robbie_joos...@hotmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, March 6, 2012 4:26 AM
Subject: Re: [ccp4bb] REFMAC Riding Hydrogens
Hi Everyone,
Pavel’s statement is likely a bit of an exaggeration, but he has a
valid (yet hard to prove point). The default in CCP4i
From: Robbie Joosten robbie_joos...@hotmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, March 6, 2012 4:26 AM
Subject: Re: [ccp4bb] REFMAC Riding Hydrogens
Hi Everyone,
Pavel’s statement is likely a bit of an exaggeration, but he has a valid (yet
hard
GUI?
Thanks again,
--Paul
From: Robbie Joosten robbie_joos...@hotmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, March 6, 2012 4:26 AM
Subject: Re: [ccp4bb] REFMAC Riding Hydrogens
Hi Everyone,
Pavel’s statement is likely a bit
4:26 AM
Subject: Re: [ccp4bb] REFMAC Riding Hydrogens
Hi Everyone,
Pavel’s statement is likely a bit of an exaggeration, but he has a valid (yet
hard to prove point). The default in CCP4i was (and is?) to use hydrogens
only if present in the input file. This is IMO not a safe default
).
Cheers,
Robbie
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel
Afonine
Sent: Monday, March 05, 2012 21:53
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] REFMAC Riding Hydrogens
Dear Tim,
good catch, thanks; I could craft that phrase more carefully! Although
Pavel’s statement is likely a bit of an exaggeration, but he has a valid
(yet hard to prove point). The default in CCP4i was (and is?) to use
hydrogens only if present in the input file. This is IMO not a safe default.
I agree: what I find confusing here is that the current CCP4i default
is
Hello CCP4 community,
I'm posting at large regarding a previously raised issue for REFMAC for which I
cannot find the conclusion in the old threads.
Specifically, does REFMAC add riding hydrogens during default refinement?
Though I've not requested that any hydrogens be added, only used if in
Hi Paul -
Refmac does indeed add riding hydrogens by default; see here:
http://www.ccp4.ac.uk/dist/html/refmac5/keywords/restraints.html#makecif
The REMARK 3 is referring to what you think it is: riding hydrogens have
been added. (They are not, however, written to the output file unless
you
On the interface under Refinement Parameters there are three options
1) Use if present
2) Do not use
3) Generate all
if you are using script then default is generate all (add them riding
positions). You can switch to other options:
make hydr all# generate all - default option
make hydr yes
Hi,
On Mon, Mar 5, 2012 at 11:52 AM, Matthew Franklin mfrank...@nysbc.orgwrote:
Adding the riding hydrogens generally gives you some improvement in R
factors even with a good quality (i.e. stereochemically correct) model.
and here are the results of more or less systematic test that prove
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Dear Pavel,
you may want to add to the structures mentioned in [1] one or two
organic structures present in the Cambridge Database.
Until recently it was customary to ignore hydrogen atoms throughout the
process of crystallographic X-‐ray structure
Dear Tim,
good catch, thanks; I could craft that phrase more carefully! Although
often it may not be quite fair to take phrases out of context: this
newsletter article was written in the context of macromolecular refinement.
And yes, recently may be a broad term -:)
All the best,
Pavel
On Mon,
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