Chainsaw problem

From: SUBSCRIBE CCP4BB Huo tong
Date: 22 December 2011 08:44

Hello everyone:
I am dealing with a MR issue. To modify the model  to my own target protein, I use the program Chainsaw provided in the CCP4 suite instead of manually mutating the residues one by one. After that, I want to run the Refmac5, but the program failed with the info:

Input coordinate does not have CRYST card
Check the input coordinate file
===> Error: Input coordinate file is not complete

I wonder if  the output file of the Chainsaw can be the input of other programs like Refmac5, or if the Chainsaw changes the file properties which leads to be an incomplete file.

I am looking forward to any advices!

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From: Eleanor Dodson


Usually the output of chainsaw is used as the input for MR - and the MR search will add the crystal information. If you are sure your model is correctly placed in your cell you can use pdbset with keyword cell a b c etc and that will outtput CRYST1 and SCALE cards.

Eleanor

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From: herohonan

Thanks a lot!

I checked the original PDB file and modified PDB file, and find that the modified file by Chainsaw has a pseudo header information generated by Chainsaw program but not the crystal information. So I copy the header information to the new file, and it works.

I also tried your advice, and it works too. I consider that our methods are same, but maybe yours can be more general....  

--

Tong Huo

Ph.D candidate

College of Life Sciences

Nankai University

Tianjin, China

At 2011-12-22 18:13:06,"Eleanor Dodson" wrote: >Usually the output of chainsaw is used as the input for MR - and the MR  >search will add the crystal information. If you are sure your model is  >correctly placed in your cell you can use pdbset with keyword cell a b c  >etc and that will outtput CRYST1 and SCALE cards. > >Eleanor > > >On 12/22/2011 08:44 AM, SUBSCRIBE CCP4BB Huo tong wrote: >> Hello everyone: >> I am dealing with a MR issue. To modify the model  to my own target protein, I use the program Chainsaw provided in the CCP4 suite instead of manually mutating the residues one by one. After that, I want to run the Refmac5, but the program failed with the info: >> >> Input coordinate does not have CRYST card >> Check the input coordinate file >> ===>  Error: Input coordinate file is not complete >> >> I wonder if  the output file of the Chainsaw can be the input of other programs like Refmac5, or if the Chainsaw changes the file properties which leads to be an incomplete file. >> >> I am looking forward to any advices!