CORAL: Fortran runtime error: Missing format for FORMATTED data transfer

[MT]

I try to use CORAL to improve an AlphaFold model to obtain a better fit with SAXS experimental data.

I am not a power user, so it is largely possible I am doing obvious mistakes.

I tried to search for same kind of topics looking for "fortran" or "line 930" but I didn't find any related...

So my problem is that one:
With some initial settings, the software works and sometimes it returns me fortran error, which happens immediately after the indication of pairs of domains to group.
I am playing with an important number of pdb files for different domains, and I saw the limitation to the maximum of 20 files.

Then I tried a configuration with exactly 20 domains, and the software returns me that error:

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 Pair of domains to group .. <            0,           0 >: 0,0
 Domains .................................... : 20 and      21
At line 930 of file /Users/atsas/svn/atsas-3.1.3-1/atsas/coral/coral.for
Fortran runtime error: Missing format for FORMATTED data transfer

Error termination. Backtrace:
#0  0x117b5435e
#1  0x117b55005
#2  0x117b55beb
#3  0x117d7a5b7
#4  0x105ee9cad
#5  0x105eef8be

Thus I reduced the number of domains to 16, the soft is actually running.

I wanted to restart it in parallel in a different folder with exactly the same setting and initial files as above (folder was duplicated and .log removed) to see the effect of a different symmetry setting, but the soft crash before I indicate the symmetry with the same error as the assay with 20 domains:

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 Pair of domains to group .. <            0,           0 >: 0,0
 Domains .................................... : 16 and      17
At line 930 of file /Users/atsas/svn/atsas-3.1.3-1/atsas/coral/coral.for
Fortran runtime error: Missing format for FORMATTED data transfer

Error termination. Backtrace:
#0  0x117b5435e
#1  0x117b55005
#2  0x117b55beb
#3  0x117d7a5b7
#4  0x105ee9cad
#5  0x105eef8be

What could be the reason of that error? Is there some masked files somewhere preventing the use of same initial files (even if I am running the two runs in different folders).

Than you for helping.

[franke]

Hi there.

Thanks for the report. First, you seem to use 3.1.3, which is quite old by now. Most recent is 3.2.1. Could you please update and try again?

That said, what likely happens is that it dies trying to tell you "'Internal error: was not able to generate a linker'". This happens when it can not find a suitable linker in the database to get started with. Either your domains are too close, or too far apart, or some things clash, or ... something else. You get the picture.

HTH

[MT]

I am using CORAL with SBGRID on a Mac (Os 10.15) and the 3.1.3 is the newer version it offers me... Other versions are for newer MacOs.

Regarding the second point, it is true I am dealing with a very overlapping structure as it is a tetramer based on a coiled-coil oligomerisation, so domains can be too close.

What puzzle me is that sometimes I am able to run the software, but it is true that it accept to run only when I fix or group some domains.

If I put only Calpha in my .pdb files, will it work? Will it remove the problem of potentially too close residues? Residues "density" will it be representative?

[franke]

Regarding the second point, it is true I am dealing with a very overlapping structure as it is a tetramer based on a coiled-coil oligomerisation, so domains can be too close.
What puzzle me is that sometimes I am able to run the software, but it is true that it accept to run only when I fix or group some domains.

Initial random placement may, randomly, happen to find a starting point from which to start?

If I put only Calpha in my .pdb files, will it work? Will it remove the problem of potentially too close residues? Residues "density" will it be representative?

Sorry, I'm not qualified to give you a definite answer on this, My intuition might say: it might work, but how much use would it be?

[MT]

I tried online version to be up to date...

When I try the config with 20 domains, I obtain that error:

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Array ( [0] => XXXa1.pdb [1] => XXXa2.pdb [2] => XXXa3.pdb [3] => XXXa4.pdb [4] => XXXa.pdb [5] => XXXb1.pdb [6] => XXXb2.pdb [7] => XXXb3.pdb [8] => XXXb4.pdb [9] => XXXb.pdb [10] => XXXc1.pdb [11] => XXXc2.pdb [12] => XXXc3.pdb [13] => XXXc4.pdb [14] => XXXc.pdb [15] => XXXd1.pdb [16] => XXXd2.pdb [17] => XXXd3.pdb [18] => XXXd4.pdb ) wrong number of uploaded pdb files: 19 2

But if you look at the screen shot I took before to submit I gave the 20 domains:


And when I try the config with 16 domains, I obtain this error:

