Re: [ccp4bb] TWIN?

[Eric Montemayor]

Maybe you have a bimolecular dimer when you expected a unimolecular
hairpin?  It’s happened before :)

https://pubmed.ncbi.nlm.nih.gov/31584014/

Eric



On Tue, Jun 8, 2021 at 10:15 AM Almudena Ponce Salvatierra <
maps.fa...@gmail.com> wrote:

> Hello everyone,
>
> I am working with an RNA-only structure, data are at 3 Angstroms, and at
> first, I thought was in the C2 space group (with 6 molecules in the AU).
>
> I can't finish building! it, because the structure seems to get in the way
> of its neighbor symmetrically! See the attached picture, please! The only 4
> residues that the structure is missing "have to go there", where one
> structure meets the other one. The R factors for this spacegroup are around
> 0.3.
>
> However, Phenix Xtriage suggests the symmetry may be higher. So I reindex
> in P622, do MR with Phaser (trying all possible space groups in that point
> group), and it finds a unique solution in space group P 65 2 2 with TFZ of
> 50 and LLG >3000. Of course, the problem persists (one molecule sort of
> interfering with the neighbor), not only that but also the refinement
> R-factors are substantially higher, 0.37.
>
> I have to say that the refinement maps look better when I am working with
> the C2 spacegroup. I can't understand, though, what is happening at that
> "supposedly interface" between the two molecules. Has anybody experienced
> anything like this in the past? Can it be a twin? Is it something else?
> and... how to fix it?
>
> Thank you very much in advance.
>
> Best wishes,
>
> Almudena
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] Associate Researcher Position in the KU Protein Structure Laboratory

[Lovell, Scott W]

The Protein Structure Laboratory (PSL) at the University of Kansas (KU) is 
seeking a full-time Associate Researcher to assist with various structural 
biology projects.  As a core laboratory, the PSL collaborates with a diverse 
range of investigators to obtain structures of their proteins of interest using 
X-ray crystallography and delivers dozens of structures annually.  
Additionally, the PSL manages the structural biology efforts for extramurally 
funded research projects particularly aimed at inhibitor development.

For a full description of the position and to apply, GO TO: 
https://employment.ku.edu/associate-researcher/19212br

Regards,
Scott

__
Scott Lovell Ph.D., Director
Protein Structure and X-Ray Crystallography Laboratory
University of Kansas
Del Shankel Structural Biology Center
2034 Becker Drive
Lawrence, KS 66047
Office: SBC 1015
email: swlov...@ku.edu
phone:  785-864-3772
fax: 785-864-8141
__




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Re: [ccp4bb] Problem with peakmax

[Mohamed Ibrahim]

Thank all,
it works perfectly, using the "<< EOF"

