from:"Mooers, Blaine H.M. \(HSC\)"

[ccp4bb] Registration open for the SSRL/LCLS User Meeting

2023-08-30 Thread Mooers, Blaine H.M. (HSC)

Registration is open for the SSRL/LCLS User's Meeting, which will be September 
24-29, 2023 (https://events.bizzabo.com/SLAC-2023/home). It will be in person 
for the first time since 2019. This meeting attracts the lightsource community 
to a single scientific event that is inclusive of many disciplines. 
Participants learn about current/future facility capabilities and the latest 
user research. Of special note is an excellent series of tutorials on the 
Sunday designed by graduate students for new users of LCLS or SSRL.  There will 
be 33 workshops and a plenary session. In addition, there is a poster session 
on Wednesday, September 27th with several poster prizes. Graduate students who 
present a poster have their registration fee waived. The poster abstract 
submission deadline is September 18th.

In addition to the very popular "Metals in Structural Biology" workshop on 
Friday, September 29, I would like to draw attention to the "Computational 
Methods in Structural Biology" workshop on Monday, September 25. It is likely 
of particular interest to some members of the CCP4BB. We have the following 
distinguished set of speakers.

Marcin Wojdyr, Global Phasing
Clemens Vonrhein, Global Phasing
Carmelo Giacovazoo, U of Bari
Lance M. Westerhof, QuantumBio Inc.
Elke De Zitter, IBS, Grenoble, France
Muyuan Chen, Stanford U.
Rachael Kretsch , Stanford U.
Cathy Lawson, RCSB Protein Data Bank

Best regards,

Blaine Mooers and Tzanko Doukov
Co-Chairs of the Computational Methods in Structural Biology  Workshop.




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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] ILLUSTRATE in PYMOL

2023-08-16 Thread Mooers, Blaine H.M. (HSC)

Hi Faisal,

You can make similar striking images with the illustrative1 and 2 options in 
Qutemol https://sourceforge.net/projects/qutemol/.
Qutemol ran on Windows10 for me this morning.
It does not run on the newer macOS operating systems.
Only the binaries are available.
It has not been updated since 2007.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: 
https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): 
https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology

From: CCP4 bulletin board  on behalf of khaja faisal 
tarique 
Sent: Wednesday, August 16, 2023 6:46 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] ILLUSTRATE in PYMOL

Thanks all. I am almost there making similar figs as in ILLUSTRATE. It is 
amazing. Just wondering if we can make similar stuffs in ChimeraX ?.

Faisal

On Tue, 15 Aug 2023, 23:22 Jared Sampson, 
mailto:jared.samp...@columbia.edu>> wrote:
Hi Faisal -

In addition to the `specular`, `ray_trace_mode`, and `ray_trace_gain` settings 
Blaine pointed out, you can also adjust the `direct` and `ambient` lighting 
settings, as well as `light_count` (which I believe only affects direct and 
specular lighting, not ambient).  For example, these worked pretty well for me:

```
set ray_trace_mode, 3
set ray_trace_gain, 0
set specular, 0
set direct, 0
set ambient, 0.9
```

Note that you'll have to ray trace (`ray`) to see the outlines.  Also it looks 
like the tRNA image on the CCSB Illustrate site uses slightly different colors 
for different parts of the molecule (phosphate, sugar, base), which is a nice 
effect.

Hope that helps.

Cheers,
Jared


On Tue, Aug 15, 2023 at 10:40 PM Mooers, Blaine H.M. (HSC) 
mailto:blaine-moo...@ouhsc.edu>> wrote:
Hi Faisal,

I made a number of such figures several years ago.
I finally found the code.

Load the molecule of interest into PyMOL
and paste the following code onto the command line
just below the command history window.
I was using our school colors: crimson and cream.
Ligands are colored crimson. Change to suit
your needs.


as surface
set_color crimsom, [165,42,42];
set_color cream, [221,203,164];
color crimsom, org;
color cream, not org;

remove solvent
set_color bground, [252,250,249];
bg_color bground;
# set the view
# orient all within 8 of org
# set the lights, ray tracing setttings
# to get the Goodsell-like rendering
unset specular
set ray_trace_gain, 0
set ray_trace_mode, 3
bg_color white
set ray_trace_color, black
set depth_cue, 0
#ray
png Goodsell1test.png, 1200,1200,600,1


Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: 
https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): 
https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Pius Padayatti mailto:ppadaya...@gmail.com>>
Sent: Tuesday, August 15, 2023 8:24 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [EXTERNAL] Re: [ccp4bb] ILLUSTRATE in PYMOL

https://pymolwiki.org/index.php/APBS<https://urldefense.com/v3/__https://pymolwiki.org/index.php/APBS__;!!GNU8KkXDZlD12Q!9eD_ProG0wUZ-JErjGALFQIrpgJlQO_bYGkQ0_iklgY0qfFv6IblDBIQ_JwWVq4rFViNFwN_v8t_mnr6vVLzKnD4$>
Pius Padayatti




On Tue, Aug 15, 2023 at 5:20 PM khaja faisal tarique 
mailto:khajafaisaltari...@gmail.com>> wrote:
Hi everyone

Is there any way to make surface representation of a protein structure similar 
to the 'Illustrate: Non-photorealistic Biomolecular Illustration' 
(https://ccsb.scripps.edu/illustrate/<https://urldefense.com/v3/__https://ccsb.scripps.edu/illustrate/__;!!GNU8KkXDZlD12Q!9eD_ProG0wUZ-JErjGALFQIrpgJlQO_bYGkQ0_iklgY0qfFv6IblDBI

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] ILLUSTRATE in PYMOL

2023-08-15 Thread Mooers, Blaine H.M. (HSC)

Hi Faisal,

I made a number of such figures several years ago.
I finally found the code.