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 === CORAL05 started at 07-Jun-2023 14:17:24
Computation mode ....................................... : Expert
Project identifier ..................................... : Coral8_1
Project description .................................... : Coral8
Initialized random seed as ..................... : 3834481987073438136
File name with objects info ............................ : coral.con
Coordinates of the 1-st subunit evaluated from ......... : XXX1_1.pdb
377 atoms read, center at 16.39 -172.23 -67.66
Coordinates of the 2-nd subunit evaluated from ......... : XXX1_2.pdb
513 atoms read, center at 9.17 -79.48 -36.27
Coordinates of the 3-rd subunit evaluated from ......... : XXX1_3.pdb
497 atoms read, center at -0.60 18.21 6.16
Coordinates of the 4-th subunit evaluated from ......... : XXX1.pdb
1099 atoms read, center at -29.18 59.66 43.15
Coordinates of the 5-th subunit evaluated from ......... : XXX2_1.pdb
377 atoms read, center at 22.10 -170.10 -72.73
Coordinates of the 6-th subunit evaluated from ......... : XXX2_2.pdb
513 atoms read, center at 7.54 -78.97 -37.44
Coordinates of the 7-th subunit evaluated from ......... : XXX2_3.pdb
497 atoms read, center at -2.27 18.09 6.15
Coordinates of the 8-th subunit evaluated from ......... : XXX2.pdb
1099 atoms read, center at 9.42 58.92 51.60
Coordinates of the 9-th subunit evaluated from ......... : XXX3_1.pdb
377 atoms read, center at 16.70 -168.17 -78.47
Coordinates of the 10-th subunit evaluated from ........ : XXX3_2.pdb
513 atoms read, center at 6.24 -79.90 -35.99
Coordinates of the 11-th subunit evaluated from ........ : XXX3_3.pdb
497 atoms read, center at -2.18 17.37 7.72
Coordinates of the 12-th subunit evaluated from ........ : XXX3.pdb
1099 atoms read, center at 17.90 75.79 15.13
Coordinates of the 13-th subunit evaluated from ........ : XXX4_1.pdb
377 atoms read, center at 10.87 -169.91 -73.52
Coordinates of the 14-th subunit evaluated from ........ : XXX4_2.pdb
513 atoms read, center at 7.84 -80.12 -34.67
Coordinates of the 15-th subunit evaluated from ........ : XXX4_3.pdb
497 atoms read, center at -0.52 17.55 7.79
Coordinates of the 16-th subunit evaluated from ........ : XXX4.pdb
1099 atoms read, center at -21.03 76.16 5.93
Domains .................................... : 16 and 17
Internal error: was not able to generate a linker

Am I doing a bad configuration, or is it due to the "too close" residues?

[MT]

Regarding the second point, it is true I am dealing with a very overlapping structure as it is a tetramer based on a coiled-coil oligomerisation, so domains can be too close.
What puzzle me is that sometimes I am able to run the software, but it is true that it accept to run only when I fix or group some domains.

Initial random placement may, randomly, happen to find a starting point from which to start?

My initial model is already in coiled-coil, so it is difficult to place it in a random way.

If I put only Calpha in my .pdb files, will it work? Will it remove the problem of potentially too close residues? Residues "density" will it be representative?

Sorry, I'm not qualified to give you a definite answer on this, My intuition might say: it might work, but how much use would it be?

It would be to have the Calpha trace to stick on it my full domains to lead to the final model.

So one more strange thing... with CORAL on line this time...
Yesterday I started two calculations (to again try to play on symmetry), with the same initial setting and files, the first one is still running and the second one crashed at the usual step:

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=== CORAL05 started at 07-Jun-2023 15:31:25
Computation mode ....................................... : Expert
Project identifier ..................................... : Coral8b
Project description .................................... : Coral8b
Initialized random seed as ..................... : 1650374610955620505
File name with objects info ............................ : coral.con
Coordinates of the 1-st subunit evaluated from ......... : xxx1_1.pdb
377 atoms read, center at 16.39 -172.23 -67.66
Coordinates of the 2-nd subunit evaluated from ......... : xxx1_2.pdb
513 atoms read, center at 9.17 -79.48 -36.27
Coordinates of the 3-rd subunit evaluated from ......... : xxx1_3.pdb
497 atoms read, center at -0.60 18.21 6.16
Coordinates of the 4-th subunit evaluated from ......... : xxx1.pdb
1099 atoms read, center at -29.18 59.66 43.15
Coordinates of the 5-th subunit evaluated from ......... : xxx2_1.pdb
377 atoms read, center at 22.10 -170.10 -72.73
Coordinates of the 6-th subunit evaluated from ......... : xxx2_2.pdb
513 atoms read, center at 7.54 -78.97 -37.44
Coordinates of the 7-th subunit evaluated from ......... : xxx2_3.pdb
497 atoms read, center at -2.27 18.09 6.15
Coordinates of the 8-th subunit evaluated from ......... : xxx2.pdb
1099 atoms read, center at 9.42 58.92 51.60
Coordinates of the 9-th subunit evaluated from ......... : xxx3_1.pdb
377 atoms read, center at 16.70 -168.17 -78.47
Coordinates of the 10-th subunit evaluated from ........ : xxx3_2.pdb
513 atoms read, center at 6.24 -79.90 -35.99
Coordinates of the 11-th subunit evaluated from ........ : xxx3_3.pdb
497 atoms read, center at -2.18 17.37 7.72
Coordinates of the 12-th subunit evaluated from ........ : xxx3.pdb
1099 atoms read, center at 17.90 75.79 15.13
Coordinates of the 13-th subunit evaluated from ........ : xxx4_1.pdb
377 atoms read, center at 10.87 -169.91 -73.52
Coordinates of the 14-th subunit evaluated from ........ : xxx4_2.pdb
513 atoms read, center at 7.84 -80.12 -34.67
Coordinates of the 15-th subunit evaluated from ........ : xxx4_3.pdb
497 atoms read, center at -0.52 17.55 7.79
Coordinates of the 16-th subunit evaluated from ........ : xxx4.pdb
1099 atoms read, center at -21.03 76.16 5.93
Subunit 1 was grouped with 5 and 13.
Subunit 2 was grouped with 6 and 14.
Subunit 3 was grouped with 7 and 15.
Subunit 5 was grouped with 1 and 9.
Subunit 6 was grouped with 2 and 10.
Subunit 7 was grouped with 3 and 11.
Subunit 9 was grouped with 5 and 13.
Subunit 10 was grouped with 6 and 14.
Subunit 11 was grouped with 7 and 15.
Subunit 13 was grouped with 9 and 1.
Subunit 14 was grouped with 10 and 2.
Subunit 15 was grouped with 11 and 3.
Number of backbone atoms generated ..................... : 1240
Averaged formfactors of DRs used
DR formfactor multiplier ............................... : 1.000
Point symmetry of the particle ......................... : P1
...

