[ccp4bb] CryoEM Scientist Position at Sosei Heptares, Cambridge UK

[Mathieu Rappas]

Sosei Heptares is an international biopharmaceutical group focused on the
design and development of new medicines originating from its proprietary G
Protein-Coupled Receptor (GPCR) targeted StaR® technology and
Structure-Based Drug Design (SBDD) platform capabilities.



We are seeking an experienced cryo-electron microscopy scientist to join
the biophysics group working on GPCR structure determination to enable drug
discovery efforts.



At Sosei Heptares we are equipped with a ThermoFisher Glacios 200keV
microscope and purpose-built sample preparation facilities. Applicants
should be proficient in the preparation and optimisation of sample grids
and have expertise in the operation of high end, high voltage electron
microscopes, high-resolution data collection including image processing,
automated pre-processing pipelines and high-resolution model reconstruction.



For further details about the position and for information on how to apply
please follow the link:

https://cezanneondemand.intervieweb.it/heptares/jobs/cryoelectron_microscopy_scientist_5637/en/



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

[ccp4bb] Postdoc position in biophysics of parasite signaling molecules at UT Southwestern

[Michael Reese]

Dear all,

    The lab of Dr. Michael Reese at UT Southwestern Medical Center 
(http://www.reeselab.org) is recruiting highly motivated postdocs to 
join our team studying the molecular mechanisms of signalling at the 
Toxoplasma-host pathogen interface. We take an interdisciplinary 
approach and combine methods from molecular genetics, cell biology, 
biochemical and biophysics to deeply interrogate Toxoplasma biology.


Current projects include:
    + Structural studies of parasite protein complexes that are 
required for the biogenesis of the vacuole in which Toxoplasma 
replicates inside its vertebrate host cells.
    + Cellular and structural studies of signaling complexes essential 
to parasite invasion of mammalian cells
    + Structure-based drug discovery for inhibitors of kinases 
essential to the apicomplexan lytic cycle (that is, the parasites that 
cause the human diseases toxoplasmosis, malaria, and cryptosporidiosis).


    This would be a great opportunity for someone with biophysics 
training to learn to work with an atypical model organism with huge 
medical relevance. Those with more cell biological experience who would 
like to integrate biophysics and biochemistry into their research are 
also more than welcome to apply.  Applicants should hold a Ph.D. (or be 
within a year of receiving their Ph.D.). If interested, please send a CV 
with cover letter and contact information for 2-3 references to 
michael.re...@utsouthwestern.edu.


    Members of the Reese lab have full access to outstanding shared 
facilities as UT Southwestern, including high-field NMR, x-ray 
crystallography (with regular synchotron access), and world-class 
cryoEM. UT Southwestern is highly collaborative institution located in 
the heart of Dallas. The Dallas metroplex is welcoming and affordable, 
with great food and arts.


As an equal opportunity employer, UT Southwestern’s employment decisions 
are made without consideration of race, color, national origin, 
religion, sex, age, veteran status, or disability.


--
Michael Reese, Ph.D.
Assistant Professor
Department of Pharmacology
University of Texas, Southwestern Medical Center
ND9.200
6001 Forest Park Road
Dallas, TX 75390-9041

Phone: 214-645-5843
Fax: 214-645-6131

www.reeselab.org



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

[ccp4bb] PhD studentship at the University of Sussex, Brighton

[Erika Mancini]

Hi All,

I'm posting this on behalf of my colleague Michelle West. Please see below. 
Thanks!

PhD Project: The overall aim of this project is to use biochemical, genomic, 
biophysical and structural biology approaches to study how interactions between 
EBV transcription factors and host cell transcriptional regulators promote B 
cell immortalisation. The project is a collaboration between the groups of 
Professor Michelle West and Dr Chrisostomos Prodromou. 

Application Deadline: 1st of April

To apply, please follow this link:

https://www.findaphd.com/phds/project/molecular-mechanisms-of-host-cell-transcription-factor-hijack-by-the-cancer-associated-epstein-barr-virus/?p107300


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

[ccp4bb] Postdoc Position at the University of Sussex, Brighton

[Erika Mancini]

Dear all,

We are looking for a Postdoctoral Research fellow to join the West and Mancini 
groups located in the School of Life Science, University of Sussex, Brighton.