Load the molecule of interest into PyMOL
and paste the following code onto the command line
just below the command history window.
I was using our school colors: crimson and cream.
Ligands are colored crimson. Change to suit
your needs.


as surface
set_color crimsom, [165,42,42];
set_color cream, [221,203,164];
color crimsom, org;
color cream, not org;

remove solvent
set_color bground, [252,250,249];
bg_color bground;
# set the view
# orient all within 8 of org
# set the lights, ray tracing setttings
# to get the Goodsell-like rendering
unset specular
set ray_trace_gain, 0
set ray_trace_mode, 3
bg_color white
set ray_trace_color, black
set depth_cue, 0
#ray
png Goodsell1test.png, 1200,1200,600,1


Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: 
https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): 
https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology

From: CCP4 bulletin board  on behalf of Pius Padayatti 

Sent: Tuesday, August 15, 2023 8:24 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [EXTERNAL] Re: [ccp4bb] ILLUSTRATE in PYMOL

https://pymolwiki.org/index.php/APBS
Pius Padayatti




On Tue, Aug 15, 2023 at 5:20 PM khaja faisal tarique 
mailto:khajafaisaltari...@gmail.com>> wrote:
Hi everyone

Is there any way to make surface representation of a protein structure similar 
to the 'Illustrate: Non-photorealistic Biomolecular Illustration' 
(https://ccsb.scripps.edu/illustrate/)
 using scripts in Pymol ? It will be really helpful if someone can share this 
with me.

Thanks

Faisal




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



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Staff scientist position for an experienced biomolecular crystallographer

2022-10-28 Thread Mooers, Blaine H.M. (HSC)

The Laboratory of Biomolecular Structure and Function (LBSF) at the University
of Oklahoma Health Sciences Center (OUHSC) seeks an experienced
crystallographer to run the daily operations of the LBSF. The position is at
the Staff Scientist level. The candidate will be responsible for working with
PIs to advance their structural biology projects. These efforts will include
routine technical operations, developing new protocols to overcome challenging
problems, and training the staff of user labs in protein purification,
crystallization, data collection, and structure determination. The ideal
candidate for this position will have a PhD and ten years of experience in
macromolecular crystallography, a strong work ethic, and the ability to
independently carry out each step of the standard crystallographic study
workflow: this a service position, not a training position. The candidate will
not be expected to write grant applications to support their position.

Pluses in a candidate's background include experience with instrument repair,
eukaryotic protein expression, membrane protein purification and LCP
crystallization, Cyro-EM, microED, SAXS, SANS, XAFS, NMR, or XFELS.

The LBSF is part of a suite of core labs supported in part by the OUHSC Vice
President of Research. The LBSF is also part of the Biomolecular Structure Core
(BSC) for the Oklahoma Center of Biomedical Research Excellence in Structural
Biology (OCSB), which is based on the main campus in Norman. The OCSB was
awarded five more years of NIH funding in May 2022. The BSC has contributed to
the awarding of 26 million dollars in grant funding and 36 publications in the
past ten years. The OCSB has been the focal point of Oklahoma's structural
biology community for nine years. The community includes 50 labs at three major
research institutions.

The BSC is a vital part of a new Center for Therapeutic Science. The center
coordinates and fosters the drug development pipeline with the BSC playing a
central role in structure-based drug design. The LBSF is working closely with
Dr. Matt Hart
(https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/hart-matthew-phd-1),
Director of the newly established Center for High Throughput Screening.

Most of the 12 major users of the LBSF have cancer-related projects. One
project led to the 2021 publication of crystal structures of RET Kinase bound
to two drug molecules recently approved by the FDA for the treatment of
non-small cell lung cancer (https://pubmed.ncbi.nlm.nih.gov/33161056/). Most of
the major users are members of the Stephenson Cancer Center, a National Cancer
Institute-designated cancer center.

The compensation level for this full-time position includes a generous benefits
package. The position is based in Oklahoma City -- an affordable place to raise
a family. To apply, please submit a cover letter, CV and contact information
(name and email) for three references to Blaine Mooers, Director of the
Laboratory of Biomolecular Structure and Function at OUHSC, at blaine-mooers at
ouhsc.edu. Also apply for Job # 223015 – Staff Scientist Structural Biology at
jobs.ou.edu. The position will remain open until filled. Application review
will begin immediately.

OUHSC is an equal opportunity employer and is committed to creating a diverse
and inclusive environment for all employees.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page:
https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF):
https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology

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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] reminder: tomorrow is last day to register for the virtual and free SSRL/LCLS Users Meeting

2022-09-24 Thread Mooers, Blaine H.M. (HSC)

Tomorrow is the last day to register for the virtual and free SSRL/LCLS Users 
Meeting

https://events.bizzabo.com/SLAC-UsersMeeting-2022/home

There are 30 half-day workshops. Of particular interest to this mailing list 
are the following

- Fundamentals at SSRL and LCLS - Part I and II
- Integrative Structural Biology – X-ray and CryoEM Techniques
- Computational Methods in the Structural Sciences
- Writing more compelling bioscience proposals for LCLS
- Plenary Session - Synergy at SLAC I and II: Cooperative Science Utilizing the 
LCLS and SSRL
- Advancing Biological and Environmental Science at SSRL: From Structure and 
Function to Metal and Nutrient Cycling
- Data analysis at LCLS
- Metals in Structural Biology I and II
- Science Communication

Registrants can login at a later time to view recordings of the talks if they 
cannot attend the
live sessions due to schedule conflicts.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
University of Oklahoma Health Sciences Center



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Poster deadline approaching for SSRL/LCLS User's Meeting

2022-09-06 Thread Mooers, Blaine H.M. (HSC)

This is a reminder of the fast approaching deadline of September 9th for poster
abstract submissions
for the SSRL/LCLS User's Meeting, September 26-30, 2022.

