Re: [ccp4bb] Refmac problem: Validation and Analysis

[Martin Malý]

Dear Marian,
This issue regarding validation report in refmac task has been fixed in 
the latest update 8.0.019. Please let us know if the problem persists.

Best wishes,
Martin

On 05/04/2024 13:19, Jon Agirre wrote:

Dear Marian,
Thanks for your report. I'm sorry you're having to deal with this 
problem. There is nothing wrong with your machine; this is an 
identified bug and we're working towards fixing it. In the meantime, 
the only workaround I can think of is to roll CCP4 back to a previous 
update, e.g. 015.

I will keep you posted,
Jon

On Fri, 5 Apr 2024 at 12:54, Marian Oliva  wrote:

Dear list,

I have a problem running the Validation and Analysis in Refmac and
I would really appreciate any feed-back from your side.

I am using CCP4i2 (CCP4-8.0.018 locally running in Ubuntu 20.04.4).

Last time I was using Refmac was in November 2023. At the time, I
posted in the list an error with the CCP4i2 interface (no
responding) that I solved by turning off the 3D picture in the
reports (as kindly suggested by Stuart McNicholas).

Now, despite the 3D picture in the reports is off, I still
experience ‘some delays’ on the interface response, though this is
not a major issue.

The real problem I’m experiencing is that after a (apparent)
normal termination of Refmac (no sign of warnings or error
messages), I find no results from the Multimeric validation.

Navigating through the jobs folders I have found that in job2
(which I guess correspond to the validation) there is:

- no prosmart related files (.out, .pdb, .py).

- the tables_as_csv_files folder is empty.

- there is no molprobity.log file. Instead, there is a
log_mtzjoin.txt file but it does not highlight any warning or
error either.

- the program.xml file only contains the heather but otherwise, it
is blank (which I guess this is the reason it is not running).

- also, in the param.xml file I found that there are 2 sets of
input data (instead of one and I don’t know why), where:

-There is no dbFileID for the input F-SIGF data (in any of them)

-In the first one the XYZIN is the XYZIN-coordinated.pdb (instead
of the xyzout_prosmart_refmac.pdb) and in the second it is the
xyzout_prosmart_refmac.pdb)

Checking the terminal while running refmac I saw the following
error message that appears just after refmac window state ‘The job
is finished’. This error repeats multiple times, with variations
in the .WebGL-alphanumerical code, from time to time and ends as
follows.

[3701:3802:0405/112315.960478:ERROR:gles2_cmd_decoder.cc
(12701)] [.WebGL-0x23e9d90]GL ERROR
:GL_INVALID_VALUE : glVertexAttrib4f: index out of range

<--- Last few GCs --->

[4500:0xc37]   177121 ms: Scavenge 2518.8 (2529.1) ->
2510.8 (2529.1) MB, 0.2 / 0.0 ms  (average mu = 0.980, current mu
= 0.948) allocation failure
[4500:0xc37]   177148 ms: Scavenge 2518.8 (2529.1) ->
2510.8 (2529.1) MB, 0.2 / 0.0 ms  (average mu = 0.980, current mu
= 0.948) allocation failure
[4500:0xc37]   177175 ms: Scavenge 2518.8 (2529.1) ->
2510.8 (2529.1) MB, 0.2 / 0.0 ms  (average mu = 0.980, current mu
= 0.948) allocation failure


<--- JS stacktrace --->

[4500:4500:0405/112334.605730:FATAL:memory.cc
(38)] Out of memory. size=0

Because at the end there is an ‘out of memory’ message, I have
increased the ram of my computer from 16GB to 32GB but the problem
persists. Another piece of info is that my computer has 8 CPU but
when running CCP4i2 it only uses one.

Does anybody have an idea of which could be the problem?

Best regards,

Marian





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--
Dr Jon Agirre (He/Him)
Royal Society University Research Fellow (assistant professor)
Main editor at Acta Crystallographica Section F: Structural Biology 
Communications

CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK



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Re: [ccp4bb] Refmac problem: Validation and Analysis

[Jon Agirre]

Dear Marian,
Thanks for your report. I'm sorry you're having to deal with this problem.
There is nothing wrong with your machine; this is an identified bug and
we're working towards fixing it. In the meantime, the only workaround I can
think of is to roll CCP4 back to a previous update, e.g. 015.
I will keep you posted,
Jon

On Fri, 5 Apr 2024 at 12:54, Marian Oliva  wrote:

> Dear list,
>
>
>
> I have a problem running the Validation and Analysis in Refmac and I would
> really appreciate any feed-back from your side.
>
>
>
> I am using CCP4i2 (CCP4-8.0.018 locally running in Ubuntu 20.04.4).
>
>
>
> Last time I was using Refmac was in November 2023. At the time, I posted
> in the list an error with the CCP4i2 interface (no responding) that I
> solved by turning off the 3D picture in the reports (as kindly suggested by
> Stuart McNicholas).
>
>
>
> Now, despite the 3D picture in the reports is off, I still experience
> ‘some delays’ on the interface response, though this is not a major issue.
>
>
>
> The real problem I’m experiencing is that after a (apparent) normal
> termination of Refmac (no sign of warnings or error messages), I find no
> results from the Multimeric validation.
>
>
>
> Navigating through the jobs folders I have found that in job2 (which I
> guess correspond to the validation) there is:
>
> - no prosmart related files (.out, .pdb, .py).
>
> - the tables_as_csv_files folder is empty.
>
> - there is no molprobity.log file. Instead, there is a log_mtzjoin.txt
> file but it does not highlight any warning or error either.
>
> - the program.xml file only contains the heather but otherwise, it is
> blank (which I guess this is the reason it is not running).
>
> - also, in the param.xml file I found that there are 2 sets of input data
> (instead of one and I don’t know why), where:
>
> -There is no dbFileID for the input F-SIGF data (in any of them)
>
> -In the first one the XYZIN is the XYZIN-coordinated.pdb (instead
> of the xyzout_prosmart_refmac.pdb) and in the second it is the
> xyzout_prosmart_refmac.pdb)
>
>
>
> Checking the terminal while running refmac I saw the following error
> message that appears just after refmac window state ‘The job is finished’.
> This error repeats multiple times, with variations in the
> .WebGL-alphanumerical code, from time to time and ends as follows.
>
>
>
> [3701:3802:0405/112315.960478:ERROR:gles2_cmd_decoder.cc(12701)]
> [.WebGL-0x23e9d90]GL ERROR :GL_INVALID_VALUE : glVertexAttrib4f: index out
> of range
>
> <--- Last few GCs --->
>
> [4500:0xc37]   177121 ms: Scavenge 2518.8 (2529.1) -> 2510.8
> (2529.1) MB, 0.2 / 0.0 ms  (average mu = 0.980, current mu = 0.948)
> allocation failure
> [4500:0xc37]   177148 ms: Scavenge 2518.8 (2529.1) -> 2510.8
> (2529.1) MB, 0.2 / 0.0 ms  (average mu = 0.980, current mu = 0.948)
> allocation failure
> [4500:0xc37]   177175 ms: Scavenge 2518.8 (2529.1) -> 2510.8
> (2529.1) MB, 0.2 / 0.0 ms  (average mu = 0.980, current mu = 0.948)
> allocation failure
>
>
> <--- JS stacktrace --->
>
> [4500:4500:0405/112334.605730:FATAL:memory.cc(38)] Out of memory. size=0
>
>
>
>
>
> Because at the end there is an ‘out of memory’ message, I have increased
> the ram of my computer from 16GB to 32GB but the problem persists. Another
> piece of info is that my computer has 8 CPU but when running CCP4i2 it only
> uses one.
>
>
>
> Does anybody have an idea of which could be the problem?
>
>
>
> Best regards,
>
> Marian
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>


-- 
Dr Jon Agirre (He/Him)
Royal Society University Research Fellow (assistant professor)
Main editor at Acta Crystallographica Section F: Structural Biology
Communications
CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK



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[ccp4bb] Refmac problem: Validation and Analysis

[Marian Oliva]

Dear list,
 
I have a problem running the Validation and Analysis in Refmac and I would 
really appreciate any feed-back from your side.
 
I am using CCP4i2 (CCP4-8.0.018 locally running in Ubuntu 20.04.4). 
 
Last time I was using Refmac was in November 2023. At the time, I posted in the 
list an error with the CCP4i2 interface (no responding) that I solved by 
turning off the 3D picture in the reports (as kindly suggested by Stuart 
McNicholas).
 
Now, despite the 3D picture in the reports is off, I still experience ‘some 
delays’ on the interface response, though this is not a major issue. 
 
The real problem I’m experiencing is that after a (apparent) normal termination 
of Refmac (no sign of warnings or error messages), I find no results from the 
Multimeric validation. 
 
Navigating through the jobs folders I have found that in job2 (which I guess 
correspond to the validation) there is:
- no prosmart related files (.out, .pdb, .py). 
- the tables_as_csv_files folder is empty.
- there is no molprobity.log file. Instead, there is a log_mtzjoin.txt file but 
it does not highlight any warning or error either. 
- the program.xml file only contains the heather but otherwise, it is blank 
(which I guess this is the reason it is not running). 
- also, in the param.xml file I found that there are 2 sets of input data 
(instead of one and I don’t know why), where:
-There is no dbFileID for the input F-SIGF data (in any of them)
-In the first one the XYZIN is the XYZIN-coordinated.pdb (instead of 
the xyzout_prosmart_refmac.pdb) and in the second it is the 
xyzout_prosmart_refmac.pdb)
 
Checking the terminal while running refmac I saw the following error message 
that appears just after refmac window state ‘The job is finished’. This error 
repeats multiple times, with variations in the .WebGL-alphanumerical code, from 
time to time and ends as follows. 
 
[3701:3802:0405/112315.960478:ERROR:gles2_cmd_decoder.cc 
(12701)] [.WebGL-0x23e9d90]GL ERROR 
:GL_INVALID_VALUE : glVertexAttrib4f: index out of range

<--- Last few GCs --->

[4500:0xc37]   177121 ms: Scavenge 2518.8 (2529.1) -> 2510.8 (2529.1) 
MB, 0.2 / 0.0 ms  (average mu = 0.980, current mu = 0.948) allocation failure
[4500:0xc37]   177148 ms: Scavenge 2518.8 (2529.1) -> 2510.8 (2529.1) 
MB, 0.2 / 0.0 ms  (average mu = 0.980, current mu = 0.948) allocation failure
[4500:0xc37]   177175 ms: Scavenge 2518.8 (2529.1) -> 2510.8 (2529.1) 
MB, 0.2 / 0.0 ms  (average mu = 0.980, current mu = 0.948) allocation failure


<--- JS stacktrace --->

[4500:4500:0405/112334.605730:FATAL:memory.cc (38)] Out of 
memory. size=0
 
 
Because at the end there is an ‘out of memory’ message, I have increased the 
ram of my computer from 16GB to 32GB but the problem persists. Another piece of 
info is that my computer has 8 CPU but when running CCP4i2 it only uses one.
 
Does anybody have an idea of which could be the problem?
 
Best regards,
Marian




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[ccp4bb] refmac output query

[Emmanuel Saridakis]

Dear All,

A quick question about Refmac on ccp4i. When refining an RNA oligonucleotide 
structure using the findwaters option, the pdb output labels all the atoms as 
HETATM (inluding the original RNA atoms which were not so labelled in the input 
pdb). It is of course trivial to correct this, but I was wondering if there is 
a hidden problem somewhere, that might influence more crucial things.

Many thanks,
Emmanuel

-- 
Dr. Emmanuel Saridakis
Institute of Nanoscience and Nanotechnology
National Centre for Scientific Research "DEMOKRITOS"
15310 Athens
GREECE



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Re: [ccp4bb] Refmac automatically handles twinning?

[Eleanor Dodson]

I am sure you have checked this but
A) is there non cryst translation? If so this can make space group
selection tricky . Could it be P3  21 or P31 21 or ...
B ) the twin indicators at data processing are pretty reliable and if that
suggests no twinning it probably isn’t there... you could process bits
separately to see if bens idea is likely.

C) I see data sets where long runs if vatches are totally wrong - Rmerge >1
etc - no idea why but you need to cut them out of the data processing

All very puzzling!
Eleanor

On Thu, 31 Mar 2022 at 05:46, Ben Bax  wrote:

> The twin fraction can vary during data collection - if the beam is smaller
> than the crystal
> For example you could have crystals which are like two very short ends of
> pencils - with flat ends together (in your case these might pencils could
> be in P3)
> In some orientations you could have the beam going through only one pencil
> (not twinned) and some orientations going through both pencils ( 50:50
> twin).
> This is not yet properly handled in the data processing.
>
>
>
> On 29 Mar 2022, at 09:39, Nicholas Keep  wrote:
>
> Just double checking that Refmac automatically handles twinning without
> the need for a keyword or a box click in i2.  I have a crystal in P32 21
> that gives poor Rfactors and maps (Rfree mid 40s) from what should be an
> excellent model. I have reprocessed in P32, P1 and C2 but all give similar
> results so it appears not to be hidden twinning.  There is no need to click
> a box or enter a keyword for this to be a check for twinning ?
>
> There is severe anisotropy and a few other problems flagged up in iSPYB so
> there may be more complex problems than twinning with these crystals
>
> Best wishes
>
> Nick
>
> --
> Prof Nicholas H. Keep
> Emeritus Professor of Biomolecular Science
> Crystallography, Institute for Structural and Molecular Biology,
> Department of Biological Sciences
> Birkbeck,  University of London,
> Malet Street,
> Bloomsbury
> LONDON
> WC1E 7HX
>
> Dept email n.k...@bbk.ac.uk
> Telephone 020-3926-3475  (Will contact me at home if working as well as my
> office)
>
> 
>
> 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
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>
> 
>
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Re: [ccp4bb] Refmac automatically handles twinning?

[Ben Bax]

The twin fraction can vary during data collection - if the beam is smaller than 
the crystal
For example you could have crystals which are like two very short ends of 
pencils - with flat ends together (in your case these might pencils could be in 
P3)
In some orientations you could have the beam going through only one pencil (not 
twinned) and some orientations going through both pencils ( 50:50 twin).
This is not yet properly handled in the data processing.



On 29 Mar 2022, at 09:39, Nicholas Keep  wrote:

Just double checking that Refmac automatically handles twinning without the 
need for a keyword or a box click in i2.  I have a crystal in P32 21 that gives 
poor Rfactors and maps (Rfree mid 40s) from what should be an excellent model. 
I have reprocessed in P32, P1 and C2 but all give similar results so it appears 
not to be hidden twinning.  There is no need to click a box or enter a keyword 
for this to be a check for twinning ?

There is severe anisotropy and a few other problems flagged up in iSPYB so 
there may be more complex problems than twinning with these crystals

Best wishes

Nick

-- 
Prof Nicholas H. Keep
Emeritus Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

Dept email n.k...@bbk.ac.uk
Telephone 020-3926-3475  (Will contact me at home if working as well as my 
office)



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[ccp4bb] Refmac automatically handles twinning?

[Nicholas Keep]

Just double checking that Refmac automatically handles twinning without 
the need for a keyword or a box click in i2.  I have a crystal in P32 21 
that gives poor Rfactors and maps (Rfree mid 40s) from what should be an 
excellent model. I have reprocessed in P32, P1 and C2 but all give 
similar results so it appears not to be hidden twinning.  There is no 
need to click a box or enter a keyword for this to be a check for twinning ?


There is severe anisotropy and a few other problems flagged up in iSPYB 
so there may be more complex problems than twinning with these crystals


Best wishes

Nick

--
Prof Nicholas H. Keep
Emeritus Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

Dept email n.k...@bbk.ac.uk
Telephone 020-3926-3475  (Will contact me at home if working as well as my 
office)



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Re: [ccp4bb] Refmac is changing the bond lengths, torsion angle of modified residues

[Prasun Kumar]

Hi
Thanx for your response. I was quite surprised to see such examples listed as 
outlier in the pdb validation report. The angles are deviating by 8-10 deg. Am 
I being so picky on this. Do you suggest me to ignore such warnings

Cheers
PK


From: Hinrichs, Winfried 
Sent: 16 November 2021 19:24
To: Prasun Kumar 
Subject: Re: [ccp4bb] Refmac is changing the bond lengths, torsion angle of 
modified residues


Dear PR,

0.1Angstrom is not a general disaster - you should talk to a chemist.

Best,
Winfried Hinrichs

--
--




Am Dienstag, den 16-11-2021 um 19:56 schrieb Prasun Kumar:
Hi Group

I am refining one of the structures that has modified amino acid and it is not 
defined in the CCP4 dictionary.
I got the restrains using ELBOW and used it for refinement. However, when I 
refine the structure using REFMAC, the bond length deviates significantly from 
the ideal/ given value in the restrains file. for example: BR-CZ bond length is 
2.01 ang (observed), but the ideal value is 1.9 ang. Bond angle and torsional 
angles are also behaving in a similar way.

Can you please suggest a method by which I can fix this issue.

I am happy to provide any other information.

Thank You
PK




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[ccp4bb] Refmac is changing the bond lengths, torsion angle of modified residues

[Prasun Kumar]

Hi Group

I am refining one of the structures that has modified amino acid and it is not 
defined in the CCP4 dictionary.
I got the restrains using ELBOW and used it for refinement. However, when I 
refine the structure using REFMAC, the bond length deviates significantly from 
the ideal/ given value in the restrains file. for example: BR-CZ bond length is 
2.01 ang (observed), but the ideal value is 1.9 ang. Bond angle and torsional 
angles are also behaving in a similar way.

Can you please suggest a method by which I can fix this issue.

I am happy to provide any other information.

Thank You
PK




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Re: [ccp4bb] refmac - use weighting term - pdb to mmcif

[Marina Gárdonyi]

I deleted a line in the keyword file which was "pdbout format mmcif".

It was my first try to convert the pdb file to an mmcif file, but it  
did not work!


Best
Marina


Zitat von "Krieger, James M" :


It could be good to say how you solved it for future users.

Best wishes
James

On Aug 6, 2021, at 09:27, Marina Gárdonyi  
<652c4b26eb10-dmarc-requ...@jiscmail.ac.uk> wrote:


Hi,

as it is often the case, the mail is out and you are able to solve  
the problem on your own. Thanks anyway!


Best
Marina

Zitat von Marina Gárdonyi <652c4b26eb10-dmarc-requ...@jiscmail.ac.uk>:


Hi,

before I will soon finish my PhD, I have to solve one more problem.

I managed to refine occupancies and tls in Refmac. I also found  
out that you can use pdb-extract to convert the pdb file to an  
mmcif file so that you can validate the structure using the  
validation server.
However, during validation, it came out that the bond lengths and  
angles are hugely different from the expected values. I had used  
the automatic weighting until then. If I do the weighting by hand  
(I tried different weighting terms), I cannot convert the pdb file  
into an mmcif file anymore, because the pdb file has a different  
structure and pdb-extract does not recognize the pdb file as such.


Does anyone know the problem and can help me?

Best
Marina

--
Marina Gárdonyi

PhD Student, Research Group Professor Dr. Klebe

Department of Pharmaceutical Chemistry

Philipps-University Marburg

Marbacher Weg 6, 35032 Marburg, Germany

Phone: +49 6421 28 21392

E-Mail: marina@pharmazie.uni-marburg.de

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Re: [ccp4bb] refmac - use weighting term - pdb to mmcif

[Marina Gárdonyi]

Hi,

as it is often the case, the mail is out and you are able to solve the  
problem on your own. Thanks anyway!


Best
Marina

Zitat von Marina Gárdonyi <652c4b26eb10-dmarc-requ...@jiscmail.ac.uk>:


Hi,

before I will soon finish my PhD, I have to solve one more problem.

I managed to refine occupancies and tls in Refmac. I also found out  
that you can use pdb-extract to convert the pdb file to an mmcif  
file so that you can validate the structure using the validation  
server.
However, during validation, it came out that the bond lengths and  
angles are hugely different from the expected values. I had used the  
automatic weighting until then. If I do the weighting by hand (I  
tried different weighting terms), I cannot convert the pdb file into  
an mmcif file anymore, because the pdb file has a different  
structure and pdb-extract does not recognize the pdb file as such.


Does anyone know the problem and can help me?