You will join a friendly and hard-working team to use biochemical, biophysical 
and structural biology methods to understand the molecular basis for 
transcription control by the cancer-associated Epstein-Barr virus and how this 
contributes to lymphoma development.

For more details please see:


ttps://www.sussex.ac.uk/about/jobs/research-fellow-in-biochemistry-ref-0933


Thanks,

Erika






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

Re: [ccp4bb] Refinement

[Raymond Brown]

Hi,

Run your data through POINTLESS to check space group.

Ray

On Sun, 3/24/19, StrBio  wrote:

 Subject: [ccp4bb] Refinement
 To: CCP4BB@JISCMAIL.AC.UK
 Date: Sunday, March 24, 2019, 12:17 AM
 
 ALL.
 I have data at 2.4 A in P21 sp gr, helical
 protein. 
 Refined to Rwork 29 Rfree 34 with nice density
 map and all nice statistics oither Rfactor (by Phenix).
 Refmac quit same. 
 Should I deposit it or look better
 data?Any suggestion?
   
 
 
 
 
 To unsubscribe from the CCP4BB list, click
 the following link:
 
 https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
 



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

[no subject]

[owner-ccp4bb]

x-uw-ex-currentlocation-365-recipient: Outside
x-microsoft-antispam-prvs:
 

x-forefront-prvs: 09888BC01D
x-forefront-antispam-report:
 
SFV:NSPM;SFS:(10009020)(346002)(136003)(396003)(3986042)(376002)(366004)(199004)(189003)(31163002)(47861)(97736004)(55016002)(2906002)(186003)(564073)(14454004)(88552002)(2351001)(68736007)(106356001)(6116002)(66066001)(7736002)(86362001)(52536014)(81156014)(8936002)(7120041)(7119041)(1005)(3846002)(8676002)(566032)(256004)(81166006)(102836004)(7696005)(25786009)(9686003)(53936002)(2501003)(75432002)(99286004)(316002)(6506007)(6436002)(19627405001)(54896002)(486006)(476003)(74316002)(105004)(236005)(26005)(105586002)(6916009)(786003)(33656002)(11255022);DIR:OUT;SFP:1101;SCL:1;SRVR:MN2PR08MB5822;H:MN2PR08MB5712.namprd08.prod.outlook.com;FPR:;SPF:None;LANG:en;PTR:InfoNoRecords;A:1;MX:1;
received-spf: None (protection.outlook.com: uw.edu does not designate permitted
  sender hosts)
x-ms-exchange-senderadcheck: 1
x-microsoft-antispam-message-info:
 