The meeting will be virtual again due to COVID, but the of the sessions will be
recorded live.
Registration is free and open to all. Register here
(https://events.bizzabo.com/SLAC-UsersMeeting-2022/home).
[https://res.cloudinary.com/bizzaboprod/image/upload/q_auto:best,c_crop,g_custom/v1648229683/nv1egrdyfdfxqgkkl8sd.png]
2022 SSRL/LCLS Users' Meeting -
Bizzabo
Join us virtually for the 2022 SSRL/LCLS Users' Meeting. Every year, thousands
of scientists from universities, laboratories, and private companies around the
world use our cutting-edge research facilities.
events.bizzabo.com

We had about 1600 registrants last year.

We will have 25 workshops, 3 poster sessions, and 3 plenary sessions.
Many of the workshops would be of interest to the members of this
bulletin board including one titled "Computational Methods in the Structural
Sciences".

Distinguished plenary speakers include Drs. John Helliwell and Linda Young.

There will be several poster prizes. The BioXFEL prizes are not
limited to work done at LCLS. Please note that the poster judging
will occur the week before the meeting so those participating in the
poster contest will need to post their poster PDF and accompanying contest
video by September 13th
and PDFs of the general posters are due September 14th.

Best regards,

Blaine

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] SSRL/LCLS User's Meeting registration is open

2022-08-19 Thread Mooers, Blaine H.M. (HSC)

The SSRL/LCLS User's Meeting will be September 26-30, 2022.
It will be virtual again due to COVID, but the of the sessions will be recorded 
live.
Registration is free 
and open to all. We had about 1600 registrants last year.

We will have 27 workshops, 3 poster sessions, and 3 plenary sessions.
Distinguished plenary speakers include Drs. John Helliwell and Linda Young.

Although the registered attendees will be able to view the videos
at a later time, please do attend during the live sessions to participate in
the question and answer periods.

There will be several poster prizes. The BioXFEL prizes are not
limited to work done at LCLS. The 
deadline
 for the submission of
poster abstracts is September 9th.

Best regards,

Blaine Mooers on behalf of the SSRL/LCLS User's Meeting Organizing Committee
and the SSRL User Executive 
Committee
 and the LCLS User Executive 
Committee




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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

2022-07-26 Thread Mooers, Blaine H.M. (HSC)

Hi Dale,

Which version of PyMOL are you using?
(PyMOL questions should really be directed to the PyMOL mailing list).
Ancient versions of PyMOL may not accept cif files via fetch unless you include 
the type=cif keyword.
To get the pdb file downloaded, try fetch 6wrh type=pdb.
I can download 6wrh into a recent incentive version of PyMOL (2.5.2) via fetch 
6wrh.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: 
https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): 
https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology

From: CCP4 bulletin board  on behalf of Dale C 
<8378c932659c-dmarc-requ...@jiscmail.ac.uk>
Sent: Tuesday, July 26, 2022 7:44 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [EXTERNAL] [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 
v8

Hi all,

I recently updated my ccp4 package to Program suite v8.0.002 and i have now run 
into a few issues with other programs. The issues are highlighted below...

- When i click 'Open in Coot' on any output through Phenix (so far only tested 
phenix.refine and phenix.phaser), i no longer see anything open. Nor do i see 
the "Connected to Phenix" button in the toolbar on Coot.

- The 'fetch' command in Pymol no longer works either (I have attached a 
screenshot of the error message here)

- Coot also seems to have an issue with not loading the amino acid restraints 
so when i click real-space refine, i get the error 'unable to find restraints 
for residue x,y,z'.

I feel they may be all related and my first thought is that it has something to 
do with my Python dependencies however I have no idea how to fix this or 
reinstall them.

Does anyone have an idea if they are all related? Or how i might fix this?

fyi I am using
- ccp4 program suit v8.0.002
- Coot 0.9.8.3
- Phenix-1.20.1-4487

Thanks in advance.

Dale.





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

This message was issued to members of 
www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are 
available at https://www.jiscmail.ac.uk/policyandsecurity/



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Phasing a difficult RNA heteroduplex structure

2022-05-06 Thread Mooers, Blaine H.M. (HSC)

Hi Charles,

Congratulations on getting an RNA heteroduplex to crystallize! Most do not 
crystallize.

You should make and look at a native Patterson map to find the off-origin 
peak(s) that give the report of tNCS.
The direction and distance of this peak from the origin can be enlightening.
For an example with two levels of tNCS from an RNA duplex, see 
https://doi.org/10.1107/S2059798316001224.

Best regards,

Blaine
.
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: 
https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): 
https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology

From: CCP4 bulletin board  on behalf of Nichols, Charlie 

Sent: Friday, May 6, 2022 6:17 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [EXTERNAL] [ccp4bb] Phasing a difficult RNA heteroduplex structure


Dear all,



I am trying to solve the structure of an RNA heteroduplex + ligand with 
approximate MW of 6800.

  *   Structure likely to have a core helical region and a couple of bases of 
single stranded material at both ends on both strands



I have datasets from visually similar crystals with different, but related unit 
cells:



Form1:

32.70 32.70 54.55 90.00 90.00 120.00 – best native ~2.9A

- different pipelines reported P62 2 2, P62 and P32 from auto-indexing

- P6222 impossible to fit 1 complete heteroduplex

- P62, most consistent indexing choice, 37% solvent, low Matthews probability 
but possible to fit 1 heteroduplex



However, Xia/Dials report tNCS



  *   If the ASU only has room for 1 copy the heteroduplex there can’t be tNCS, 
does this therefore mean we must have twinning?
  *   There is a reasonable similarity NMR structure in the PDB, this is ~45A 
long
  *   I am therefore guessing that the duplexes are most probably making 
end-end contacts to form long fibres that are ~aligned along the Z-axis and 
that the crystal either contains fibres bound both ways up, or that the duplex 
can bind either way up to create the fibres, the twinning then superposes the 
two orientations to create two identical repeats mimicking tNCS  – does this 
seem a reasonable interpretation?