Best
Marina

--
Marina Gárdonyi

PhD Student, Research Group Professor Dr. Klebe

Department of Pharmaceutical Chemistry

Philipps-University Marburg

Marbacher Weg 6, 35032 Marburg, Germany

Phone: +49 6421 28 21392

E-Mail: marina@pharmazie.uni-marburg.de

http://www.agklebe.de/



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--
Marina Gárdonyi

PhD Student, Research Group Professor Dr. Klebe

Department of Pharmaceutical Chemistry

Philipps-University Marburg

Marbacher Weg 6, 35032 Marburg, Germany

Phone: +49 6421 28 21392

E-Mail: marina@pharmazie.uni-marburg.de

http://www.agklebe.de/



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[ccp4bb] refmac - use weighting term - pdb to mmcif

[Marina Gárdonyi]

Hi,

before I will soon finish my PhD, I have to solve one more problem.

I managed to refine occupancies and tls in Refmac. I also found out  
that you can use pdb-extract to convert the pdb file to an mmcif file  
so that you can validate the structure using the validation server.
However, during validation, it came out that the bond lengths and  
angles are hugely different from the expected values. I had used the  
automatic weighting until then. If I do the weighting by hand (I tried  
different weighting terms), I cannot convert the pdb file into an  
mmcif file anymore, because the pdb file has a different structure and  
pdb-extract does not recognize the pdb file as such.


Does anyone know the problem and can help me?

Best
Marina

--
Marina Gárdonyi

PhD Student, Research Group Professor Dr. Klebe

Department of Pharmaceutical Chemistry

Philipps-University Marburg

Marbacher Weg 6, 35032 Marburg, Germany

Phone: +49 6421 28 21392

E-Mail: marina@pharmazie.uni-marburg.de

http://www.agklebe.de/



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Re: [ccp4bb] refmac twin refinement vs resolution limit

[Yuji Kado]

Dear Eleanor,

Thank you so much.
As you said, it is a problem that the number of reflections estimated by FreeR 
set is different from an actual that of reflections because of the low 
resolution discrepancy. Moreover, twin refinement includes a problem about some 
overlapping of diffraction spot.

But fortunately, I solved it. I just add twin tolerance parameter to refmac. In 
my case, parameters of L and H test slightly increase and the space group is 
P21, suggesting that it seems not to a merohedral twinning but a 
pseudo-merohedral twinning. In the case of pseudo merohedral, higher tolerance 
sometimes causes resolution stretch problem. After the refinement, resolution 
range and electron density map look fine so that I concluded that's the reason.

Regards,
Yuji



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Re: [ccp4bb] refmac twin refinement vs resolution limit

[Eleanor Dodson]

Well - I am not sure whether this has anything to do with twin refinement
but resolution limits are often a bit iffy.
First the low resolution discrepancy. The Free R is  generated to a
lower and higher resolution than any observation. The FreeR set is meant to
be complete for any possible index regardless of whether there IS an
observation or not. (There are good reasons for this - if your data set is
very incomplete it is better to have "reflections" included in
map calculations with values DFc rather than omitting them altogether - ie
effectively using them with intensity set to zero.) But it does look a bit
bizarre in the printed limits..
I dont think it matters - the number of observations is not changed.

However for twin refinement things are a bit more complicated. Every
"reflection" is actually a sum of two (or more) overlapping observations, I
(h k l) and I(h(twin) k(twin) l(twin) )  and I really do not know what
REFMAC will do if one of the pair is not observed..

And there are even more complicated scenarios if your twin is
non-merahedral!

Eleanor

On Mon, 29 Mar 2021 at 08:21, Yuji Kado  wrote:

> When I use refmac restrained refinement with intensity based twin
> refinement,
> resolution limit has been changed from 71.4519- 1.9996 to 47.392-1.986.
>
> From Log file, before refinement, Scaling and SigmaA resln: 71.4519
> 1.9996, seems to be correct.
> But in the middle of log file, around Fom and SigmaA vs resolution,
> Resolution limits are from 47.392 to 1.986.
>
> Output mtz file also shows different resolution range 71.46-1.925.
> Amplitude based twin refinement is also failed.
> Even if I input resolution range at Refinement parameters in refmac, the
> problem still occurs.
>
> I also read someone's similar problem, but it has been solved because of
> the update of refmac.
> What should I do to correspond with resolution range between the output of
> aimless and refmac restrained refinement?
>
> regards,
> Yuji
>
> 
>
> 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] refmac twin refinement vs resolution limit

[Yuji Kado]

When I use refmac restrained refinement with intensity based twin refinement,
resolution limit has been changed from 71.4519- 1.9996 to 47.392-1.986.

From Log file, before refinement, Scaling and SigmaA resln: 71.4519 1.9996, 
seems to be correct.
But in the middle of log file, around Fom and SigmaA vs resolution, Resolution 
limits are from 47.392 to 1.986.

Output mtz file also shows different resolution range 71.46-1.925.
Amplitude based twin refinement is also failed.
Even if I input resolution range at Refinement parameters in refmac, the 
problem still occurs.

I also read someone's similar problem, but it has been solved because of the 
update of refmac.
What should I do to correspond with resolution range between the output of 
aimless and refmac restrained refinement?

regards,
Yuji



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Re: [ccp4bb] Refmac not handling microheterogeneity?

[Ian Tickle]

; 0.50 27.65 N
> >
> > ATOM 2355 CA ATHR A 279 136.909 167.684 153.607 0.50 28.45 C
> >
> > ATOM 2356 C ATHR A 279 135.937 167.731 154.799 0.50 31.92 C
> >
> > ATOM 2357 O ATHR A 279 136.426 167.682 155.949 0.50 32.52 O
> >
> > ATOM 2358 CB ATHR A 279 136.906 166.273 153.009 0.50 27.04 C
> >
> > ATOM 2359 OG1ATHR A 279 137.119 165.333 154.066 0.50 28.59 O
> >
> > ATOM 2360 CG2ATHR A 279 137.957 166.077 151.931 0.50 27.69 C
> >
> > ATOM 2361 N BLYS A 279 138.238 168.081 154.020 0.50 32.20 N
> >
> > ATOM 2362 CA BLYS A 279 136.870 167.701 153.585 0.50 36.51 C
> >
> > ATOM 2363 C BLYS A 279 135.930 167.793 154.787 0.50 38.18 C
> >
> > ATOM 2364 O BLYS A 279 136.377 168.014 155.910 0.50 42.23 O
> >
> > ATOM 2365 CB BLYS A 279 136.887 166.298 152.984 0.50 40.70 C
> >
> > ATOM 2366 CG BLYS A 279 137.909 166.091 151.872 0.50 46.05 C
> >
> > ATOM 2367 CD BLYS A 279 138.177 164.645 151.591 0.50 50.67 C
> >
> > ATOM 2368 CE BLYS A 279 139.166 164.047 152.568 0.50 59.69 C
> >
> > ATOM 2369 NZ BLYS A 279 140.515 163.892 151.967 0.50 59.05 N
> >
> >
> >
> >
> > In case 1 OD1 A is immediately followed bu OD1B
> >
> >
> > In second case - all As listed then all Bs
> >
> >
> > Eleanor
> >
> >
> >
> >
> > On Wed, 2 Dec 2020 at 14:34, Robbie Joosten <
> robbie_joos...@hotmail.com <mailto:robbie_joos...@hotmail.com>> wrote:
> >
> > Hi Ian,
> >
> > AFAIK there is no clean solution for this and I imagine this
> problem goes very deep into the internal representation of the model in
> REFMAC. That said, 1 in 6 missing PDB-REDO entries is caused by this
> problem, so a solution would be very welcome.
> >
> > Cheers,
> > Robbie
> >
> >  > -Original Message-
> >  > From: CCP4 bulletin board  CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Ian
> >  > Tickle
> >  > Sent: Wednesday, December 2, 2020 15:02
> >  > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> >  > Subject: [ccp4bb] Refmac not handling microheterogeneity?
> >  >
> >  >
> >  > Dear All
> >  >
> >  > I just downloaded a PDB file (7A5V) from the EBI server,
> tried to run Refmac
> >  > on it and got the error:
> >  >
> >  > ERROR: in chain A residue: 279 different residues have the
> same number
> >  > There is an error in the input coordinate file
> >  >
> >  > At least one the chains has 2 residues with the same number
> ===> Error:
> >  > Problem with coordinate file
> >  >
> >  >
> >  > and indeed residue A279 has:
> >  >
> >  > ATOM   2354  N  ATHR A 279 138.241 168.068 154.050  0.50
> 27.65   N
> >  >
> >  > and
> >  > ATOM   2361  N  BLYS A 279 138.238 168.081 154.020  0.50
> 32.20   N
> >  > and the same for all the other atoms in the residues.
> >  >
> >  > Searching the CCP4BB archives for "microheterogeneity" I see
> that this has
> >  > been discussed before and apparently it should "just work" if
> there are alt
> >  > atom indicators (check) and occupancies add up to <= 1
> (check).  I must say I
> >  > also was of the impression that it "just worked" so I'm a bit
> confused now
> >  > why it doesn't.
> >  >
> >  > Version info:

Re: [ccp4bb] Refmac not handling microheterogeneity?

[Keitaro Yamashita]

5.910 0.50 42.23 O

ATOM 2365 CB BLYS A 279 136.887 166.298 152.984 0.50 40.70 C

ATOM 2366 CG BLYS A 279 137.909 166.091 151.872 0.50 46.05 C

ATOM 2367 CD BLYS A 279 138.177 164.645 151.591 0.50 50.67 C

ATOM 2368 CE BLYS A 279 139.166 164.047 152.568 0.50 59.69 C

ATOM 2369 NZ BLYS A 279 140.515 163.892 151.967 0.50 59.05 N




In case 1 OD1 A is immediately followed bu OD1B


In second case - all As listed then all Bs


Eleanor




On Wed, 2 Dec 2020 at 14:34, Robbie Joosten mailto:robbie_joos...@hotmail.com>> wrote:

Hi Ian,

AFAIK there is no clean solution for this and I imagine this problem 
goes very deep into the internal representation of the model in REFMAC. That 
said, 1 in 6 missing PDB-REDO entries is caused by this problem, so a solution 
would be very welcome.

Cheers,
Robbie

 > -Original Message-
 > From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Ian
 > Tickle
 > Sent: Wednesday, December 2, 2020 15:02
     > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
 > Subject: [ccp4bb] Refmac not handling microheterogeneity?
 >
 >
 > Dear All
 >
 > I just downloaded a PDB file (7A5V) from the EBI server, tried to 
run Refmac
 > on it and got the error:
 >
 > ERROR: in chain A residue: 279 different residues have the same 
number
 > There is an error in the input coordinate file
 >
 > At least one the chains has 2 residues with the same number ===> 
Error:
 > Problem with coordinate file
 >
 >
 > and indeed residue A279 has:
 >
 > ATOM   2354  N  ATHR A 279     138.241 168.068 154.050  0.50 27.65   
        N
 >
 > and
 > ATOM   2361  N  BLYS A 279     138.238 168.081 154.020  0.50 32.20   
        N
 > and the same for all the other atoms in the residues.
 >
 > Searching the CCP4BB archives for "microheterogeneity" I see that 
this has
 > been discussed before and apparently it should "just work" if there 
are alt
 > atom indicators (check) and occupancies add up to <= 1 (check).  I 
must say I
 > also was of the impression that it "just worked" so I'm a bit 
confused now
 > why it doesn't.
 >
 > Version info:
 > DISTRIB_DESCRIPTION="Ubuntu 20.04.1 LTS"
 > ### CCP4 7.1.008: Refmac          version 5.8.0267 : 24/08/20##
 >
 > Is there some other hack I need to do to get it to work?
 >
 > Cheers
 >
 > -- Ian
 >
 >
 >
 >
 > 
 >
 >
 > 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] Refmac not handling microheterogeneity?

[Ian Tickle]

Sorry Eleanor, same problem in 'interleaved' order (except for 2 extra
atoms in LYS).

Strangely the error message is now repeated 91 times, even though there are
only 16 atoms (7+9) in the 2 residues: previously I only got the message
once !

Guess I must have imagined that it worked - it's called 'expectation bias' !

Thanks anyway.

-- Ian


On Wed, 2 Dec 2020 at 18:34, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> Only a hunch but this works:
>
> ATOM 1036 OD1AASN A 172 -7.722 13.371 -18.195 0.50 5.12 O
>
> ATOM 1037 OD1BASN A 172 -7.152 14.800 -15.791 0.50 7.63 O
>
>
> And here you have:ATOM 2354 N ATHR A 279 138.241 168.068 154.050 0.50
> 27.65 N
>
> ATOM 2355 CA ATHR A 279 136.909 167.684 153.607 0.50 28.45 C
>
> ATOM 2356 C ATHR A 279 135.937 167.731 154.799 0.50 31.92 C
>
> ATOM 2357 O ATHR A 279 136.426 167.682 155.949 0.50 32.52 O
>
> ATOM 2358 CB ATHR A 279 136.906 166.273 153.009 0.50 27.04 C
>
> ATOM 2359 OG1ATHR A 279 137.119 165.333 154.066 0.50 28.59 O
>
> ATOM 2360 CG2ATHR A 279 137.957 166.077 151.931 0.50 27.69 C
>
> ATOM 2361 N BLYS A 279 138.238 168.081 154.020 0.50 32.20 N
>
> ATOM 2362 CA BLYS A 279 136.870 167.701 153.585 0.50 36.51 C
>
> ATOM 2363 C BLYS A 279 135.930 167.793 154.787 0.50 38.18 C
>
> ATOM 2364 O BLYS A 279 136.377 168.014 155.910 0.50 42.23 O
>
> ATOM 2365 CB BLYS A 279 136.887 166.298 152.984 0.50 40.70 C
>
> ATOM 2366 CG BLYS A 279 137.909 166.091 151.872 0.50 46.05 C
>
> ATOM 2367 CD BLYS A 279 138.177 164.645 151.591 0.50 50.67 C
>
> ATOM 2368 CE BLYS A 279 139.166 164.047 152.568 0.50 59.69 C
>
> ATOM 2369 NZ BLYS A 279 140.515 163.892 151.967 0.50 59.05 N
>
>
>
>
> In case 1 OD1 A is immediately followed bu OD1B
>
>
> In second case - all As listed then all Bs
>
>
> Eleanor
>
>
>
>
> On Wed, 2 Dec 2020 at 14:34, Robbie Joosten 
> wrote:
>
>> Hi Ian,
>>
>> AFAIK there is no clean solution for this and I imagine this problem goes
>> very deep into the internal representation of the model in REFMAC. That
>> said, 1 in 6 missing PDB-REDO entries is caused by this problem, so a
>> solution would be very welcome.
>>
>> Cheers,
>> Robbie
>>
>> > -Original Message-
>> > From: CCP4 bulletin board  On Behalf Of Ian
>> > Tickle
>> > Sent: Wednesday, December 2, 2020 15:02
>> > To: CCP4BB@JISCMAIL.AC.UK
>> > Subject: [ccp4bb] Refmac not handling microheterogeneity?
>> >
>> >
>> > Dear All
>> >
>> > I just downloaded a PDB file (7A5V) from the EBI server, tried to run
>> Refmac
>> > on it and got the error:
>> >
>> > ERROR: in chain A residue: 279 different residues have the same number
>> > There is an error in the input coordinate file
>> >
>> > At least one the chains has 2 residues with the same number ===> Error:
>> > Problem with coordinate file
>> >
>> >
>> > and indeed residue A279 has:
>> >
>> > ATOM   2354  N  ATHR A 279 138.241 168.068 154.050  0.50 27.65
>>  N
>> >
>> > and
>> > ATOM   2361  N  BLYS A 279 138.238 168.081 154.020  0.50 32.20
>>  N
>> > and the same for all the other atoms in the residues.
>> >
>> > Searching the CCP4BB archives for "microheterogeneity" I see that this
>> has
>> > been discussed before and apparently it should "just work" if there are
>> alt
>> > atom indicators (check) and occupancies add up to <= 1 (check).  I must
>> say I
>> > also was of the impression that it "just worked" so I'm a bit confused
>> now
>> > why it doesn't.
>> >
>> > Version info:
>> > DISTRIB_DESCRIPTION="Ubuntu 20.04.1 LTS"
>> > ### CCP4 7.1.008: Refmac  version 5.8.0267 : 24/08/20##
>> >
>> > Is there some other hack I need to do to get it to work?
>> >
>> > Cheers
>> >
>> > -- Ian
>> >
>> >
>> >
>> >
>> > 
>> >
>> >
>> > 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:
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Re: [ccp4bb] Refmac not handling microheterogeneity?

[Eleanor Dodson]

Only a hunch but this works:

ATOM 1036 OD1AASN A 172 -7.722 13.371 -18.195 0.50 5.12 O

ATOM 1037 OD1BASN A 172 -7.152 14.800 -15.791 0.50 7.63 O


And here you have:ATOM 2354 N ATHR A 279 138.241 168.068 154.050 0.50 27.65
N

ATOM 2355 CA ATHR A 279 136.909 167.684 153.607 0.50 28.45 C

ATOM 2356 C ATHR A 279 135.937 167.731 154.799 0.50 31.92 C

ATOM 2357 O ATHR A 279 136.426 167.682 155.949 0.50 32.52 O

ATOM 2358 CB ATHR A 279 136.906 166.273 153.009 0.50 27.04 C

ATOM 2359 OG1ATHR A 279 137.119 165.333 154.066 0.50 28.59 O

ATOM 2360 CG2ATHR A 279 137.957 166.077 151.931 0.50 27.69 C

ATOM 2361 N BLYS A 279 138.238 168.081 154.020 0.50 32.20 N

ATOM 2362 CA BLYS A 279 136.870 167.701 153.585 0.50 36.51 C

ATOM 2363 C BLYS A 279 135.930 167.793 154.787 0.50 38.18 C

ATOM 2364 O BLYS A 279 136.377 168.014 155.910 0.50 42.23 O

ATOM 2365 CB BLYS A 279 136.887 166.298 152.984 0.50 40.70 C

ATOM 2366 CG BLYS A 279 137.909 166.091 151.872 0.50 46.05 C

ATOM 2367 CD BLYS A 279 138.177 164.645 151.591 0.50 50.67 C

ATOM 2368 CE BLYS A 279 139.166 164.047 152.568 0.50 59.69 C

ATOM 2369 NZ BLYS A 279 140.515 163.892 151.967 0.50 59.05 N




In case 1 OD1 A is immediately followed bu OD1B


In second case - all As listed then all Bs


Eleanor




On Wed, 2 Dec 2020 at 14:34, Robbie Joosten 
wrote:

> Hi Ian,
>
> AFAIK there is no clean solution for this and I imagine this problem goes
> very deep into the internal representation of the model in REFMAC. That
> said, 1 in 6 missing PDB-REDO entries is caused by this problem, so a
> solution would be very welcome.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of Ian
> > Tickle
> > Sent: Wednesday, December 2, 2020 15:02
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] Refmac not handling microheterogeneity?
> >
> >
> > Dear All
> >
> > I just downloaded a PDB file (7A5V) from the EBI server, tried to run
> Refmac
> > on it and got the error:
> >
> > ERROR: in chain A residue: 279 different residues have the same number
> > There is an error in the input coordinate file
> >
> > At least one the chains has 2 residues with the same number ===> Error:
> > Problem with coordinate file
> >
> >
> > and indeed residue A279 has:
> >
> > ATOM   2354  N  ATHR A 279 138.241 168.068 154.050  0.50 27.65
>  N
> >
> > and
> > ATOM   2361  N  BLYS A 279 138.238 168.081 154.020  0.50 32.20
>  N
> > and the same for all the other atoms in the residues.
> >
> > Searching the CCP4BB archives for "microheterogeneity" I see that this
> has
> > been discussed before and apparently it should "just work" if there are
> alt
> > atom indicators (check) and occupancies add up to <= 1 (check).  I must
> say I
> > also was of the impression that it "just worked" so I'm a bit confused
> now
> > why it doesn't.
> >
> > Version info:
> > DISTRIB_DESCRIPTION="Ubuntu 20.04.1 LTS"
> > ### CCP4 7.1.008: Refmac  version 5.8.0267 : 24/08/20##
> >
> > Is there some other hack I need to do to get it to work?
> >
> > Cheers
> >
> > -- Ian
> >
> >
> >
> >
> > 
> >
> >
> > 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] Refmac not handling microheterogeneity?

