Re: [ccp4bb] aimless scale without merging data running Fail

[Phil Evans]

Dear Jiang 

If you gave Mosflm the “correct” space group, then you can skip the Pointless 
step, but I don’t think the pipelines in ccp4i and certainly ccp4i2 let you do 
that. However, it shouldn’t hurt.

I don’t think you can skip the merging step in Aimless, and anyway it is that 
step which generates the Table 1 statistics. You don’t have to use the output 
file, of course

I do recommend the newer ccp4i2 interface (not so new now), it produces much 
better reports, and the Table 1 can be exported as a CSV file for direct import 
into a paper

Good luck
Phil

Sent from my iPad

> On 16 Jun 2021, at 23:35, Jiang Xu  wrote:
> 
> 
> Hello Phil, 
> I just read my email and found I may not ask the question clearly. So my 
> question is, should I use the integrated data from Imosflm, or should I use 
> the output from Pointless as the input of Aimless to do scale without merging 
> the data?
> Thank you,
> Best,
> Jiang
> Lin Chen Research Group
> University of Southern California 
> 
>> On Wed, Jun 16, 2021 at 2:51 PM Jiang Xu  wrote:
>> Hello Phil,
>>Thank you for the comments. I noticed that the ccp4 package I used was 
>> 7.0. After upgrading to the latest version, the problem was solved.
>>I also have another question about Aimless. I want to use aimless to 
>> scale without merging the data for generating the "table1" of my data. I 
>> noticed that in your original publication, one way of doing the scale is to 
>> use the "Quick Scale" button in Imosflm, in which the output from Pointless 
>> will be the input of Aimless. However, I also noticed that some posts claim 
>> that the input of Aimless could also be from the integrated data file from 
>> Imosflm. I tried both ways and found no problem. So which way is the correct 
>> way for my purpose?
>>Thank you,
>> Best,
>> Jiang
>> Lin Chen Research Group
>> University of Southern California   
>> 
>>> On Wed, Jun 16, 2021 at 12:10 PM Phil Evans  wrote:
>>> I think it’s trying to write a file TILEIMAGE.img to a directory where you 
>>> aren’t allowed to write. I can’t remember what is done in ccp4i - I believe 
>>> it should work ok in ccp4i2, which produces better reports, and is 
>>> generally recommended as a replacement for ccp4i
>>> 
>>> As a workaround, you might be able to assign the file to somewhere you are 
>>> allowed to write. Before running ccp4i, type something like (for tosh / 
>>> cash, not sure about bash)
>>> 
>>> setenv TILEIMAGE /some/suitable/directory/TILEIMAGE.img
>>> 
>>> This file is an image of the correction factors for a tiled ccd detector
>>> 
>>> I can look at this next week, to see if I can work out what is happening 
>>> 
>>> Phil
>>> 
>>> Sent from my iPad
>>> 
> On 16 Jun 2021, at 18:52, Jiang Xu  wrote:
> 
 
 Hello guys,
I am having some problems running Aimless from the CCP4i packages. I 
 want to scale without merging the data. The input mtz file for aimless was 
 either the mtz file directly from Imosflm integration, or from Pointless 
 from a previous run on Imosflm. I ran both pointless and aimless 
 successfully on the Imosflm UI, after integration. However I just couldn't 
 do it from the CCP4i. From the log it seems there's always an error 
 message:  "#CCP4I TERMINATION STATUS 0 "OpenFile: cannot open file 
 TILEIMAGE.img"
I googled this line and found no hit. So does anyone know what's 
 happening and how to solve this problem?
 Thank you,
 Best,
 Jiang Xu
 Lin Chen Research Group
 University of Southern California
 
 
 To unsubscribe from the CCP4BB list, click the following link:
 https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
 
 



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Re: [ccp4bb] Looking for proteins for undergraduate biochemistry lab

[Brian Shoichet]

FWIW, many of the beta-lactamases fall into the same category: single step
purification on an affinity resin, a few litres can give you 100 mg
quantities, great spectrophotometric assay, several good substrates and
many inhibitors, both covalent (teaching kinetics) and non-covalent.