--> This one is still running...

Code: Select all

 === CORAL05 started at 07-Jun-2023 15:39:25
Computation mode ....................................... : Expert
Project identifier ..................................... : Coral8b_1
Project description .................................... : Coral8b
Initialized random seed as ..................... : 4051717911715586633
File name with objects info ............................ : coral.con
Coordinates of the 1-st subunit evaluated from ......... : xxx1_1.pdb
377 atoms read, center at 16.39 -172.23 -67.66
Coordinates of the 2-nd subunit evaluated from ......... : xxx1_2.pdb
513 atoms read, center at 9.17 -79.48 -36.27
Coordinates of the 3-rd subunit evaluated from ......... : xxx1_3.pdb
497 atoms read, center at -0.60 18.21 6.16
Coordinates of the 4-th subunit evaluated from ......... : xxx1.pdb
1099 atoms read, center at -29.18 59.66 43.15
Coordinates of the 5-th subunit evaluated from ......... : xxx2_1.pdb
377 atoms read, center at 22.10 -170.10 -72.73
Coordinates of the 6-th subunit evaluated from ......... : xxx2_2.pdb
513 atoms read, center at 7.54 -78.97 -37.44
Coordinates of the 7-th subunit evaluated from ......... : xxx2_3.pdb
497 atoms read, center at -2.27 18.09 6.15
Coordinates of the 8-th subunit evaluated from ......... : xxx2.pdb
1099 atoms read, center at 9.42 58.92 51.60
Coordinates of the 9-th subunit evaluated from ......... : xxx3_1.pdb
377 atoms read, center at 16.70 -168.17 -78.47
Coordinates of the 10-th subunit evaluated from ........ : xxx3_2.pdb
513 atoms read, center at 6.24 -79.90 -35.99
Coordinates of the 11-th subunit evaluated from ........ : xxx3_3.pdb
497 atoms read, center at -2.18 17.37 7.72
Coordinates of the 12-th subunit evaluated from ........ : xxx3.pdb
1099 atoms read, center at 17.90 75.79 15.13
Coordinates of the 13-th subunit evaluated from ........ : xxx4_1.pdb
377 atoms read, center at 10.87 -169.91 -73.52
Coordinates of the 14-th subunit evaluated from ........ : xxx4_2.pdb
513 atoms read, center at 7.84 -80.12 -34.67
Coordinates of the 15-th subunit evaluated from ........ : xxx4_3.pdb
497 atoms read, center at -0.52 17.55 7.79
Coordinates of the 16-th subunit evaluated from ........ : xxx4.pdb
1099 atoms read, center at -21.03 76.16 5.93
Subunit 1 was grouped with 5 and 13.
Subunit 2 was grouped with 6 and 14.
Subunit 3 was grouped with 7 and 15.
Subunit 5 was grouped with 1 and 9.
Subunit 6 was grouped with 2 and 10.
Subunit 7 was grouped with 3 and 11.
Subunit 9 was grouped with 5 and 13.
Subunit 10 was grouped with 6 and 14.
Subunit 11 was grouped with 7 and 15.
Subunit 13 was grouped with 9 and 1.
Subunit 14 was grouped with 10 and 2.
Subunit 15 was grouped with 11 and 3.
Domains .................................... : 16 and 17
Internal error: was not able to generate a linker

--> This one crashed.

How could it be possible?... Is it due to that difference:

Code: Select all

Initialized random seed as ..................... : 1650374610955620505

Vs

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Initialized random seed as ..................... : 4051717911715586633