N2EKucNE4eeXni03yFt5iQyNwdAymibbyVaQtN7uJxzZNm2kSIDELMNvzR0m/t0vs+KzitAR5vtoGLAqUYJpHQjpqAhCQF39b5h6yWY3dzpQYUXMuQli5tAWzskp229PcL7DpVtDE1dVAV8VoLyYXeS6Wl81pilBHsjyYxiaA62PyO8DcWdcBAHEO8lvxa00OxmWzpO9gvz8WfAXoXrAOj8oZ7IcJVy/SBqASbGDor7ARMeRJ4g5vblN96aBdU8MR7kP/hd+RiVWtIeNDnEVBzSRXYsN4FDk39wBlX+21yelKbRqGEV65a5n8xVIFaZn4Gf9oND/FJOXeU8mj8obldwXwZbSUkCl9QnrmesbqAfFLFpMGndfEcXsDN5UhnAsSvXVGkQNI1oMnR7ntzEXcwOaGXMlqwYY+j0OEtisjTU=
Content-Type: multipart/alternative; 
boundary="_000_MN2PR08MB57123255D53A6BA2C7E8A147D85F0MN2PR08MB5712namp_"
MIME-Version: 1.0
X-MS-Exchange-CrossTenant-Network-Message-Id:
 0c1dd92d-259a-4c55-29fe-08d6b1f9cefb
X-MS-Exchange-CrossTenant-originalarrivaltime: 26 Mar 2019 14:46:19.6113 (UTC)
X-MS-Exchange-CrossTenant-fromentityheader: Hosted
X-MS-Exchange-CrossTenant-id: f6b6dd5b-f02f-441a-99a0-162ac5060bd2
X-MS-Exchange-CrossTenant-mailboxtype: HOSTED
X-MS-Exchange-Transport-CrossTenantHeadersStamped: MN2PR08MB5822
X-OriginatorOrg: uw.edu
X-PMX-Version: 6.4.6.2792898, Antispam-Engine: 2.7.2.2107409,
   Antispam-Data: 2019.3.26.143916, AntiVirus-Engine: 5.60.0,
   AntiVirus-Data: 2019.3.26.561
X-PMX-Server: mxout26.s.uw.edu
X-Uwash-Spam: Gauge=I, Probability=9%, Report=' CN_TLD 0.1,
  HTML_70_90 0.1, HTML_NO_HTTP 0.1, RCVD_FROM_IP_DATE 0.1,
  SUPERLONG_LINE 0.05, BODYTEXTH_SIZE_3000_MORE 0,
  BODYTEXTP_SIZE_3000_LESS 0, BODY_SIZE_1_PLUS 0,
  DKIM_SIGNATURE 0, FROM_EDU_TLD 0, NO_URI_HTTPS 0, SPF_NEUTRAL 0,
  WEBMAIL_SOURCE 0, WEBMAIL_XOIP 0, WEBMAIL_X_IP_HDR 0,
  __ANY_URI 0, __CT 0, __CTYPE_HAS_BOUNDARY 0, __CTYPE_MULTIPART 0,
  __CTYPE_MULTIPART_ALT 0, __DQ_NEG_HEUR 0, __DQ_NEG_IP 0,
  __FUR_RDNS_OUTLOOK 0, __HAS_FROM 0, __HAS_HTML 0, __HAS_MSGID 0,
  __HAS_XOIP 0, __HTML_TAG_DIV 0, __INT_PROD_LOC 0, __MIME_HTML 0,
  __MIME_TEXT_H 0, __MIME_TEXT_H1 0, __MIME_TEXT_H2 0,
  __MIME_TEXT_P 0, __MIME_TEXT_P1 0, __MIME_TEXT_P2 0,
  __MIME_VERSION 0, __PHISH_SPEAR_TEAM 0, __RDNS_WEBMAIL 0,
  __SANE_MSGID 0, __STYLE_RATWARE_NEG 0, __STYLE_TAG 0,
  __SUBJ_ALPHA_END 0, __TAG_EXISTS_HTML 0, __TO_MALFORMED_2 0,
  __TO_NAME 0, __TO_NO_NAME 0, __URI_NO_WWW 0, __URI_NS '
Message-ID:  

Date: Tue, 26 Mar 2019 14:46:19 +
Reply-To: Wenqing Xu 
Sender:   CCP4 bulletin board 
From: Wenqing Xu 
Subject: [ccp4bb] Job posting: Founding Director of PDB China
To:   CCP4BB@JISCMAIL.AC.UK
Precedence: list
List-Help: ,
   
List-Unsubscribe: 
List-Subscribe: 
List-Owner: 
List-Archive: 
X-MXTHUNDER-Identifier:  
_
X-MXTHUNDER-IP-Rating:  0, 212.247.25.116, Ugly c=0.357145 p=-0.375 Source 
Normal
X-MXTHUNDER-Scan-Result:  0
X-MXTHUNDER-Rules: 
0-0-0-28341-c
X-MXTHUNDER-Clean:  Yes
X-MXTHUNDER-Group:  OK

--_000_MN2PR08MB57123255D53A6BA2C7E8A147D85F0MN2PR08MB5712namp_
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Founding Director, Protein Data Bank China


We are currently seeking an experienced structural biologist to become the =
founding Director of Protein Data Bank China (PDBc). The successful candida=
te will work with the Worldwide Protein Data Bank (wwPDB) Core Members (RCS=
B PDB and BMRB in the US, PDBe in Europe, and PDBj in Japan) to satisfy the=
 requirements for PDBc to become a member of the wwPDB organization. wwPDB =
members jointly manage the wwPDB Core Archives, provide expert 

Re: [ccp4bb] map rotation

[Zhijie Li]

Hi Jan,


As Paul pointed out, you can use COOT to accomplish what you want. Particularly 
you can take a look at the following functions in section 6 of the COOT manual 
(these are in scheme):



(set-map-mask-atom-radius radius)


(mask-map-by-molecule imol-map imol-model invert-mask?)