[Robbie Joosten]

Hi Ian,

AFAIK there is no clean solution for this and I imagine this problem goes very 
deep into the internal representation of the model in REFMAC. That said, 1 in 6 
missing PDB-REDO entries is caused by this problem, so a solution would be very 
welcome.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Ian
> Tickle
> Sent: Wednesday, December 2, 2020 15:02
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Refmac not handling microheterogeneity?
> 
> 
> Dear All
> 
> I just downloaded a PDB file (7A5V) from the EBI server, tried to run Refmac
> on it and got the error:
> 
> ERROR: in chain A residue: 279 different residues have the same number
> There is an error in the input coordinate file
> 
> At least one the chains has 2 residues with the same number ===> Error:
> Problem with coordinate file
> 
> 
> and indeed residue A279 has:
> 
> ATOM   2354  N  ATHR A 279 138.241 168.068 154.050  0.50 27.65   N
> 
> and
> ATOM   2361  N  BLYS A 279 138.238 168.081 154.020  0.50 32.20   N
> and the same for all the other atoms in the residues.
> 
> Searching the CCP4BB archives for "microheterogeneity" I see that this has
> been discussed before and apparently it should "just work" if there are alt
> atom indicators (check) and occupancies add up to <= 1 (check).  I must say I
> also was of the impression that it "just worked" so I'm a bit confused now
> why it doesn't.
> 
> Version info:
> DISTRIB_DESCRIPTION="Ubuntu 20.04.1 LTS"
> ### CCP4 7.1.008: Refmac  version 5.8.0267 : 24/08/20##
> 
> Is there some other hack I need to do to get it to work?
> 
> Cheers
> 
> -- Ian
> 
> 
> 
> 
> 
> 
> 
> 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] Refmac not handling microheterogeneity?

[Ian Tickle]

Dear All

I just downloaded a PDB file (7A5V) from the EBI server, tried to run
Refmac on it and got the error:

ERROR: in chain A residue: 279 different residues have the same number
There is an error in the input coordinate file
At least one the chains has 2 residues with the same number
===> Error: Problem with coordinate file

and indeed residue A279 has:

ATOM   2354  N  ATHR A 279 138.241 168.068 154.050  0.50 27.65
 N
and
ATOM   2361  N  BLYS A 279 138.238 168.081 154.020  0.50 32.20
 N
and the same for all the other atoms in the residues.

Searching the CCP4BB archives for "microheterogeneity" I see that this has
been discussed before and apparently it should "just work" if there are alt
atom indicators (check) and occupancies add up to <= 1 (check).  I must say
I also was of the impression that it "just worked" so I'm a bit confused
now why it doesn't.

Version info:
DISTRIB_DESCRIPTION="Ubuntu 20.04.1 LTS"
### CCP4 7.1.008: Refmac  version 5.8.0267 : 24/08/20##

Is there some other hack I need to do to get it to work?

Cheers

-- Ian



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Re: [ccp4bb] Refmac use - water addition

[Christian Roth]

Hi Luca,
as Eleanor mentioned, in the i2 interface there is in the option menu an
add water button. That will automatically run the coot find waters script
similar to the old interface.  Paul did use some very sensible values to
look for blobs, which might be waters. These ones are used (basically the
same defaults if you press the interactive find waters button in Coot
alone).  Afterwards there is another quick 5 cycle refmac run to refine
position and B-values of the added waters.
The R value is the R work. If the value does not reach the given values
during the refinement process, the  additional water picking step is
skipped. The R value is based on your experience and one has to take
resolution, status of the model etc. into account. It is often not helpful
to add waters at an early stage of model building and refinement when R
values are hight or the model is very incomplete.
Does that make sense?

Best
Christian

On Sat, Sep 12, 2020 at 8:38 PM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> You don’t say quite how you are doing this. There is an option in the i2
> pipeline to add waters using coot when the r factor falls below some
> assigned value.
> This is done using COOT.
> One can debate whether it is a useful option or whether the user would be
> better o open COOT and supervise the water search..
> Eleanor
>
> On Sat, 12 Sep 2020 at 16:56, Jon Cooper <
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hello, I'm not totally up-to-the minute with this but I didn't know that
>> refmac itself added waters so maybe it's another program in an i2 pipeline,
>> or something. However, I know another excellent refinement program that
>> does ;-) and an excellent graphics program that does, too ;-0
>>
>> In the past, we have added well-defined water molecule when the R-factor
>> goes into the mid-to-low thirties, or lower.
>>
>> Anything above 2 sigma in a delta-F map making sensible H-bonds is likely
>> to be real but you can lower that cutoff a bit (~1.5) if your resolution is
>> not brilliant.
>>
>> Glad to be corrected on this.
>>
>> Best wishes, Jon Cooper.
>>
>> jon.b.coo...@protonmail.com
>>
>>
>>
>>
>>
>>  Original Message 
>> On 12 Sep 2020, 11:06, Luca Mazzei < luca.mazz...@unibo.it> wrote:
>>
>>
>> Dear CCP4 people,
>>
>>
>> I am approaching in these days to the new CCP4i2 interface and, in
>> particular, to REFMAC. Can anyone quickly explain what the factor R, that
>> must be chosen in order to automatically add water molecules, is? How can I
>> relate this value with the previous DELFWT and FWT map values?
>>
>>
>> Thanks,
>>
>>
>> Luca
>>
>>
>> Luca Mazzei - PhD
>>
>>
>> Department of Pharmacy and Biotechnology
>>
>>
>> University of Bologna
>> 
>>
>>
>> Viale Giuseppe Fanin, 40 - 40127
>> 
>>
>>
>> Bologna - Italy
>> 
>>
>>
>> 
>>
>>
>> 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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>>
>>
>>
>>
>>
>>
>>
>> --
>>
>>
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Re: [ccp4bb] Refmac use - water addition

[Eleanor Dodson]

You don’t say quite how you are doing this. There is an option in the i2
pipeline to add waters using coot when the r factor falls below some
assigned value.
This is done using COOT.
One can debate whether it is a useful option or whether the user would be
better o open COOT and supervise the water search..
Eleanor

On Sat, 12 Sep 2020 at 16:56, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello, I'm not totally up-to-the minute with this but I didn't know that
> refmac itself added waters so maybe it's another program in an i2 pipeline,
> or something. However, I know another excellent refinement program that
> does ;-) and an excellent graphics program that does, too ;-0
>
> In the past, we have added well-defined water molecule when the R-factor
> goes into the mid-to-low thirties, or lower.
>
> Anything above 2 sigma in a delta-F map making sensible H-bonds is likely
> to be real but you can lower that cutoff a bit (~1.5) if your resolution is
> not brilliant.
>
> Glad to be corrected on this.
>
> Best wishes, Jon Cooper.
>
> jon.b.coo...@protonmail.com
>
>
>
>
>
>  Original Message 
> On 12 Sep 2020, 11:06, Luca Mazzei < luca.mazz...@unibo.it> wrote:
>
>
> Dear CCP4 people,
>
>
> I am approaching in these days to the new CCP4i2 interface and, in
> particular, to REFMAC. Can anyone quickly explain what the factor R, that
> must be chosen in order to automatically add water molecules, is? How can I
> relate this value with the previous DELFWT and FWT map values?
>
>
> Thanks,
>
>
> Luca
>
>
> Luca Mazzei - PhD
>
>
> Department of Pharmacy and Biotechnology
>
>
> University of Bologna
> 
>
>
> Viale Giuseppe Fanin, 40 - 40127
> 
>
>
> Bologna - Italy
> 
>
>
> 
>
>
> 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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>
>
>
>
>
>
>
> --
>
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Re: [ccp4bb] Refmac use - water addition

[Luca Mazzei]

Dear Jon,

thanks for your answer. Maybe I have been too quick in writing my last message. 
The point is that with the old CCP4 interface, I would have been able to run 
Coot-findwaters to automatically add and remove water molecules at certain 
DELFWT and FWT rmsd tresholds, respectively, through REFMAC interface. Now, 
with the new interface, Coot-findwaters is not made explicit anywhere, and 
DELFWT and FWT rmsd tresholds seem not to be changeable. There’s only "R lower 
than” that is surely what you say = Rfactor (%) lower than 30%. I would not 
want to create misunderstandings, I am just asking for things which are not 
clear to me (maybe given my limited experience), starting from the assumption 
that my knowledge in refinement, model building and, more in general, protein 
crystallography, can always improve. 

Thanks for the precious help,

Luca Mazzei

Luca Mazzei - PhD
Department of Pharmacy and Biotechnology
University of Bologna
Viale Giuseppe Fanin, 40 - 40127
Bologna - Italy



> Il giorno 12 set 2020, alle ore 17:55, Jon Cooper 
>  ha scritto:
> 
> Hello, I'm not totally up-to-the minute with this but I didn't know that 
> refmac itself added waters so maybe it's another program in an i2 pipeline, 
> or something. However, I know another excellent refinement program that does 
> ;-) and an excellent graphics program that does, too ;-0
> 
> In the past, we have added well-defined water molecule when the R-factor goes 
> into the mid-to-low thirties, or lower. 
> 
> Anything above 2 sigma in a delta-F map making sensible H-bonds is likely to 
> be real but you can lower that cutoff a bit (~1.5) if your resolution is not 
> brilliant.
> 
> Glad to be corrected on this.
> 
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
> 
> 
> 
> 
> 
>  Original Message 
> On 12 Sep 2020, 11:06, Luca Mazzei < luca.mazz...@unibo.it> wrote:
> 
> Dear CCP4 people,
> 
> I am approaching in these days to the new CCP4i2 interface and, in 
> particular, to REFMAC. Can anyone quickly explain what the factor R, that 
> must be chosen in order to automatically add water molecules, is? How can I 
> relate this value with the previous DELFWT and FWT map values?
> 
> Thanks,
> 
> Luca
> 
> Luca Mazzei - PhD
> Department of Pharmacy and Biotechnology
> University of Bologna
> Viale Giuseppe Fanin, 40 - 40127
> Bologna - Italy
> 
> 
> 
> 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 
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Re: [ccp4bb] Refmac use - water addition

[Jon Cooper]

Hello, I'm not totally up-to-the minute with this but I didn't know that refmac 
itself added waters so maybe it's another program in an i2 pipeline, or 
something. However, I know another excellent refinement program that does ;-) 
and an excellent graphics program that does, too ;-0

In the past, we have added well-defined water molecule when the R-factor goes 
into the mid-to-low thirties, or lower.

Anything above 2 sigma in a delta-F map making sensible H-bonds is likely to be 
real but you can lower that cutoff a bit (~1.5) if your resolution is not 
brilliant.

Glad to be corrected on this.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

 Original Message 
On 12 Sep 2020, 11:06, Luca Mazzei wrote:

> Dear CCP4 people,
>
> I am approaching in these days to the new CCP4i2 interface and, in 
> particular, to REFMAC. Can anyone quickly explain what the factor R, that 
> must be chosen in order to automatically add water molecules, is? How can I 
> relate this value with the previous DELFWT and FWT map values?
>
> Thanks,
>
> Luca
>
> Luca Mazzei - PhD
> Department of Pharmacy and Biotechnology
> University of Bologna
> Viale Giuseppe Fanin, 40 - 40127
> Bologna - Italy
>
> 
>
> 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 
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[ccp4bb] Refmac use - water addition

[Luca Mazzei]

Dear CCP4 people, 

I am approaching in these days to the new CCP4i2 interface and, in particular, 
to REFMAC. Can anyone quickly explain what the factor R, that must be chosen in 
order to automatically add water molecules, is? How can I relate this value 
with the previous DELFWT and FWT map values?

Thanks,

Luca 

Luca Mazzei - PhD
Department of Pharmacy and Biotechnology
University of Bologna
Viale Giuseppe Fanin, 40 - 40127
Bologna - Italy



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Re: [ccp4bb] Refmac Ideal Geometry Library

[Robert Nicholls]

Hi Dale,

Yes Refmac uses the dictionaries found in lib/data/monomers
Of course these targets may differ from those used by validation tools.
If you identify anything that's clearly wrong then do let us know!

Regards,
Rob


> On 25 Jul 2020, at 17:22, Dale Tronrud  wrote:
> 
> Hi,
> 
>   I'm seeking insight into some geometry outliers in my Refmac refined
> model.  It would be nice to have confidence in the target values used by
> Refmac.  Does Refmac use the library distributed by CCP4 in
> lib/data/monomers, or do it have its own library squirreled away somewhere?
> 
> Dale Tronrud
> 
> 
> 
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[ccp4bb] Refmac Ideal Geometry Library

[Dale Tronrud]

Hi,

   I'm seeking insight into some geometry outliers in my Refmac refined
model.  It would be nice to have confidence in the target values used by
Refmac.  Does Refmac use the library distributed by CCP4 in
lib/data/monomers, or do it have its own library squirreled away somewhere?

Dale Tronrud



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[ccp4bb] [refmac developers] unrestrained anisotropic

[Bernhard Rupp]

Hi Fellows,

 

Q for the Refmac cognosci:

 

Just curious: If I run unrestrained anisotropic refi on 1 A data, some
barely supported ligands display insane and physically impossible ADPs,

worthy of the ORTEP of the century. As cigars penetrate discs, it seems that
Hirschfeld criteria on

aniso ADPs are violated. 

 

Are they also turned off when I select unrestrained - they should remain in
effect regardless of

how bad or unsupported my atoms are? Do I need to change/adjust/optimize the
RBON/RIGU keywrd?

 

Best, BR

 

--

Bernhard Rupp

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] Refmac and hydrogens -developers

[James Holton]

The first thing you want to do when debugging hydrogens in refmac5 is to 
make sure it outputs whatever it was doing:

MAKE HOUT Y

This is not the default.  Normally, refmac will take a PDB file without 
any hydrogens in it, quietly add them before doing refinement, and then 
delete them before outputting the final coordinates.  Why so secretive?  
Probably because someone complained about having to look at all that 
fuzzy hydrogen nonsense in the graphics.  In fact, I know some 
crystallographers who refuse to believe that the element hydrogen even 
exists. Never seen it. Including them in refinement has even been called 
"too many parameters". Nowadays, of course, we know having hydrogens 
involved in the geometry is a good thing.  This is especially true at 
poor resolution.


The other important hydrogen keyword to know is:
MAKE HYDR A

This is the default.  "A" means add all hydrogens, regardless of what is 
in the input pdb file.  Normally, these get deleted before output, so 
you don't notice it.  The other choices are:
MAKE HYDR N: which is basically "do not do the hydrogen thing".  Any 
hydrogens in the input file will be ignored, and they will also not be 
in the output file (even if you use MAKE HOUT Y), because they were 
never there.
MAKE HYDR Y : this is the one that will use the hydrogens listed in the 
pdb file.  Here there lies a danger!  Not every program names hydrogens 
the same way, so some might be quietly ignored.  The only way to know if 
they were is to use MAKE HOUT Y.


So, if you want to define and use your own hydrogens through many rounds 
of refmac, you want to use:

MAKE HYDR Y
MAKE HOUT Y

But, if your starting PDB has no hydrogens in it you want your first 
round to have:

MAKE HYDR A
MAKE HOUT Y

If you inspect the occupancies of the output hydrogens you may find that 
some are zero, and every once ina while one is somewhere between 1 and 
0.  I have not seen documentation for this, but it appears that refmac 
might be quietly doing some sort of occupancy refinement on hydrogens 
that may or may not be there.  Titratable ones for example.  The 
philisophy explained to me once by Garib is that since it is twice as 
bad to put in an electron that isn't there vs leaving out one that is 
you want to err on the side of dropping hydrogens that don't seem to fit.


HTH,

-James Holton
MAD Scientist


On 5/20/2020 7:07 PM, Bernhard Rupp wrote:


Hi Fellows,

for an experiment, I am running 0.9 A data with unrestrained Refmac 
(yes I know should/could use SHELXL, but let’s drop that for now).


When I select ‘ignore even if present in file’ in a PDB that has 
hydrogens, I get the identical results than with ’use if present’ or 
‘generate all’.


The log informs me that the instructions were properly issued, the 
output PDB does not have Hs, but Rs and map are exactly the same


as with selection of if present or generate all H. Does not seem to 
make sense.


If I cull the hydrogens from the input PDB and ‘use if present’ or 
‘ignore’, the stats and map are different and no H in output as 
requested -  all as expected.


Maybe that can be reproduced and, if it is not a feature, fixed.

Best, BR

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org 

+1 925 209 7429

+43 676 571 0536

--

Real knowledge is to know

the extent of one's ignorance

--




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Re: [ccp4bb] Refmac and hydrogens -developers

[Eleanor Dodson]

Yes - I am having problems with hydrogens in REFMAC recently - has
something changed?
My problem is this: Build a rough model for some residues into a lousy map.
(R ~ 32% etc..)
I know it is rough with clashes and bad geometry but trust refinement to
improve things a bit..
However if the run includes instruction BUILD hydrogens the structure sort
of explodes - R up to 39%.
If I dont do that REFMAC does fix things a bit - R drops a bit - ready for
more corrections..

I assume that now the hydrogens are generating restraints and these
restraints are blowing things up.

Surely hydrogens should not be allowed to do this?
Eleanor


On Thu, 21 May 2020 at 03:07, Bernhard Rupp 
wrote:

> Hi Fellows,
>
>
>
> for an experiment, I am running 0.9 A data with unrestrained Refmac (yes I
> know should/could use SHELXL, but let’s drop that for now).
>
>
>
> When I select ‘ignore even if present in file’ in a PDB that has
> hydrogens, I get the identical results than with ’use if present’ or
> ‘generate all’.
>
>
>
> The log informs me that the instructions were properly issued, the output
> PDB does not have Hs, but Rs and map are exactly the same
>
> as with selection of if present or generate all H. Does not seem to make
> sense.
>
>
>
> If I cull the hydrogens from the input PDB and ‘use if present’ or
> ‘ignore’, the stats and map are different and no H in output as requested
> -  all as expected.
>
>
>
> Maybe that can be reproduced and, if it is not a feature, fixed.
>
>
>
> Best, BR
>
> --
>
> Bernhard Rupp
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Real knowledge is to know
>
> the extent of one's ignorance
>
> --
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Refmac and hydrogens -developers

[Bernhard Rupp]

Hi Fellows,

 

for an experiment, I am running 0.9 A data with unrestrained Refmac (yes I
know should/could use SHELXL, but let's drop that for now).

 

When I select 'ignore even if present in file' in a PDB that has hydrogens,
I get the identical results than with 'use if present' or 'generate all'.

 

The log informs me that the instructions were properly issued, the output
PDB does not have Hs, but Rs and map are exactly the same 

as with selection of if present or generate all H. Does not seem to make
sense.

 

If I cull the hydrogens from the input PDB and 'use if present' or 'ignore',
the stats and map are different and no H in output as requested -  all as
expected.

 

Maybe that can be reproduced and, if it is not a feature, fixed.

 

Best, BR

--

Bernhard Rupp

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Real knowledge is to know 

the extent of one's ignorance 

--

 




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[ccp4bb] Refmac per-cycle and all-cycle statistics.

[Jonathan Cooper]

I was wondering why everything appears twice in the report, as below ;-?
https://www.ucl.ac.uk/~rmhajc0/percycle.jpg




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Re: [ccp4bb] Refmac in i2

[Jonathan Cooper]

 The numbers do make sense now: AaA, AbA, etc, correspond to different HETATM 
groups and (what was confusing me a lot) the No. atoms includes riding 
hydrogens. 
On Thursday, 2 May 2019, 23:27:49 BST, Jonathan Cooper 
 wrote:  
 
 In the output statistics part of the GUI there is table of mean B-factors, e.g.
Chain mean B (No. atoms) AAA 23.6( 2596 )AaA 35.4( 29 )AbA 35.2( 10 )AcA 18.9( 
10 )AdA 58.5( 10 )AeA 39.5( 119 )BBB 25.5( 2545 )BaB 42.0( 10 )BbB 46.9( 5 )BcB 
37.3( 92 )
There is an A- and a B-chain in the structure, each with their own waters, but 
can someone explain the AaA, AbA,...AeA, BaB...BcB  notation please, since it 
is not obvious how this relates to the contents of the PDB file. Thank you.

