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", "sh
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: ccp4bb@jiscmail.a
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
Dear kas,
I don't understand why you say that. Spaces may require a little more
typing (the quotes), althouh e.g. the bash automatically inserts them
when you expand a file / directory name with the TAB-key, but linux has
no personal issues with spaces.
Best,
Tim
On 01/24/2015 08:10 PM, Kenneth
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 guess
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
--- Begin Message ---
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 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 reflect
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 ano
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 ccp4-6.
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