Re: [ccp4bb] High Temperature Factors with TLS

[Rezaul Karim]

If  the correct atoms are in place, resetting the b factors of those atoms/residues to a constant e.g. 5.00 and refining in phenix with individual B-factors ON should take care of these.Best,RezaSent from my iPhoneOn Aug 2, 2023, at 7:42 AM, Thomas, Leonard M.  wrote:




Hello All,


A general questions though phenix.refine is being used for refinement.  A student I am working with has a structure that was solved and initially refined using TLS and NCS parameters.  They were given the structure to gain some experience in refinement
 and they have been asking me some questions, I was not involved in the initial work.  While everything seems to be happy and the model is correct with good refinement statistics for the most part one thing that I am unsure of is some of the heavier atoms (Phosphate
 and Sulfer) have very high temperature factors when looking at individual residues or ligands.  The temperature factors are at least twice as high as the lighter atoms they are associated with.  


I am at a loss to explain what is going on, I really have not used TLS refinement a lot so there is that.  Resolution is about 2.5 angstroms with good completeness.


Thoughts?


Thank You in advance
Len Thomas






Leonard Thomas, Ph.D.
Biomolecular Structure Core, Director
Oklahoma COBRE in Structural Biology
Price
 Family Foundation Institute of Structural Biology
University
 of Oklahoma
Department
 of Chemistry and Biochemistry
101
 Stephenson Parkway
Norman,
 OK 73019-5251
Office:
 (405)325-1126
lmtho...@ou.edu
http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl









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Re: [ccp4bb] Cannot select any recommended SG for the protein BsAlaDH

[Phil Jeffrey]

1.  Completeness is primarily an issue with using the right point group 
and crystal system, not the actual space group (e.g. in primitive point 
group mmm the space groups P222, P2221, P21212, P212121 should all have 
essentially the same completeness).
2.  If "refinalize" in CrysAlisPro doesn't let you choose the right 
point group and system, then you should process the data with another 
program.  XDS, MOSFLM, DIALS, autoPROC etc might work, and I have to 
believe they'd be better at scaling your data.
3.  If you can export the unscaled data from CrysAlisPro you might be 
able to feed it into POINTLESS and AIMLESS for scaling


4.  On the model front, go find an AlphaFold model, they have worked for 
me multiple times in molecular replacement so far.


Phil Jeffrey
Princeton



On 8/2/23 3:00 PM, CENGIZ KAAN FERAH wrote:

Hello,
So I'm trying to get the data processed that I gathered from XRD for the 
protein BsAlaDH. Unfortunately from the method that I know of on 
CrysAlisPro I cannot select the recommended space group for the protein. 
This results in the data not being complete. Still I can get good unit 
cells and the degrees. Another problem is that this protein has no 
structure published on PDB. And the homolog proteins do not have high 
similarities. By that way I cannot really find a suitable space group. 
Can someone give me a hand on this issue.

Thank you.




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[ccp4bb] Cannot select any recommended SG for the protein BsAlaDH

[CENGIZ KAAN FERAH]

Hello,
So I'm trying to get the data processed that I gathered from XRD for the
protein BsAlaDH. Unfortunately from the method that I know of on
CrysAlisPro I cannot select the recommended space group for the protein.
This results in the data not being complete. Still I can get good unit
cells and the degrees. Another problem is that this protein has no
structure published on PDB. And the homolog proteins do not have high
similarities. By that way I cannot really find a suitable space group. Can
someone give me a hand on this issue.
Thank you.



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[ccp4bb] PyMol tutorials?

[Patrick Loll]

Hi everyone,

Can the hive mind recommend particular video tutorials that introduce PyMol? 
I’m looking for a beginner-level introduction, suitable for undergrads or 
early-career grad students. 

My hope is that some kind soul(s) can save me from slogging through hours on 
YouTube in order to find a suitable resource. 

Thanks in advance,

Pat 

[This is me bowing to the fact that younger people appear to like to get their 
information by watching videos, even though I much prefer to READ].