  



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[ccp4bb] Refmac in i2

[Jonathan Cooper]

In the output statistics part of the GUI there is table of mean B-factors, e.g.
Chain mean B (No. atoms) AAA 23.6( 2596 )AaA 35.4( 29 )AbA 35.2( 10 )AcA 18.9( 
10 )AdA 58.5( 10 )AeA 39.5( 119 )BBB 25.5( 2545 )BaB 42.0( 10 )BbB 46.9( 5 )BcB 
37.3( 92 )
There is an A- and a B-chain in the structure, each with their own waters, but 
can someone explain the AaA, AbA,...AeA, BaB...BcB  notation please, since it 
is not obvious how this relates to the contents of the PDB file. Thank you.




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Re: [ccp4bb] Refmac dictionary

[Sam Tang]

Hi

My apologies. This is indeed a silly question. It appears I forgot to
remove the extra O when linking them together!

Sam


On Wed, 3 Apr 2019 at 07:21, Sam Tang  wrote:

> Dear all
>
> Hello again.
>
> We have another protein-RNA dataset which we are trying to refine. For
> this dataset we have three OMU nucleotides modelled. We got the monomer
> from Coot 'Get Monomer'. Refmac returned the following error:
> ERROR : atom :OP3  OMU 2  CCC  is absent in the library
> ERROR : atom :OP3  OMU 3  CCC  is absent in the library
>
> The library version is 5.44. I tried to download a OMU.cif (from this link
> https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/dictionary.html)
> for use in Refmac but the same error occurs.
>
> So... what should I try now?
>
> Many thanks in advance!
>
> Sam
>



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[ccp4bb] Refmac dictionary

[Sam Tang]

Dear all

Hello again.

We have another protein-RNA dataset which we are trying to refine. For this
dataset we have three OMU nucleotides modelled. We got the monomer from
Coot 'Get Monomer'. Refmac returned the following error:
ERROR : atom :OP3  OMU 2  CCC  is absent in the library
ERROR : atom :OP3  OMU 3  CCC  is absent in the library

The library version is 5.44. I tried to download a OMU.cif (from this link
https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/dictionary.html)
for use in Refmac but the same error occurs.

So... what should I try now?

Many thanks in advance!

Sam



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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

[Clemens Vonrhein]

Dear Herman,

On Thu, Feb 07, 2019 at 10:26:09AM +, Herman Schreuder wrote:
> I did understand your question correctly and (at least for ligands)
> the procedure I and also Diana Tomchick described, worked. However,
> I just did a test with both Refmac and Buster and it seems that
> these programs have now so far been perfected that “errors” like
> this cannot occur anymore.

You might not have seen the reply to Ed's original question on the
BUSTER discussion mailing list [1]. It is not fully automatic and
might look slightly complicated (the intention was to give the full
background information for such a problem) - so doesn't qualify as a
"native" solution that Ed was looking for.

It is of course possible to handle micro-heterogeneity in BUSTER
(and also in REFMAC - after all: most structures marked with
"MICROHETEROGENEITY" in the PDB have been refined with it). If this
becomes a more common and pressing need for our users, development
of a "native" solution would move higher up the priority list list
in the future. It is very good to hear from users (like Ed) when
something doesn't quite work as expected - even if they then decide
to switch to another package/program for a particular problem.

Cheers

Clemens, Peter & Gerard

[1] 
http://www.globalphasing.com/pipermail/buster-discuss/2019-February/thread.html

> So it seems that the poor crystallographers who have crystallized proteins 
> which are heterogeneous at certain positions, will have to switch to Phenix.



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[ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

[Herman . Schreuder]

Ed,

I did understand your question correctly and (at least for ligands) the 
procedure I and also Diana Tomchick described, worked. However, I just did a 
test with both Refmac and Buster and it seems that these programs have now so 
far been perfected that “errors” like this cannot occur anymore.

So it seems that the poor crystallographers who have crystallized proteins 
which are heterogeneous at certain positions, will have to switch to Phenix.

Best,
Herman


Von: Edwin Pozharski [mailto:pozharsk...@gmail.com]
Gesendet: Mittwoch, 6. Februar 2019 18:19
An: Schreuder, Herman /DE
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [EXTERNAL] [ccp4bb] refmac same residue different names

Herman,

thanks - however, it seems like I have poorly worded my question.  I do know 
how to generate alternate conformers, what the PDB ATOM record format is etc.  
The point was that when I have alternate conformers that carry the same residue 
ID but different residue types, Refmac exits with the error.  The question was 
whether there is a "native" solution to this that does not include some pdb 
file acrobatics (i.e. separating the alternative type into a separate residue 
and enforcing connectivity using elaborate LINK records).   Based on what I see 
so far, there likely isn't any such native option.  Whether these situations 
are common enough to warrant (possibly elaborate) software changes is a 
separate question.

Cheers,

Ed.

---
I don't know why the sacrifice didn't work. The science seemed so solid.
Julien XIII, Lord of the Lemurs

On Wed, Feb 6, 2019 at 2:36 AM 
mailto:herman.schreu...@sanofi.com>> wrote:
Dear Edwin,

I do not know whether your question has been answered already, but the answer 
is simple: you have to define alternative conformations. Easiest is to generate 
them in coot with the “add alternate conformation” option in the right panel. 
You may have to delete the original unlabeled alternative conformation first 
though.
Alternatively, if you want to keep the original coordinates, or if the 
alternative residue is different: say a Leu versus a Phe you can open the pdb 
file with an editor and generate the alternative conformation yourself:
One of the residues gets an “A” in front of the residue name, e.g. ALEU, and 
the alternative residue a “B”, say BLEU. You also have to reset the occupancies 
to 0.5 for both conformations (or different fractions which add up to one).

Good luck!
Herman

Von: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag von 
Edwin Pozharski
Gesendet: Montag, 4. Februar 2019 22:35
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: [EXTERNAL] [ccp4bb] refmac same residue different names

Belated happy 2019, everyone.

For whatever obscure reason, I need to refine a model that has two different 
residue types as alternate conformers with the same residue ID.  Presented with 
a pdb file that has such feature, Refmac fails saying this

 ERROR: in chain A residue: 443
different residues have the same number

There is an error in the input coordinate file
At least one the chains has 2 residues with the same number
Check above to see error
===> Error: Problem with coordinate file

There are several ways of getting around this I can think of.  Perhaps 
duplicate chain with strict NCS for all but the residue in question could work. 
 Perhaps adding this residue as two separate chains and then adding enough LINK 
records to keep things in place could.  Either solution here is inelegant and 
requires reformating pdb file back to sanity prior to deposition.

Is there some way to allow different geometries for alternate conformers that 
is native to Refmac?

Cheers,

Ed.

PS.  I know that phenix.refine takes the mixed name pdb file straight up.  I 
still want to be able to refine such structure with refmac (and buster, 
actually, but that's a question I already asked in the appropriate forum.


Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /



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Re: [ccp4bb] [EXTERNAL] [ccp4bb] refmac same residue different names

[Mark Wilson]

Hi Diana,
At the risk of thread-jacking Ed’s question, yes, PHENIX handles this
seamlessly for us as well.  However, REFMAC5 doesn’t like this scenario,
with or without alt. confs. or insertion codes.  There are some models
where I’d really like to use REFMAC5 for refining these mixed species
models, and it’s not clear to me how to do so.  It sounds like Ed is
encountering similar issues.
Best regards,
Mark

Mark A. Wilson
Associate Professor
Department of Biochemistry/Redox Biology Center
University of Nebraska
N118 Beadle Center
1901 Vine Street
Lincoln, NE 68588
(402) 472-3626
mwilso...@unl.edu 






On 2/6/19, 11:32 AM, "CCP4 bulletin board on behalf of Diana Tomchick"

wrote:

>
>
>
>The scenario I presented earlier works like a charm in refinement with
>the Phenix program suite. For example, I have used it for both mixed
>populations of ligands (e.g., AAMP and BADP) as well as phosphorylation
>(ASER and BSEP).
>
>
>Diana
>
>**
>Diana R. Tomchick
>Professor
>Departments of Biophysics and Biochemistry
>UT Southwestern Medical Center
>5323 Harry Hines Blvd.
>Rm. ND10.214A
>Dallas, TX 75390-8816
>diana.tomch...@utsouthwestern.edu
>(214) 645-6383 (phone)
>(214) 645-6353 (fax)
>
>
>On Feb 6, 2019, at 11:19 AM, Edwin Pozharski 
>wrote:
>
>Herman,
>
>
>thanks - however, it seems like I have poorly worded my question.  I do
>know how to generate alternate conformers, what the PDB ATOM record
>format is etc.  The point was that when I have alternate conformers that
>carry the same residue ID but
> different residue types, Refmac exits with the error.  The question was
>whether there is a "native" solution to this that does not include some
>pdb file acrobatics (i.e. separating the alternative type into a separate
>residue and enforcing connectivity using
> elaborate LINK records).   Based on what I see so far, there likely
>isn't any such native option.  Whether these situations are common enough
>to warrant (possibly elaborate) software changes is a separate question.
>
>
>Cheers,
>
>
>Ed.
>
>
>---
>
>I don't know why the sacrifice didn't work. The science seemed so solid.
>
>Julien XIII, Lord of the Lemurs
>
>
>
>
>On Wed, Feb 6, 2019 at 2:36 AM  wrote:
>
>
>Dear Edwin,
> 
>I do not know whether your question has been answered already, but the
>answer is simple: you have to define alternative conformations. Easiest is
> to generate them in coot with the “add alternate conformation” option in
>the right panel. You may have to delete the original unlabeled
>alternative conformation first though.
>
>Alternatively, if you want to keep the original coordinates, or if the
>alternative residue is different: say a Leu versus a Phe you can open the
>pdb
> file with an editor and generate the alternative conformation yourself:
>One of the residues gets an “A” in front of the residue name, e.g. ALEU,
>and the alternative residue a “B”, say BLEU. You also have to reset the
>occupancies
> to 0.5 for both conformations (or different fractions which add up to
>one).
> 
>Good luck!
>Herman
> 
>Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
>Im Auftrag von Edwin Pozharski
>Gesendet: Montag, 4. Februar 2019 22:35
>An: 
>CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
>Betreff: [EXTERNAL] [ccp4bb] refmac same residue different names
> 
>Belated happy 2019, everyone.
> 
>
>For whatever obscure reason, I need to refine a model that has two
>different residue types as alternate conformers with the same residue ID.
> Presented with a pdb file that has such feature, Refmac fails saying this
>
> 
>
>
> ERROR: in chain A residue: 443
>different residues have the same number
>
>There is an error in the input coordinate file
>At least one the chains has 2 residues with the same number
>Check above to see error
>===> Error: Problem with coordinate file
>
>
>
> 
>
>There are several ways of getting around this I can think of.  Perhaps
>duplicate chain with strict NCS for all but the residue in question could
>work.  Perhaps adding this residue as two separate chains and then adding
>enough LINK records
> to keep things in place could.  Either solution here is inelegant and
>requires reformating pdb file back to sanity prior to deposition.
>
> 
>
>Is there some way to allow different geometries for alternate conformers
>that is native to Refmac?
>
> 
>
>Cheers,
>
> 
>
>Ed.
>
> 
>
>PS.  I know that phenix.refine takes the mixed name pdb file straight up.
> I still want to be able to refine such structure with refmac (and
>buster

Re: [ccp4bb] [EXTERNAL] [ccp4bb] refmac same residue different names

[Diana Tomchick]

The scenario I presented earlier works like a charm in refinement with the 
Phenix program suite. For example, I have used it for both mixed populations of 
ligands (e.g., AAMP and BADP) as well as phosphorylation (ASER and BSEP).

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu>
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Feb 6, 2019, at 11:19 AM, Edwin Pozharski 
mailto:pozharsk...@gmail.com>> wrote:

Herman,

thanks - however, it seems like I have poorly worded my question.  I do know 
how to generate alternate conformers, what the PDB ATOM record format is etc.  
The point was that when I have alternate conformers that carry the same residue 
ID but different residue types, Refmac exits with the error.  The question was 
whether there is a "native" solution to this that does not include some pdb 
file acrobatics (i.e. separating the alternative type into a separate residue 
and enforcing connectivity using elaborate LINK records).   Based on what I see 
so far, there likely isn't any such native option.  Whether these situations 
are common enough to warrant (possibly elaborate) software changes is a 
separate question.

Cheers,

Ed.

---
I don't know why the sacrifice didn't work. The science seemed so solid.
Julien XIII, Lord of the Lemurs

On Wed, Feb 6, 2019 at 2:36 AM 
mailto:herman.schreu...@sanofi.com>> wrote:
Dear Edwin,

I do not know whether your question has been answered already, but the answer 
is simple: you have to define alternative conformations. Easiest is to generate 
them in coot with the “add alternate conformation” option in the right panel. 
You may have to delete the original unlabeled alternative conformation first 
though.
Alternatively, if you want to keep the original coordinates, or if the 
alternative residue is different: say a Leu versus a Phe you can open the pdb 
file with an editor and generate the alternative conformation yourself:
One of the residues gets an “A” in front of the residue name, e.g. ALEU, and 
the alternative residue a “B”, say BLEU. You also have to reset the occupancies 
to 0.5 for both conformations (or different fractions which add up to one).

Good luck!
Herman

Von: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag von 
Edwin Pozharski
Gesendet: Montag, 4. Februar 2019 22:35
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: [EXTERNAL] [ccp4bb] refmac same residue different names

Belated happy 2019, everyone.

For whatever obscure reason, I need to refine a model that has two different 
residue types as alternate conformers with the same residue ID.  Presented with 
a pdb file that has such feature, Refmac fails saying this

 ERROR: in chain A residue: 443
different residues have the same number

There is an error in the input coordinate file
At least one the chains has 2 residues with the same number
Check above to see error
===> Error: Problem with coordinate file

There are several ways of getting around this I can think of.  Perhaps 
duplicate chain with strict NCS for all but the residue in question could work. 
 Perhaps adding this residue as two separate chains and then adding enough LINK 
records to keep things in place could.  Either solution here is inelegant and 
requires reformating pdb file back to sanity prior to deposition.

Is there some way to allow different geometries for alternate conformers that 
is native to Refmac?

Cheers,

Ed.

PS.  I know that phenix.refine takes the mixed name pdb file straight up.  I 
still want to be able to refine such structure with refmac (and buster, 
actually, but that's a question I already asked in the appropriate forum.


Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /



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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

[Mark Wilson]

I agree. We have encountered refinement problems similar to those Ed
describes for models with mixtures of modified cysteine species, which is
a fairly common occurrence.
Best regards,
Mark

Mark A. Wilson
Associate Professor
Department of Biochemistry/Redox Biology Center
University of Nebraska
N118 Beadle Center
1901 Vine Street
Lincoln, NE 68588
(402) 472-3626
mwilso...@unl.edu 






On 2/6/19, 11:19 AM, "CCP4 bulletin board on behalf of Palm, Gottfried"
 wrote:

>The situation might not be so rare, if you consider 50% Lys and 50%
>Acetyl-Lys or other post-translational modifications.
>
>Gottfried
>
>On Wednesday, 06-02-2019 at 18:05 Diana Tomchick wrote:
>
>If you have the odd case where one residue (of the same number in the
>polypeptide chain) is a Leu and the alternative residue is a Phe, then it
>would be ALEU and BPHE, both residues would have the same residue number,
>and reset the occupancies to fractions
> that sum to 1.0.
>
>
>Diana
>
>**
>Diana R. Tomchick
>Professor
>Departments of Biophysics and Biochemistry
>UT Southwestern Medical Center
>5323 Harry Hines Blvd.
>Rm. ND10.214A
>Dallas, TX 75390-8816
>diana.tomch...@utsouthwestern.edu
>(214) 645-6383 (phone)
>(214) 645-6353 (fax)
>
>
>On Feb 6, 2019, at 1:36 AM,
>herman.schreu...@sanofi.com <mailto:herman.schreu...@sanofi.com> wrote:
>
>Dear Edwin,
> 
>I do not know whether your question has been answered already, but the
>answer is simple: you have to define alternative conformations. Easiest
>is to generate
> them in coot with the “add alternate conformation” option in the right
>panel. You may have to delete the original unlabeled alternative
>conformation first though.
>Alternatively, if you want to keep the original coordinates, or if the
>alternative residue is different: say a Leu versus a Phe you can open the
>pdb file with
> an editor and generate the alternative conformation yourself:
>One of the residues gets an “A” in front of the residue name, e.g. ALEU,
>and the alternative residue a “B”, say BLEU. You also have to reset the
>occupancies to
> 0.5 for both conformations (or different fractions which add up to one).
> 
>Good luck!
>Herman
> 
>Von: CCP4 bulletin board
> [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Edwin
> Pozharski
>Gesendet: Montag, 4. Februar 2019 22:35
>An: CCP4BB@JISCMAIL.AC.UK
>Betreff: [EXTERNAL] [ccp4bb] refmac same residue different names
> 
>Belated happy 2019, everyone.
> 
>
>For whatever obscure reason, I need to refine a model that has two
>different residue types as alternate conformers with the same residue ID.
> Presented with a pdb file that has such feature, Refmac fails saying this
>
> 
>
>
> ERROR: in chain A residue: 443
>different residues have the same number
>
>There is an error in the input coordinate file
>At least one the chains has 2 residues with the same number
>Check above to see error
>===> Error: Problem with coordinate file
>
>
>
> 
>
>There are several ways of getting around this I can think of.  Perhaps
>duplicate chain with strict NCS for all but the residue in question could
>work.  Perhaps adding this residue as two separate chains and then adding
>enough LINK records to keep things in
> place could.  Either solution here is inelegant and requires reformating
>pdb file back to sanity prior to deposition.
>
> 
>
>Is there some way to allow different geometries for alternate conformers
>that is native to Refmac?
>
> 
>
>Cheers,
>
> 
>
>Ed.
>
> 
>
>PS.  I know that phenix.refine takes the mixed name pdb file straight up.
> I still want to be able to refine such structure with refmac (and
>buster, actually, but that's a question I already asked in the
>appropriate forum.
>
> 
>
>
>Edwin Pozharski, PhD, Assistant Professor
>University of Maryland, Baltimore
>--
>When the Way is forgotten duty and justice appear;
>Then knowledge and wisdom are born along with hypocrisy.
>When harmonious relationships dissolve then respect and devotion arise;
>When a nation falls to chaos then loyalty and patriotism are born.
>-- / Lao Tse /
>
>
>
>
> 
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
><https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_c
>gi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX
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>33Wexf2P2dxZ7xNYA

Re: [ccp4bb] [EXTERNAL] [ccp4bb] refmac same residue different names

[Edwin Pozharski]

Herman,

thanks - however, it seems like I have poorly worded my question.  I do
know how to generate alternate conformers, what the PDB ATOM record format
is etc.  The point was that when I have alternate conformers that carry the
same residue ID but different residue types, Refmac exits with the error.
The question was whether there is a "native" solution to this that does not
include some pdb file acrobatics (i.e. separating the alternative type into
a separate residue and enforcing connectivity using elaborate LINK
records).   Based on what I see so far, there likely isn't any such native
option.  Whether these situations are common enough to warrant (possibly
elaborate) software changes is a separate question.

Cheers,

Ed.