Best regards,
Mohamed

On Tue, Jun 8, 2021 at 8:32 PM CCP4BB <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> The text following the "<<" in Eleanor's and Phil's example is known as a
> "heredoc" in Unix or Linux-speak (I had been using them for decades before
> I found out what they're called...). You can replace both "EOF-pmx"s in
> Phil's example and both "eof"s in Eleanor's with any text you like.
>
> See https://linuxize.com/post/bash-heredoc/.
>
> Harry
> --
> Dr Harry Powell
>
> On 8 Jun 2021, at 19:22, Fischmann, Thierry <
> 22f7fda0a875-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> echo “keyword1 arguments\nkeyword2 arguments\n etc. \nEND” | peakmax
> MAPIN myfile.ccp4 XYZOUT myfiles_omit_atom.pdb
>
> should work as well
>
>
>
> Thierry
>
>
>
> *From:* CCP4 bulletin board  * On Behalf Of *Philip
> D. Jeffrey
> *Sent:* Tuesday, June 8, 2021 2:16 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Problem with peakmax
>
>
>
> *EXTERNAL EMAIL* – Use caution with any links or file attachments.
>
> Paul was a little too terse, perhaps.
>
> In script form
>
>
>
> peakmax MAPIN myfile.ccp4 XYZOUT myfiles_omit_atom.pdb << EOF-pmx
>
> keywords in here
>
> EOF-pmx
>
>
>
> at least that's what works for me in Csh.  Bash proselytizers will correct
> me as necessary...
>
>
>
> Phil Jeffrey
>
> Princeton
>
>
> --
>
> *From:* CCP4 bulletin board  on behalf of Mohamed
> Ibrahim 
> *Sent:* Tuesday, June 8, 2021 2:06 PM
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* Re: [ccp4bb] Problem with peakmax
>
>
>
> Thanks Paul,
>
> Is it possible to add Ctrl-D to my bash script?
>
>
>
> Best regards,
>
>
>
> On Tue, Jun 8, 2021 at 8:03 PM Mohamed Ibrahim <
> mohamed.ibra...@hu-berlin.de> wrote:
>
> Thanks Paul,
>
> Is it possible to add Ctrl-D to my bash script?
>
>
>
> Best regards,
>
>
>
> On Tue, Jun 8, 2021 at 7:51 PM Paul Emsley 
> wrote:
>
> On Tue, 2021-06-08 at 19:34 +0200, Mohamed Ibrahim wrote:
> >
> > I am trying to get the peak values from omit maps. The peakmax from the
> GUI works fine. However, I tried to run
> > peakmax from the terminal, and it stuck when returning P1. Same map file
> works fine, when I use the GUI. Any ideas,
> > how to solve this problem?
> >
> > command used
> > peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
> >
>
> Ctrl-D
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>
>
>
>
> --
>
> ​
>
> *​*
>
> *--*
>
> *Dr. Mohamed Ibrahim*
>
> *Postdoctoral Researcher*
>
>
>
>
>
>
>
>
>
> *Humboldt University  *
>
>
>
>
>
> *Berlin, Germany*
>
>
>
>
>
> *Tel: +**49 30 209347931 *
>
>
>
>
> --
>
> ​
>
> *​*
>
> *--*
>
> *Dr. Mohamed Ibrahim*
>
> *Postdoctoral Researcher*
>
>
>
>
>
>
>
>
>
> *Humboldt University  *
>
>
>
>
>
> *Berlin, Germany*
>
>
>
>
>
> *Tel: +**49 30 209347931 *
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> Notice:  This e-mail message, together with any attachments, contains
> information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth,
> New Jersey, USA 07033), and/or its affiliates Direct contact information
> for affiliates is available at
> http://www.merck.com/contact/contacts.html) that may be confidential,
> proprietary copyrighted and/or legally privileged. It is intended solely
> for the use of the individual or entity named on this message. If you are
> not the intended recipient, and have received this message in error,
> please notify us immediately by reply e-mail and then delete it from
> your system.
>
> --
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> To unsubscribe from the CCP4BB list, click the following link:
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>
> --
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-- 
​
*​--*
*Dr. Mohamed Ibrahim*
*Postdoctoral Researcher   *

*Humboldt University   *
*Berlin, Germany  *

*Tel: +49 30 209347931 *



To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] Problem with peakmax

[CCP4BB]

The text following the "<<" in Eleanor's and Phil's example is known as a 
"heredoc" in Unix or Linux-speak (I had been using them for decades before I 
found out what they're called...). You can replace both "EOF-pmx"s in Phil's 
example and both "eof"s in Eleanor's with any text you like.

See https://linuxize.com/post/bash-heredoc/.