---
Patrick J. Loll, Ph. D.  (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu



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[ccp4bb] Postdoctoral position in drug discovery

[Harp, Joel M]

Postdoctoral position in drug discovery An opening is available in the drug 
discovery laboratory of Dr. Stephen Fesik for a post-doc in the field of 
protein x-ray crystallography.  Responsibilities will include protein 
production, fragment screening by NMR, and all aspects of x-ray crystallography 
including preparation of protein-ligand complexes, crystallization, 
home/synchrotron data collection, and structure determination. Additional 
experience in molecular biology including construct design, cloning, 
site-directed mutagenesis and modeling is a plus.  The ideal candidate should 
be self-motivated and be able to communicate efficiently in a highly 
collaborative environment. Please send cv to 
jason.p...@vanderbilt.edu


The Vanderbilt campus is located in Nashville Tennessee. Also known as Music 
City, Nashville is a fast growing and dynamic environment with plenty of 
cultural attractions and opportunities for outdoor recreation.




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Re: [ccp4bb] High Temperature Factors with TLS

[Jon Cooper]

Hello, is it definitely due to the TLS refinement? I guess you have tried 
without TLS and don't see the same effect i.e. the B-factors are more 
consistent. It would be good to know.

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

Sent from Proton Mail mobile

 Original Message 
On 2 Aug 2023, 15:42, Thomas, Leonard M. wrote:

> Hello All,
>
> A general questions though phenix.refine is being used for refinement. A 
> student I am working with has a structure that was solved and initially 
> refined using TLS and NCS parameters. They were given the structure to gain 
> some experience in refinement and they have been asking me some questions, I 
> was not involved in the initial work. While everything seems to be happy and 
> the model is correct with good refinement statistics for the most part one 
> thing that I am unsure of is some of the heavier atoms (Phosphate and Sulfer) 
> have very high temperature factors when looking at individual residues or 
> ligands. The temperature factors are at least twice as high as the lighter 
> atoms they are associated with.
>
> I am at a loss to explain what is going on, I really have not used TLS 
> refinement a lot so there is that. Resolution is about 2.5 angstroms with 
> good completeness.
>
> Thoughts?
>
> Thank You in advance
> Len Thomas
>
> Leonard Thomas, Ph.D.
> Biomolecular Structure Core, Director
>
> Oklahoma COBRE in Structural Biology
> Price Family Foundation Institute of Structural Biology
> University of Oklahoma
> Department of Chemistry and Biochemistry
> 101 Stephenson Parkway
> Norman, OK 73019-5251
> Office: (405)325-1126
> lmtho...@ou.edu
> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl
>
> ---
>
> 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] High Temperature Factors with TLS

[Robbie Joosten]

Although the effect should be quite small, is the wavelength in your reflection 
file consistent with the actual wavelength? 

Another option is that specific filters on atom types were used in the TLS 
refinement. I would refine the models with another program 
(REFMAC/Buster/PDB-REDO) to see if the B-factor anomaly remains.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Daniel M.
> Himmel, Ph. D.
> Sent: Wednesday, August 2, 2023 17:06
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] High Temperature Factors with TLS
> 
> One possible explanation for high B-factors, assuming the coordinates are
> refined correctly, is partial occupancy and high mobility (dynamics) at those
> heavy atom sites.
> 
> Also, one should check Fo-Fc maps of those positions.  Are other atom types
> substituting for some of those heavy atoms (such as sulfate instead of
> phosphate)?
> 
> 
> Daniel
> 
> ___
> 
> Daniel M. Himmel, Ph. D.
> 
> Principal, Himmel Sci Med Com, LLC
> 
> E-mail:  danielmhim...@gmail.com
> 
> 
> URL   :  https://www.HimmelSciMedCom.com
> 
> 
> 
> On Wed, Aug 2, 2023 at 10:42 AM Thomas, Leonard M.   > wrote:
> 
> 
>   Hello All,
> 
>   A general questions though phenix.refine is being used for refinement.
> A student I am working with has a structure that was solved and initially 
> refined
> using TLS and NCS parameters.  They were given the structure to gain some
> experience in refinement and they have been asking me some questions, I was
> not involved in the initial work.  While everything seems to be happy and the
> model is correct with good refinement statistics for the most part one thing
> that I am unsure of is some of the heavier atoms (Phosphate and Sulfer) have
> very high temperature factors when looking at individual residues or ligands.
> The temperature factors are at least twice as high as the lighter atoms they 
> are
> associated with.
> 
>   I am at a loss to explain what is going on, I really have not used TLS
> refinement a lot so there is that.  Resolution is about 2.5 angstroms with 
> good
> completeness.
> 
>   Thoughts?
> 
>   Thank You in advance
>   Len Thomas
> 
>   Leonard Thomas, Ph.D.
>   Biomolecular Structure Core, Director
> 
>   Oklahoma COBRE in Structural Biology
>   Price Family Foundation Institute of Structural Biology
>   University of Oklahoma
>   Department of Chemistry and Biochemistry
>   101 Stephenson Parkway
>   Norman, OK 73019-5251
>   Office: (405)325-1126
>   lmtho...@ou.edu 
>   http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl
> 
> 
> 
> 
> 
>   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] High Temperature Factors with TLS

[Thomas, Leonard M.]

