Exported mmCIF not compatible with other software

[sitins07@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 0.91 (2019-07-13)
Description
mmCIF files created in ChimreaX couldn't be used in other software tools like Coot of phenix_real_space_refine. In case of Coot it doesn't open them and Phenix can recognize only first submodel e.g. #1.1 from model 1 but doesn't see #1.2 etc. Also there are no way to convert submodel into a chain of existing model to fix this. These function exist in normal chimera but it can't save mmCIF files. Is there any way to combine and save coordinates from several pdb and mmCIF files into one mmCIF file? I realy like and appreciate your work on ChimeraX, Thank you for your work and looking forward fot your answer.    

OpenGL version: 3.3.0 NVIDIA 397.93
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Greg Couch]

Can you give me more information about why Coot can't open ChimeraX's mmCIF output? If it is not an NMR ensemble, does it work? Is there any diagnostic output from Coot?

Someone else will need to address the molecular editing issues.

[sitins07@…]

Dear gregc,

Using ChimeraX 0.91 I opened several Cryo-EM structures (different ribosome
complexes) I removed different parts of each of them using select and
delete commands. Then I saved 3 modified models into one cif file using
command: save file.cif format mmcif models #1,2,3.
Trying to reproduce bug I just opened pdb entry 5afi.cif shifted it a bit
and saved as cif. It also caused opening issue in coot. I use Coot 0.8.9
and 0.8.9.2 it just gives a message "Failed to read coordinates ..."

Respectfully yours,
Valentyn Petrychenko


ср, 17 лип. 2019 о 19:56 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> пише:

[tic20@…]

Playing around with a test example (5y5s), I get the following in Coot's 
stdout when I try to load the .cif as saved by ChimeraX:

INFO:: Reading coordinate file: 
/home/tic20/structure_dump/test_cif/5y5s.cif
WARNING:: Error reading small-molecule cif 
"/home/tic20/structure_dump/test_cif/5y5s.cif"
There was an error reading /home/tic20/structure_dump/test_cif/5y5s.cif.
ERROR 26 READ: Unrecognized item(s) in CIF file.
          LINE #61176
      _pdbx_struct_assembly_gen.asym_id_list A, B, C, D, E, F, G, H, I, 
J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, AA, BA, CA, DA, EA, 
FA, GA, HA, IA, JA, KA, LA, MA, NA, OA, PA, QA, RA, SA, TA, UA, VA, WA, 
XA, YA, ZA, AB, BB, CB, DB, EB, FB, GB, HB, IB, JB, KB, LB, MB, NB, OB, 
PB, QB, RB, SB, TB, UB, VB, WB, XB, YB, ZB, AC, BC, CC, DC, EC, FC, GC, 
HC, IC, JC, KC, LC, MC, NC, OC, PC, QC, RC, SC, TC, UC, VC, WC, XC, YC, 
ZC, AD, BD, CD, DD, ED, FD, GD, HD, ID, JD, KD, LD, MD, ND, OD, PD, QD, 
RD

No Spacegroup found for this PDB file
There was a coordinates read error

If I edit the offending line to treat it as a multi-line string (even 
though it isn't) as seen in the "official" 5y5s.cif from the PDB:

_pdbx_struct_assembly_gen.asym_id_list
;A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB,AC,BC,CC,DC,EC,FC,GC,HC,IC,JC,KC,LC,MC,NC,OC,PC,QC,RC,SC,TC,UC,VC,WC,XC,YC,ZC,AD,BD,CD,DD,ED,FD,GD,HD,ID,JD,KD,LD,MD,ND,OD,PD,QD,RD,SD,TD,UD,VD,WD,XD,YD,ZD,AE,BE,CE,DE,EE,FE,GE,HE,IE,JE,KE,LE,ME,NE,OE,PE,QE,RE,SE,TE,UE,VE,WE,XE,YE,ZE,AF,BF,CF,DF,EF,FF,GF,HF,IF,JF,KF,LF,MF,NF,OF,PF,QF,RF,SF,TF,UF,VF,WF,XF,YF,ZF,AG,BG,CG,DG,EG,FG,GG,HG,IG,JG,KG,LG,MG,NG,OG,PG,QG,RG,SG,TG,UG,VG,WG,XG,YG,ZG,AH,BH,CH,DH,EH,FH,GH,HH
;

... then Coot is happy (and no longer seems to think it's a 
small-molecule CIF file). Honestly seems like a bug in Coot rather than 
in ChimeraX, but perhaps it would be better to do it the way the wwPDB 
does it in any case?



On 2019-07-18 09:50, ChimeraX wrote:

[sitins07@…]

1. Windows Coot is buggy, so might be. But would it be possible to operate
PDB/CIF files like in Chimera to merge models, rename/renumber chains? And
possible recover of PDB/CIF files that have problems?
2. Also my test file 5afi gave another error and couldn't open it at all.
3. Another thing if I save several models in one CIF Phenix doesn't see any
model except the first one.

Respectfully yours,
Valentyn Petrychenko


чт, 18 лип. 2019 о 11:21 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> пише:

[pett]

I have added an RFE ticket for porting Chimera's copy/combine functionality. (#2236)

[Greg Couch]

I revised the pdbx_struct_assembly_gen.asym_id_list value to be on a separate line. So Coot should be happier now.