SUPCOMB error: unable to read pdb files

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA
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Anne M
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Posts: 9
Joined: 2012.06.05 16:46

SUPCOMB error: unable to read pdb files

#1 Post by Anne M » 2017.04.20 15:02

Hello Atsas guys,
I am trying to superimpose a dammif-created model and a crystal structure.
I type:
>supcomb 4igg.pdb HA_100D2O_NoSymm_dammif.pdb
And I get the error message:
error: unable to read input file: 4igg.pdb

I tried to inverse file order and it is the first file (so the other one) which cannot be read.

What am I doing wrong there?
I attach the files in case...
Thanks a lot for your help.

Anne
Attachments
HA_100D2O_NoSymm_dammif.pdb
(28.55 KiB) Downloaded 75 times
4igg.pdb
(980.46 KiB) Downloaded 66 times

sasha
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Posts: 46
Joined: 2014.03.05 17:56

Re: SUPCOMB error: unable to read pdb files

#2 Post by sasha » 2017.04.21 16:00

Dear Anne,

I assume that the files are indeed available in the directory where you are executing SUPCOMB (in case of doubt, please check with "ls" or "dir" commands).

As an alternative, you can try the SUPALM program.
If the problem persists, please let us know what version of ATSAS you are using (supcomb -v) and on which platform (Linux, Windows or Mac?) so we can reproduce the problem and fix it.

I am attaching the rotated ab-initio model you provided, just in case.

Best,

sasha
Attachments
HA_100D2O_NoSymm_dammifr.pdb
(29.68 KiB) Downloaded 59 times

Anne M
Member
Posts: 9
Joined: 2012.06.05 16:46

Re: SUPCOMB error: unable to read pdb files

#3 Post by Anne M » 2017.04.27 11:57

Dear Sasha,
Thank you for your answer.
Yes, I have both pdb files and the .exe all in the same directory.
I tried supalm but this time I had the error: "insufficient number of argument". In the help, I saw that I need to enter parameters to calculate the scattering curve of the model, but I have it (it is my experimental curve) so I do not want it. I really just want to superimpose the bead-model and the crystal structure. So it can use all the default values... I do not see what else I should enter.
The version I use is Atsas 2.7.2 (r7883), on windows 7. Should I download a more recent one?
Thank you very much for the rotated model, but I have many others to do, so please, let me know if you see a solution...
Regards
Anne

Anne M
Member
Posts: 9
Joined: 2012.06.05 16:46

Re: SUPCOMB error: unable to read pdb files

#4 Post by Anne M » 2017.04.27 12:04

Dear Sasha,
I opened a new command shell and run the same command again and this time it worked!!!
It is mysterious, but it is solved!
Thank you very much.
Regards
Anne

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