So the Phosphates are actually the end of the ADP which the Sulfer atoms are 
Cystiene suffers.   The Fo-Fc maps show large positive peaks for each position 
also.  The TLS groups is the whole protein chain, there are 4 in the asymmetric 
unit as the biological unit I think is a dimer of 2 different chains.  ADP and 
FAD are bound and are separate from what I can tell.

Len


On Aug 2, 2023, at 10:05 AM, Daniel M. Himmel, Ph. D. 
mailto:danielmhim...@gmail.com>> wrote:

One possible explanation for high B-factors, assuming the coordinates are 
refined correctly, is partial occupancy and high mobility (dynamics) at those 
heavy atom sites.

Also, one should check Fo-Fc maps of those positions.  Are other atom types 
substituting for some of those heavy atoms (such as sulfate instead of 
phosphate)?

Daniel
___
Daniel M. Himmel, Ph. D.
Principal, Himmel Sci Med Com, LLC
E-mail:  danielmhim...@gmail.com
URL   :  
https://www.HimmelSciMedCom.com


On Wed, Aug 2, 2023 at 10:42 AM Thomas, Leonard M. 
mailto:lmtho...@ou.edu>> wrote:
Hello All,

A general questions though phenix.refine is being used for refinement.  A 
student I am working with has a structure that was solved and initially refined 
using TLS and NCS parameters.  They were given the structure to gain some 
experience in refinement and they have been asking me some questions, I was not 
involved in the initial work.  While everything seems to be happy and the model 
is correct with good refinement statistics for the most part one thing that I 
am unsure of is some of the heavier atoms (Phosphate and Sulfer) have very high 
temperature factors when looking at individual residues or ligands.  The 
temperature factors are at least twice as high as the lighter atoms they are 
associated with.

I am at a loss to explain what is going on, I really have not used TLS 
refinement a lot so there is that.  Resolution is about 2.5 angstroms with good 
completeness.

Thoughts?

Thank You in advance
Len Thomas

Leonard Thomas, Ph.D.
Biomolecular Structure Core, Director
Oklahoma COBRE in Structural Biology
Price Family Foundation Institute of Structural Biology
University of Oklahoma
Department of Chemistry and Biochemistry
101 Stephenson Parkway
Norman, OK 73019-5251
Office: (405)325-1126
lmtho...@ou.edu
http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl




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Re: [ccp4bb] anomalous map in Coot - Linux vs. Win difference?

[Paul Emsley]

On 02/08/2023 13:53, Andrea Smith wrote:

Dear all,

I used refmac in CCP4Cloud and then I opened the generated .pdb and 
.mtz from the CCP4Cloud job both in Linux Coot 0.9.6. and WinCoot 
0.9.6. I can see different anomalous maps in Coot and Wincoot - see 
attached printscreen where on the left there is a green electron 
density between the aspartates while on the right there is none. I 
tried to search if this is a bug but couldn't find info about this.




Did you press "Apply" in both cases?

To check/set the contour level, normally I just scroll the scroll wheel.

Paul.



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Re: [ccp4bb] High Temperature Factors with TLS

[Daniel M. Himmel, Ph. D.]

One possible explanation for high B-factors, assuming the coordinates are
refined correctly, is partial occupancy and high mobility (dynamics) at
those heavy atom sites.

Also, one should check Fo-Fc maps of those positions.  Are other atom types
substituting for some of those heavy atoms (such as sulfate instead of
phosphate)?

Daniel

___

Daniel M. Himmel, Ph. D.

