Wrong default criteria

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-04)
Description
swapaa docs say the default criteria option is dchp.  But using

swapaa /A:53 GLU criteria dchp

gives an error about no volume specified while omitting the criteria option works.  So I'm confused what is the actual default criteria.  Leaving out the d criteria

swapaa /A:53 GLU criteria chp

also does not give the same behavior as omitting the criteria option -- this command is much faster and does not spew countless messages about hbond acceptors.

So what really is the default criteria?  I'm trying to figure out why it is using hbonds when I expect all rotamers to have clashes.  I can see their may be number of clash ties, but it even seems to use hbonds if I use "score sum" which I would not expect to produce ties, unless there are rotamers with 0 clashes.


Log:
UCSF ChimeraX version: 0.91 (2019-09-04)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6h6b format mmCIF fromDatabase pdb

6h6b title:  
Structure of alpha-synuclein fibrils [more info...]  
  
Chain information for 6h6b #1  
---  
Chain | Description  
A B C D E F G H I J | Alpha-synuclein  
  
  

> swapaa /A:53 GLU criteria dchp

Using Dunbrack library  
/A ALA 53: phi -136.3, psi 131.6 trans  
Density criteria requested but no volume model specified  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[goddard@…]

Why is

 swapaa /A:53 GLU criteria chp

so much faster than if I omit the criteria option?  The status messages suggest it does not consider hbonds with “criteria chp” for this structure while with no criteria option it does consider hbonds.

[Eric Pettersen]

It's because my sysadmin fingers typed dhcp in the code rather than dchp! Fixed now.

The command knows whether you explicitly specified criteria or not. If you explicitly specify 'd' and don't provide the 'density' keyword info, it complains. Elaine's documentation isn't accurate there. I'm think I'm going to make it so that if you have exactly one map open then you needn't specify the 'density' keyword (assuming 'd' is in the criteria). Anyway, this will get worked on.

[Eric Pettersen]

Upgraded the way the 'd' criteria is handled. If one map is open, uses that. If multiple maps are open, then the 'density' keyword needs to be used to pick one. If no maps are open, an error is raised if the criteria was provided explicitly, otherwise it is silently skipped.

Will alert Elaine to the behavior change.