---
I don't know why the sacrifice didn't work. The science seemed so solid.
Julien XIII, Lord of the Lemurs

On Wed, Feb 6, 2019 at 2:36 AM  wrote:

> Dear Edwin,
>
>
>
> I do not know whether your question has been answered already, but the
> answer is simple: you have to define alternative conformations. Easiest is
> to generate them in coot with the “add alternate conformation” option in
> the right panel. You may have to delete the original unlabeled alternative
> conformation first though.
>
> Alternatively, if you want to keep the original coordinates, or if the
> alternative residue is different: say a Leu versus a Phe you can open the
> pdb file with an editor and generate the alternative conformation yourself:
>
> One of the residues gets an “A” in front of the residue name, e.g. ALEU,
> and the alternative residue a “B”, say BLEU. You also have to reset the
> occupancies to 0.5 for both conformations (or different fractions which add
> up to one).
>
>
>
> Good luck!
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Edwin Pozharski
> *Gesendet:* Montag, 4. Februar 2019 22:35
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] [ccp4bb] refmac same residue different names
>
>
>
> Belated happy 2019, everyone.
>
>
>
> For whatever obscure reason, I need to refine a model that has two
> different residue types as alternate conformers with the same residue ID.
> Presented with a pdb file that has such feature, Refmac fails saying this
>
>
>
>  ERROR: in chain A residue: 443
> different residues have the same number
>
> There is an error in the input coordinate file
> At least one the chains has 2 residues with the same number
> Check above to see error
> ===> Error: Problem with coordinate file
>
>
>
> There are several ways of getting around this I can think of.  Perhaps
> duplicate chain with strict NCS for all but the residue in question could
> work.  Perhaps adding this residue as two separate chains and then adding
> enough LINK records to keep things in place could.  Either solution here is
> inelegant and requires reformating pdb file back to sanity prior to
> deposition.
>
>
>
> Is there some way to allow different geometries for alternate conformers
> that is native to Refmac?
>
>
>
> Cheers,
>
>
>
> Ed.
>
>
>
> PS.  I know that phenix.refine takes the mixed name pdb file straight up.
> I still want to be able to refine such structure with refmac (and buster,
> actually, but that's a question I already asked in the appropriate forum.
>
>
>
>
> Edwin Pozharski, PhD, Assistant Professor
> University of Maryland, Baltimore
> --
> When the Way is forgotten duty and justice appear;
> Then knowledge and wisdom are born along with hypocrisy.
> When harmonious relationships dissolve then respect and devotion arise;
> When a nation falls to chaos then loyalty and patriotism are born.
> -- / Lao Tse /
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=533Wexf2P2dxZ7xNYAOkGTAhejw65fhzx7fdVjiaqR0=3CLcdo1WJ40rHm6l4rs8gd7nqHBgf_cZbvJjRgUfgHg=>
>



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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

[Palm, Gottfried]

The situation might not be so rare, if you consider 50% Lys and
50% Acetyl-Lys or other post-translational modifications. 
Gottfried

On Wednesday, 06-02-2019 at 18:05 Diana Tomchick wrote:


 If you have the odd case where one residue (of the same number in the
polypeptide chain) is a Leu and the alternative residue is a Phe, then
it would be ALEU and BPHE, both residues would have the same residue
number, and reset the occupancies to fractions that sum to 1.0. 

Diana

  **
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)


On Feb 6, 2019, at 1:36 AM, herman.schreu...@sanofi.com wrote:

   Dear Edwin,
  
 I do not know whether your question has been answered already, but
the answer is simple: you have to define alternative conformations.
Easiest is to generate them in coot with the “add alternate
conformation” option in the right panel. You may have to delete the
original unlabeled alternative conformation first though.
 Alternatively, if you want to keep the original coordinates, or if
the alternative residue is different: say a Leu versus a Phe you can
open the pdb file with an editor and generate the alternative
conformation yourself:
 One of the residues gets an “A” in front of the residue name,
e.g. ALEU, and the alternative residue a “B”, say BLEU. You also
have to reset the occupancies to 0.5 for both conformations (or
different fractions which add up to one).
  
 Good luck!
 Herman
  
 Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
von Edwin Pozharski
Gesendet: Montag, 4. Februar 2019 22:35
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] refmac same residue different names
  
   Belated happy 2019, everyone.
   

  For whatever obscure reason, I need to refine a model that has two
different residue types as alternate conformers with the same residue
ID.  Presented with a pdb file that has such feature, Refmac fails
saying this

   

 

   ERROR: in chain A residue: 443
        different residues have the same number

There is an error in the input coordinate file
At least one the chains has 2 residues with the same number
Check above to see error
===> Error: Problem with coordinate file


 
   

  There are several ways of getting around this I can think of. 
Perhaps duplicate chain with strict NCS for all but the residue in
question could work.  Perhaps adding this residue as two separate
chains and then adding enough LINK records to keep things in place
could.  Either solution here is inelegant and requires reformating
pdb file back to sanity prior to deposition.

   

  Is there some way to allow different geometries for alternate
conformers that is native to Refmac?

   

  Cheers,

   

  Ed.

   

  PS.  I know that phenix.refine takes the mixed name pdb file
straight up.  I still want to be able to refine such structure with
refmac (and buster, actually, but that's a question I already asked in
the appropriate forum.

   

   
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion
arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /




  
 
-
 


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Medical Center

 
 
 
 
 
  

The future of medicine, today.

 
  

 

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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

[Diana Tomchick]

If you have the odd case where one residue (of the same number in the 
polypeptide chain) is a Leu and the alternative residue is a Phe, then it would 
be ALEU and BPHE, both residues would have the same residue number, and reset 
the occupancies to fractions that sum to 1.0.

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu>
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Feb 6, 2019, at 1:36 AM, 
herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com> wrote:

Dear Edwin,

I do not know whether your question has been answered already, but the answer 
is simple: you have to define alternative conformations. Easiest is to generate 
them in coot with the “add alternate conformation” option in the right panel. 
You may have to delete the original unlabeled alternative conformation first 
though.
Alternatively, if you want to keep the original coordinates, or if the 
alternative residue is different: say a Leu versus a Phe you can open the pdb 
file with an editor and generate the alternative conformation yourself:
One of the residues gets an “A” in front of the residue name, e.g. ALEU, and 
the alternative residue a “B”, say BLEU. You also have to reset the occupancies 
to 0.5 for both conformations (or different fractions which add up to one).

Good luck!
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Edwin 
Pozharski
Gesendet: Montag, 4. Februar 2019 22:35
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: [EXTERNAL] [ccp4bb] refmac same residue different names

Belated happy 2019, everyone.

For whatever obscure reason, I need to refine a model that has two different 
residue types as alternate conformers with the same residue ID.  Presented with 
a pdb file that has such feature, Refmac fails saying this

 ERROR: in chain A residue: 443
different residues have the same number

There is an error in the input coordinate file
At least one the chains has 2 residues with the same number
Check above to see error
===> Error: Problem with coordinate file

There are several ways of getting around this I can think of.  Perhaps 
duplicate chain with strict NCS for all but the residue in question could work. 
 Perhaps adding this residue as two separate chains and then adding enough LINK 
records to keep things in place could.  Either solution here is inelegant and 
requires reformating pdb file back to sanity prior to deposition.

Is there some way to allow different geometries for alternate conformers that 
is native to Refmac?

Cheers,

Ed.

PS.  I know that phenix.refine takes the mixed name pdb file straight up.  I 
still want to be able to refine such structure with refmac (and buster, 
actually, but that's a question I already asked in the appropriate forum.


Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=533Wexf2P2dxZ7xNYAOkGTAhejw65fhzx7fdVjiaqR0=3CLcdo1WJ40rHm6l4rs8gd7nqHBgf_cZbvJjRgUfgHg=>



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Medical Center



The future of medicine, today.




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[ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

[Herman . Schreuder]

Dear Edwin,

I do not know whether your question has been answered already, but the answer 
is simple: you have to define alternative conformations. Easiest is to generate 
them in coot with the “add alternate conformation” option in the right panel. 
You may have to delete the original unlabeled alternative conformation first 
though.
Alternatively, if you want to keep the original coordinates, or if the 
alternative residue is different: say a Leu versus a Phe you can open the pdb 
file with an editor and generate the alternative conformation yourself:
One of the residues gets an “A” in front of the residue name, e.g. ALEU, and 
the alternative residue a “B”, say BLEU. You also have to reset the occupancies 
to 0.5 for both conformations (or different fractions which add up to one).

Good luck!
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Edwin 
Pozharski
Gesendet: Montag, 4. Februar 2019 22:35
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] refmac same residue different names

Belated happy 2019, everyone.

For whatever obscure reason, I need to refine a model that has two different 
residue types as alternate conformers with the same residue ID.  Presented with 
a pdb file that has such feature, Refmac fails saying this

 ERROR: in chain A residue: 443
different residues have the same number

There is an error in the input coordinate file
At least one the chains has 2 residues with the same number
Check above to see error
===> Error: Problem with coordinate file

There are several ways of getting around this I can think of.  Perhaps 
duplicate chain with strict NCS for all but the residue in question could work. 
 Perhaps adding this residue as two separate chains and then adding enough LINK 
records to keep things in place could.  Either solution here is inelegant and 
requires reformating pdb file back to sanity prior to deposition.

Is there some way to allow different geometries for alternate conformers that 
is native to Refmac?

Cheers,

Ed.

PS.  I know that phenix.refine takes the mixed name pdb file straight up.  I 
still want to be able to refine such structure with refmac (and buster, 
actually, but that's a question I already asked in the appropriate forum.


Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /



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[ccp4bb] refmac same residue different names

[Edwin Pozharski]

Belated happy 2019, everyone.

For whatever obscure reason, I need to refine a model that has two
different residue types as alternate conformers with the same residue ID.
Presented with a pdb file that has such feature, Refmac fails saying this

 ERROR: in chain A residue: 443
> different residues have the same number
>
> There is an error in the input coordinate file
> At least one the chains has 2 residues with the same number
> Check above to see error
> ===> Error: Problem with coordinate file


There are several ways of getting around this I can think of.  Perhaps
duplicate chain with strict NCS for all but the residue in question could
work.  Perhaps adding this residue as two separate chains and then adding
enough LINK records to keep things in place could.  Either solution here is
inelegant and requires reformating pdb file back to sanity prior to
deposition.

Is there some way to allow different geometries for alternate conformers
that is native to Refmac?

Cheers,

Ed.

PS.  I know that phenix.refine takes the mixed name pdb file straight up.
I still want to be able to refine such structure with refmac (and buster,
actually, but that's a question I already asked in the appropriate forum.


Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /



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[ccp4bb] Refmac jelly body parameters

[Guenter Fritz]

Dear Refmac developers,

I am trying to reproduce some successful refmac runs but cannot get the 
previous results despite playing around with the parameters.


I did those runs in Feb 2014 (Refmac 5.8.0049) but unfortunately have 
overwritten the log files in a backup. I still have the pdbs, mtz and my 
notes.


I was using jelly body and Prosmart at a resolution of 3.1 A,  which 
worked superb and I could track some unexpected conformational changes. 
In several successive runs each with 100 cycles Rwork and Rfree were 
decreasing slowly and continuously and finally showed two rigid body 
movements.


When I now repeat those runs (same pdb, same mtz input files and using 
the prosmart restraint file from the former runs) I get very similar 
Rwork/Refree but not the rigid body movements of these domains again in 
the resulting pdb.


If I loosen the restraints in jelly body  Rwork decreases but Rfree 
stays, indicating some overfitting. And also in the resulting pdbs the 
previously observbed conformational change is not observed. I tried also 
to increase the number of cycles to some insane numbers (>600), but this 
did not improve the situation.


Any ideas what might go wrong? I am really fond of jelly body and would 
like now to check a series of new data sets at low resolution for the 
extent of the observed (and verified) conformational change.


Best regards,

Guenter







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[ccp4bb] Refmac resolution limit doesn't match data processing

[Joël Benjamin Heim]

Dear all,


for one of my projects Refmac (ccp4i2) shows a low resolution limit lower than 
Aimless, which I used for scaling. How is this possible? Since this causes 
problems for the pdb deposition, how can I fix it?


Best,

Joel



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Re: [ccp4bb] Refmac refinement: reduced disulfides

[Ursula Neu]

Hi Joel,

I'm working on a similar structure at the moment.

If refining in refmac, you could add a line to the pdb such as:

LINKRSG ACYS A  22 SG ACYS A  96SS

and tell the program to only use links defined in the pdb file.

If refining in phenix, you could set the parameter for the disulfide
distance cutoff from 3.0 to 2.4 A so that the automatic detection only
finds the "real" disulfides.

Good luck!

Ulla



> Dear all,
>
> I am refining structures containing disulfides using refmac. Many of the
> disulfides are partly broken due to radiation damage.
>
> I tried modeling alternative conformations (i.e. one cysteine pair in a
> disulfide and the other pair as free thiols), but after refinement the
> reduced form is forced back to its original position forming a disulfide
> bridge and resulting in difference density in the fo-fc map.
>
> How do I prevent a disulfide bond from being defined for the free thiol?
>
>
>
> Best regards,
>
> Joel Heim
>
> University of Oslo
>
> 
>
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[ccp4bb] Refmac refinement: reduced disulfides

[Joël Benjamin Heim]

Dear all,

I am refining structures containing disulfides using refmac. Many of the 
disulfides are partly broken due to radiation damage.

I tried modeling alternative conformations (i.e. one cysteine pair in a 
disulfide and the other pair as free thiols), but after refinement the reduced 
form is forced back to its original position forming a disulfide bridge and 
resulting in difference density in the fo-fc map.

How do I prevent a disulfide bond from being defined for the free thiol?



Best regards,

Joel Heim

University of Oslo



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[ccp4bb] refmac error

[Leonid Sazanov]

Hi, after updating to ccp4/7.0, I get this error when trying to run Refmac:

Dictionary path has not been defined
Check the environment variable CLIBD_MON
Current value of CLIBD_MON is
/mnt/nfs/clustersw/shared/ccp4/7.0/ccp4-7.0/lib/data/monomers
It should be set to wherever_dict/dic/
===> Error: Wrong path for the dictionary files
 Refmac:  Wrong path for the dictionary files

How to resolve this?
Many thanks!



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Re: [ccp4bb] Refmac: problem with anisotropic refinement of heavy atoms.

[M T]

Sorry, I moved the image before the sending of the mail and then I was not
attached.

2018-04-04 11:26 GMT+02:00 M T :

> Hello,
>
> I am refining a structure at 2.1Å, using Refmac and manual constructions
> in coot.
> I have few Ca, Cl and Mg in my structure and some of them have a clearly
> anisotropic distribution, then I decided to use ANISOU line in pdb file
> only for these atoms.
> In refinement parameters of Refmac I set "mixed (isotropic/anisotropic)
> temperature factors".
> And I have a problem with some of them which are obviously badly refined
> (see attached picture).
>
> What could be the reason of that? What should I badly set?
>
> Thank you for your help.
>

[ccp4bb] Refmac: problem with anisotropic refinement of heavy atoms.

[M T]

Hello,

I am refining a structure at 2.1Å, using Refmac and manual constructions in
coot.
I have few Ca, Cl and Mg in my structure and some of them have a clearly
anisotropic distribution, then I decided to use ANISOU line in pdb file
only for these atoms.
In refinement parameters of Refmac I set "mixed (isotropic/anisotropic)
temperature factors".
And I have a problem with some of them which are obviously badly refined
(see attached picture).

What could be the reason of that? What should I badly set?

Thank you for your help.

Re: [ccp4bb] Refmac: removing selected ligand hydrogens after making a link

[James Holton]

After outputting the hydrogens, delete the ones you don't want and from 
then on do refinement with:


make hout Y
make hydr Y

When you do that, refmac will keep the hydrogens you put in, and also 
put them in the output.


-James Holton

MAD Scientist


On 3/29/2018 2:11 PM, Phil Jeffrey wrote:
I've got a couple of instances where I have non-standard amino acids, 
nevertheless present in the monomer dictionary, that have additional 
non-peptide covalent linkages.  I've figured out how to define these, 
but if I opt to output hydrogens as a diagnostic I see that Refmac 
doesn't delete the ligand hydrogens that were present at the linkage 
point.


Nothing catastrophic happens in refinement but extra atoms lying along 
other covalent bonds makes me a little queasy.


Is there something (non-obvious) in additional user-defined .cif 
library that I can use to do this ?  Do I simply define a new version 
of the monomer (w/o errant hydrogen) and hope that it overwrites the 
previous definition ?


I'm doing this at borderline atomic resolution.

Thanks
Phil Jeffrey
Princeton

[ccp4bb] Refmac: removing selected ligand hydrogens after making a link

[Phil Jeffrey]

I've got a couple of instances where I have non-standard amino acids, 
nevertheless present in the monomer dictionary, that have additional 
non-peptide covalent linkages.  I've figured out how to define these, 
but if I opt to output hydrogens as a diagnostic I see that Refmac 
doesn't delete the ligand hydrogens that were present at the linkage point.


Nothing catastrophic happens in refinement but extra atoms lying along 
other covalent bonds makes me a little queasy.


Is there something (non-obvious) in additional user-defined .cif library 
that I can use to do this ?  Do I simply define a new version of the 
monomer (w/o errant hydrogen) and hope that it overwrites the previous 
definition ?


I'm doing this at borderline atomic resolution.

Thanks
Phil Jeffrey
Princeton

[ccp4bb] refmac mixed anisotropic refinement

[Abhishek Anan]

Dear all,

How does one exclude water from anisotropic refinement in refmac5.8 under
ccp4-7.0

Here is the relevant section from the com file,

refi -
type REST -
resi MLKF -
meth CGMAT -
bref MIXED anisou residues from 100 A to 200 A

This does not work and the logfile has the following warning,

Data line---

 refi type REST resi MLKF meth CGMAT bref MIXED anisou RESID

 UES 100 A to 200 A

 Unknown subkeyword of REFI

 ? ANIS ?

 Wrong residual option

 Unknown subkeyword of REFI

 ? A?

 Unknown subkeyword of REFI

 ? TO   ?

 Unknown subkeyword of REFI

 ? 200  ?

 Unknown subkeyword of REFI

 ? A?

Is there any other way of defining the residue range or excluding only water?

Thank you for your help,

Abhishek

Re: [ccp4bb] refmac-extra-params

[Dr A.A. Jalan]

 

Dear Prof Emsley 

That worked! 

Thanks 

Abhishek 

On 2017-08-24 17:42, Paul Emsley wrote: 

> On 24/08/17 16:29, Dr A.A. Jalan wrote:
> 
>> I am trying to change the default refmac run parameters in coot. For this, I 
>> created a refmac-extra-params file in the directory from where coot is 
>> launched. (set! refmac-extra-params (list "MAKE HYDROGENS ALL" "REFI BREF 
>> ANIS"))
> 
> You can set refmac-extra-params in 2 ways. Either add to your ~/.coot file:
> 
> (set! refmac-extra-params (list "MAKE HYDROGENS ALL" "REFI BREF ANISO"))
> 
> or recreate a file called refmac-extra-params (like you have done) with 
> contents
> 
> MAKE HYDROGENS ALL
> REFI BREF ANISO
> 
> Sorry if that was not clear in the documentation.
> 
> Regards,
> 
> Paul.

 

Re: [ccp4bb] refmac-extra-params

[Paul Emsley]

On 24/08/17 16:29, Dr A.A. Jalan wrote:


I am trying to change the default refmac run parameters in coot. For 
this, I created a refmac-extra-params file in the directory from where 
coot is launched.


(set! refmac-extra-params (list "MAKE HYDROGENS ALL" "REFI BREF ANIS"))



You can set refmac-extra-params in 2 ways. Either add to your ~/.coot file:

(set! refmac-extra-params (list "MAKE HYDROGENS ALL" "REFI BREF ANISO"))

or recreate a file called refmac-extra-params (like you have done) with 
contents


MAKE HYDROGENS ALL
REFI BREF ANISO

Sorry if that was not clear in the documentation.

Regards,

Paul.

[ccp4bb] refmac-extra-params

[Dr A.A. Jalan]

 

Dear all, 

I am trying to change the default refmac run parameters in coot. For
this, I created a refmac-extra-params file in the director from where
coot is launched. 

(set! refmac-extra-params (list "MAKE HYDROGENS ALL" "REFI BREF ANIS")) 

But these modification are ignored through the following message in the
log file, 

Data line--- MAKE HYDROGENS NO
 Data line--- NCYCLES 0
 Data line--- WEIGHT AUTO 5
 Data line--- (set! refmac-extra-params (list "MAKE HYDROGENS ALL" "REFI
BREF ANIS"))
===> Warning: Unrecognized keyword: (SET
 Data line--- END 

I was wondering if I am missing something. I have also tried "set"
without the "!" and "define" but in vain. 

