Dear Patrick,
those entries are entered by the user and not very reliable. E.g. I
would not say 'CCP4 refined' but 'refmac5 refined' or 'restrain
refined', as much as 'SHELXL refined' and 'phenix.refine refined'. This
makes two different ways between the two of us - take all depositors and
I
Hi Tim,
Thank you for the clarification.
Is there a way to extract from the PDB all the CCP4/Phenix structures then?
From your answer I take it there is no way?
Patrick
-Original Message-
From: t...@shelx.uni-ac.gwdg.de
Sent: Sat, 24 Jan 2015 20:35:54 +0100
To:
Spaces are not friendly to linux.
kas
--
Kenneth A. Satyshur, M.S.,Ph.D.
Senior Scientist
University of Wisconsin
Madison, Wisconsin 53706
608-215-5207
---BeginMessage---
Dear Kas,
that's probably a bug in CCP4, in that file names ought to be enclosed
in single quotes when passed to a program.
Hi all,
I am wondering what the conditions are when Rfree is less than Rwork. I
have seen this when trying certain models to solve my structure, but I am
not sure why this occurs, or if this is valid or not.
Thanks,
Jarrod Mousa
U. of Florida
Hi,
not directly related but I wanted to know how to extract from the PDB all the
PHENIX/CCP4 refined structures currently deposited.
Do I use the text search in quarry to get the result or do I use the software?
I tried it for both but seems to give different results (no's).
I tried for
Hi Jarrod,
If this occurs in a not yet refined model, this is not a problem. It is an
indication that your test set is free yet. If Rfree stays lower than R at the
later stages of model building and refinement this typically means that your
test set is not independent, that is, test set
Dear kas,
I just noticed your email was not in response to my previous mail, but a
forward, so I may have misinterpreted these few words in their intention
when I replied.
Cheers,
Tim
On 01/24/2015 08:10 PM, Kenneth A. Satyshur wrote:
Spaces are not friendly to linux.
kas
--
Kenneth A.
Hi Patrick,
while I agree with Tim this task may be a bit less straightforward than it
appears, I think you can get ballpark numbers by looping over all PDB
entries and searching for a keyword in PROGRAM card. All you need is to
make an upfront definition of what you count as phenix, ccp4, shelx,
Hi there,
Following your kind suggestions, logging out and logging in again solved
the problem. Thanks !
Fred.
On 23/01/15 18:07, vellieux wrote:
Hello,
I just installed ccp4-6.5
I get an error at run time (relating to $PATH I suppose, see below)
that still contains occurrences of
