I thank everyone for their comments about the problems I was having finding the water molecules as the map and the model were displaced. I solved the problem by using a different model in phaser-MR. After that everything coincided after I did the refmac.
Best
Denis Rousseau
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of [log in to unmask]
Sent: Tuesday, March 08, 2016 9:53 AM
To: [log in to unmask]
Subject: [ccp4bb] AW: [ccp4bb] Water molecules
Dear Mohamed,
At your stage of refinement, I would worry about the still very high Rfactors and not so much about the waters. You still have quite some way to go in terms of rebuilding, water searching etc. Once your Rfree is in the low twenties and you still have found very few water molecules, then you may start worrying about the waters.
Denis, what do you mean by that map and structure do not coincide? Are your atoms not in density when you view them with coot? Are the waters at some other place as your protein model? Lacking more information, I could give the following hints:
1) Did you load the mtz and pdb file, produced by refmac or some other refinement program in coot?
2) If the waters are at some other position as your protein molecule, try the "modeling - arrange waters around protein" option in coot.
3) If you cannot find back your protein molecule, try the "draw - go to atom" option to center on a protein residue.
If this all does not work, you will need to give us more details: which mtz and pdb files did you load, what exactly is the problem? What did you try but did not work etc?
Best,
Herman
-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Denis Rousseau
Gesendet: Dienstag, 8. März 2016 15:07
An: [log in to unmask]
Betreff: Re: [ccp4bb] Water molecules
I have the same problem. It appears that the map and the structure do not coincide. However, when I try to move the structure with the CCP4 module I cannot get them to coincide. I can see where the map is buy clicking on one of the blobs after I do the water search. So I also need advice.
Denis Rousseau
________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Mohamed Noor [[log in to unmask]]
Sent: Tuesday, March 08, 2016 1:20 AM
To: [log in to unmask]
Subject: [ccp4bb] Water molecules
Dear all
I am working on a 2-A structure with an octameric arrangement (363 residues per chain). There are only about 20 water molecules in total, which does not correspond to the rule-of-thumb of one water per residue (Carugo and Bordo 1999). Is this something to worry about?
The R/Rfree is currently at around 30/32 %. The protein chains are almost complete except for some difficult loops in some chains.
Thanks.
Mohamed
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