Harry
--
Dr Harry Powell

> On 8 Jun 2021, at 19:22, Fischmann, Thierry 
> <22f7fda0a875-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> echo “keyword1 arguments\nkeyword2 arguments\n etc. \nEND” | peakmax MAPIN 
> myfile.ccp4 XYZOUT myfiles_omit_atom.pdb
> should work as well
>  
> Thierry
>  
> From: CCP4 bulletin board  On Behalf Of Philip D. 
> Jeffrey
> Sent: Tuesday, June 8, 2021 2:16 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Problem with peakmax
>  
> EXTERNAL EMAIL – Use caution with any links or file attachments.
> Paul was a little too terse, perhaps.
> In script form
>  
> peakmax MAPIN myfile.ccp4 XYZOUT myfiles_omit_atom.pdb << EOF-pmx
> keywords in here
> EOF-pmx
>  
> at least that's what works for me in Csh.  Bash proselytizers will correct me 
> as necessary...
>  
> Phil Jeffrey
> Princeton
>  
> From: CCP4 bulletin board  on behalf of Mohamed 
> Ibrahim 
> Sent: Tuesday, June 8, 2021 2:06 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] Problem with peakmax
>  
> Thanks Paul, 
> Is it possible to add Ctrl-D to my bash script?
>  
> Best regards, 
>  
> On Tue, Jun 8, 2021 at 8:03 PM Mohamed Ibrahim  
> wrote:
> Thanks Paul, 
> Is it possible to add Ctrl-D to my bash script?
>  
> Best regards, 
>  
> On Tue, Jun 8, 2021 at 7:51 PM Paul Emsley  wrote:
> On Tue, 2021-06-08 at 19:34 +0200, Mohamed Ibrahim wrote:
> > 
> > I am trying to get the peak values from omit maps. The peakmax from the GUI 
> > works fine. However, I tried to run
> > peakmax from the terminal, and it stuck when returning P1. Same map file 
> > works fine, when I use the GUI. Any ideas,
> > how to solve this problem?
> > 
> > command used 
> > peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
> > 
> 
> Ctrl-D
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> https://www.jiscmail.ac.uk/policyandsecurity/
> 
>  
> --
> ​
> ​
> --
> Dr. Mohamed Ibrahim
> Postdoctoral Researcher   
>
>   
>
>  
> Humboldt University 
>
>
> Berlin, Germany   
>  
>   
> Tel: +49 30 209347931 
> 
>  
> --
> ​
> ​
> --
> Dr. Mohamed Ibrahim
> Postdoctoral Researcher   
>
>   
>
>  
> Humboldt University 
>
>
> Berlin, Germany   
>  
>   
> Tel: +49 30 209347931 
>  
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
>  
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> Notice:  This e-mail message, together with any attachments, contains
> information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, 
> New Jersey, USA 07033), and/or its affiliates Direct contact information
> for affiliates is available at 
> http://www.merck.com/contact/contacts.html) that may be confidential,
> proprietary copyrighted and/or legally privileged. It is intended solely
> for the use of the individual or entity named on this message. If you are
> not the intended recipient, and have received this message in error,
> please notify us immediately by reply e-mail and then delete it from 
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Re: [ccp4bb] Problem with peakmax

[Fischmann, Thierry]

echo “keyword1 arguments\nkeyword2 arguments\n etc. \nEND” | peakmax MAPIN 
myfile.ccp4 XYZOUT myfiles_omit_atom.pdb
should work as well

Thierry

From: CCP4 bulletin board  On Behalf Of Philip D. Jeffrey
Sent: Tuesday, June 8, 2021 2:16 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problem with peakmax

EXTERNAL EMAIL – Use caution with any links or file attachments.
Paul was a little too terse, perhaps.
In script form

peakmax MAPIN myfile.ccp4 XYZOUT myfiles_omit_atom.pdb << EOF-pmx
keywords in here
EOF-pmx

at least that's what works for me in Csh.  Bash proselytizers will correct me 
as necessary...

Phil Jeffrey
Princeton


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Mohamed Ibrahim 
mailto:m.essam.ibra...@gmail.com>>
Sent: Tuesday, June 8, 2021 2:06 PM
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Problem with peakmax

Thanks Paul,
Is it possible to add Ctrl-D to my bash script?

Best regards,

On Tue, Jun 8, 2021 at 8:03 PM Mohamed Ibrahim 
mailto:mohamed.ibra...@hu-berlin.de>> wrote:
Thanks Paul,
Is it possible to add Ctrl-D to my bash script?

