[ccp4bb] New Technical staff position at PPSCF facility EPFL Lausanne Switzerland

[Pojer Florence]

Dear CCP4 community,

The Protein Production and Structure Core Facility has a new open position for 
a technical staff (CDI, 80-100%, location EPFL Lausanne Switzerland).
 The main duties will be to advise, assist and follow-up X-ray crystallisation 
projects for various users; as well as to produce and purify  recombinant 
proteins from a variety of hosts.

Here is the link to apply:
https://recruiting.epfl.ch/Vacancies/833/Description/2


All the best, Florence Pojer
__

Florence Pojer -PhD-
Head of the Protein Production and Structure Core Facility
EPFL/SV/PPSCF - Station 19
1015 Lausanne - Switzerland - CH
florence.po...@epfl.ch
 - +41 78909096349 - +41216931976



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Re: [ccp4bb] Live stream of CCP4 Study Weekend?

[Karen McIntyre - UKRI STFC]

All the videos from the CCP4 Study Weekend 2019 are now available on the CCP4 
YouTube channel.

Only the videos where the speakers have expressly given permission for them to 
be uploaded are there.

Regards
 
Karen McIntyre
Science & Technology Facilties Council
Scientific Computing Department – CCP4
RCaH 1.22
 
Tel +44 (0) 1235 44 5790
Fax  +44 (0) 1235 56 7720

• @ccp4_mx

STFC is part of UK Research and Innovation 
For more information visit https://stfc.ukri.org/
 



**Please note that I only work mornings until 1.30pm**


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay 
Diederichs
Sent: 22 January 2019 16:58
To: ccp4bb
Subject: Re: [ccp4bb] Live stream of CCP4 Study Weekend?

Dear Melanie,

I'm still waiting for the recorded videos from the past Study Weekend ... am I 
looking in the wrong place? ( https://sas.stfc.ac.uk/vportal/index.jsp ) If 
they will appear there, is there any estimate when this will happen?

thanks,

Kay

On Wed, 9 Jan 2019 10:16:59 +, melanie.voll...@diamond.ac.uk 
 wrote:

>Dear Kay,
>
>
>Yes, all the videos will be recorded, unless a speaker objects to it (at least 
>it used to be that way).
>
>Use the same link from the twitter feed and click at the top on 'Videos' and 
>you will get all of the past webinars/videos from various STFC events. You can 
>see the study weekend videos from the past two years for example.
>
>
>Melanie
>
>
>From: CCP4 bulletin board  on behalf of Kay Diederichs 
>
>Sent: 09 January 2019 10:13:28
>To: ccp4bb
>Subject: Re: [ccp4bb] Live stream of CCP4 Study Weekend?
>
>The redirection of http://sas.stfc.ac.uk/p.jsp?i=2 works for me now, in Chrome 
>on Linux: after clicking "Get Flash", I get a popup asking whether I want to 
>allow Flash to run, and then the Video and Audio starts.
>
>Next question: due to some obligations, I cannot watch some interesting talks 
>in real time - are the video streams stored somewhere so I can watch them 
>later?
>
>thanks,
>
>Kay
>
>
>On Wed, 9 Jan 2019 10:27:41 +0100, Kay Diederichs 
> wrote:
>
>>Sorry, I need some additional help with this.
>>
>>If I use my browser (Firefox or Chrome on Linux) to go to 
>>http://sas.stfc.ac.uk/p.jsp?i=2 it gets redirected to 
>>https://sas.stfc.ac.uk/vportal/VideoPlayer.jsp?ccsid=C-5d13ead9-b217-4b5b-bceb-bb37e04bbefe:-1
>>
>>On that page, I tried "Videos" and "Go" but nothing happens.
>>
>>Does this work for anyone, and if so, how?
>>
>>thanks,
>>
>>Kay
>>
>>On 1/9/19 10:11 AM, Luca Jovine wrote:
>>> From another tweet of just a few sec ago:
>>>
>>> The live stream of this years #ccp4sw is now available at 
>>> sas.stfc.ac.uk/p.jsp?i=2 . Check out 
>>> previous proceedings in @ActaCrystD at bit.ly/2CdGU2n 
>>>  - papers from last year's meeting are appearing at 
>>> bit.ly/2H5Nr51  pic.twitter.com/6tLLc53Cnh 
>>> 
>>>
>>> -Luca
>>>
>>> 
>>> Luca Jovine, Ph.D.
>>> Professor of Structural Biology & EMBO Member
>>> Karolinska Institutet
>>> Department of Biosciences and Nutrition & Center for Innovative Medicine
>>> Medicinaren 25 Neo
>>> Blickag�ngen 16, SE-141 83 Huddinge, Sweden
>>> E-mail: luca.jov...@ki.se 
>>> W3: http://jovinelab.org
>>> 
>>>
 On 9 Jan 2019, at 10:08, Tim Gruene >>> > wrote:

 Hi Mark,

 Seriously on Twitter only?
 Sic transit gloria mundi.

 Best,
 Tim

 On Wednesday, January 9, 2019 9:50:02 AM CET Mark J van Raaij wrote:
> Good morning and happy 2019,
>
> There was an announcement on Twitter yesterday:
> https://twitter.com/ccp4_mx 
> (second post as of writing this)
>
> pointing here:
> https://stfc.ukri.org/about-us/our-purpose-and-priorities/requesting-informa
> tion-from-uk-research-and-innovation/webinars/
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij
> Editor of Acta Crystallographica F, Structural Biology Communications
> http://journals.iucr.org/f/
>
>> On 9 Jan 2019, at 09:39, Kay Diederichs 
>> wrote:
>>
>> Good morning everybody,
>>
>> I haven't seen any announcement about the streaming of the Study Weekend
>> ... I'd be really interested to watch and listen!
>>
>> Any hints?
>>
>> thanks,
>>
>> Kay
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/c

[ccp4bb] X-ray generator and imaging plates available

[Norbert Straeter]

Dear CCP4bb readers,

we are in the process of decommissioning our in-house X-ray source and would 
like to offer it to the community:

Bruker MicroStar X-ray generator (non-functional, i.e. for repair or 
replacement parts)
2 Helios Mx Cu X-Ray optics for Microstar
Mardtb Imaging Plate Detector

If you are interested please email stra...@bbz.uni-leipzig.de

I would note that we offer this equipment on an as is basis and interested 
parties would be responsible for transportation and associated costs. The 
instrument is located in Leipzig, Germany.

Best wishes,

Norbert



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[ccp4bb] 2 Postdoctoral Fellowships in Structural Biology and Drug Development at the University of Oslo, Centre for Molecular Medicine Norway (NCMM)

[Luecke, Hartmut]

Structural Biology and Drug Development at the University of Oslo

[cid:45310D88-A655-46CE-828B-07D61B8B9026]

2 Postdoctoral Fellowships

Inhibitor discovery targeting the Helicobacter pylori pH acclimation system (a 
pH-gated urea channel and a cytoplasmic urease)1
1Strugatsky et al. “Structure of the proton-gated urea channel from the gastric 
pathogen Helicobacter pylori” (2013) Nature 493, 255–258.

Online application required, deadline 28 Feb 2019:

https://www.jobbnorge.no/en/available-jobs/job/164159/two-2-postdoctoral-fellowships-in-structural-biology-and-drug-development

--
Prof. Hartmut Luecke
Structural Biology and Drug Discovery Group
Norwegian Centre for Molecular Medicine (NCMM), Nordic EMBL Partnership
and Institute of Clinical Medicine, University of Oslo
Dept. of Medical Biochemistry, Oslo University Hospital
Oslo, Norway




This message may contain confidential information and is for the sole use of 
the intended recipient(s). If you are not the intended recipient, do not use, 
distribute, or copy this e-mail. Please notify the UC Irvine Health – 
Compliance and Privacy Office via email at hacomplia...@uci.edu or by phone 
888-456-7006 immediately if you have received this e-mail in error. E-mail 
transmission cannot be guaranteed to be secure or error-free as information 
could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or 
contain viruses. The sender therefore does not accept liability for any errors 
or omissions in the contents of this message, which arise as a result of e-mail 
transmission.



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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
(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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UT Southwestern


Medical Center



The future of medicine, today.




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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&A=1
> 
>



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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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-
 

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-
 

  
  

UT Southwestern 

 
 
  

Medical Center

 
 
 
 
 
  

The future of medicine, today.

 
  

 

-
 

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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  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:
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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
(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] 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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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 
>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 patrioti