brian

On Wed, Jun 16, 2021 at 6:23 PM Peat, Tom (Manufacturing, Parkville)
 wrote:

> I agree with Roger that human CAII is easy to express in E. coli at high
> level and does not need a tag for purification- and that it is a good
> lesson for students to purify proteins without tags (they sometimes have
> better activity and crystallise better without having the tag).
> It is also easy to find things in a catalogue for binding studies (many
> small molecules with a sulfonamide moiety will bind) and assays are
> relatively straightforward to perform.
> Good recommendation!
> cheers, tom
>
> Tom Peat, PhD
> Proteins Group
> Biomedical Program, CSIRO
> 343 Royal Parade
> Parkville, VIC, 3052
> +613 9662 7304
> +614 57 539 419
> tom.p...@csiro.au
>
> --
> *From:* CCP4 bulletin board  on behalf of Roger
> Rowlett 
> *Sent:* Thursday, June 17, 2021 10:45 AM
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* Re: [ccp4bb] Looking for proteins for undergraduate
> biochemistry lab
>
> Human carbonic anhdydrase II is very expressible in *E. coli,* and
> purifiable in one step via affinity chromatography with
> para-aminobenzenesulfonamide affinity resin (which is relatively easy to
> make, and reusable for many years.) It can be assayed by stopped-flow
> spectrophotometry for CO2 hydration, by a timed colorimetric assay, or you
> can investigate it's esterase activity with p-nitrophenylacetate. This
> enzyme, as well as most other carbonic anhdydrases, is also easy to purify
> by a classical combination of anion exchange (Q-sepharose), hydrophobic
> interaction (butylsepharose), and gel exclusion polishing. The latter would
> be a good exercise for students in general protein purification
> optimization, which is an increasingly lost art. (Just had a conversation
> with one of the protein chemists ast BioGen who pretty much observed the
> same thing.) We routinely did classical purifications on tagless
> overexpressed proteins for crystallography work. The time saved in His-Tag
> purification is sometimes lost in cleaving the tag to make tagless protein
> for crystallography.
>
> A paper describing the purification procedure can be found in J. Chem. Ed.
> (https://doi.org/10.1021/ed075p1021) for the similar bovine carbonic
> anhydrase. An fun long-term undergraduate research training project might
> involve improving the esterase activity through student-initiated point
> mutations.
>
> I did this kind of parallel protein mutation project with my students in a
> biochemistry research training studio course I taught, often  with one of
> my research target proteins. Teaching lab students can do all sorts of
> crazy things you might never prioritize in your funded research. Some of
> these crazy things turn out to be fun and interesting. One of my students
> insisted on making a mutation in a protein that seemed to have low chances
> of leading to a successful publication based on prior work. Lo and behold,
> that mutation turned out to be gold, and he was published within the year.
> I still can't believe it not only worked, but crystallized easily from the
> first screen and optimization for structure determination. Go figure.
>
> ___
> Roger S. Rowlett
> Gordon & Dorothy Kline Professor, Emeritus
> Department of Chemistry
> Colgate University
> 13 Oak Drive
> Hamilton, NY 13346
>
> email: rrowl...@colgate.edu
>
> On Wed, Jun 16, 2021 at 7:09 PM Chun Luo  wrote:
>
> Many phosphatases, such as lambda phosphatase, have good soluble
> expression in E. coli. Their activity can be shown by simply colorimetric
> assay.
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *P. H
> *Sent:* Wednesday, June 16, 2021 3:19 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Looking for proteins for undergraduate biochemistry
> lab
>
>
>
> Hello All,
>
>
>
> We are looking for some candidate proteins for an undergraduate level
> advanced biochemistry lab. They should be expressed in bacteria, simple
> enough to purify and it will be nice to perform some simple
> characterization experiments(binding assays, enzymatic assays).
>
> Any suggestions?
>
>
>
> Thank you in advance.
>
> Prerna gupta
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Looking for proteins for undergraduate biochemistry lab

[Peat, Tom (Manufacturing, Parkville)]