Best regards,

On Tue, Jun 8, 2021 at 7:51 PM Paul Emsley 
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
On Tue, 2021-06-08 at 19:34 +0200, Mohamed Ibrahim wrote:
>
> I am trying to get the peak values from omit maps. The peakmax from the GUI 
> works fine. However, I tried to run
> peakmax from the terminal, and it stuck when returning P1. Same map file 
> works fine, when I use the GUI. Any ideas,
> how to solve this problem?
>
> command used
> peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
>

Ctrl-D



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--
​
​
--
Dr. Mohamed Ibrahim
Postdoctoral Researcher




Humboldt University


Berlin, Germany


Tel: +49 30 209347931


--
​
​
--
Dr. Mohamed Ibrahim
Postdoctoral Researcher




Humboldt University


Berlin, Germany


Tel: +49 30 209347931



To unsubscribe from the CCP4BB list, click the following link:
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Notice:  This e-mail message, together with any attachments, contains
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New Jersey, USA 07033), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system.




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Re: [ccp4bb] Problem with peakmax

[Eleanor Dodson]

peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"  <
wrote:

> Paul was a little too terse, perhaps.
> In script form
>
> peakmax MAPIN myfile.ccp4 XYZOUT myfiles_omit_atom.pdb << EOF-pmx
> keywords in here
> EOF-pmx
>
> at least that's what works for me in Csh.  Bash proselytizers will correct
> me as necessary...
>
> Phil Jeffrey
> Princeton
>
> --
> *From:* CCP4 bulletin board  on behalf of Mohamed
> Ibrahim 
> *Sent:* Tuesday, June 8, 2021 2:06 PM
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* Re: [ccp4bb] Problem with peakmax
>
> Thanks Paul,
> Is it possible to add Ctrl-D to my bash script?
>
> Best regards,
>
> On Tue, Jun 8, 2021 at 8:03 PM Mohamed Ibrahim <
> mohamed.ibra...@hu-berlin.de> wrote:
>
> Thanks Paul,
> Is it possible to add Ctrl-D to my bash script?
>
> Best regards,
>
> On Tue, Jun 8, 2021 at 7:51 PM Paul Emsley 
> wrote:
>
> On Tue, 2021-06-08 at 19:34 +0200, Mohamed Ibrahim wrote:
> >
> > I am trying to get the peak values from omit maps. The peakmax from the
> GUI works fine. However, I tried to run
> > peakmax from the terminal, and it stuck when returning P1. Same map file
> works fine, when I use the GUI. Any ideas,
> > how to solve this problem?
> >
> > command used
> > peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
> >
>
> Ctrl-D
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>
>
>
> --
> ​
> * ​ --*
> *Dr. Mohamed Ibrahim*
> *Postdoctoral Researcher *
>
> *Humboldt University *
> *Berlin, Germany *
> *Tel: +49 30 209347931 *
>
>
>
> --
> ​
> * ​ --*
> *Dr. Mohamed Ibrahim*
> *Postdoctoral Researcher *
>
> *Humboldt University *
> *Berlin, Germany *
>
> *Tel: +49 30 209347931  *
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
> --
>
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>



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Re: [ccp4bb] Problem with peakmax

[Philip D. Jeffrey]

Paul was a little too terse, perhaps.
In script form

peakmax MAPIN myfile.ccp4 XYZOUT myfiles_omit_atom.pdb << EOF-pmx
keywords in here
EOF-pmx

at least that's what works for me in Csh.  Bash proselytizers will correct me 
as necessary...

Phil Jeffrey
Princeton


From: CCP4 bulletin board  on behalf of Mohamed Ibrahim 

Sent: Tuesday, June 8, 2021 2:06 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Problem with peakmax

Thanks Paul,
Is it possible to add Ctrl-D to my bash script?