(transform-map imol rotation-matrix trans point radius)

(transform-map-using-lsq-matrix imol-ref ref-chain ref-resno-start 
ref-resno-end imol-mov mov-chain mov-resno-start mov-resno-end imol-map 
about-pt radius)




Please take a look at the attached python example.  It can be run with COOT 
graphical interface by:


coot scr.py


You can run it without COOT graphical interface by un-commenting the exit() 
line at the end, then:


coot --no-graphics -s scr.py

If you see any part of the resulting transformed map being cut in the protein 
region, play with the rotation center (supply your coordinates [x,y,z] to 
replace the rotation_center() function.  In this script, the current rotation 
center is set upon reading the last pdb.).


BTW, if you see jagged map after rotation, that's probably because the map 
sampling frequency before the rotation is too low. When you rotate a map, there 
is always a resolution loss, because of the rastering nature of the maps 
(imagine rotating a mesh then resample it to become another mesh of the same 
spacing, how can you keep all the information?). So you had better use a very 
high sampling frequency when you are preparing a map that is going to be 
rotated. Since we often start from a MTZ file, you may even start by computing 
the starting map by specifying the sampling frequency to be more than 5x of the 
highest resolution to be very safe. On the other hand, if you use COOT i guess 
an interpolation is going to be done internally before the rotation (however 
interpolation is, maybe to some degree, not as good as computing a very 
over-sampled map from MTZ, I think.).


Zhijie



From: CCP4 bulletin board  on behalf of Jan Abendroth 

Sent: Tuesday, March 26, 2019 2:05 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] map rotation

Thanks, Eleanor!
what i really want to do with this script is to compare ligand binding sites 
from many structures in several space groups. So, I want to move coordinates 
and density onto one reference molecule. Since we ran into issues, I used this 
dimer structure as a simple test case.

The script you outlined, only recreates the same density w/o any rotation.

mapmask \

mapin AB_full-cell.ccp4 \

xyzin B.pdb \

mskout B.msk \

<< eof

border 5

eof


maprot \

mapin AB_full-cell.ccp4 \

mskin B.msk \

mapout B_rot.map \

<< eof

MODE to

AVER

rota euler 152.440   110.24328.112

TRANS  -42.212 5.510   -57.243

end

eof


Btw, I had to remove the rota euler 0 0 0 / trans 0 0 0 lines. Maprot 
complained about too many operators.

The odd thing -to me- is that when I shift a map around molecule B or the dimer 
(mapmask with border 5) with a small amount ( euler 1 0 0  or trans 0.5 0.5 
0.5) the map does not look jagged at the edges of the molecule, while it does 
when I rotate the full amount to match B on A:

maprot  \

wrkin  AB-5.map \

mapout AB_rot.map \

 << eof

CELL xtal 61.0100   142.360068.280090.97.198090.

GRID xtal 100 228 112

MODE to

AVER

rota euler  1 0 0

TRANS   0 0 0

end

eof

Cheers,
Jan

On Mon, Mar 25, 2019 at 3:49 AM Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:
Hmm - I find maprot extremely confusing, but remember a wrkmap does not use any 
symmetry so maybe that is why some is lost.

I would have done this, but I havent tested it. And the documentation is 
SERIOUSLY confusing!!

