Folks
Sorry about that last git action. I stumbled over a previous merge and
merged it again. I now know have to deal.
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-48
Dear SHIJUN,
I am not aware of any processing software which actually prevents you from
merging different data sets. It's quite a normal procedure.
Kind regards,
Tim
On Tuesday, November 08, 2016 08:45:33 PM 张士军 wrote:
> Hi ccp4 guys
>
> I have a crystal whose spacegroup is I4,and the cell di
it depends a bit on what the reason for the data getting “bad” is.
- if it’s radiation damage, you may need to collect with less intense x-rays or
take shorter images. Merging isomorphous datasets may also help, but this is
not always straightforward, for example because different crystals may ha
Hi ccp4 guys
I have a crystal whose spacegroup is I4,and the cell dimension are
a=b=83，while ,the C axis is 315.SO the diffraction data is very bad when the
crystal started to rotate to some degree ,and it is difficult to process the
data .So I wondering there any strategy to resolve this kind
lundi 2 mars 2015 10:24
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] merge weak anomalous signal from multiple datasets
Hi Charles,
Actually I also tried the method of Q. Liu et al and got one structure solved
after merging 3 different datasets. The only thing different in my case is the
Se-SAD phasin
Hi Charles,
Actually I also tried the method of Q. Liu et al and got one structure
solved after merging 3 different datasets. The only thing different in my
case is the Se-SAD phasing instead of Br. But the signal was also weak due
to the disorder of incorporated Se in the protein crystals (I supp
Hi Charles,
I don't know what multiscale does. Probably the right thing. If the
anomalous signal is weaker after scaling of multiple datasets,
non-isomorphism might be at fault. Try Blend to scale your datasets.
Blend is part of ccp4 and gives good graphical diagnostic feedback.
Andreas
Dear CCP4 users,
Recently, I got some datasets with weak anomalous Br signal. I tried to
merge them according to Q. Liu et al Science 336, p1033 (2012). I am using
the script multiscale@SSRL. The merged dataset has WEAKER anomalous
signals.
Liu et al used SCALA for scaling and merging while mult
due number. It makes it easier to deal with them in the future.
>
>Cheers,
>Robbie
>
>> -Original Message-
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>> Ed Pozharski
>> Sent: Thursday, October 23, 2014 13:37
>> To: CCP4BB@JIS
One option is to change the chain IDs and residue numbers manually using a text
editor like nedit.
Sent from Jack's iPad
On Oct 23, 2014, at 6:03 AM, luzuok mailto:luzuo...@126.com>>
wrote:
Dear all,
Sorry to ask a simple question. There are many SO4 in my PDB file, one
belongs to a differ
.AC.UK] On Behalf Of
> Ed Pozharski
> Sent: Thursday, October 23, 2014 13:37
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Merge PDB chains
>
> Edit the ATOM records?
>
>
> Sent on a Sprint Samsung Galaxy S® III
>
>
> Original message ---
Dear Lu,
- you could just edit the pdb-file by hand in a suitable texteditor (which is
what I usually do, in MacOSX TextEdit).
- smarter people may find a functionality in COOT, PDBSET or other existing
program that can do it.
- even smarter people would probably write a script or little program
Edit the ATOM records?
Sent on a Sprint Samsung Galaxy S® III
Original message From: luzuok
Date:10/23/2014 6:51 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Merge PDB
chains
Dear all,
Sorry to ask a simple question. There are many SO4 in my PDB file
Dear all,
Sorry to ask a simple question. There are many SO4 in my PDB file, one
belongs to a different chain. I want to merge them into one chain, can anyone
tell me how to do this?
Best regards!
Lu Zuokun
--
卢作焜
南开大学新生物站A202
Hello Deng,
Process them as usual with e.g. Mosflm, then sort them together (you
may need to rebatch one of the runs) and do one Scala run - this will
put all of the measurement on a common scale and write out data
suitable for refinement. For pointgroups with ambiguous origin choices
(e.g. P4) yo
Hi CCP4bb,
I have two dataset from one crystal with different distance.now i am wondering
how to merge the two dataset into one file,and use it to refinement.
thanks a lot!
deng
Calculate - Merge Molecules
Herman
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
jab
Sent: Thursday, August 25, 2011 4:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] merge chains in coot
Hi
I've tried to find where to merge chains in
Hi
I've tried to find where to merge chains in coot, eg merge built co-factor
to protein chain, or
merge all my ions (Na, Cl, Mg etc) together.
Any pointers?
Thanks
Jim Brannigan
Dear All,
I have two questions:
1) I have collected multiple, native datasets (5) from the same
crystal (different parts of the crystals exposed with different
transmission and oscillation angles). Each dataset on its own is close
to complete (96-98 %). Naturally, differences in exposure,
Hi,
you first need to be sure that both datasets are indexed the same way
(this depends on your spacegroup). During the processing step, you have
to give each dataset different batch numbers (directly from imosflm) or
you can rebatch them after processing (Data
Reduction/Utilities/Sort-Modify
You can combine them together using the ccp4i task "Find or Match Laue group"
which runs Pointless. This will also try to choose the Laue group and possibly
the space group. If the space group is P21 2 21 (not chosen by mosflm which can
only choose the Laue group), you can choose in Pointless to
I have collected two sets of data, high-res and low-res, with the same
crystal and integrated them separately with imosflm. Now I want to merge
and scale the two MTZ files with Scala in ccp4i GUI. But I do not know how
to input 2 MTZ files through the Scala input GUI window (under Data
Reductio
Hi,
Replies to your specific queries are interspersed with your text below.
> Message du 19/12/09 05:19
> De : "Jinzhong Lin"
> A : CCP4BB@JISCMAIL.AC.UK
> Copie à :
> Objet : [ccp4bb] merge data from multiple isomorphous crystals.
>
>
> Dear all,
>
Dear all,
I have a crystal that can diffract to 3.0A for the first few frames at
synchrotron, after procession only up to 3.6A data are useful. The
structure has been solved by MAD. In order to get a 3.0A dataset, I am
going to collect the first few images from dozens of isomorphous
crystals and me
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