Best regards,

On Tue, Jun 8, 2021 at 8:03 PM Mohamed Ibrahim 
mailto:mohamed.ibra...@hu-berlin.de>> wrote:
Thanks Paul,
Is it possible to add Ctrl-D to my bash script?

Best regards,

On Tue, Jun 8, 2021 at 7:51 PM Paul Emsley 
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
On Tue, 2021-06-08 at 19:34 +0200, Mohamed Ibrahim wrote:
>
> I am trying to get the peak values from omit maps. The peakmax from the GUI 
> works fine. However, I tried to run
> peakmax from the terminal, and it stuck when returning P1. Same map file 
> works fine, when I use the GUI. Any ideas,
> how to solve this problem?
>
> command used
> peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
>

Ctrl-D



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--
​
​
--
Dr. Mohamed Ibrahim
Postdoctoral Researcher




Humboldt University


Berlin, Germany


Tel: +49 30 209347931


--
​
​
--
Dr. Mohamed Ibrahim
Postdoctoral Researcher




Humboldt University


Berlin, Germany


Tel: +49 30 209347931



To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Problem with peakmax

[Mohamed Ibrahim]

Thanks Paul,
Is it possible to add Ctrl-D to my bash script?

Best regards,

On Tue, Jun 8, 2021 at 8:03 PM Mohamed Ibrahim 
wrote:

> Thanks Paul,
> Is it possible to add Ctrl-D to my bash script?
>
> Best regards,
>
> On Tue, Jun 8, 2021 at 7:51 PM Paul Emsley 
> wrote:
>
>> On Tue, 2021-06-08 at 19:34 +0200, Mohamed Ibrahim wrote:
>> >
>> > I am trying to get the peak values from omit maps. The peakmax from the
>> GUI works fine. However, I tried to run
>> > peakmax from the terminal, and it stuck when returning P1. Same map
>> file works fine, when I use the GUI. Any ideas,
>> > how to solve this problem?
>> >
>> > command used
>> > peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
>> >
>>
>> Ctrl-D
>>
>> 
>>
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>
>
> --
> ​
> *​--*
> *Dr. Mohamed Ibrahim*
> *Postdoctoral Researcher   *
>
> *Humboldt University   *
> *Berlin, Germany  *
> *Tel: +49 30 209347931 *
>


-- 
​
*​--*
*Dr. Mohamed Ibrahim*
*Postdoctoral Researcher   *

*Humboldt University   *
*Berlin, Germany  *

*Tel: +49 30 209347931 *



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Re: [ccp4bb] Problem with peakmax

[Paul Emsley]

On Tue, 2021-06-08 at 19:34 +0200, Mohamed Ibrahim wrote:
> 
> I am trying to get the peak values from omit maps. The peakmax from the GUI 
> works fine. However, I tried to run
> peakmax from the terminal, and it stuck when returning P1. Same map file 
> works fine, when I use the GUI. Any ideas,
> how to solve this problem?
> 
> command used 
> peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
> 

Ctrl-D



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[ccp4bb] Problem with peakmax

[Mohamed Ibrahim]

Dear All,

I am trying to get the peak values from omit maps. The peakmax from the GUI
works fine. However, I tried to run peakmax from the terminal, and it stuck
when returning P1. Same map file works fine, when I use the GUI. Any ideas,
how to solve this problem?

command used
peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"

Thank you!

-- 
*--*
*Dr. Mohamed Ibrahim*
*Postdoctoral Researcher   *

*Humboldt University   *
*Berlin, Germany  *

*Tel: +49 30 209347931 *



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Re: [ccp4bb] TWIN?

[Eleanor Dodson]

First spacegrouop -  trigonal spacegroups can also be indexed as C2 so it
isnt so surprising that a P6/mmm should masquerade as C2.
I would look very carefull at the POINTLESS symmetry scores and see if some
are more convincing than others.

But how I hate RNA & DNA - molecular replacement struggles because often
the molecules pack to form a pseudo-continuous chain so it is easy when
searching with one copy to finish up a residue or so out of register..
Do the B factors give you a clue about error?

