 3 subunit H  
K | eukaryotic translation initiation factor 3 subunit K  
L | uncharacterized protein  
M | eukaryotic translation initiation factor 3 subunit M  
  
  

> matchmaker #2/L to #1.1/7

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker closed_PHX_RFM_M_0_0001.pdb, chain 7 (#1.1) with 5a5t, chain L
(#2), sequence alignment score = 1888.6  
RMSD between 323 pruned atom pairs is 1.086 angstroms; (across all 372 pairs:
1.403)  
  

> close #2




OpenGL version: 3.3.0 NVIDIA 440.44
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Elaine Meng]

This is already available, albeit maybe not in the most obvious way. When the results are returned, in that panel you have to go to the columns menu (icon looks like some black horizontal bars) and check/uncheck to control which columns are shown, including Resolution.

[Elaine Meng]

it's documented, at least:
​http://rbvi.ucsf.edu/chimerax/docs/user/tools/blastprotein.html#results