Please could anyone point me to a solution. 

best regards, 

Abhishek 
 

Re: [ccp4bb] refmac output

[Eleanor Dodson]

the CCP4 gui does just that - provides map coeffs by default..
You can seek out the full REFMAC output if needed but it is not there by
default.
Eleanor

On 3 August 2017 at 02:04, Pavel Afonine  wrote:

> Hi Ed,
>
> your suggestion makes perfect sense to me, and it's trivial to add an
> option to do what you want. This will be available in next Phenix nightly
> build (clearly not tomorrow given today's power outage).
>
> Command line: use "write_map_coefficients_only=True" (by default is is
> False).
>
> Refinement GUI: Configure -> Output -> Other options -> tick "Write map
> coefficients only" box.
>
> Pavel
>
>
> On Wed, Aug 2, 2017 at 1:12 PM, Edwin Pozharski 
> wrote:
>
>>
>> Just to clarify, how do you use the extra columns in this scenario?  My
>> suggestion was to have the output file that includes only the map
>> coefficient columns, so you still can look at the map.  IIRC, FP/SIGFP
>> columns from refmac output are actually modified from the input (scaled
>> with Boverall), so it was not recommended to use refmac output as input of
>> any kind.
>>
>> Also, to provide context, my comment resulted from dealing with a large
>> chunk of data that included ~200 output mtz files - which is Gb-sized
>> tarball that had to be uploaded/downloaded.  Not the end of the world, but
>> cutting it in half seemed like a good idea at the time. :)  Not hard to
>> script that, of course.
>>
>> I am not necessarily advocating for skinny files to be the default, but
>> as it stands, refmac/buster/phenix do not even provide the option of doing
>> it (It's entirely possible that I am wrong here on specifics and will get
>> corrected by Garib, Gerard and Pavel).
>>
>> Cheers,
>>
>> Ed.
>>
>> Edwin Pozharski, PhD, Assistant Professor
>> University of Maryland, Baltimore
>> --
>> When the Way is forgotten duty and justice appear;
>> Then knowledge and wisdom are born along with hypocrisy.
>> When harmonious relationships dissolve then respect and devotion arise;
>> When a nation falls to chaos then loyalty and patriotism are born.
>> -- / Lao Tse /
>>
>>
>

Re: [ccp4bb] refmac output

[Pavel Afonine]

Hi Ed,

your suggestion makes perfect sense to me, and it's trivial to add an
option to do what you want. This will be available in next Phenix nightly
build (clearly not tomorrow given today's power outage).

Command line: use "write_map_coefficients_only=True" (by default is is
False).

Refinement GUI: Configure -> Output -> Other options -> tick "Write map
coefficients only" box.

Pavel

On Wed, Aug 2, 2017 at 1:12 PM, Edwin Pozharski 
wrote:

>
> Just to clarify, how do you use the extra columns in this scenario?  My
> suggestion was to have the output file that includes only the map
> coefficient columns, so you still can look at the map.  IIRC, FP/SIGFP
> columns from refmac output are actually modified from the input (scaled
> with Boverall), so it was not recommended to use refmac output as input of
> any kind.
>
> Also, to provide context, my comment resulted from dealing with a large
> chunk of data that included ~200 output mtz files - which is Gb-sized
> tarball that had to be uploaded/downloaded.  Not the end of the world, but
> cutting it in half seemed like a good idea at the time. :)  Not hard to
> script that, of course.
>
> I am not necessarily advocating for skinny files to be the default, but as
> it stands, refmac/buster/phenix do not even provide the option of doing it
> (It's entirely possible that I am wrong here on specifics and will get
> corrected by Garib, Gerard and Pavel).
>
> Cheers,
>
> Ed.
>
> Edwin Pozharski, PhD, Assistant Professor
> University of Maryland, Baltimore
> --
> When the Way is forgotten duty and justice appear;
> Then knowledge and wisdom are born along with hypocrisy.
> When harmonious relationships dissolve then respect and devotion arise;
> When a nation falls to chaos then loyalty and patriotism are born.
> -- / Lao Tse /
>
>

Re: [ccp4bb] refmac output

[Ethan A Merritt]

On Wednesday, 02 August, 2017 16:12:30 Edwin Pozharski wrote:
> Just to clarify, how do you use the extra columns in this scenario?  My
> suggestion was to have the output file that includes only the map
> coefficient columns, so you still can look at the map.  IIRC, FP/SIGFP
> columns from refmac output are actually modified from the input (scaled
> with Boverall), so it was not recommended to use refmac output as input of
> any kind.

The scaled Fs are useful to recalculate R as a function of whatever, and
to calculate alternative R values (e.g. for Hamilton R test or comparison
to shelxl R1 R2). It's nice to carry though DANO and SIGDANO so that one
can generate anomalous maps. In general I'd rather err on the side of
including everything rather than discarding something that may be useful
later.  In any case it's trivial to run one additional script to filter
unwanted columns if file size really is a controlling factor.

Ethan




> 
> Also, to provide context, my comment resulted from dealing with a large
> chunk of data that included ~200 output mtz files - which is Gb-sized
> tarball that had to be uploaded/downloaded.  Not the end of the world, but
> cutting it in half seemed like a good idea at the time. :)  Not hard to
> script that, of course.
> 
> I am not necessarily advocating for skinny files to be the default, but as
> it stands, refmac/buster/phenix do not even provide the option of doing it
> (It's entirely possible that I am wrong here on specifics and will get
> corrected by Garib, Gerard and Pavel).
> 
> Cheers,
> 
> Ed.
> 
> Edwin Pozharski, PhD, Assistant Professor
> University of Maryland, Baltimore
> --
> When the Way is forgotten duty and justice appear;
> Then knowledge and wisdom are born along with hypocrisy.
> When harmonious relationships dissolve then respect and devotion arise;
> When a nation falls to chaos then loyalty and patriotism are born.
> -- / Lao Tse /

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] refmac output

[Edwin Pozharski]

Just to clarify, how do you use the extra columns in this scenario?  My
suggestion was to have the output file that includes only the map
coefficient columns, so you still can look at the map.  IIRC, FP/SIGFP
columns from refmac output are actually modified from the input (scaled
with Boverall), so it was not recommended to use refmac output as input of
any kind.

Also, to provide context, my comment resulted from dealing with a large
chunk of data that included ~200 output mtz files - which is Gb-sized
tarball that had to be uploaded/downloaded.  Not the end of the world, but
cutting it in half seemed like a good idea at the time. :)  Not hard to
script that, of course.

I am not necessarily advocating for skinny files to be the default, but as
it stands, refmac/buster/phenix do not even provide the option of doing it
(It's entirely possible that I am wrong here on specifics and will get
corrected by Garib, Gerard and Pavel).

Cheers,

Ed.

Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /

Re: [ccp4bb] refmac output

[Diana Tomchick]

Yes, I agree! This (“Please look at my structure, and here are my files from 
the last cycle of refinement") happens to me almost every week. :)

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Aug 1, 2017, at 10:48 AM, James Holton  wrote:

As someone who uses those "superfluous" columns all the time, I would like to 
chime in in favor of keeping the default output columns of refmac.  If only I 
had a nickle for every time someone asked me to "look at" a structure and only 
gave me the output files of refinement.  Kind of ties your hands.

I have always been a fan of erring on the side of providing information in 
output files.  How hard is it to delete something? How hard is it to get it 
back after you deleted it?

My two cents,

-James Holton
MAD Scientist

On 7/31/2017 8:57 AM, Edwin Pozharski wrote:
> I know space is cheap these days, but is there a reason for Refmac to 
> generate all those extra columns in the output mtz file?  Refmac (as well as 
> phenix.refine and buster-tnt) output mtz file is almost always used for only 
> one purpose - look at the map in coot.  You only need 4 columns for that, not 
> 14.  Other columns are useful for testing, but why not make them optional?
>
> This would certainly be a low priority - one can easily delete extra columns 
> using, say, sftools.
>
> Cheers,
>
> Ed.
>
> ---
> Hurry up, before we all come to our senses!
> Julien, King of Lemurs
>




UT Southwestern


Medical Center



The future of medicine, today.

Re: [ccp4bb] refmac output

[James Holton]

As someone who uses those "superfluous" columns all the time, I would 
like to chime in in favor of keeping the default output columns of 
refmac.  If only I had a nickle for every time someone asked me to "look 
at" a structure and only gave me the output files of refinement.  Kind 
of ties your hands.


I have always been a fan of erring on the side of providing information 
in output files.  How hard is it to delete something? How hard is it to 
get it back after you deleted it?


My two cents,

-James Holton
MAD Scientist

On 7/31/2017 8:57 AM, Edwin Pozharski wrote:
I know space is cheap these days, but is there a reason for Refmac to 
generate all those extra columns in the output mtz file?  Refmac (as 
well as phenix.refine and buster-tnt) output mtz file is almost always 
used for only one purpose - look at the map in coot.  You only need 4 
columns for that, not 14.  Other columns are useful for testing, but 
why not make them optional?


This would certainly be a low priority - one can easily delete extra 
columns using, say, sftools.


Cheers,

Ed.

---
Hurry up, before we all come to our senses!
Julien, King of Lemurs

Re: [ccp4bb] refmac output

[Pavel Afonine]

>
> I know space is cheap these days, but is there a reason for Refmac to
> generate all those extra columns in the output mtz file?  Refmac (as well
> as phenix.refine and buster-tnt) output mtz file is almost always used for
> only one purpose - look at the map in coot.  You only need 4 columns for
> that, not 14.  Other columns are useful for testing, but why not make them
> optional?
>

a phenix.refine run creates an MTZ file with four kinds of data:

1) Copy of input data. Why? For convenience and consistency. Inputs may not
necessarily be in MTZ format and may be spread across multiple files of
different format.

2) Data that were actually used in refinement. Why? A user has options to
cut resolution from both ends, as well as apply cutting by sigma. Plus,
phenix.refine may choose not to use a handful of reflections as outliers
(Read, 1999). So it may be good to have set of reflections that were used
in given refinement run.

3) Model in reciprocal space: Fmodel. Why? This is a reciprocal space
representation of what's in PDB file except that it is richer because
contains not only atomic model (Fcalc) but also solvent contributions (bulk
and non-uniform) as well as all scales. Fmodel taken from this array and
Fobs from "2)" are expected to reproduce reported R-factor exactly.

4) Fourier map coefficients (2mFobs-DFmodel, mFobs-DFmodel, anomalous map
if applicable).

"1)" and "3)" can be optional:
- with trivial scripting one can obtain Fmodel using data from "2)" and
"4)".
- "1)" duplicates inputs. It's not unreasonable to assume they are
still available by the time you finalize your structure.
But.. as you pointed out space is cheap and personally I find it much
easier to have relevant arrays of data centralized in one place (file)
rather than scattered across hard drive.

All the best,
Pavel

Re: [ccp4bb] refmac output

[Jon Agirre]

Perhaps a good opportunity for getting rid of (scaled) F and SIGF too?

Certain pipelines need Refmac's phase estimates (Buccaneer and Crank2 off
the top of my head), but I can't see how activating an 'expert mode' or
'developer mode' in order to get them would be a problem for their authors.

Cheers,

Jon


On 31 July 2017 at 16:57, Edwin Pozharski  wrote:

> I know space is cheap these days, but is there a reason for Refmac to
> generate all those extra columns in the output mtz file?  Refmac (as well
> as phenix.refine and buster-tnt) output mtz file is almost always used for
> only one purpose - look at the map in coot.  You only need 4 columns for
> that, not 14.  Other columns are useful for testing, but why not make them
> optional?
>
> This would certainly be a low priority - one can easily delete extra
> columns using, say, sftools.
>
> Cheers,
>
> Ed.
>
> ---
> Hurry up, before we all come to our senses!
> Julien, King of Lemurs
>
>


-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Twitter: @alwaysonthejazz
+44 (0) 1904 32 8270

[ccp4bb] refmac output

[Edwin Pozharski]

I know space is cheap these days, but is there a reason for Refmac to
generate all those extra columns in the output mtz file?  Refmac (as well
as phenix.refine and buster-tnt) output mtz file is almost always used for
only one purpose - look at the map in coot.  You only need 4 columns for
that, not 14.  Other columns are useful for testing, but why not make them
optional?

This would certainly be a low priority - one can easily delete extra
columns using, say, sftools.

Cheers,

Ed.

---
Hurry up, before we all come to our senses!
Julien, King of Lemurs

Re: [ccp4bb] REFMAC? COOT? and TER records

[Eleanor Dodson]

Thank you Robbie.
I guess ligands do not (or should not) appear in SEQRES therefore should
not have a TER record.

Eleanor

On 19 June 2017 at 11:04, Robbie Joosten <robbie_joos...@hotmail.com> wrote:

> Hi Eleanor,
>
> From PDB format 3.3:
> * Every chain of ATOM/HETATM records presented on SEQRES records is
> terminated with a TER record.
> * The TER records occur in the coordinate section of the entry, and
> indicate the last residue presented for each polypeptide and/or nucleic
> acid chain for which there are determined coordinates. For proteins, the
> residue defined on the TER record is the carboxy-terminal residue; for
> nucleic acids it is the 3'-terminal residue.
> * For a cyclic molecule, the choice of termini is arbitrary.
> * Terminal oxygen atoms are presented as OXT for proteins, and as O5’ or
> OP3 for nucleic acids. These atoms are present only if the last residue in
> the polymer is truly the last residue in the SEQRES.
> * The TER record has the same residue name, chain identifier, sequence
> number and insertion code as the terminal residue. The serial number of the
> TER record is one number greater than the serial number of the ATOM/HETATM
> preceding the TER.
>
> It seems that many programs are indeed overenthusiastic and also putting
> them behind non-polymer residues or carbohydrates. TER records also appear
> (IMO incorrectly) after linker residues that are in SEQRES, but are not
> amino acids. This indeed causes side effects. I also noticed that COOT
> leaves TER records if you add C-terminal residues. This can cause Refmac to
> think that the residues should not be connected.
>
> Cheers,
> Robbie
>
>
> > -Original Message-
> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> > Eleanor Dodson
> > Sent: Monday, June 19, 2017 11:42
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] REFMAC? COOT? and TER records
> >
> > These do seem to multiply wonderfully in the PDB output files and
> > sometimees to have have strange effects/ affects in COOT?
> >
> >
> > As I understand there should be a TER record after a protein chain? but
> not
> > after a ligand.
> >
> >
> > Dont know about carbohydrate chains.
> >
> >
> > Eleanor
> >
> >
> > The correspondence about N linked glycosylation brought it up..
> >
> >
> >
> >
> >
> >
>
>

Re: [ccp4bb] REFMAC? COOT? and TER records

[Robbie Joosten]

Hi Eleanor,

From PDB format 3.3:
* Every chain of ATOM/HETATM records presented on SEQRES records is terminated 
with a TER record.
* The TER records occur in the coordinate section of the entry, and indicate 
the last residue presented for each polypeptide and/or nucleic acid chain for 
which there are determined coordinates. For proteins, the residue defined on 
the TER record is the carboxy-terminal residue; for nucleic acids it is the 
3'-terminal residue.
* For a cyclic molecule, the choice of termini is arbitrary.
* Terminal oxygen atoms are presented as OXT for proteins, and as O5’ or OP3 
for nucleic acids. These atoms are present only if the last residue in the 
polymer is truly the last residue in the SEQRES.
* The TER record has the same residue name, chain identifier, sequence number 
and insertion code as the terminal residue. The serial number of the TER record 
is one number greater than the serial number of the ATOM/HETATM preceding the 
TER.

It seems that many programs are indeed overenthusiastic and also putting them 
behind non-polymer residues or carbohydrates. TER records also appear (IMO 
incorrectly) after linker residues that are in SEQRES, but are not amino acids. 
This indeed causes side effects. I also noticed that COOT leaves TER records if 
you add C-terminal residues. This can cause Refmac to think that the residues 
should not be connected.

Cheers,
Robbie


> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Eleanor Dodson
> Sent: Monday, June 19, 2017 11:42
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] REFMAC? COOT? and TER records
> 
> These do seem to multiply wonderfully in the PDB output files and
> sometimees to have have strange effects/ affects in COOT?
> 
> 
> As I understand there should be a TER record after a protein chain? but not
> after a ligand.
> 
> 
> Dont know about carbohydrate chains.
> 
> 
> Eleanor
> 
> 
> The correspondence about N linked glycosylation brought it up..
> 
> 
> 
> 
> 
> 

[ccp4bb] REFMAC? COOT? and TER records

[Eleanor Dodson]

These do seem to multiply wonderfully in the PDB output files and
sometimees to have have strange effects/ affects in COOT?

As I understand there should be a TER record after a protein chain? but not
after a ligand.

Dont know about carbohydrate chains.

Eleanor

The correspondence about N linked glycosylation brought it up..

Re: [ccp4bb] Refmac library

[Paul Emsley]

On 01/05/2017 13:51, brian walker wrote:

Is there a 3 letter code for D-methionine in refmac library. It is not listed 
in library,
while all the others are?


Here's the meta solution if you have Coot:

File -> Search Monomer Library -> "D-methionone" -> Search

gives

MED


Paul.

Re: [ccp4bb] Refmac library

[Robbie Joosten]

Hi Brian,

It's called MED.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> brian walker
> Sent: Monday, May 01, 2017 14:52
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Refmac library
> 
> Is there a 3 letter code for D-methionine in refmac library. It is not listed 
> in
> library, while all the others are?

[ccp4bb] Refmac library

[brian walker]

Is there a 3 letter code for D-methionine in refmac library. It is not
listed in library, while all the others are?

[ccp4bb] Refmac twin refine works for Amplitude based but not Intensity based

[Xiao Lei]

Dear CCP4bb members,

I have a dataset of 3A, twinned data (twin fraction 0.15) set of space
group P6222, I solved the structure by phaser (TFZ>10, LLG>1000) with space
group P32 and build model to Rfree/R 30% 26%.  I then tried twin refinement
in Refmac, after I tried amplitude based refine the Rfree/R drops to 24%
17% with output files of .mtz map, .pdb and .cif. Everything is normal in
amplitude based refine.

I also tried intensity based twin refine, the log of Refmac shows the
process is successful (I attach below) but only .cif is in output, I could
not find .mtz and .pdb (I even check the path but I still could not find
the files), in addition, there is no report of Rfree/R in the results panel:

**

* Information from CCP4Interface script

***

Writing final coordinates (XYZOUT) to XXX.pdb

***

***

* Information from CCP4Interface script

***

Writing final phases (HKLOUT) to XXX.mtz

***

#CCP4I TERMINATION STATUS 1

#CCP4I TERMINATION TIME 02 Mar 2017  18:10:04

#CCP4I TERMINATION OUTPUT_FILES  XXX.cif

#CCP4I MESSAGE Task completed successfully


Is this a bug? I use CCP4 7.0.030 in ubuntu.

Re: [ccp4bb] Refmac refinement R factors going up..... TLS issue?

[Eleanor Dodson]

And I usually accept the TLS domain definition, but reset all B factors and
start B factor refinement again - ie dont use the actual TLS numbers
returned..
Ideally I guess the B reset could be done using TLSANL

There seems to be confusion over the interaction between the iso B and
those TLS generated ones..
Eleanor



On 18 June 2015 at 22:08, Boaz Shaanan bshaa...@bgu.ac.il wrote:

 Hi Christian,

 I usually send the pdb back to the tlsmd server after any manipulation of
 the model just to be on the safe side. I'm not sure whether that'll make
 any difference in your case but it's perhaps worth trying.

Cheers,

 Boaz


 Boaz Shaanan, Ph.D.
 Dept. of Life Sciences
 Ben-Gurion University of the Negev
 Beer-Sheva 84105
 Israel

 E-mail: bshaa...@bgu.ac.il
 Phone: 972-8-647-2220  Skype: boaz.shaanan
 Fax:   972-8-647-2992 or 972-8-646-1710





 
 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Christian
 Roth [christian.r...@bbz.uni-leipzig.de]
 Sent: Thursday, June 18, 2015 11:30 PM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] Refmac refinement R factors going up. TLS issue?