And with only 3A data it will be hard to check the base identities.. Maybe
set base occupancies to 0.00 one at a time , refine then see what you see
in the difference map. Maybe you might detect a possible
different interpretation
Eleanor


On Tue, 8 Jun 2021 at 16:28, CRAIG A BINGMAN <
21371e2fba31-dmarc-requ...@jiscmail.ac.uk> wrote:

> It’s difficult to tell exactly what is happening from your description and
> the attached image. Both your description and the image are OK. It’s just
> that there are a lot of ways for things to go off the rails.
>
> Are the molecules stacked end-to-end? In that case, you may have an
> incommensurate structure where the molecule is disordered around a
> pseudo-continuous helical axis running through the crystal.
>
> But from this view, it looks like at least two bases are swung out to the
> left. I’d omit the interaction region, refine what you can model well as
> well as you can, and see if the maps for this region clear up. Keep in mind
> that your model might be out of register, so look at the shapes of the
> bases carefully to see if you need adjust that.
>
> On Jun 8, 2021, at 10:14 AM, maps.fa...@gmail.com wrote:
>
> Hello everyone,
>
> I am working with an RNA-only structure, data are at 3 Angstroms, and at
> first, I thought was in the C2 space group (with 6 molecules in the AU).
>
> I can't finish building! it, because the structure seems to get in the way
> of its neighbor symmetrically! See the attached picture, please! The only 4
> residues that the structure is missing "have to go there", where one
> structure meets the other one. The R factors for this spacegroup are around
> 0.3.
>
> However, Phenix Xtriage suggests the symmetry may be higher. So I reindex
> in P622, do MR with Phaser (trying all possible space groups in that point
> group), and it finds a unique solution in space group P 65 2 2 with TFZ of
> 50 and LLG >3000. Of course, the problem persists (one molecule sort of
> interfering with the neighbor), not only that but also the refinement
> R-factors are substantially higher, 0.37.
>
> I have to say that the refinement maps look better when I am working with
> the C2 spacegroup. I can't understand, though, what is happening at that
> "supposedly interface" between the two molecules. Has anybody experienced
> anything like this in the past? Can it be a twin? Is it something else?
> and... how to fix it?
>
> Thank you very much in advance.
>
> Best wishes,
>
> Almudena
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>  16.43.21.png>
>
>
>
> --
>
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Re: [ccp4bb] looking for proteins with no homologues in pdb

[Debanu Das]

You can download such proteins/sequences from the CASP website:
https://predictioncenter.org/

At the JCSG, we participated for many years in the annual CASP competition,
where we would use/hold our novel experimental crystal structures (before
PDB deposition, almost all our ~1500 targets/PDB depositions had < 20%
sequence identity to existing PDB entries, from novel Pfam/CATH) as tests
by protein structure prediction/modeling groups around the world
participating in CASP to try to predict before PDB release, thereby
allowing a direct comparison with the prediction algorithm and the
experimental structure.

Best,
Debanu
--
Debanu Das

On Mon, Jun 7, 2021 at 1:11 PM Scott Horowitz  wrote:

> For testing purposes, we want to solve structures of proteins that are not
> in the PDB and have no significant sequence homologues in the PDB (i.e. a
> blast of the pdb will get no significant hits). Does anyone happen know a
> good way to find such proteins efficiently? Having an interesting function
> isn't needed.
>
> Thanks,
> Scott
>
> Scott Horowitz, Ph.D.
>
> Assistant Professor
>
> Department of Chemistry & Biochemistry
>
> Knoebel Institute for Healthy Aging
>
> University of Denver
>
>
>
> ECS Building
>
> 2155 E. Wesley Ave
>
> Denver, CO 80208
>
> Phone: 303-871-4326
>
> Fax: 303-871-7915
>
> Zoom Room: https://udenver.zoom.us/my/scotthorowitz
>
> Email: scott.horow...@du.edu
>
> Office: Room 561   Lab: Room 505
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] TWIN?