I agree with Roger that human CAII is easy to express in E. coli at high level 
and does not need a tag for purification- and that it is a good lesson for 
students to purify proteins without tags (they sometimes have better activity 
and crystallise better without having the tag).
It is also easy to find things in a catalogue for binding studies (many small 
molecules with a sulfonamide moiety will bind) and assays are relatively 
straightforward to perform.
Good recommendation!
cheers, tom

Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Roger Rowlett 

Sent: Thursday, June 17, 2021 10:45 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Looking for proteins for undergraduate biochemistry lab

Human carbonic anhdydrase II is very expressible in E. coli, and purifiable in 
one step via affinity chromatography with para-aminobenzenesulfonamide affinity 
resin (which is relatively easy to make, and reusable for many years.) It can 
be assayed by stopped-flow spectrophotometry for CO2 hydration, by a timed 
colorimetric assay, or you can investigate it's esterase activity with 
p-nitrophenylacetate. This enzyme, as well as most other carbonic anhdydrases, 
is also easy to purify by a classical combination of anion exchange 
(Q-sepharose), hydrophobic interaction (butylsepharose), and gel exclusion 
polishing. The latter would be a good exercise for students in general protein 
purification optimization, which is an increasingly lost art. (Just had a 
conversation with one of the protein chemists ast BioGen who pretty much 
observed the same thing.) We routinely did classical purifications on tagless 
overexpressed proteins for crystallography work. The time saved in His-Tag 
purification is sometimes lost in cleaving the tag to make tagless protein for 
crystallography.

A paper describing the purification procedure can be found in J. Chem. Ed. 
(https://doi.org/10.1021/ed075p1021) for the similar bovine carbonic anhydrase. 
An fun long-term undergraduate research training project might involve 
improving the esterase activity through student-initiated point mutations.

I did this kind of parallel protein mutation project with my students in a 
biochemistry research training studio course I taught, often  with one of my 
research target proteins. Teaching lab students can do all sorts of crazy 
things you might never prioritize in your funded research. Some of these crazy 
things turn out to be fun and interesting. One of my students insisted on 
making a mutation in a protein that seemed to have low chances of leading to a 
successful publication based on prior work. Lo and behold, that mutation turned 
out to be gold, and he was published within the year. I still can't believe it 
not only worked, but crystallized easily from the first screen and optimization 
for structure determination. Go figure.

___
Roger S. Rowlett
Gordon & Dorothy Kline Professor, Emeritus
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

email: rrowl...@colgate.edu

On Wed, Jun 16, 2021 at 7:09 PM Chun Luo 
mailto:c...@accelagen.com>> wrote:

Many phosphatases, such as lambda phosphatase, have good soluble expression in 
E. coli. Their activity can be shown by simply colorimetric assay.



From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of P. H
Sent: Wednesday, June 16, 2021 3:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Looking for proteins for undergraduate biochemistry lab



Hello All,



We are looking for some candidate proteins for an undergraduate level advanced 
biochemistry lab. They should be expressed in bacteria, simple enough to purify 
and it will be nice to perform some simple characterization experiments(binding 
assays, enzymatic assays).

Any suggestions?



Thank you in advance.

Prerna gupta





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] Looking for proteins for undergraduate biochemistry lab

[Roger Rowlett]

Human carbonic anhdydrase II is very expressible in *E. coli,* and
purifiable in one step via affinity chromatography with
para-aminobenzenesulfonamide affinity resin (which is relatively easy to
make, and reusable for many years.) It can be assayed by stopped-flow
spectrophotometry for CO2 hydration, by a timed colorimetric assay, or you
can investigate it's esterase activity with p-nitrophenylacetate. This
enzyme, as well as most other carbonic anhdydrases, is also easy to purify
by a classical combination of anion exchange (Q-sepharose), hydrophobic
interaction (butylsepharose), and gel exclusion polishing. The latter would
be a good exercise for students in general protein purification
optimization, which is an increasingly lost art. (Just had a conversation
with one of the protein chemists ast BioGen who pretty much observed the
same thing.) We routinely did classical purifications on tagless
overexpressed proteins for crystallography work. The time saved in His-Tag
purification is sometimes lost in cleaving the tag to make tagless protein
for crystallography.