Do I understand you want to ADD the density for mol B to that of Mol A


mapmask mapin whole-cell.map
xyzin A.pdb
mskout A-mol.msk

Then
maprot
mapin whole-cell.map
mskin A-mol.msk ! only density withing this mask is 
interesting
mapout A-mol.map

MODE to

AVER

rota euler 0 0 0! to pick up mol A density

trans 0 0 0


rota euler 152.440   110.24328.112   ! to rotate map by B to A rotation

TRANS  -42.212 5.510   -57.243

end




On Mon, 25 Mar 2019 at 04:58, Jan Abendroth 
mailto:jan.abendr...@gmail.com>> wrote:
Hi all,
thanks for the feedback. Suggestions like coot or pymol won't work for us well, 
since we will have to do this with dozens of structures/maps.So, I'd rather 
have this scripted.

Still running into some issues that I think relate to maprot.
My understanding is that I first have to create a map covering molecule B that 
I want to map on A. Checking the extend of the map in chimera confirms that 
this worked:


mapmask \

mapin 2mol_2mFo-DFc.map \

xyzin 2mol_B.pdb \

mapout 2mol_2mFo-DFc_B.map \

<< eof

border 5

eof


Next, I need to rotate/translate the map in maprot. Since in maprot, mapin 
requires a map that covers the unit cell, I use wrkin and 'mode to' as below. 
In this script, 

[ccp4bb] One day symposium Cryo-EM in Drug Discovery

[H. Raaijmakers]

CRYO-EM IN DRUG DISCOVERY SCIENTIFIC SYMPOSIUM

Apr 23, 2019 

MIT Samberg Conference Center 

Cambridge, MA 02142 

This one-day scientific symposium will highlight the role cryo-EM can
play in the drug discovery process. Leaders in the biopharma industry
will highlight their successes and experiences utilizing this
ground-breaking technology. 

Topics include: 

* Cryo-EM in Biopharma: Progress and Lessons Learned
* Cryo-EM by Outsourcing: Panel Discussion
* Bottlenecks: Sample preparation, Throughput, Data Infrastructure 
* Hot Topics: micro-Electron Diffraction

Program and registration [1] 

Cheers, 

Hans Raaijmakers
Staff scientist Cryo-EM Pharma
Thermofisher Scientific
hans.raaijmak...@thermofisher.com 

Links:
--
[1]
https://www.thermofisher.com/nl/en/home/about-us/events/industrial/pharma-symposium-at-mit.html?cta=button_2elqtrack=true



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

Re: [ccp4bb] CCP4BB Digest - 24 Mar 2019 to 25 Mar 2019 (#2019-91)

[dturk]

Jan,

you my wish to try MAIN as an alternative "http://www-bmb.ijs.si/;. The 
superimposition parameters obtained from either FatCat or MAIN directly are 
directly saved into the form that is used in map rotation and translation. Maps 
do not have to be in a unit cell (it may be simpler though).

The scripts are generated during setup of an interactive session when 
generating NCS operators (in the case the molecules do not contain highly 
identical sequences  FatCat/CE interface has to be used). The scripts can be 
called during non-interactive use too.

If you have any questions or you need additional information to the manual 
please ask. 

best, dusan




Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://stef.ijs.si/ 
Head of Centre for Protein  and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of 
Proteins, Scientific Director
http://www.cipkebip.org/
e-mail: dusan.t...@ijs.si
phone: +386 1 477 3857   Dept. of Biochem.& Mol.& Struct. Biology
fax:  +386 1 477 3984   Jozef Stefan Institute
Jamova 39, 1 000 Ljubljana,Slovenia
Skype: dusan.turk (voice over internet: www.skype.com


