Save mmCIF selected atoms only

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-07-16)
Description
Want to be able to save selected atoms only in mmCIF format

save file.cif model #1 selectedOnly true

This works for PDB format but selectedOnly is not available for mmCIF.

This problem was reported by Jing He.

Log:
UCSF ChimeraX version: 0.91 (2019-07-16)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 4v68 format mmCIF fromDatabase pdb

Summary of feedback from opening 4v68 fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "PHA" near line 170882  
  
4v68 title:  
T. thermophilus 70S ribosome in complex with mRNA, tRNAs and EF-
Tu.GDP.kirromycin ternary complex, fitted to a 6.4 A Cryo-EM map. [more
info...]  
  
Chain information for 4v68 #1  
---  
Chain | Description  
A0 | MRNA codon  
AA | 16S rRNA  
AB | 30S ribosomal protein S2  
AC | 30S ribosomal protein S3  
AD | 30S ribosomal protein S4  
AE | 30S ribosomal protein S5  
AF | 30S ribosomal protein S6  
AG | 30S ribosomal protein S7  
AH | 30S ribosomal protein S8  
AI | 30S ribosomal protein S9  
AJ | 30S ribosomal protein S10  
AK | 30S ribosomal protein S11  
AL | 30S ribosomal protein S12  
AM | 30S ribosomal protein S13  
AN | 30S ribosomal protein S14  
AO | 30S ribosomal protein S15  
AP | 30S ribosomal protein S16  
AQ | 30S ribosomal protein S17  
AR | 30S ribosomal protein S18  
AS | 30S ribosomal protein S19  
AT | 30S ribosomal protein S20  
AU | 30S ribosomal protein Thx  
AV | P-site TRNA  
AW | E-site TRNA  
AX | synthetic MRNA  
AY | At-site TRNA  
AZ | Elongation factor Tu-A  
B0 | 50S ribosomal protein L27  
B1 | 50S ribosomal protein L28  
B2 | 50S ribosomal protein L29  
B3 | 50S ribosomal protein L30  
B4 | 50S ribosomal protein L31  
B5 | 50S ribosomal protein L32  
B6 | 50S ribosomal protein L33  
B7 | 50S ribosomal protein L34  
B8 | 50S ribosomal protein L35  
B9 | 50S ribosomal protein L36  
BA | 23S rRNA  
BB | 5S rRNA  
BC | 50S ribosomal protein L1  
BD | 50S ribosomal protein L2  
BE | 50S ribosomal protein L3  
BF | 50S ribosomal protein L4  
BG | 50S ribosomal protein L5  
BH | 50S ribosomal protein L6  
BI | 50S ribosomal protein L9  
BL | 50S ribosomal protein L11  
BN | 50S ribosomal protein L13  
BO | 50S ribosomal protein L14  
BP | 50S ribosomal protein L15  
BQ | 50S ribosomal protein L16  
BR | 50S ribosomal protein L17  
BS | 50S ribosomal protein L18  
BT | 50S ribosomal protein L19  
BU | 50S ribosomal protein L20  
BV | 50S ribosomal protein L21  
BW | 50S ribosomal protein L22  
BX | 50S ribosomal protein L23  
BY | 50S ribosomal protein L24  
BZ | 50S ribosomal protein L25  
  
Non-standard residues in 4v68 #1  
---  
BME — β-mercaptoethanol  
MAU — N-methyl kirromycin (aurodox; 1-methylmocimycin; antibiotic X-5108;
goldinodox; goldinomycin)  
  
  




OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tom Goddard]

Jing He was trying to save individual chains of ribosome structure 4v68. She is using the split command to work around the limitation that mmCIF save does not offer the selectedOnly option. Saving PDB format has the selectedOnly option but cannot handle 2-letter chain ids.

[Greg Couch]

Added support for selectedOnly and displayedOnly.