A paper describing the purification procedure can be found in J. Chem. Ed. (
https://doi.org/10.1021/ed075p1021) for the similar bovine carbonic
anhydrase. An fun long-term undergraduate research training project might
involve improving the esterase activity through student-initiated point
mutations.

I did this kind of parallel protein mutation project with my students in a
biochemistry research training studio course I taught, often  with one of
my research target proteins. Teaching lab students can do all sorts of
crazy things you might never prioritize in your funded research. Some of
these crazy things turn out to be fun and interesting. One of my students
insisted on making a mutation in a protein that seemed to have low chances
of leading to a successful publication based on prior work. Lo and behold,
that mutation turned out to be gold, and he was published within the year.
I still can't believe it not only worked, but crystallized easily from the
first screen and optimization for structure determination. Go figure.

___
Roger S. Rowlett
Gordon & Dorothy Kline Professor, Emeritus
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

email: rrowl...@colgate.edu

On Wed, Jun 16, 2021 at 7:09 PM Chun Luo  wrote:

> Many phosphatases, such as lambda phosphatase, have good soluble
> expression in E. coli. Their activity can be shown by simply colorimetric
> assay.
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *P. H
> *Sent:* Wednesday, June 16, 2021 3:19 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Looking for proteins for undergraduate biochemistry
> lab
>
>
>
> Hello All,
>
>
>
> We are looking for some candidate proteins for an undergraduate level
> advanced biochemistry lab. They should be expressed in bacteria, simple
> enough to purify and it will be nice to perform some simple
> characterization experiments(binding assays, enzymatic assays).
>
> Any suggestions?
>
>
>
> Thank you in advance.
>
> Prerna gupta
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Looking for proteins for undergraduate biochemistry lab

[Chun Luo]

Many phosphatases, such as lambda phosphatase, have good soluble expression in 
E. coli. Their activity can be shown by simply colorimetric assay. 

 

From: CCP4 bulletin board  On Behalf Of P. H
Sent: Wednesday, June 16, 2021 3:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Looking for proteins for undergraduate biochemistry lab

 

Hello All,

 

We are looking for some candidate proteins for an undergraduate level advanced 
biochemistry lab. They should be expressed in bacteria, simple enough to purify 
and it will be nice to perform some simple characterization experiments(binding 
assays, enzymatic assays). 

Any suggestions?

 

Thank you in advance.

Prerna gupta

 

  _  

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB 
 &A=1 




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Re: [ccp4bb] aimless scale without merging data running Fail

[Jiang Xu]

Hello Phil,
I just read my email and found I may not ask the question clearly. So
my question is, should I use the integrated data from Imosflm, or should I
use the output from Pointless as the input of Aimless to do scale without
merging the data?
Thank you,
Best,
Jiang
Lin Chen Research Group
University of Southern California

On Wed, Jun 16, 2021 at 2:51 PM Jiang Xu  wrote:

> Hello Phil,
>Thank you for the comments. I noticed that the ccp4 package I used was
> 7.0. After upgrading to the latest version, the problem was solved.
>I also have another question about Aimless. I want to use aimless to
> scale without merging the data for generating the "table1" of my data. I
> noticed that in your original publication, one way of doing the scale is to
> use the "Quick Scale" button in Imosflm, in which the output from Pointless
> will be the input of Aimless. However, I also noticed that some posts claim
> that the input of Aimless could also be from the integrated data file from
> Imosflm. I tried both ways and found no problem. So which way is the
> correct way for my purpose?
>Thank you,
> Best,
> Jiang
> Lin Chen Research Group
> University of Southern California
>
> On Wed, Jun 16, 2021 at 12:10 PM Phil Evans  wrote:
>
>> I think it’s trying to write a file TILEIMAGE.img to a directory where
>> you aren’t allowed to write. I can’t remember what is done in ccp4i - I
>> believe it should work ok in ccp4i2, which produces better reports, and is
>> generally recommended as a replacement for ccp4i
>>
>> As a workaround, you might be able to assign the file to somewhere you
>> are allowed to write. Before running ccp4i, type something like (for tosh /
>> cash, not sure about bash)
>>
>> setenv TILEIMAGE /some/suitable/directory/TILEIMAGE.img
>>
>> This file is an image of the correction factors for a tiled ccd detector
>>
>> I can look at this next week, to see if I can work out what is happening
>>
>> Phil
>>
>> Sent from my iPad
>>
>> On 16 Jun 2021, at 18:52, Jiang Xu  wrote:
>>
>> 
>> Hello guys,
>>I am having some problems running Aimless from the CCP4i packages. I
>> want to scale without merging the data. The input mtz file for aimless was
>> either the mtz file directly from Imosflm integration, or from Pointless
>> from a previous run on Imosflm. I ran both pointless and aimless
>> successfully on the Imosflm UI, after integration. However I just couldn't
>> do it from the CCP4i. From the log it seems there's always an error
>> message:  "#CCP4I TERMINATION STATUS 0 "OpenFile: cannot open file
>> TILEIMAGE.img"
>>I googled this line and found no hit. So does anyone know what's
>> happening and how to solve this problem?
>> Thank you,
>> Best,
>> Jiang Xu
>> Lin Chen Research Group
>> University of Southern California
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> 
>>
>>



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[ccp4bb] Looking for proteins for undergraduate biochemistry lab

[P. H]

Hello All,

We are looking for some candidate proteins for an undergraduate level
advanced biochemistry lab. They should be expressed in bacteria, simple
enough to purify and it will be nice to perform some simple
characterization experiments(binding assays, enzymatic assays).
Any suggestions?

Thank you in advance.
Prerna gupta



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
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Re: [ccp4bb] aimless scale without merging data running Fail

[Jiang Xu]

Hello Phil,
   Thank you for the comments. I noticed that the ccp4 package I used was
7.0. After upgrading to the latest version, the problem was solved.
   I also have another question about Aimless. I want to use aimless to
scale without merging the data for generating the "table1" of my data. I
noticed that in your original publication, one way of doing the scale is to
use the "Quick Scale" button in Imosflm, in which the output from Pointless
will be the input of Aimless. However, I also noticed that some posts claim
that the input of Aimless could also be from the integrated data file from
Imosflm. I tried both ways and found no problem. So which way is the
correct way for my purpose?
   Thank you,
Best,
Jiang
Lin Chen Research Group
University of Southern California

On Wed, Jun 16, 2021 at 12:10 PM Phil Evans  wrote:

> I think it’s trying to write a file TILEIMAGE.img to a directory where you
> aren’t allowed to write. I can’t remember what is done in ccp4i - I believe
> it should work ok in ccp4i2, which produces better reports, and is
> generally recommended as a replacement for ccp4i
>
> As a workaround, you might be able to assign the file to somewhere you are
> allowed to write. Before running ccp4i, type something like (for tosh /
> cash, not sure about bash)
>
> setenv TILEIMAGE /some/suitable/directory/TILEIMAGE.img
>
> This file is an image of the correction factors for a tiled ccd detector
>
> I can look at this next week, to see if I can work out what is happening
>
> Phil
>
> Sent from my iPad
>
> On 16 Jun 2021, at 18:52, Jiang Xu  wrote:
>
> 
> Hello guys,
>I am having some problems running Aimless from the CCP4i packages. I
> want to scale without merging the data. The input mtz file for aimless was
> either the mtz file directly from Imosflm integration, or from Pointless
> from a previous run on Imosflm. I ran both pointless and aimless
> successfully on the Imosflm UI, after integration. However I just couldn't
> do it from the CCP4i. From the log it seems there's always an error
> message:  "#CCP4I TERMINATION STATUS 0 "OpenFile: cannot open file
> TILEIMAGE.img"
>I googled this line and found no hit. So does anyone know what's
> happening and how to solve this problem?
> Thank you,
> Best,
> Jiang Xu
> Lin Chen Research Group
> University of Southern California
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
>
>