> On 26 Mar 2019, at 01:00, CCP4BB automatic digest system 
>  wrote:
> 
> Date:Sun, 24 Mar 2019 21:57:45 -0700
> From:Jan Abendroth 
> Subject: Re: map rotation
> 
> Hi all,
> thanks for the feedback. Suggestions like coot or pymol won't work for us
> well, since we will have to do this with dozens of structures/maps.So, I'd
> rather have this scripted.
> 
> Still running into some issues that I think relate to maprot.
> My understanding is that I first have to create a map covering molecule B
> that I want to map on A. Checking the extend of the map in chimera confirms
> that this worked:
> 
> 
> mapmask \
> 
> mapin 2mol_2mFo-DFc.map \
> 
> xyzin 2mol_B.pdb \
> 
> mapout 2mol_2mFo-DFc_B.map \
> 
> << eof
> 
> border 5
> 
> eof
> 
> 
> Next, I need to rotate/translate the map in maprot. Since in maprot, mapin
> requires a map that covers the unit cell, I use wrkin and 'mode to' as
> below. In this script, the cell and grid values are the same mapdump
> provides me for the map. The rotation and translation are from superpose,
> RMSD of that superposition is 0.5Å.
> 
> 
> maprot  \
> 
> wrkin  2mol_2mFo-DFc_B.map \
> 
> mapout 2mol_2FoFc_rot.map \
> 
> << eof
> 
> CELL xtal 61.0100   142.360068.280090.97.198090.
> 
> GRID xtal 100 228 112
> 
> MODE to
> 
> AVER
> 
> rota euler 152.440   110.24328.112
> 
> TRANS  -42.212 5.510   -57.243
> 
> eof
> 
> 
> The issue now is that the superposed map for the center of molecule A looks
> great. Towards the edges of the molecule it gets weaker, does not match up
> with the molecule or stops entirely. Again, molecule and maps between A and
> B, as visualized in Coot by NCS hopping, are very similar.
> 
> 
> I am still quite puzzled by what is happening. I guess I am missing
> something in maprot. Any input would be appreciated. This is public data,
> so I would be happy to share the data.
> 
> 
> Cheers,
> 
> Jan
> 
> 
> 
> On Wed, Mar 20, 2019 at 9:26 PM Jan Abendroth 
> wrote:
> 
>> Hi all,
>> this should be easy, scripting the rotation of a map.
>> Purpose for this is: Superimpose several structures of the same protein
>> that crystallized in different space groups, and then drag the maps along.
>> As a simple test, I took a dimeric protein and try to superimpose molecule
>> B along with the map on molecule A.
>> 
>> The execution should be straightforward:
>> a) take a map that covers the unit cell (fft),
>> b) generate a mask around molecule B (mapmask),
>> c) apply rotation/translation that I obtain from superimposing molecule B
>> on molecule A.
>> 
>> The issue is that the obtained map covers both molecule A and B (not a big
>> deal), more importantly, it cuts of certain areas on both molecules.
>> Molecule A and B have low RMSDs (0.5Å).
>> 
>> I must be missing something fairly obvious, have not been able to see
>> what. Feedback would be much appreciated. Scripts are below.
>> 
>> Thanks!
>> Jan



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

Re: [ccp4bb] map rotation

[Jan Abendroth]

Thanks, Eleanor!
what i really want to do with this script is to compare ligand binding
sites from many structures in several space groups. So, I want to move
coordinates and density onto one reference molecule. Since we ran into
issues, I used this dimer structure as a simple test case.

The script you outlined, only recreates the same density w/o any rotation.

mapmask \

mapin AB_full-cell.ccp4 \

xyzin B.pdb \

mskout B.msk \

<< eof

border 5

eof


maprot \

mapin AB_full-cell.ccp4 \

mskin B.msk \

mapout B_rot.map \

<< eof

MODE to

AVER

rota euler 152.440   110.24328.112

TRANS  -42.212 5.510   -57.243

end

eof


Btw, I had to remove the rota euler 0 0 0 / trans 0 0 0 lines. Maprot
complained about too many operators.

The odd thing -to me- is that when I shift a map around molecule B or the
dimer (mapmask with border 5) with a small amount ( euler 1 0 0  or trans
0.5 0.5 0.5) the map does not look jagged at the edges of the molecule,
while it does when I rotate the full amount to match B on A:

maprot  \

wrkin  AB-5.map \

mapout AB_rot.map \

 << eof

CELL xtal 61.0100   142.360068.280090.97.198090.