I have a dataset with Zn/Mg exchange and good anomalous signal to ~3.8A, ShelX 
finds good sites but DM / phase-extension with the 2.9A native data creates a 
mess and there is little difference between the two hands – can you give any 
advice on how I might try to proceed with experimental phasing in this case?



Form2:

62.40 62.40 54.82 90.00 90.00 120.00 – best native ~2.5A

- Auto-indexes as P62 / P64, higher resolution data than Form1

- Again, Xia/Dials report tNCS

- Cell has a doubling of a/b dimensions but c is the same

- Molecular replacement fails completely

- Cobalt-hexammine soak gave strong anomalous signal but only to ~6A, again 
ShelX finds good sites, but DM / phase-extension gives a mess

- From the pathology of Form1, I am concerned that we have exactly the same 
issue with overlaid flipped orientations along the Z-axis



Any advice on how to proceed would be greatly appreciated.



Thanks, take care,



Dr Charlie Nichols

Charles River Laboratories



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Opportunity for experienced crystallographer

2021-11-30 Thread Mooers, Blaine H.M. (HSC)

Associate Director of the Laboratory of Biomolecular Structure and Function

The Laboratory of Biomolecular Structure and Function (LBSF) at the University
of Oklahoma Health Sciences Center (OUHSC) seeks an experienced
crystallographer to run the daily operations of the LBSF. The position is at
the Assistant Professor of Research level. The candidate will be responsible
for working with PIs to advance their structural biology projects. These
efforts will include routine technical operations, developing new protocols to
overcome challenging problems, and training the staff of user labs in protein
purification, crystallization, data collection, and structure determination.
The ideal candidate for this position will have a PhD and ten years of
experience in macromolecular crystallography. The candidate will not be
expected to write grant applications. Pluses in a candidate's background
include experience with membrane protein purification and LCP crystallization,
experience with Cyro-EM, or experience with other structural biology methods
like microED, SAXS, SANS, XAFS, NMR, or XFELS.

The LBSF is part of a suite of core labs supported in part by the OUHSC Vice
President of Research. The LBSF is also part of the Biomolecular Structure Core
(BSC) for the Oklahoma Center of Biomedical Research Excellence in Structural
Biology (OCSB), which is based on the main campus in Norman. The BSC has
contributed to the awarding of 23 million dollars in grant funding and 33
publications in the past nine years. The OCSB has been the focal point of
Oklahoma's structural biology community for nine years. The community includes
50 labs at three major research institutions.

The BSC will be a vital part of a new Center for Therapeutic Science. The
center will coordinate and foster the drug development pipeline with the BSC
playing a central role in structure-based drug design. The LBSF will be working
closely with Dr. Matt Hart
(https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/hart-matthew-phd-1),
Director of the newly established Center for High Throughput Screening.

Most of the 12 major users of the LBSF have cancer-related projects. One
project led to the 2021 publication of crystal structures of RET Kinase bound
to two drug molecules recently approved by the FDA for the treatment of
non-small cell lung cancer. Most of the major users are members of the
Stephenson Cancer Center, a National Cancer Institute-designated cancer center.

The compensation level for this full-time position includes a generous benefits
package. The position is based in Oklahoma City -- an affordable place to raise
a family. To apply, please submit a cover letter, CV and contact information
(name and email) for three references to Blaine Mooers, Director of the
Laboratory of Biomolecular Structure and Function at OUHSC, at blaine-mooers at
http://ouhsc.edu. The position will remain open until filled. Application
review will begin immediately.

OUHSC is an equal opportunity employer and is committed to creating a diverse
and inclusive environment for all employees.

Best regards,

Blaine

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] last day to register for the SSRL/LCLS User Meeting

2021-09-17 Thread Mooers, Blaine H.M. (HSC)

Dear CCP4BB,

Today is the last day to register for the SSRL/LCLS User Meeting that starts on
Monday.
It is free. https://events.bizzabo.com/SLAC-UsersMeeting-2021/home.

The poster session runs 12 - 1 PM Pacific Time M-Th.
You use the gathertown software to attend it.
Navigation of the poster session is like playing a 1990s computer game.

I was on the poster judging team.
We spent this week judging the posters virtually.
We made our selections of the finalist today.
All of the semifinalist posters were excellent.

Best regards,

Blaine
SSRL UEC member and past chair.

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Experienced crystallographer needed

2021-08-11 Thread Mooers, Blaine H.M. (HSC)

Dear all,

Please share this job announcement with potential candidates.

Associate Director of the Laboratory of Biomolecular Structure and Function

The Laboratory of Biomolecular Structure and Function (LBSF) at the University
of Oklahoma Health Sciences Center (OUHSC) seeks an experienced
crystallographer to run the daily operations of the LBSF. The position is at
the Assistant Professor of Research level. The candidate will be responsible
for working with PIs to advance their structural biology projects. These
efforts will include routine technical operations, developing new protocols to
overcome challenging problems, and training the staff of user labs in protein
purification, crystallization, data collection, and structure determination.
The ideal candidate for this position will have a PhD and ten years of
experience in macromolecular crystallography. The candidate will not be
expected to write grant applications. Pluses in a candidate's background
include experience with membrane protein purification and LCP crystallization,
experience with Cyro-EM, or experience with other structural biology methods.