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Re: [ccp4bb] aimless scale without merging data running Fail

[Phil Evans]

I think it’s trying to write a file TILEIMAGE.img to a directory where you 
aren’t allowed to write. I can’t remember what is done in ccp4i - I believe it 
should work ok in ccp4i2, which produces better reports, and is generally 
recommended as a replacement for ccp4i

As a workaround, you might be able to assign the file to somewhere you are 
allowed to write. Before running ccp4i, type something like (for tosh / cash, 
not sure about bash)

setenv TILEIMAGE /some/suitable/directory/TILEIMAGE.img

This file is an image of the correction factors for a tiled ccd detector

I can look at this next week, to see if I can work out what is happening 

Phil

Sent from my iPad

> On 16 Jun 2021, at 18:52, Jiang Xu  wrote:
> 
> 
> Hello guys,
>I am having some problems running Aimless from the CCP4i packages. I want 
> to scale without merging the data. The input mtz file for aimless was either 
> the mtz file directly from Imosflm integration, or from Pointless from a 
> previous run on Imosflm. I ran both pointless and aimless successfully on the 
> Imosflm UI, after integration. However I just couldn't do it from the CCP4i. 
> From the log it seems there's always an error message:  "#CCP4I TERMINATION 
> STATUS 0 "OpenFile: cannot open file TILEIMAGE.img"
>I googled this line and found no hit. So does anyone know what's happening 
> and how to solve this problem?
> Thank you,
> Best,
> Jiang Xu
> Lin Chen Research Group
> University of Southern California
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
> 



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[ccp4bb] aimless scale without merging data running Fail

[Jiang Xu]

Hello guys,
   I am having some problems running Aimless from the CCP4i packages. I
want to scale without merging the data. The input mtz file for aimless was
either the mtz file directly from Imosflm integration, or from Pointless
from a previous run on Imosflm. I ran both pointless and aimless
successfully on the Imosflm UI, after integration. However I just couldn't
do it from the CCP4i. From the log it seems there's always an error
message:  "#CCP4I TERMINATION STATUS 0 "OpenFile: cannot open file
TILEIMAGE.img"
   I googled this line and found no hit. So does anyone know what's
happening and how to solve this problem?
Thank you,
Best,
Jiang Xu
Lin Chen Research Group
University of Southern California



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#CCP4I VERSION CCP4Interface 7.0.078
#CCP4I SCRIPT LOG aimless
#CCP4I DATE 16 Jun 2021  10:32:41
#CCP4I USER linchenlab
#CCP4I PROJECT alpha1actx
#CCP4I JOB_ID 17
#CCP4I SCRATCH /tmp/linchenlab
#CCP4I HOSTNAME linchenlab
#CCP4I PID 10938


 
 ###
 ###
 ###
 ### CCP4 7.0.078: POINTLESSversion 1.11.21 : 10/05/19##
 ###
 User: unknown  Run date: 16/ 6/2021 Run time: 10:32:41 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 
235-242.
 as well as any specific reference in the program write-up.

 Command line arguments 
HKLOUT /tmp/linchenlab/alpha1actx_17_2_mtz.tmp
XMLOUT /home/linchenlab/ccp4/jiangxu/alpha1actx/alpha1actx_17_pointless.xml

Release Date: 10th May 2019

 Input command lines 

HKLIN /home/linchenlab/ccp4/jiangxu/alpha1actx/pointless_run_11_1.mtz
## This script run with the command   ##
# /usr/bin/CCP4/ccp4-7.0/bin/pointless HKLOUT 
"/tmp/linchenlab/alpha1actx_17_2_mtz.tmp" XMLOUT &
"/home/linchenlab/ccp4/jiangxu/alpha1actx/alpha1actx_17_pointless.xml"


 End of input


**
**
* POINTLESS  *
*  1.11.21   *
**
*   Determine Laue group from unmerged intensities   *
* Phil Evans MRC LMB, Cambridge  *
* Uses cctbx routines by Ralf Grosse-Kunstleve et al.*
**
**