GRID xtal 100 228 112

MODE to

AVER

rota euler  1 0 0

TRANS   0 0 0

end

eof

Cheers,
Jan

On Mon, Mar 25, 2019 at 3:49 AM Eleanor Dodson 
wrote:

> Hmm - I find maprot extremely confusing, but remember a wrkmap does not
> use any symmetry so maybe that is why some is lost.
>
> I would have done this, but I havent tested it. And the documentation is
> SERIOUSLY confusing!!
>
> Do I understand you want to ADD the density for mol B to that of Mol A
>
>
> mapmask mapin whole-cell.map
> xyzin A.pdb
> mskout A-mol.msk
>
> Then
> maprot
> mapin whole-cell.map
> mskin A-mol.msk ! only density withing this mask
> is interesting
> mapout A-mol.map
>
> MODE to
>
> AVER
>
> rota euler 0 0 0! to pick up mol A density
>
> trans 0 0 0
>
>
> rota euler 152.440   110.24328.112   ! to rotate map by B to A
> rotation
>
> TRANS  -42.212 5.510   -57.243
>
> end
>
>
>
>
>
> On Mon, 25 Mar 2019 at 04:58, Jan Abendroth 
> wrote:
>
>> Hi all,
>> thanks for the feedback. Suggestions like coot or pymol won't work for us
>> well, since we will have to do this with dozens of structures/maps.So, I'd
>> rather have this scripted.
>>
>> Still running into some issues that I think relate to maprot.
>> My understanding is that I first have to create a map covering molecule B
>> that I want to map on A. Checking the extend of the map in chimera confirms
>> that this worked:
>>
>>
>> mapmask \
>>
>> mapin 2mol_2mFo-DFc.map \
>>
>> xyzin 2mol_B.pdb \
>>
>> mapout 2mol_2mFo-DFc_B.map \
>>
>> << eof
>>
>> border 5
>>
>> eof
>>
>>
>> Next, I need to rotate/translate the map in maprot. Since in maprot,
>> mapin requires a map that covers the unit cell, I use wrkin and 'mode to'
>> as below. In this script, the cell and grid values are the same mapdump
>> provides me for the map. The rotation and translation are from superpose,
>> RMSD of that superposition is 0.5Å.
>>
>>
>> maprot  \
>>
>> wrkin  2mol_2mFo-DFc_B.map \
>>
>> mapout 2mol_2FoFc_rot.map \
>>
>>  << eof
>>
>> CELL xtal 61.0100   142.360068.280090.97.198090.
>>
>> GRID xtal 100 228 112
>>
>> MODE to
>>
>> AVER
>>
>> rota euler 152.440   110.24328.112
>>
>> TRANS  -42.212 5.510   -57.243
>>
>> eof
>>
>>
>> The issue now is that the superposed map for the center of molecule A
>> looks great. Towards the edges of the molecule it gets weaker, does not
>> match up with the molecule or stops entirely. Again, molecule and maps
>> between A and B, as visualized in Coot by NCS hopping, are very similar.
>>
>>
>> I am still quite puzzled by what is happening. I guess I am missing
>> something in maprot. Any input would be appreciated. This is public
>> data, so I would be happy to share the data.
>>
>>
>> Cheers,
>>
>> Jan
>>
>>
>>
>> On Wed, Mar 20, 2019 at 9:26 PM Jan Abendroth 
>> wrote:
>>
>>> Hi all,
>>> this should be easy, scripting the rotation of a map.
>>> Purpose for this is: Superimpose several structures of the same protein
>>> that crystallized in different space groups, and then drag the maps along.
>>> As a simple test, I took a dimeric protein and try to superimpose
>>> molecule B along with the map on molecule A.
>>>
>>> The execution should be straightforward:
>>> a) take a map that covers the unit cell (fft),
>>> b) generate a mask around molecule B (mapmask),
>>> c) apply rotation/translation that I obtain from superimposing molecule
>>> B on molecule A.
>>>
>>> The issue is that the obtained map covers both molecule A and B (not a
>>> big deal), more importantly, it cuts of certain areas on both molecules.
>>> Molecule A and B have low RMSDs (0.5Å).
>>>
>>> I must be missing something fairly obvious, have not been able to see
>>> what. Feedback would be much appreciated. Scripts are below.
>>>
>>> Thanks!
>>> Jan
>>>
>>>