Principal, Himmel Sci Med Com, LLC

E-mail:  danielmhim...@gmail.com

URL   :  https://www.HimmelSciMedCom.com


On Wed, Aug 2, 2023 at 10:42 AM Thomas, Leonard M.  wrote:

> Hello All,
>
> A general questions though phenix.refine is being used for refinement.  A
> student I am working with has a structure that was solved and initially
> refined using TLS and NCS parameters.  They were given the structure to
> gain some experience in refinement and they have been asking me some
> questions, I was not involved in the initial work.  While everything seems
> to be happy and the model is correct with good refinement statistics for
> the most part one thing that I am unsure of is some of the heavier atoms
> (Phosphate and Sulfer) have very high temperature factors when looking at
> individual residues or ligands.  The temperature factors are at least twice
> as high as the lighter atoms they are associated with.
>
> I am at a loss to explain what is going on, I really have not used TLS
> refinement a lot so there is that.  Resolution is about 2.5 angstroms with
> good completeness.
>
> Thoughts?
>
> Thank You in advance
> Len Thomas
>
> Leonard Thomas, Ph.D.
> Biomolecular Structure Core, Director
> Oklahoma COBRE in Structural Biology
> Price Family Foundation Institute of Structural Biology
> University of Oklahoma
> Department of Chemistry and Biochemistry
> 101 Stephenson Parkway
> Norman, OK 73019-5251
> Office: (405)325-1126
> lmtho...@ou.edu
> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl
>
>
> --
>
> 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] High Temperature Factors with TLS

[Eleanor Dodson]

You need to tell us more details - is this a deposited structure?
Eleanor

On Wed, 2 Aug 2023 at 15:42, Thomas, Leonard M.  wrote:

> Hello All,
>
> A general questions though phenix.refine is being used for refinement.  A
> student I am working with has a structure that was solved and initially
> refined using TLS and NCS parameters.  They were given the structure to
> gain some experience in refinement and they have been asking me some
> questions, I was not involved in the initial work.  While everything seems
> to be happy and the model is correct with good refinement statistics for
> the most part one thing that I am unsure of is some of the heavier atoms
> (Phosphate and Sulfer) have very high temperature factors when looking at
> individual residues or ligands.  The temperature factors are at least twice
> as high as the lighter atoms they are associated with.
>
> I am at a loss to explain what is going on, I really have not used TLS
> refinement a lot so there is that.  Resolution is about 2.5 angstroms with
> good completeness.
>
> Thoughts?
>
> Thank You in advance
> Len Thomas
>
> Leonard Thomas, Ph.D.
> Biomolecular Structure Core, Director
> Oklahoma COBRE in Structural Biology
> Price Family Foundation Institute of Structural Biology
> University of Oklahoma
> Department of Chemistry and Biochemistry
> 101 Stephenson Parkway
> Norman, OK 73019-5251
> Office: (405)325-1126
> lmtho...@ou.edu
> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl
>
>
> --
>
> 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] High Temperature Factors with TLS

[Thomas, Leonard M.]

Hello All,

A general questions though phenix.refine is being used for refinement.  A 
student I am working with has a structure that was solved and initially refined 
using TLS and NCS parameters.  They were given the structure to gain some 
experience in refinement and they have been asking me some questions, I was not 
involved in the initial work.  While everything seems to be happy and the model 
is correct with good refinement statistics for the most part one thing that I 
am unsure of is some of the heavier atoms (Phosphate and Sulfer) have very high 
temperature factors when looking at individual residues or ligands.  The 
temperature factors are at least twice as high as the lighter atoms they are 
associated with.

I am at a loss to explain what is going on, I really have not used TLS 
refinement a lot so there is that.  Resolution is about 2.5 angstroms with good 
completeness.

Thoughts?

Thank You in advance
Len Thomas

Leonard Thomas, Ph.D.
Biomolecular Structure Core, Director
Oklahoma COBRE in Structural Biology
Price Family Foundation Institute of Structural Biology
University of Oklahoma
Department of Chemistry and Biochemistry
101 Stephenson Parkway
Norman, OK 73019-5251
Office: (405)325-1126
lmtho...@ou.edu
http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl




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Re: [ccp4bb] anomalous map in Coot - Linux vs. Win difference?

[Randy John Read]

I’ve just been playing with a difference map to check something. If you fail to 
set the map as a difference map (either when opening the map initially, or 
using Calculate->Map Tools->Set map is a difference map), there’s nothing in 
the Display Manager->Properties window that tells you. I was wondering if that 
could be the issue, if the contour colour chosen when it isn’t set as a 
difference map doesn’t show up against the other map.