Reflection list generated from file: 
/home/linchenlab/ccp4/jiangxu/alpha1actx/pointless_run_11_1.mtz

Title: Untitled

   Space group from HKLIN file : P 21 21 21
   Cell:45.59   46.91  149.84   90.00   90.00   90.00
   Resolution range in file: 74.922.26

Time for reading file(s):0.393 secs

===

>*> Summary of test data read in:
   Resolution range accepted:74.922.26

   Number of reflections  = 15828
   Number of observations =157818
   Number of parts=324574
   Number of batches in file  =   269
   Number of datasets = 1
 
  Project: New Crystal: New Dataset: New
  Run number:   1 consists of batches 1 - 269
 Resolution range for run:74.922.26
 Phi range:90.51 to   359.51   Time range:90.51 to   359.51
 Closest reciprocal axis to spindle: b* (angle   16.7 degrees)
   Unit cell for dataset:45.59   46.91  149.84   90.00   90.00   90.00
 Wavelength:  0.3


Numbers of observations marked in the FLAG column
By default all flagged observations are rejected
Observations may be counted in more than one category

 Flagged  Accepted   Maximum   MaxAccepted
   BGratio too large  0   0   1.800   0.000
   PKratio too large 53   0   5.100   0.000
   Negative < 5sigma  1   0
   Gradient too large 3   0   0.047   0.000
   Profile-fitted overloads   1   1
   Spots on edge   3324   0
   XDS misfits (outliers) 0   0


===

Number of reflections  = 1582

[ccp4bb] Bioinformatician position at PDBe

[John Berrisford]

Dear Colleagues,

 

We have a bioinformatician position available in the PDBe team at the
European Bioinformatics Institute (EBI) on the Wellcome Genome Campus near
Cambridge.

 

We are looking for a scientific programmer/bioinformatician with a strong
structural biology background and software engineering skills.

 

The successful candidate will create and improve biological data processing
pipelines, perform data analysis, and develop user-facing web pages for the
PDBe - Knowledge Base (PDBe-KB) resource.

 

The closing date for applications is 14th July 2021. For more information on
the position, please visit:

 

 
https://www.embl.org/jobs/position/EBI01851 

 

Kind regards,

 

John

 

--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

  http://www.pdbe.org

 
http://www.facebook.com/proteindatabank

  http://twitter.com/PDBeurope

 




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[ccp4bb] Fwd: [ccpem] Glutamate receptor cryo-EM at the MRC LMB

[Krieger, James M]

Hi everyone,

I’m forwarding this position in structural biology and drug development at the 
LMB in Cambridge with my former PhD supervisor, Ingo Greger, in collaboration w 
AstraZeneca in case anyone is interested who is not on CCPEM. It’s a very 
dynamic, interdisciplinary group that I highly recommend.

Believe wishes
James


Begin forwarded message:

From: Ingo Greger 
Date: June 15, 2021 at 07:59:20 GMT+1
To: cc...@jiscmail.ac.uk
Subject: [ccpem] Glutamate receptor cryo-EM at the MRC LMB
Reply-To: i...@mrc-lmb.cam.ac.uk

Hi all

We're looking for a postdoc interested in glutamate receptor structure,
pharmacology and drug development. This is a close collaboration between
the LMB and AstraZeneca, Cambridge:

https://www.nature.com/naturecareers/job/investigator-scientist-medical-research-council-741162

This for 1 year initially with prospect of extension.
Please get in touch for further details: i...@mrc-lmb.cam.ac.uk

References:
Zhang, D., et al. (2021). Gating and modulation of a hetero-octameric AMPA
glutamate receptor
Nature, https://doi.org/10.1038/s41586-021-03613-0

Dohrke, J-N., et al. (2020). Characterizing the binding and function of
TARPγ8-selective AMPA receptor modulators.
J. Biol. Chem. 295(43):14565-14577

Herguedas, B., et al. (2019). Architecture of the heteromeric GluA1/2 AMPA
receptor in complex with the auxiliary subunit TARP-γ8.
Science 364(6438): pii: eaav9011.


Best,
Ingo Greger



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