The LBSF is part of a suite of core labs supported in part by the OUHSC Vice
President of Research. The LBSF is also part of the Biomolecular Structure Core
(BSC) for the Oklahoma Center of Biomedical Research Excellence in Structural
Biology (OCSB), which is based on the main campus in Norman. The BSC has
contributed to the awarding of 23 million dollars in grant funding and 33
publications in the past nine years. The OCSB has been the focal point of
Oklahoma's structural biology community for nine years. The community includes
50 labs at three major research institutions.

The BSC will be a vital part of a new Center for Therapeutic Science. The
center will coordinate and foster the drug development pipeline with the BSC
playing a central role in structure-based drug design. Most of the 12 major
users of the LBSF have cancer-related projects. One project led to the 2021
publication of crystal structures of RET Kinase bound to two drug molecules
recently approved by the FDA for the treatment of non-small cell lung cancer.
Most of the major users are members of the Stephenson Cancer Center, a National
Cancer Institute-designated cancer center.

The compensation level for this full-time position includes a generous benefits
package. The position is based in Oklahoma City -- an affordable place to raise
a family. To apply, please submit a cover letter, CV and contact information
(name and email) for three references to Blaine Mooers, Director of the
Laboratory of Biomolecular Structure and Function at OUHSC, at blaine-mooers at
ouhsc.edu. The position will remain open until filled. Application review will
begin immediately.

OUHSC is an equal opportunity employer and is committed to creating a diverse
and inclusive environment for all employees.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

2021-05-26 Thread Mooers, Blaine H.M. (HSC)

If you have PyMOL installed, you can paste the bash function below into your 
.bashrc file, enter 'source .bashrc', and then enter 'bu PDB-ID'.
All that you have to remember a month from now is 'bu'. 

Otherwise, you can replace the pymol command with one of the other commands 
that have been suggested and replace the filename stem with $1.


bu()
{
echo "Write out the biological unit for a PDB file from PyMOL."
if [ $# -lt 1 ]; then
  echo 1>&2 "$0: not enough arguments"
  echo "Supply the PDB-ID."
  echo "Example: bu 3nd4"
  return 2
elif [ $# -gt 1 ]; then
  echo 1>&2 "$0: too many arguments"
  echo "Supply the PDB-ID."
  echo "Example: bu 3nd4"
fi
pymol -c -d "fetch $1,type=pdb1;set all_states,on;save $1bu.pdb,state=0"
}


Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
University of Oklahoma Health Sciences Center

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Marcin Wojdyr 
[woj...@gmail.com]
Sent: Wednesday, May 26, 2021 2:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] writing coordinates of full biomol into one 
(PDB) file

another one:

gemmi convert --assembly=N input.pdb output.pdb


On Wed, 26 May 2021 at 07:30, Frank von Delft
 wrote:
>
> Thanks for the quick responses!  I was looking for a command-line tool
> (should have said).  Here's the list:
>
> 1. phenix.pdb.biomt_reconstruction
> 2. 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__Makemultimer.py=DwIBaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8=wMMX-ub8O19NLtJDQdelGfFOni2RMO7EVgZG1XZ1Uu4=
>  : 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__watcut.uwaterloo.ca_tools_makemultimer_docs=DwIBaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8=XQ41GNcbJlsckrDR76D9n7YD0eKVop24nJpUYi5pTPA=
>   >
> 3. Quat in pymol: 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_BiologicalUnit_Quat=DwIBaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8=K4dJU4Mq8Mi4SgQB6UFnQcTzfnkCfius8_QsRmWs_ZQ=
>   >
> 4. BiologicalUnit in pymol:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_BiologicalUnit=DwIBaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8=yOPGY2fznON_wKdKHEXsGbfEj9dij-0NHHTuqHdH6tM=
>   >
>
> (CCP4bb is amazing)
>
> Frank
>
> On 25/05/2021 20:44, Frank von Delft wrote:
> > Hello all - this presumably has a really simple solution:
> >
> > For a PDB file with a (correct) biomolecular assembly record (REMARK
> > 350), what program do I use to generate and write out the coordinates
> > of the biomolecular assembly (or one of them).
> >
> > Thanks
> > Frank
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwIBaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8=Zc5y9vtC54wj1EQkTlPSy1gDJXFDHGKDWtpCUt0pGWs=
> >
> > This message was issued to members of 
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.jiscmail.ac.uk_CCP4BB=DwIBaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8=3Td7Xm6df98q55Qfp858BRcgJ58KOFH7GgL3f0Ye0Hc=
> >  , a
> > mailing list hosted by 
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.jiscmail.ac.uk=DwIBaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8=Z3kyHvED39ClsehF-iN5Xjv91IQoLwRhJStxQNsZ0Hc=
> >  , terms & conditions are
> > available at 
>

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

2020-11-25 Thread Mooers, Blaine H.M. (HSC)

Dear Nika,

The question is about a Fo-Fc map and the replies have been focused on such 
maps.
However, I question why you are bothering with Fo-Fc maps.
The ligand was soaked into the crystal. There is probably an isomorphous apo 
data set available. 
A [Fo(ligand complex) - Fo(apo)]*exp(alpha_apo,calc) map should be consulted in 
preference to various Fo-Fc maps corrected for phase bias.
It would be even better to substitute in the experimental phases for the apo 
structure if
they are available.

Fo-Fo maps may be nosier than Fo-Fc maps. but they are more reliable when you 
are
trying to decide if a ligand is present. 

I recommend reading the following book chapter:

@incollection{rould2003isomorphous,
  title={Isomorphous difference methods},
  author={Rould, Mark A and Carter Jr, Charles W},
  booktitle={Methods in enzymology},
  volume={374},
  pages={145--163},
  year={2003},
  publisher={Elsevier}
}

I second Robbie's "bloody obvious" rule. 
Sounds like you have an occupancy issue.
If you collected data from multiple crystals of the complex
as is the standard practice these days,
process and check each one. There can be large differences 
in ligand occupancy between crystals from different drops. 

