Hi Everyone,
I hope everyone gets this email.
Below are the two answers I got on how to solve my problem using ccp4.I
actually emailed another person who wanted to know how I did it. So I got
to transfer what I learned immediately. But his email was offline not
through the forum.
The answers
Begin forwarded message:
From: "Charles W. Carter, Jr"
Date: February 19, 2010 10:28:55 AM EST
To: "George M. Sheldrick"
Subject: Re: [ccp4bb] anomalous difference fourier maps
I'm also inclined to join this discussion. I agree with both Gérard
and George. I
Dear Ivan,
It is great to have confirmation that you got answers to your initial
question that enabled you to solve your problem. The idea of the BB is that,
in exchange for the gift of other people's contribution to solving your
problem, you are expected to share the solution with the other
I guess it is a BB hosted by CCP4, but I think it serves a much wider
community of structural biologists, and it is valuable for that
community that there are suggestions about how to solve problems using
SHELX, or BUSTER or PHENIX software.. Certainly I learn new tricks.
So speaking as a CCP4
ok I think I should say something here.For some reason I was unable to find
REPLY-ALL button and my reply did not go to everyone first so I had to write
another message.I got the answer to my original query and I used CCP4 (CAD)
and coot as suggested by Jan.
Having said that I did not know that you
I guess Phenix people are just trying to help. After all they are not selling us
Zinger sewing machines (zin...@sewing CO, my apology) nor they are trying
to push us Kirby (http://www.consumeraffairs.com/in_home/kirby.htm, no apology)
vacuum cleaners using naive chastity of CCP4BB site.
They are
On Fri, 2010-02-19 at 10:37 -0500, Edward A. Berry wrote:
> The problem is not that the phenix team was so quick
> to promote their software, but rather that now 14 hours after the
> original
> post, no one has answered the CCP4 question.
The original poster returned to indicate that he had recei
The guidelines for the CCP4BB are extremely broad and certainly include
discussion of other software packages. Since the original poster's question
had to do with a specific problem with CCP4, it would have been appropriate
for Pavel to prefix his reply with something like "I hope you receive an
a
I am inclined to agree with Gerard. Of course if there is a specific
question to CCP4bb about SHELX, I try to answer it. Since I am too
lazy to maintain my own bb, this is very convenient. However I have
stopped 'poaching', for example for the thread in question I resisted
the temptation to point
Hi Dirk,
When it happens that I reply to a ccp4bb message and that the answer, or
solution I may have (which I think is "better" or "more appropriate")
involves using non-ccp4 programs, I do it off-list. By replying
privately to the person who asked the question.
Fred.
Dirk Kostrewa wrote:
Dear Gerard,
I can only agree with you - I've also noticed a growing and sometimes
irritating cross-advertisement of non-CCP4 programs on the CCP4BB over
the last months (mainly Phenix). Unless, the specific task that was
asked for, can only be (reasonably) solved with non-CCP4 programs, such
Dear all,
This is a remark I have wanted to make for a long time but managed so
far to repress. However, this case is absolutely clear: Ivan was not asking
for general advice on how to carry out a general task, but how to perform a
specific task with the CCP4 software.
In response we ge
Hi Ivan,
two ways (at least) to do it in PHENIX:
- phenix.refine always computes anomalous difference Fourier map
(provided that your input data file contains Fobs(+) and Fobs(-)). The
command below will do it:
phenix.refine model.pdb data.mtz strategy=none
main.number_of_macro_cycles=0 out
Hello,
I wanted to make an anomalous difference fourier map of a structure with
zinc bound to it. However I have not been successful in making the map and I
would really appreciate your help if anyone could suggest me where I am
going wrong.
I solved this zinc bound structure, by molecular repla
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