Randy

> On 2 Aug 2023, at 14:32, Andrea Smith  wrote:
> 
> Dear Eleanor,
> 
> yes, I made the printscreen with the setting that shows both maps contoured 
> at 0.08 = 3 rmsd.
> 
> I also attach a printscreen from a site where I believe a Zn ion is bound 
> (from my condition). Can see that Wincoot is drawing the map wrong...
> Andrea
> 
> 
> 
> On Wednesday, August 02, 2023 15:28 CEST, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>  
>> 
>> Hmmm -are the two ano maps contoured at the same level? 
>> You can check this by setting the SCROLL option to the ano map.
>>  The 2mFo-DFc maps look pretty identical..which suggests the two input mtz 
>> files are similar.
>> You can get more information by viewing the inputs to make sure the values 
>> are the same..
>> Eleanor
>>   On Wed, 2 Aug 2023 at 13:53, Andrea Smith  
>> wrote:
>> Dear all,
>> 
>> I used refmac in CCP4Cloud and then I opened the generated .pdb and .mtz 
>> from the CCP4Cloud job both in Linux Coot 0.9.6. and WinCoot 0.9.6. I can 
>> see different anomalous maps in Coot and Wincoot - see attached printscreen 
>> where on the left there is a green electron density between the aspartates 
>> while on the right there is none. I tried to search if this is a bug but 
>> couldn't find info about this.
>> 
>> Am I doing something wrong? Do I have a local software issue?
>> 
>> Any advice would be appreciated, best,
>> Andrea
>>  To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>  To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
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-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk




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Re: [ccp4bb] anomalous map in Coot - Linux vs. Win difference?

[Jon Cooper]

It looks like it is not applying the 90 degree phase shift for anomalous data.

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

Sent from Proton Mail mobile

 Original Message 
On 2 Aug 2023, 14:32, Andrea Smith wrote:

> Dear Eleanor,
>
> yes, I made the printscreen with the setting that shows both maps contoured 
> at 0.08 = 3 rmsd.
>
> I also attach a printscreen from a site where I believe a Zn ion is bound 
> (from my condition). Can see that Wincoot is drawing the map wrong...
> Andrea
>
> On Wednesday, August 02, 2023 15:28 CEST, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hmmm -are the two ano maps contoured at the same level?
>> You can check this by setting the SCROLL option to the ano map.
>>
>> The 2mFo-DFc maps look pretty identical..which suggests the two input mtz 
>> files are similar.
>> You can get more information by viewing the inputs to make sure the values 
>> are the same..
>> Eleanor
>>
>> On Wed, 2 Aug 2023 at 13:53, Andrea Smith  wrote:
>>
>>> Dear all,
>>>
>>> I used refmac in CCP4Cloud and then I opened the generated .pdb and .mtz 
>>> from the CCP4Cloud job both in Linux Coot 0.9.6. and WinCoot 0.9.6. I can 
>>> see different anomalous maps in Coot and Wincoot - see attached printscreen 
>>> where on the left there is a green electron density between the aspartates 
>>> while on the right there is none. I tried to search if this is a bug but 
>>> couldn't find info about this.
>>>
>>> Am I doing something wrong? Do I have a local software issue?
>>>
>>> Any advice would be appreciated, best,
>>> Andrea
>>>
>>> ---
>>>
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>>
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Re: [ccp4bb] anomalous map in Coot - Linux vs. Win difference?

[Eleanor Dodson]

Hmmm -are the two ano maps contoured at the same level?
You can check this by setting the SCROLL option to the ano map.

The 2mFo-DFc maps look pretty identical..which suggests the two input mtz
files are similar.
You can get more information by viewing the inputs to make sure the values
are the same..
Eleanor


On Wed, 2 Aug 2023 at 13:53, Andrea Smith  wrote:

> Dear all,
>
> I used refmac in CCP4Cloud and then I opened the generated .pdb and .mtz
> from the CCP4Cloud job both in Linux Coot 0.9.6. and WinCoot 0.9.6. I can
> see different anomalous maps in Coot and Wincoot - see attached printscreen
> where on the left there is a green electron density between the aspartates
> while on the right there is none. I tried to search if this is a bug but
> couldn't find info about this.
>
> Am I doing something wrong? Do I have a local software issue?
>
> Any advice would be appreciated, best,
> Andrea
>
> --
>
> 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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