 Hi all,

 I refine a structure with TLS and restrained refinement in Refmac. After
 the run finished, I fixed a few outliers manually in Coot, saved that
 file and used that with the original TLS file from TLSMD for the next
 round of refinement. As soon as the restrained refinement starts the
 R-factors are going up and stabilise than at a higher values compared to
 the previous run.
 If I switch of the TLS refinement and just do restrained refinement with
 the same input files the R-values start initially at a higher values and
 than decrease till they stabilise. Unfortunately the final values are
 about 1.5 % higher, compared to the run with TLS before manual
 rebuilding. So TLS seems to me beneficial and I would like to use it,
 but somehow a strange combination of wrong files?, wrong
 parametrization? or whatever prevent me of doing that.
 Has anyone an idea what might be the cause of that strange behaviour.

 Thank you very much in advance.

 Cheers

 Christian

Re: [ccp4bb] Refmac refinement R factors going up..... TLS issue? update

[Christian Roth]

Hi all,

I looked again careful in the respective files and it turns out that all 
B-Factors of the protein chains which are treated with TLS are refined 
to the lowest possible value of 2.00 for all atoms!
A workaround is to use the option to set the initial B-factor to 20.0 in 
the GUI and than the refinement finally works. I haven't yet figured out 
what goes wrong in Refmac, but it seems in the B-Factor refinement step 
something gets not treated quite right.


Cheers

Christian


Am 18.06.2015 um 21:58 schrieb Shane Caldwell:

Hi Christian, I've seen this behaviour as well. I'm not an expert but I
rationalized the situation as the TLS parameters for an incomplete model
getting overfit as the missing/wrong parts of the model pull on the TLS
parameters. REFMAC doesn't alternate between TLS and coordinate
refinement, so you can get stuck in a local minimum that moving atoms
and refining individual B-factors won't get you out of. As more of the
model is built correctly, the drift of this refinement gets less and less.

I've found that refining comparatively few TLS cycles (I usually do 3)
before the restrained refinement tends to avoid this problem most of the
time - don't let the TLS refinement converge. Sometimes I'll let the
coordinate step converge, then run another TLS refinement to bootstrap
things along, but usually the stats only marginally improve at that
point. In cases where I've made substantial rebuilds, it's sometimes
been necessary to turn off TLS and refine without it like you do, then
re-introduce the same TLS groups, setting the B-factors to fixed values.
Not really ideal, but it gets there. Hopefully others have some more
theoretically-sound advice.

A good thing to look at doing, especially if TLS is behaving weirdly, is
to check with the PARVATI server
(http://skuld.bmsc.washington.edu/parvati/). If your TLS group
boundaries set off flags, you have some more work to do on the refinement.


Shane Caldwell
McGill University

On Thu, Jun 18, 2015 at 4:30 PM, Christian Roth
christian.r...@bbz.uni-leipzig.de
mailto:christian.r...@bbz.uni-leipzig.de wrote:

Hi all,

I refine a structure with TLS and restrained refinement in Refmac.
After the run finished, I fixed a few outliers manually in Coot,
saved that file and used that with the original TLS file from TLSMD
for the next round of refinement. As soon as the restrained
refinement starts the R-factors are going up and stabilise than at a
higher values compared to the previous run.
If I switch of the TLS refinement and just do restrained refinement
with the same input files the R-values start initially at a higher
values and than decrease till they stabilise. Unfortunately the
final values are about 1.5 % higher, compared to the run with TLS
before manual rebuilding. So TLS seems to me beneficial and I would
like to use it, but somehow a strange combination of wrong files?,
wrong parametrization? or whatever prevent me of doing that.
Has anyone an idea what might be the cause of that strange behaviour.

Thank you very much in advance.

Cheers

Christian




--
Christian Roth
Strukturanalytik von Biopolymeren
Fakultät für Chemie und Mineralogie
Universität Leipzig
Deutscher Platz 5
04103 Leipzig

Email christian.r...@bbz.uni-leipzig.de

Re: [ccp4bb] Refmac refinement R factors going up..... TLS issue?

[Shane Caldwell]

Hi Christian, I've seen this behaviour as well. I'm not an expert but I
rationalized the situation as the TLS parameters for an incomplete model
getting overfit as the missing/wrong parts of the model pull on the TLS
parameters. REFMAC doesn't alternate between TLS and coordinate refinement,
so you can get stuck in a local minimum that moving atoms and refining
individual B-factors won't get you out of. As more of the model is built
correctly, the drift of this refinement gets less and less.

I've found that refining comparatively few TLS cycles (I usually do 3)
before the restrained refinement tends to avoid this problem most of the
time - don't let the TLS refinement converge. Sometimes I'll let the
coordinate step converge, then run another TLS refinement to bootstrap
things along, but usually the stats only marginally improve at that point.
In cases where I've made substantial rebuilds, it's sometimes been
necessary to turn off TLS and refine without it like you do, then
re-introduce the same TLS groups, setting the B-factors to fixed values.
Not really ideal, but it gets there. Hopefully others have some more
theoretically-sound advice.

A good thing to look at doing, especially if TLS is behaving weirdly, is to
check with the PARVATI server (http://skuld.bmsc.washington.edu/parvati/).
If your TLS group boundaries set off flags, you have some more work to do
on the refinement.


Shane Caldwell
McGill University

On Thu, Jun 18, 2015 at 4:30 PM, Christian Roth 
christian.r...@bbz.uni-leipzig.de wrote:

 Hi all,

 I refine a structure with TLS and restrained refinement in Refmac. After
 the run finished, I fixed a few outliers manually in Coot, saved that file
 and used that with the original TLS file from TLSMD for the next round of
 refinement. As soon as the restrained refinement starts the R-factors are
 going up and stabilise than at a higher values compared to the previous run.
 If I switch of the TLS refinement and just do restrained refinement with
 the same input files the R-values start initially at a higher values and
 than decrease till they stabilise. Unfortunately the final values are about
 1.5 % higher, compared to the run with TLS before manual rebuilding. So TLS
 seems to me beneficial and I would like to use it, but somehow a strange
 combination of wrong files?, wrong parametrization? or whatever prevent me
 of doing that.
 Has anyone an idea what might be the cause of that strange behaviour.

 Thank you very much in advance.

 Cheers

 Christian

[ccp4bb] Refmac refinement R factors going up..... TLS issue?

[Christian Roth]

Hi all,

I refine a structure with TLS and restrained refinement in Refmac. After 
the run finished, I fixed a few outliers manually in Coot, saved that 
file and used that with the original TLS file from TLSMD for the next 
round of refinement. As soon as the restrained refinement starts the 
R-factors are going up and stabilise than at a higher values compared to 
the previous run.
If I switch of the TLS refinement and just do restrained refinement with 
the same input files the R-values start initially at a higher values and 
than decrease till they stabilise. Unfortunately the final values are 
about 1.5 % higher, compared to the run with TLS before manual 
rebuilding. So TLS seems to me beneficial and I would like to use it, 
but somehow a strange combination of wrong files?, wrong 
parametrization? or whatever prevent me of doing that.

Has anyone an idea what might be the cause of that strange behaviour.

Thank you very much in advance.

Cheers

Christian

Re: [ccp4bb] Refmac refinement R factors going up..... TLS issue?

[Boaz Shaanan]

Hi Christian,

I usually send the pdb back to the tlsmd server after any manipulation of the 
model just to be on the safe side. I'm not sure whether that'll make any 
difference in your case but it's perhaps worth trying.

   Cheers,

Boaz 


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710






From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Christian Roth 
[christian.r...@bbz.uni-leipzig.de]
Sent: Thursday, June 18, 2015 11:30 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Refmac refinement R factors going up. TLS issue?

Hi all,

I refine a structure with TLS and restrained refinement in Refmac. After
the run finished, I fixed a few outliers manually in Coot, saved that
file and used that with the original TLS file from TLSMD for the next
round of refinement. As soon as the restrained refinement starts the
R-factors are going up and stabilise than at a higher values compared to
the previous run.
If I switch of the TLS refinement and just do restrained refinement with
the same input files the R-values start initially at a higher values and
than decrease till they stabilise. Unfortunately the final values are
about 1.5 % higher, compared to the run with TLS before manual
rebuilding. So TLS seems to me beneficial and I would like to use it,
but somehow a strange combination of wrong files?, wrong
parametrization? or whatever prevent me of doing that.
Has anyone an idea what might be the cause of that strange behaviour.

Thank you very much in advance.

Cheers

Christian

Re: [ccp4bb] Refmac fatal error with newly added ligand

[Robbie Joosten]

Hi Sze Yi,

There is already a compound named LIG in the Refmac dictionary. So either
you have to choose a new name or you overrule the dictionary by supplying a
restraint file in your Refmac run.

Cheers,
Robbie

 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 Lau Sze Yi (SIgN)
 Sent: Monday, June 08, 2015 12:00
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] Refmac fatal error with newly added ligand
 
 Hello,
 
 I generated my new ligand using smiles string in Phenix with elbow to
 generate my ligand cif and pdb file. I then open these in Coot along with
my
 protein model and mtz and fitted this new ligand into my density.
 However Refmac failed with the following details in my log file:
 
 PDB_code:4F80
   PDB_name:IMMUNE SYSTEM
   PDB_date:16-MAY-12
   
   ERROR : atom :C01  LIG 1  EE   is absent in the library
   ERROR : atom :C02  LIG 1  EE   is absent in the library
   ERROR : atom :C03  LIG 1  EE   is absent in the library
   ERROR : atom :C04  LIG 1  EE   is absent in the library
   ERROR : atom :C05  LIG 1  EE   is absent in the library
   ERROR : atom :O06  LIG 1  EE   is absent in the library
   ERROR : atom :P07  LIG 1  EE   is absent in the library
   ERROR : atom :O08  LIG 1  EE   is absent in the library
   ERROR : atom :O09  LIG 1  EE   is absent in the library
   ERROR : atom :O10  LIG 1  EE   is absent in the library
   ATTENTION: atom:C28  LIG 1  EE   is missing in the
structure
   ATTENTION: atom:C26  LIG 1  EE   is missing in the
structure
   ATTENTION: atom:C24  LIG 1  EE   is missing in the
structure
   ATTENTION: atom:C22  LIG 1  EE   is missing in the
structure
   ATTENTION: atom:C21  LIG 1  EE   is missing in the
structure
   ATTENTION: atom:C4   LIG 1  EE   is missing in the
structure
   ATTENTION: atom:N3   LIG 1  EE   is missing in the
structure
   ATTENTION: atom:C20  LIG 1  EE   is missing in the
structure
   ATTENTION: atom:C17  LIG 1  EE   is missing in the
structure
   ATTENTION: atom:C5   LIG 1  EE   is missing in the
structure
   ATTENTION: atom:C6   LIG 1  EE   is missing in the
structure
   ATTENTION: atom:N1   LIG 1  EE   is missing in the
structure
   ATTENTION: atom:C7   LIG 1  EE   is missing in the
structure
   ATTENTION: atom:C15  LIG 1  EE   is missing in the
structure
   ATTENTION: atom:C13  LIG 1  EE   is missing in the
structure
   ATTENTION: atom:N12  LIG 1  EE   is missing in the
structure
   ATTENTION: atom:C10  LIG 1  EE   is missing in the
structure
   ATTENTION: atom:C8   LIG 1  EE   is missing in the
structure
   Number of chains  :   5
   Total number of monomers  : 217
   Number of atoms   :2162
   Number of missing atoms   :  18
   Number of rebuilt atoms   : 908
   Number of unknown atoms   :  10
   Number of deleted atoms   :   0
  IERR =1
 
 There is an error. See above
 === Error: Fatal error. Cannot continue BFONT COLOR=#FF!--
 SUMMARY_BEGIN--
  Refmac_5.8.0123:  Fatal error. Cannot continue
 Times: User:   2.1s System:0.1s Elapsed: 0:04
 /pre
 /html
 
 What went wrong? Am I missing any steps in my ligand fitting?
 Appreciate your feedback.
 
 Regards,
 Sze Yi
 

[ccp4bb] Refmac fatal error with newly added ligand

[Lau Sze Yi (SIgN)]

Hello,

I generated my new ligand using smiles string in Phenix with elbow to generate 
my ligand cif and pdb file. I then open these in Coot along with my protein 
model and mtz and fitted this new ligand into my density.
However Refmac failed with the following details in my log file:

PDB_code:4F80
  PDB_name:IMMUNE SYSTEM
  PDB_date:16-MAY-12
  
  ERROR : atom :C01  LIG 1  EE   is absent in the library
  ERROR : atom :C02  LIG 1  EE   is absent in the library
  ERROR : atom :C03  LIG 1  EE   is absent in the library
  ERROR : atom :C04  LIG 1  EE   is absent in the library
  ERROR : atom :C05  LIG 1  EE   is absent in the library
  ERROR : atom :O06  LIG 1  EE   is absent in the library
  ERROR : atom :P07  LIG 1  EE   is absent in the library
  ERROR : atom :O08  LIG 1  EE   is absent in the library
  ERROR : atom :O09  LIG 1  EE   is absent in the library
  ERROR : atom :O10  LIG 1  EE   is absent in the library
  ATTENTION: atom:C28  LIG 1  EE   is missing in the structure
  ATTENTION: atom:C26  LIG 1  EE   is missing in the structure
  ATTENTION: atom:C24  LIG 1  EE   is missing in the structure
  ATTENTION: atom:C22  LIG 1  EE   is missing in the structure
  ATTENTION: atom:C21  LIG 1  EE   is missing in the structure
  ATTENTION: atom:C4   LIG 1  EE   is missing in the structure
  ATTENTION: atom:N3   LIG 1  EE   is missing in the structure
  ATTENTION: atom:C20  LIG 1  EE   is missing in the structure
  ATTENTION: atom:C17  LIG 1  EE   is missing in the structure
  ATTENTION: atom:C5   LIG 1  EE   is missing in the structure
  ATTENTION: atom:C6   LIG 1  EE   is missing in the structure
  ATTENTION: atom:N1   LIG 1  EE   is missing in the structure
  ATTENTION: atom:C7   LIG 1  EE   is missing in the structure
  ATTENTION: atom:C15  LIG 1  EE   is missing in the structure
  ATTENTION: atom:C13  LIG 1  EE   is missing in the structure
  ATTENTION: atom:N12  LIG 1  EE   is missing in the structure
  ATTENTION: atom:C10  LIG 1  EE   is missing in the structure
  ATTENTION: atom:C8   LIG 1  EE   is missing in the structure
  Number of chains  :   5
  Total number of monomers  : 217
  Number of atoms   :2162
  Number of missing atoms   :  18
  Number of rebuilt atoms   : 908
  Number of unknown atoms   :  10
  Number of deleted atoms   :   0
 IERR =1

There is an error. See above
=== Error: Fatal error. Cannot continue
BFONT COLOR=#FF!--SUMMARY_BEGIN--
 Refmac_5.8.0123:  Fatal error. Cannot continue
Times: User:   2.1s System:0.1s Elapsed: 0:04
/pre
/html

What went wrong? Am I missing any steps in my ligand fitting?
Appreciate your feedback.

Regards,
Sze Yi

[ccp4bb] Refmac- riding hydrogen

[Sasha Pausch]

Dear CCP4bb,

When we select 'generate all hydrogen atoms' option in Refmac5, does it use
riding hydrogen model in refinement?




-- 
Regards,

Sasha Pausch

Re: [ccp4bb] Refmac- riding hydrogen

[Robbie Joosten]

Hi Sasha,

Yes, it does and I highly recommend using this option all the time. It really 
makes the VdW restraints much more effective.

Cheers,
Robbie

 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 Sasha Pausch
 Sent: Wednesday, April 15, 2015 16:27
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] Refmac- riding hydrogen
 
 Dear CCP4bb,
 
 When we select 'generate all hydrogen atoms' option in Refmac5, does it use
 riding hydrogen model in refinement?
 
 
 
 
 
 --
 
 Regards,
 
 Sasha Pausch

[ccp4bb] refmac rigid body module in ccp4i interface

[Ingo P. Korndoerfer]

hello,

could i ask the developers to check for me that the rigid body refinement 
module in the latest update works correctly. when i open the rigid body menu
i see no possibility to neither define my own domains nor select auto. rather i 
see all kinds of options for auto map sharpening etc.

my feeling is something got mixed up in the tcl/tk scripts behind or so ...

p.s. i fixed that for me now by copying the relevant tasks from the previous 
installation, but still ...

1000 thanks

ingo

[ccp4bb] REFMAC - TWIN OPTION

[Santarsiero, Bernard D.]

Can someone point me to bulletpoint documentation on using the twin
refinement in CCP4?

Here's what I did.

1.  I'm in space group P3, and the see a very clean diffraction pattern
that looks like one single lattice. Very clean spots, so merohedral
twinning.

2.  You can use various programs to estimate the twin fraction and select
various twin laws.

3.  You run DETWIN in the UTILITIES section of DATA REDUCTION and
ANALYSIS. I have both intensities IMEAN and amplitudes FMEAN, and selected
amplitudes. The FMEAN changes to something like FMEAN_detw. You have to
select a twin fraction, but does it matter what the twin factor you assign
is?  (It seems to get refined, or just estimated, in refinement?)

4.  There are potentially 3 twin laws, so do you run DETWIN three times? 
You can, in fact, get amplitudes that are FMEAN_detw_detw_detw.  I've run
it once and three times, and seems to give the same result in REFMAC
refinement.

5.  Select the Free R subset. Will uniqueify choose correctly?

6.  In REFMAC, it looks for the F_detw amplitude, or you can select it.
Then it seems to select and test three twin laws, even if you only ran
DETWIN once, with one selected twin law. It tests if the twin laws give
low R(merge).  If not, it tosses them out. It seems like the R(merge)
calculation depends on the starting model, and not just on the modified
Fobs data. It also seems like it tries to calculate the twin fraction, and
then refine the structure. Or, is it just giving an estimate, and I need
to go back to original data and rerun DETWIN?

7.  I tried to work with intensities instead of amplitudes, and it can
blow up. I've also refined, got a good refinement (3 twin laws, each with
twin fraction around 0.1, Rcryst = 19%, Rfree = 21%), rebuilt one chain of
the structure, and it blows up, suggesting no twinning, but Rs around 35%.

Does REFMAC refine the twin fraction?
Do I have to assign a twin fraction in DETWIN, or does it just set up the
relationships between reflections and amplitudes?
Should I try to work with intensities or amplitudes.  The calculation is
presumably done on intensities, but seems to be more unstable using that
option.

I haven't tried the PHENIX option. Just a quick step-by-step guide on what
to do would be useful.

Thanks,

Bernie
-- 
Bernard D. Santarsiero
Research Professor
Center for Structural Biology
University of Illinois at Chicago
MC870  3070MBRB  900 South Ashland Avenue
Chicago, IL 60607-7173  USA
(312) 413-0339 (office)
(312) 413-9303 (FAX)
http://www.uic.edu/labs/bds
http://scholar.google.com/citations?user=fGauLBMJ

[ccp4bb] AW: [ccp4bb] REFMAC - TWIN OPTION

[Herman . Schreuder]

Dear Berni,

DETWIN will detwin your Fobs, which can be done if the twin fraction is 
sufficiently far from 0.5. However, as you discovered, you need to know the 
twin fraction, which is by convention specified by the smaller fraction. Once 
your data is detwinned, it should just be that, a file with regular fobs and 
not twinned anymore, so in Refmac you should not use any TWIN keywords.

However, this is not the best way to proceed. The best way is to provide Refmac 
with your twinned dataset and let Refmac figure it all out for you! As you 
mentioned, Refmac will test the different possible twinning operators and will 
refine the twinning fraction. In my hands it works very well and is extremely 
easy even for crystals with multiple twinning operators.

Good luck!
Herman



-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
Santarsiero, Bernard D.
Gesendet: Mittwoch, 17. September 2014 14:20
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] REFMAC - TWIN OPTION

Can someone point me to bulletpoint documentation on using the twin refinement 
in CCP4?

Here's what I did.

1.  I'm in space group P3, and the see a very clean diffraction pattern that 
looks like one single lattice. Very clean spots, so merohedral twinning.

2.  You can use various programs to estimate the twin fraction and select 
various twin laws.

3.  You run DETWIN in the UTILITIES section of DATA REDUCTION and ANALYSIS. I 
have both intensities IMEAN and amplitudes FMEAN, and selected amplitudes. The 
FMEAN changes to something like FMEAN_detw. You have to select a twin fraction, 
but does it matter what the twin factor you assign is?  (It seems to get 
refined, or just estimated, in refinement?)