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of John R Helliwell 
[jrhelliw...@gmail.com]
Sent: Wednesday, November 25, 2020 4:36 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] phenix.refine with ligand with ambiguous 
electron density

Hello Robbie,
Yes exactly, I agree. I thought that was what the poster faced: density with 
insufficient detail and not extending sufficiently for the whole ligand.
To make the discussion thread more focussed a screenshot or two would assist us.
Greetings,
John

Emeritus Professor John R Helliwell DSc




On 25 Nov 2020, at 09:03, Robbie Joosten  wrote:


I’m with Dale on this, the scientifically prudent thing is to set the rules and 
then play by them. Not to change the rules as you go. Of course, in a teaching 
environment where you know the correct answer, it is good to be educational and 
learn how to dig a bit more.

However, in a scientific setting this digging is not to come to a strong 
conclusion, but only to see if you should pursue the project and do additional 
experiments (e.g. longer soaks or using a higher ligand concentration). In this 
case the topic starter has poor density and fitting the ligand and refining 
gives negative difference density. Surely that is not enough evidence to reject 
the null hypothesis “the ligand is not bound”. In other words, there is no 
strong evidence that the ligand is bound. Perhaps you can look at the occupancy 
, but that is probably as far as you should go. The polder map is useful to get 
rid of the effect of the solvent mask blurring actual ligand density. But after 
fitting the ligand you shouldn’t need the polder map. Blurring and sharpening 
is something to make sense of the density shape to better fit your ligand, not 
to conclude whether or not you ligand is there.

On a whole, for ligands we should try to stick to the so-called “bloody 
obvious” test: if the density is not bloody obvious, your ligand is not there. 
At least not all the time.

Cheers,
Robbie


From: CCP4 bulletin board  On Behalf Of Jon Cooper
Sent: Wednesday, November 25, 2020 05:20
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Hello Dale, the statistical rigour you describe is, of course, excellent, but 
in a learning environment, if someone gets a negative result, you have to go 
into overdrive to check that everything has been done correctly, since there is 
a fair chance that human error is the cause. It may be a terrible practice, but 
it would seem to be an important part of the process? Even as a relative 
newcomer to the field (well, since the mid-80's ;-) I have seen many people 
getting nothing in their initial difference maps, even if the ligand is there. 
Frequently it was just the contour level being too high and, depending on how 
far back you go, the solution varied from showing someone how to roll the mouse 
wheel in Coot to having the map recontoured at a computer centre 200 miles away 
and posted back on a magnetic tape, which took about 10 days - a timescale on 
which some people just gave up and did something else! I can't help thinking it 
would be a shame to robotically accept every negative result at face value, not 
least if you're doing something important like curing a pandemic. However, back 
to the original question which I think was whether polder map coefficients 
could be used as refinement targets

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Contouring Patterson map?

2020-10-10 Thread Mooers, Blaine H.M. (HSC)

Hi Gloria,

The lack of repsonse to your question sadly suggests that not many people have 
made a Harker section recently.

You could probably make a fancier plot with matplotlib in Pytbon or Gnuplot, but
I use Map Slicer under the Visuallization pulldown in the ccp4i gui to make 
old-fashion contour plots of Harker sections.

You have to play around with the scale and and other settings to get what you 
need, especially if you have a 
unit cell angles that not equal to 90 degrees. In such a case, you may have to 
spend an hour tweaking these parameters. 
If you can live with a bitmap image of the map, you can always take a snapshot 
of the image in the gui, which is 
not always replicated completely in the exported postscript file. If needed, 
you can also edit the postscript file in a text editor.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Gloria Borgstahl 
[gborgst...@gmail.com]
Sent: Thursday, October 08, 2020 4:21 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] Contouring Patterson map?

What is the best way to display Harker sections... these days?



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Displaying solvent channels in protein crystal

2020-09-02 Thread Mooers, Blaine H.M. (HSC)

Hi Steve,

Take a look at MAP_CHANNELS: a computation tool to aid in the visualization and 
characterization of solvent channels in macromolecular crystals
by Douglas H. Juersa and Jon Ruffin  doi: 10.1107/S160057671402281X.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Carr, Stephen 
(MRC,RAL,RCAH) [stephen.c...@rc-harwell.ac.uk]
Sent: Wednesday, September 02, 2020 4:16 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] Displaying solvent channels in protein crystal

Dear all,

I would like to display the solvent channels in a protein crystal and get a 
good estimate of their dimensions.  There are lots of widgets for looking at 
channels and voids within a protein, but it appears not so much for calculating 
the solvent channels between proteins.  If anyone could offer some advice on 
the easiest way to do this I would be grateful.

best wishes,

Steve

Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717
This email and any attachments may contain confidential, copyrightand or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorized recipient of the addressee, 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to this email.

Any views or opinions presented are solely those of the author and do not 
necessarily represent those of the Research Complex at Harwell.

There is no guarantee that this email or any attachments are free from viruses 
and we cannot accept liability for any damage which you may sustain as a result 
of software viruses which may be transmitted in or with the message.

We use an electronic filing system. Please send electronic versions of 
documents, unless paper is specifically requested.