[CRAIG A BINGMAN]

It’s difficult to tell exactly what is happening from your description and the 
attached image. Both your description and the image are OK. It’s just that 
there are a lot of ways for things to go off the rails.

Are the molecules stacked end-to-end? In that case, you may have an 
incommensurate structure where the molecule is disordered around a 
pseudo-continuous helical axis running through the crystal.

But from this view, it looks like at least two bases are swung out to the left. 
I’d omit the interaction region, refine what you can model well as well as you 
can, and see if the maps for this region clear up. Keep in mind that your model 
might be out of register, so look at the shapes of the bases carefully to see 
if you need adjust that.

On Jun 8, 2021, at 10:14 AM, maps.fa...@gmail.com 
wrote:

Hello everyone,

I am working with an RNA-only structure, data are at 3 Angstroms, and at first, 
I thought was in the C2 space group (with 6 molecules in the AU).

I can't finish building! it, because the structure seems to get in the way of 
its neighbor symmetrically! See the attached picture, please! The only 4 
residues that the structure is missing "have to go there", where one structure 
meets the other one. The R factors for this spacegroup are around 0.3.

However, Phenix Xtriage suggests the symmetry may be higher. So I reindex in 
P622, do MR with Phaser (trying all possible space groups in that point group), 
and it finds a unique solution in space group P 65 2 2 with TFZ of 50 and LLG 
>3000. Of course, the problem persists (one molecule sort of interfering with 
the neighbor), not only that but also the refinement R-factors are 
substantially higher, 0.37.

I have to say that the refinement maps look better when I am working with the 
C2 spacegroup. I can't understand, though, what is happening at that 
"supposedly interface" between the two molecules. Has anybody experienced 
anything like this in the past? Can it be a twin? Is it something else? and... 
how to fix it?

Thank you very much in advance.

Best wishes,

Almudena



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Re: [ccp4bb] looking for proteins with no homologues in pdb

[Rigden, Dan]

One short cut would be to focus on Pfam families that do not yet have a 3D 
representative. They can be browsed eg

https://pfam.xfam.org/family/browse?browse=a

or you can also install Pfam locally as MySQL for programmatic access.


Choosing Families rather than Domains would make it easier to get proteins 
matching only a single Pfam entry


If you wanted to be more stringent you could exclude any families that were in 
Clans that had a structural representative.


Dan


Prof Daniel Rigden  (He/Him)
Department of Biochemistry and Systems Biology
Institute of Systems, Molecular and Integrative Biology
Room 101, Biosciences Building
University of Liverpool
Crown St., Liverpool, L69 7ZB

(+44) 151 795 4467
www.liverpool.ac.uk/integrative-biology/staff/daniel-rigden/



From: CCP4 bulletin board  on behalf of Scott Horowitz 

Sent: 07 June 2021 21:00:42
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] looking for proteins with no homologues in pdb

For testing purposes, we want to solve structures of proteins that are not in 
the PDB and have no significant sequence homologues in the PDB (i.e. a blast of 
the pdb will get no significant hits). Does anyone happen know a good way to 
find such proteins efficiently? Having an interesting function isn't needed.

Thanks,
Scott

Scott Horowitz, Ph.D.
Assistant Professor
Department of Chemistry & Biochemistry
Knoebel Institute for Healthy Aging
University of Denver

ECS Building
2155 E. Wesley Ave
Denver, CO 80208
Phone: 303-871-4326
Fax: 303-871-7915
Zoom Room: https://udenver.zoom.us/my/scotthorowitz
Email: scott.horow...@du.edu
Office: Room 561   Lab: Room 505




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Re: [ccp4bb] self-inhibitory fragments from a protein - clarification

[Andrew Lovering]

Dear All

just to clarify, I'd be most interested in examples resulting from proteolysis, 
rather than say, packing effects

Best
Andy



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