4.  There are potentially 3 twin laws, so do you run DETWIN three times? 
You can, in fact, get amplitudes that are FMEAN_detw_detw_detw.  I've run it 
once and three times, and seems to give the same result in REFMAC refinement.

5.  Select the Free R subset. Will uniqueify choose correctly?

6.  In REFMAC, it looks for the F_detw amplitude, or you can select it.
Then it seems to select and test three twin laws, even if you only ran DETWIN 
once, with one selected twin law. It tests if the twin laws give low R(merge).  
If not, it tosses them out. It seems like the R(merge) calculation depends on 
the starting model, and not just on the modified Fobs data. It also seems like 
it tries to calculate the twin fraction, and then refine the structure. Or, is 
it just giving an estimate, and I need to go back to original data and rerun 
DETWIN?

7.  I tried to work with intensities instead of amplitudes, and it can blow up. 
I've also refined, got a good refinement (3 twin laws, each with twin fraction 
around 0.1, Rcryst = 19%, Rfree = 21%), rebuilt one chain of the structure, and 
it blows up, suggesting no twinning, but Rs around 35%.

Does REFMAC refine the twin fraction?
Do I have to assign a twin fraction in DETWIN, or does it just set up the 
relationships between reflections and amplitudes?
Should I try to work with intensities or amplitudes.  The calculation is 
presumably done on intensities, but seems to be more unstable using that option.

I haven't tried the PHENIX option. Just a quick step-by-step guide on what to 
do would be useful.

Thanks,

Bernie
--
Bernard D. Santarsiero
Research Professor
Center for Structural Biology
University of Illinois at Chicago
MC870  3070MBRB  900 South Ashland Avenue Chicago, IL 60607-7173  USA
(312) 413-0339 (office)
(312) 413-9303 (FAX)
http://www.uic.edu/labs/bds
http://scholar.google.com/citations?user=fGauLBMJ

Re: [ccp4bb] REFMAC - TWIN OPTION

[Chris Fage]

Hi Bernie,

I agree with Herman. I think you will be all set if you simply change the no 
twin refinement option near the top of the Refmac interface to intensity 
based or amplitude based twin refinement. Refmac will determine the 
appropriate twin operators/fractions and refine. 

Best,
Chris 

 On Sep 17, 2014, at 14:19, Santarsiero, Bernard D. b...@uic.edu wrote:
 
 Can someone point me to bulletpoint documentation on using the twin
 refinement in CCP4?
 
 Here's what I did.
 
 1.  I'm in space group P3, and the see a very clean diffraction pattern
 that looks like one single lattice. Very clean spots, so merohedral
 twinning.
 
 2.  You can use various programs to estimate the twin fraction and select
 various twin laws.
 
 3.  You run DETWIN in the UTILITIES section of DATA REDUCTION and
 ANALYSIS. I have both intensities IMEAN and amplitudes FMEAN, and selected
 amplitudes. The FMEAN changes to something like FMEAN_detw. You have to
 select a twin fraction, but does it matter what the twin factor you assign
 is?  (It seems to get refined, or just estimated, in refinement?)
 
 4.  There are potentially 3 twin laws, so do you run DETWIN three times? 
 You can, in fact, get amplitudes that are FMEAN_detw_detw_detw.  I've run
 it once and three times, and seems to give the same result in REFMAC
 refinement.
 
 5.  Select the Free R subset. Will uniqueify choose correctly?
 
 6.  In REFMAC, it looks for the F_detw amplitude, or you can select it.
 Then it seems to select and test three twin laws, even if you only ran
 DETWIN once, with one selected twin law. It tests if the twin laws give
 low R(merge).  If not, it tosses them out. It seems like the R(merge)
 calculation depends on the starting model, and not just on the modified
 Fobs data. It also seems like it tries to calculate the twin fraction, and
 then refine the structure. Or, is it just giving an estimate, and I need
 to go back to original data and rerun DETWIN?
 
 7.  I tried to work with intensities instead of amplitudes, and it can
 blow up. I've also refined, got a good refinement (3 twin laws, each with
 twin fraction around 0.1, Rcryst = 19%, Rfree = 21%), rebuilt one chain of
 the structure, and it blows up, suggesting no twinning, but Rs around 35%.
 
 Does REFMAC refine the twin fraction?
 Do I have to assign a twin fraction in DETWIN, or does it just set up the
 relationships between reflections and amplitudes?
 Should I try to work with intensities or amplitudes.  The calculation is
 presumably done on intensities, but seems to be more unstable using that
 option.
 
 I haven't tried the PHENIX option. Just a quick step-by-step guide on what
 to do would be useful.
 
 Thanks,
 
 Bernie
 -- 
 Bernard D. Santarsiero
 Research Professor
 Center for Structural Biology
 University of Illinois at Chicago
 MC870  3070MBRB  900 South Ashland Avenue
 Chicago, IL 60607-7173  USA
 (312) 413-0339 (office)
 (312) 413-9303 (FAX)
 http://www.uic.edu/labs/bds
 http://scholar.google.com/citations?user=fGauLBMJ

Re: [ccp4bb] Refmac buccaneer combination

[Kevin Cowtan]

Can you send me the rest of the logfile?

I think I've seen an error like this where the number of atoms built
dropped to zero, in which case there is something seriously wrong with the
input phases. But I expect there are other ways to trigger a refmac fail -
I can't tell for sure without more information.

Thanks,
Kevin


On 17 March 2014 22:12, Debajyoti Dutta debajyoti_dutt...@rediffmail.comwrote:

 Hi all,

 I am running autobuild and refinement in buccaneer/refmac pipeline. Does
 anybody have any idea about the following error .

 Refmac_5.8.0069: Check input coordinates
 Traceback (most recent call last):
 File /Applications/ccp4-6.4.0/bin/buccaneer_pipeline, line 199, in
 control.run_program_template( refmac_all )
 File /Applications/ccp4-6.4.0/share/python/CCP4pipeline.py, line 740, in
 run_program_template
 self.run_program( prgm, argx, cmdx )
 File /Applications/ccp4-6.4.0/share/python/CCP4pipeline.py, line 729, in
 run_program
 raise( StandardError( 'Fail in program '+prgm+'' ) )
 StandardError: Fail in program

 Thanks in advance.

 Best

 Debajyoti

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Re: [ccp4bb] Refmac buccaneer combination

[Debajyoti Dutta]

Hi Ronan and Kavin,

I checked the input files and found that i was assigning wrong column labels in 
buccaneer for which the error was popping up. I was able to fix it now.

Thanks a lot. 

Debajyoti 


On Tue, 18 Mar 2014 21:09:15 +0530  wrote
 
  

   
  
Hi Debajyoti,

  

  Thanks for sending the file. It's clearly a problem for Buccaneer
  to build anything into the map you've provided it with. It fails
  to find any residues and as a result the output PDB file from
  Buccaneer is empty. Refmac then complains about 0 atoms. Is it
  poor map that you are providing? It might help if you provide it
  with a starting model to build from, e.g. a molecular replacement
  solution. Otherwise try ARP/wARP wit the same data. 

  

  Best wishes,

  

  Ronan

  

   

  

  On 18/03/14 21:41, Debajyoti Dutta wrote:



  
  

  Hi Ronan,

  

  Please find the log file attached.

  

  Thanks for your reply.

  

  Best

  

  Debajyoti

  

  On Tue, 18 Mar 2014 16:03:18 +0530 wrote

   

  

  

  

  

  Hi Debajyoti,

  

  

  

  This is a problem with the PDB file that Buccaneer is passing to

  Refmac for refinement. It's possible that Buccaneer couldn't build

  anything into the map in which case the PDB file will have no

  coordinates in it and Refmac will fail as a consequence. However,

  to make a proper assessment of the problem it would be best if you

  could send us the entire Buccaneer log file for the job.  

  

  

  

  Best wishes,

  

  

  

  Ronan

  

  

  

  On 18/03/14 07:12, Debajyoti Dutta wrote:

  

  

  

  

  Hi all,

  

  

  

  I am running autobuild and refinement in buccaneer/refmac

  pipeline. Does anybody have any idea about the following error .

  

  

  

  Refmac_5.8.0069: Check input coordinates

  

  Traceback (most recent call last):

  

  File /Applications/ccp4-6.4.0/bin/buccaneer_pipeline, line 199,

  in 

  

  control.run_program_template( refmac_all )

  

  File /Applications/ccp4-6.4.0/share/python/CCP4pipeline.py,

  line 740, in run_program_template

  

  self.run_program( prgm, argx, cmdx )

  

  File /Applications/ccp4-6.4.0/share/python/CCP4pipeline.py,

  line 729, in run_program

  

  raise( StandardError( 'Fail in program ' ) )

  

  StandardError: Fail in program 

  

  

  

  Thanks in advance.

  

  

  

  Best

  

  

  

  Debajyoti

  

  

  

  

  

  

  

  

  

  

  

  

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Scanned by iCritical.


 
 

[ccp4bb] Refmac buccaneer combination

[Debajyoti Dutta]

Hi all,

I am running autobuild and refinement in buccaneer/refmac pipeline. Does 
anybody have any idea about the following error .

 Refmac_5.8.0069:  Check input coordinates
Traceback (most recent call last):
  File /Applications/ccp4-6.4.0/bin/buccaneer_pipeline, line 199, in 
control.run_program_template( refmac_all )
  File /Applications/ccp4-6.4.0/share/python/CCP4pipeline.py, line 740, in 
run_program_template
self.run_program( prgm, argx, cmdx )
  File /Applications/ccp4-6.4.0/share/python/CCP4pipeline.py, line 729, in 
run_program
raise( StandardError( 'Fail in program ' ) )
StandardError: Fail in program 

Thanks in advance.

Best

Debajyoti

[ccp4bb] Refmac bond restraints across special positions?

[Oleg Tsodikov]

Colleagues,

We have determined a structure of a palindromic DNA molecule, in which one
half of the DNA is in the asymmetric unit. Is there a way to tell REFMAC
that there are covalent bonds across asymmetric units? Without such LINK
records in the PDB file, REFMAC treats this as a non-covalent interaction
and pushes the two DNA halfs apart. The data are at a fairly high
resolution, which helps, but the repulsion is still there.

Any advice would be greatly appreciated! I imagine this situation is quite
rare in macromolecular crystallography.

Oleg
-- 
Oleg Tsodikov, Ph.D.
Associate Professor of Pharmaceutical Sciences
University of Kentucky College of Pharmacy
Department of Pharmaceutical Sciences
BioPharm Bldg, Room 425
789 S. Limestone
Lexington, KY 40536

Re: [ccp4bb] Refmac bond restraints across special positions?

[Craig Bingman]

I haven’t tried this in a long time, but in the old days, we would have simply 
refined one strand.

On Mar 12, 2014, at 4:05 PM, Oleg Tsodikov olegtsodi...@gmail.com wrote:

 Colleagues,
 
 We have determined a structure of a palindromic DNA molecule, in which one 
 half of the DNA is in the asymmetric unit. Is there a way to tell REFMAC that 
 there are covalent bonds across asymmetric units? Without such LINK records 
 in the PDB file, REFMAC treats this as a non-covalent interaction and pushes 
 the two DNA halfs apart. The data are at a fairly high resolution, which 
 helps, but the repulsion is still there.
 
 Any advice would be greatly appreciated! I imagine this situation is quite 
 rare in macromolecular crystallography.
 
 Oleg
 -- 
 Oleg Tsodikov, Ph.D.
 Associate Professor of Pharmaceutical Sciences
 University of Kentucky College of Pharmacy
 Department of Pharmaceutical Sciences
 BioPharm Bldg, Room 425
 789 S. Limestone
 Lexington, KY 40536
 
 

Re: [ccp4bb] Refmac bond restraints across special positions?

[Das, Debanu]

Hi,

 Is there a way to tell REFMAC that there are covalent bonds across asymmetric 
 units?

Try this (example from 3gbi.pdb) for DNA:

LINK PDC B 119 O3'  DA B 125 1555   2555  1.61  
LINK O3'  DA B 125 PDC B 119 1555   3555  1.61  
LINK PDG C 209 O3'  DT D 108 1555   3555  1.61  
LINK O3'  DT D 108 PDG C 209 1555   2555  1.61  

Best,
Debanu.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Craig 
Bingman
Sent: Wednesday, March 12, 2014 2:10 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac bond restraints across special positions?

I haven't tried this in a long time, but in the old days, we would have simply 
refined one strand.

On Mar 12, 2014, at 4:05 PM, Oleg Tsodikov olegtsodi...@gmail.com wrote:

 Colleagues,
 
 We have determined a structure of a palindromic DNA molecule, in which one 
 half of the DNA is in the asymmetric unit. Is there a way to tell REFMAC that 
 there are covalent bonds across asymmetric units? Without such LINK records 
 in the PDB file, REFMAC treats this as a non-covalent interaction and pushes 
 the two DNA halfs apart. The data are at a fairly high resolution, which 
 helps, but the repulsion is still there.
 
 Any advice would be greatly appreciated! I imagine this situation is quite 
 rare in macromolecular crystallography.
 
 Oleg
 --
 Oleg Tsodikov, Ph.D.
 Associate Professor of Pharmaceutical Sciences University of Kentucky 
 College of Pharmacy Department of Pharmaceutical Sciences BioPharm 
 Bldg, Room 425
 789 S. Limestone
 Lexington, KY 40536
 
 

[ccp4bb] refmac-linux-I'm out of touch question

[Joel Tyndall]

Hi folks,

I am wanting to ask for some linux help as I want to try a newer version of 
refmac (5.8) to test it against a refinement problem I have. My problem is that 
I rarely use linux these days and I'm at a loss as  to how to run the latest 
version as my knowledge of linux has disappeared.

I have downloaded the binaries for refmac 5.8 which gives me refmacgfortran and 
libcheckgfortran. And now I am stuck. Would someone be so kind as to instruct 
me on where to put these, if they need compiling etc?

Many thanks

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

Re: [ccp4bb] refmac-linux-I'm out of touch question

[Robbie Joosten]

Hi Joel,

You can just replace your current 'refmac5' and 'libcheck' files. Perhaps after 
making a backup. They are in the 'bin' directory of your CCP4 installation.
The easiest way to find them is using 'which refmac5'.

HtH,
Robbie

Verzonden met mijn Windows Phone

Van: Joel Tyndall
Verzonden: 10-7-2013 23:49
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] refmac-linux-I'm out of touch question

Hi folks,

I am wanting to ask for some linux help as I want to try a newer version of 
refmac (5.8) to test it against a refinement problem I have. My problem is that 
I rarely use linux these days and I'm at a loss as  to how to run the latest 
version as my knowledge of linux has disappeared.

I have downloaded the binaries for refmac 5.8 which gives me refmacgfortran and 
libcheckgfortran. And now I am stuck. Would someone be so kind as to instruct 
me on where to put these, if they need compiling etc?

Many thanks

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

Re: [ccp4bb] Refmac error

[Martin Moche]

Dear colleagues,

I have the same problems as Peer Mittl once had. 

Was this solved and what was the solution?

Running arpWarp the job terminates with the message:
Refmac_5.7.0032:   Open failed: File: 
/software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif


However the mon_lib_list.cif is readable to my user?
[x_marmo@triolith3 CCP4]$ more 
/software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
global_
_lib_name  mon_lib
_lib_version   5.39
_lib_update06/11/12
#-



Here is the output of the ls -l command suggested by Tim Gruene
[x_marmo@triolith3 CCP4]$ ls -l 
/software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
-rw-r--r-- 1 raber nsc 1078257 May 15 08:15 
/software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif




At the end of the warpNtrace logfile is the following information:
[x_marmo@triolith3 CCP4]$ tail -22 
/home/x_marmo/MexR/CCP4/2_warpNtrace_refine.last.log
B value  outliers  10.000
NCS outliers   20.000
---

 Input file :arp_0.pdb_start
  Size of lib_com.fh(bytes) : 118100416
 Open failed: Unit:   7, File: 
/software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif 
(logical: 
/software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif)
BFONT COLOR=#FF!--SUMMARY_BEGIN--
 Refmac_5.7.0032:   Open failed: File: 
/software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif  
   
Times: User:   0.3s System:0.0s Elapsed: 0:00  
/pre
/html
!--SUMMARY_END--/FONT/B

BFONT COLOR=#FF!--SUMMARY_BEGIN--
QUITTING ... ARP/wARP module stopped with an error message:
REFMAC5

*** Look for error message in the file: 
/home/x_marmo/MexR/CCP4/2_warpNtrace_refine.last.log
[x_marmo@triolith3 CCP4]$ 



What is wrong here?

Best regards,
Martin

Re: [ccp4bb] Refmac error

[Martin Moche]

Thanks Alexander,

I got the solution #2 below as well from my colleague Johan Raber :)

Cheers,
Martin

 solution #2 ##

Hi Martin,

A colleague of mine suggested this could be a known OS bug related to opening 
files on a read-only mounted file system (such as /software on Triolith). We 
have a workaround for this until that bug is fixed by RedHat. Please try to
do:

$ export 
LD_PRELOAD=/software/tools/ldpreload/openrocrwrap/libopenrocrwrapsilent.so

before running CCP4i again, and tell us if this fixed the problem.

/Johan

-Original Message-
From: Alexander Batyuk [mailto:bat...@bioc.uzh.ch] 
Sent: den 15 maj 2013 10:34
To: Martin Moche
Subject: Re: [ccp4bb] Refmac error


Dear Martin,

I think we solved it by changing the file's permissions (for mon_lib_list.cif) 
to rwxrwxrwx

Best wishes,

Alex




On 15 May 2013, at 10:25, Martin Moche martin.mo...@ki.se wrote:

 Dear colleagues,
 
 I have the same problems as Peer Mittl once had. 
 
 Was this solved and what was the solution?
 
 Running arpWarp the job terminates with the message:
 Refmac_5.7.0032:   Open failed: File: 
 /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
 
 
 However the mon_lib_list.cif is readable to my user?
 [x_marmo@triolith3 CCP4]$ more 
 /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
 global_
 _lib_name  mon_lib
 _lib_version   5.39
 _lib_update06/11/12
 #-
 
 
 
 Here is the output of the ls -l command suggested by Tim Gruene
 [x_marmo@triolith3 CCP4]$ ls -l 
 /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
 -rw-r--r-- 1 raber nsc 1078257 May 15 08:15 
 /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
 
 
 
 
 At the end of the warpNtrace logfile is the following information:
 [x_marmo@triolith3 CCP4]$ tail -22 
 /home/x_marmo/MexR/CCP4/2_warpNtrace_refine.last.log
 B value  outliers  10.000
 NCS outliers   20.000
 ---
 
 Input file :arp_0.pdb_start
  Size of lib_com.fh(bytes) : 118100416
 Open failed: Unit:   7, File: 
 /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif 
 (logical: 
 /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif)
 BFONT COLOR=#FF!--SUMMARY_BEGIN--
 Refmac_5.7.0032:   Open failed: File: 
 /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
  
 Times: User:   0.3s System:0.0s Elapsed: 0:00  
 /pre
 /html
 !--SUMMARY_END--/FONT/B
 
 BFONT COLOR=#FF!--SUMMARY_BEGIN--
 QUITTING ... ARP/wARP module stopped with an error message:
 REFMAC5
 
 *** Look for error message in the file: 
 /home/x_marmo/MexR/CCP4/2_warpNtrace_refine.last.log
 [x_marmo@triolith3 CCP4]$ 
 
 
 
 What is wrong here?
 
 Best regards,
 Martin

--
Alex Batyuk
The Plueckthun Lab
www.bioc.uzh.ch/plueckthun

[ccp4bb] Refmac error

[Peer Mittl]

 Dear Colleagues, 

For some reason Refmac refuses to read the file mon_lib_list.cif athough the 
file exists. The error message is as follows:

 Open failed: Unit:   7, File: 
/share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif (logical: 
/share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif)
BFONT COLOR=#FF!--SUMMARY_BEGIN--
Last system error message: Illegal seek
 Refmac_5.7.0029:   Open failed: File: 
/share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
   
 Refmac_5.7.0029:   Open failed: File: 
/share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif 

Any advice would be welcome.

-Peer