This email may have a protective marking, for an explanation, please see:
http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Macports and Fink - failed building open source pymol on MacOS Catalina

2020-06-14 Thread Mooers, Blaine H.M. (HSC)

Hi Javier,

Because this is an issue about open-source pymol, 
open an issue on the open-source GitHub site and report the problem

https://github.com/schrodinger/pymol-open-source/issues


Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Javier Gonzalez 
[bio...@gmail.com]
Sent: Saturday, June 13, 2020 6:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] Macports and Fink - failed building open source 
pymol on MacOS Catalina

Hello,
I'm attempting to build pymol on a laptop running MacOS Catalina 10.15.5,
Processor 2.8GHz Quad-Core Intel i7, Graphics Intel Iris Pro 1536 MB
I downloaded the latest version of Xcode 11.1

I tried from Fink (fink install pymol-py27) and Macports (sudo port install 
pymol), as indicated here: 
https://pymolwiki.org/index.php/MAC_Install

Both scripts run to download all dependencies but at the end fail with 
different messages (see below). Any ideas? Is it doable or am I just following 
outdated instructions?
Thanks in advance!
Javier

Fink: fails at compiling term-readkey-pm5184-2.37-1
-
-
Failed: phase compiling: term-readkey-pm5184-2.37-1 failed

Before reporting any errors, please run "fink selfupdate" and try again.
Also try using "fink configure" to set your maximum build jobs to 1 and
attempt to build the package again.
If you continue to have issues, please check to see if the FAQ on Fink's
website solves the problem.  If not, ask on one (not both, please) of
these mailing lists:

The Fink Users List 
mailto:fink-us...@lists.sourceforge.net>>
The Fink Beginners List 
mailto:fink-beginn...@lists.sourceforge.net>>,

with a carbon copy to the maintainer:

Christian Schaffner 
mailto:chri...@users.sourceforge.net>>

Note that this is preferable to emailing just the maintainer directly,
since most fink package maintainers do not have access to all possible
hardware and software configurations.

Please try to include the complete error message in your report.  This
generally consists of a compiler line starting with e.g. "gcc" or "g++"
followed by the actual error output from the compiler.

Also include the following system information:
Package manager version: 0.45.1
Distribution version: selfupdate-rsync Fri Jun 12 21:49:17 2020, 10.15, x86_64
Trees: local/main stable/main
Xcode.app:
 11.5
Xcode command-line tools: 11.5.0.0.1.1588476445
Max. Fink build jobs:  8
-
-
Macports: apparently there is an issue with py38-pyqt5
--->  Computing dependencies for pymol
The following dependencies will be installed:  py38-pyqt5
Continue? [Y/n]:
--->  Fetching archive for py38-pyqt5
--->  Attempting to fetch py38-pyqt5-5.14.2_0.darwin_19.x86_64.tbz2 from 
https://packages.macports.org/py38-pyqt5
--->  Attempting to fetch py38-pyqt5-5.14.2_0.darwin_19.x86_64.tbz2 from 
http://aus.us.packages.macports.org/macports/packages/py38-pyqt5
--->  Attempting to fetch py38-pyqt5-5.14.2_0.darwin_19.x86_64.tbz2 from

Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies

2019-02-02 Thread Mooers, Blaine H.M. (HSC)

Hi Eric,

You can lookup the symmetry operator in the International Tables 
(http://img.chem.ucl.ac.uk/sgp/LARGE/sgp.htm).
Alternatively, you can use coot to find the crystallographic symmetry operator 
that generates the second half of your tetramer.

Draw/Cell & Symmetry and then generate the symmetry mates.

Select File/Save Symmetry Coordinates

Click on the right symmetry mate.
Coot will display the symmetry operator in the panel below the viewport of the 
GUI.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

office: (405) 271-8300   lab: (405) 271-8313
e-mail:  blaine-moo...@ouhsc.edu 
Faculty webpage: https://tinyurl.com/BMBmooers
Google Scholar: https://tinyurl.com/GSbmooers
X-ray lab (LBSF): https://tinyurl.com/ouhsclbsf
SSRL-LCLS User Meeting: https://conf.slac.stanford.edu/ssrl-lcls-2018/
EasyPyMOL: https://github.com/MooersLab
Molecular Graphics Course Links: https://tinyurl.com/molgr
Small Angle Scattering Links: https://tinyurl.com/ouhscsaxs



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Klontz, Erik 
[erik.klo...@som.umaryland.edu]
Sent: Saturday, February 02, 2019 3:04 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] Generating rotation/translation matrices for 
biological assemblies


Hi all,


I'm working on a protein that I believe is tetrameric based on AUC, gel 
filtration, and crystallography. However, although my asymmetric unit has 4 
chains, I cannot form the tetramer within the asymmetric unit. Instead, the 
asymmetric unit has two half-tetramers ('dimers'), and each full tetramer is 
completed by pairing up with another half-tetramer from a symmetry mate. If I 
load this structure into PISA, it recognizes that each of the 'dimers' forms a 
stable assembly, but cannot seem to assemble the tetramer. However, if I the 
generate symmetry mates in pymol to create a new PDB for the biological 
tetramer and give this to PISA, it recognizes a stable tetramer.


Specifically, chains A and C in the original PDB pair with chains A and C of 
the second symmetry mate generated in pymol, while chains B and D in the 
original pair with chains B and D of the third symmetry mate. How do I use this 
knowledge to generate a 3x4 rotation with translation matrix for PDB deposition?


Thanks,
Erik Klontz




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

Re: [ccp4bb] [EXTERNAL] [ccp4bb] cryo suggestions for lithium sulphate xt condition containing 1.8 - 2 M Li2SO4

2018-10-30 Thread Mooers, Blaine H.M. (HSC)

Hi Almu,

In my hands, 2M LiSO4 is not enough.

If your crystals cannot survive transfer to higher concentrations, transfer 
them to 1.8 M NaMalonate at the same pH and then transfer or add aliquots of Na 
Malonate stock at higher concentration until the drop has about 3.5 - 3.8 M Na 
Malonate. The optimal final concentration may vary from system to system. This 
protocol has worked for us many times.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

office: (405) 271-8300   lab: (405) 271-8313
e-mail:  blaine-moo...@ouhsc.edu 
alternate e-mail: bmooe...@gmail.com 

Faculty webpage: https://tinyurl.com/BMBmooers
Google Scholar: https://tinyurl.com/GSbmooers
SSRL User Executive Committee: 
https://www-ssrl.slac.stanford.edu/content/about-ssrl/advisory-panels/ssrl-users-organization
SSRL-LCLS User Meeting: https://conf.slac.stanford.edu/ssrl-lcls-2018/
EasyPyMOL: https://github.com/MooersLab
Molecular Graphics Course Links: https://tinyurl.com/molgr
Small Angle Scattering Links: https://tinyurl.com/ouhscsaxs
X-ray lab (LBSF): https://tinyurl.com/ouhsclbsf

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Almudena Ponce 
Salvatierra [maps.fa...@gmail.com]
Sent: Tuesday, October 30, 2018 6:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] cryo suggestions for lithium sulphate xt condition 
containing 1.8 - 2 M Li2SO4

Dear all,

I have looked into the archive and I've tried to collect suggestions for cryo 
protecting crystals that grew in 1.8 M Lithium sulphate containing mother 
liquor or 2M.

What would make more sense? Transferring it into a cryo solution that consists 
of mother liquor and a higher concentration of Lithium sulphate?

Or, would this concentration of Lithium sulphate be enough as a cryo-protectant 
and after slight dehydration I could flash freeze them?

Thank you very much in advance.

Best

Almu



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

Re: [ccp4bb] [EXTERNAL] [ccp4bb] suggestions for cryoprotectant

2018-10-22 Thread Mooers, Blaine H.M. (HSC)

Hi Firdous,

What Diana suggested may work if done carefully; however, I failed to transfer 
crystals from 1.5 LiSO4 salts to higher concentrations of LiSO4 in many 
attempts.
I did have success in transferring said crystals to 1.5 M sodium malonate then 
to incrementally to 2.8 or 3.2 M sodium malonate.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

office: (405) 271-8300   lab: (405) 271-8313
e-mail:  blaine-moo...@ouhsc.edu 
alternate e-mail: bmooe...@gmail.com 

Faculty webpage: https://tinyurl.com/BMBmooers
Google Scholar: https://tinyurl.com/GSbmooers
SSRL User Executive Committee: 
https://www-ssrl.slac.stanford.edu/content/about-ssrl/advisory-panels/ssrl-users-organization
SSRL-LCLS User Meeting: https://conf.slac.stanford.edu/ssrl-lcls-2018/
EasyPyMOL: https://github.com/MooersLab
Molecular Graphics Course Links: https://tinyurl.com/molgr
Small Angle Scattering Links: https://tinyurl.com/ouhscsaxs
X-ray lab (LBSF): https://tinyurl.com/ouhsclbsf

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Firdous Tarique 
[kahkashantari...@gmail.com]
Sent: Friday, October 19, 2018 4:57 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] suggestions for cryoprotectant

Dear members

I have got beautiful crystal hits in SaltRx screens which are not diffracting 
to a good resoultion. All of them are salt based condition and I am not able to 
formulate a good cryoprotectant for these crystals. I also think that in my 
case the poor resolution is due to a poor cryoprotectant selection.

The conditions are as follows:

1> 4M Ammonium Acetate 100mM Bis Tris Propane pH 7.0
2>0.5M KCN 100mM Tris pH8.5
3>1.5M LiSo4 100mM Bris Tris Propane pH 7.0
4>4M Sodium Nitrate 100mM Tris pH8.5
5>1.5M Sodium Nitrate 100mM Sodium acetate pH 4.6

There are few more conditions but so far not able to see good diffraction with 
using lower peg and glycerol based cryoprotectants.

Can anybody suggest me good cryos conditions for salt based crystallization 
conditions or anything good for SaltRx crystallization hits.

Thanks

Firdous



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

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Python3 and MTZ

2018-06-06 Thread Mooers, Blaine H.M. (HSC)

Hi Kay,

clipper_tools is python3 compliant.

https://github.com/clipper-python

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
University of Oklahoma Health Sciences Center
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Faculty webpage   X-ray lab (LBSF)  COBRE in Structural Biology
SSRL UEC Facebook Page  SSRL UEC  SSRL SAC  LCLS UEC
EasyPyMOL Molecular Graphics  Small Angle Scattering
office: (405) 271-8300   lab: (405) 271-8313   e-mail: blaine-moo...@ouhsc.edu


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kay Diederichs 
[kay.diederi...@uni-konstanz.de]
Sent: Wednesday, June 06, 2018 7:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] Python3 and MTZ

Dear all,

I haven't tried to read MTZ files from Python until now, but for a new
project in my lab I'd like to do that - and with Python3.

Googling around, it seems that iotbx from cctbx is not (yet)
Python3-compatible.

So, what are my options?

thanks,

Kay
--
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

This e-mail is digitally signed. If your e-mail client does not have the
necessary capabilities, just ignore the attached signature "smime.p7s".




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

Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac

2015-05-20 Thread Mooers, Blaine H.M. (HSC)

I have had good experiences with MathJak for html. It too gives beautiful 
renderings on webpages of equations 
encoded in LaTeX. It is very easy to use. It grew out of jsMath.

http://www.mathjax.org/

Best regards,

Blaine Mooers



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of William G. Scott 
[wgsc...@ucsc.edu]
Sent: Wednesday, May 20, 2015 7:32 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac

 On May 20, 2015, at 5:38 AM, Randy Read rj...@cam.ac.uk wrote:

 Thanks, as always, to everyone for a thoughtful discussion!


Alternatively, as a scientific community, perhaps it is finally time for us to 
untwist Clippy, bending him backwards and forwards until he snaps at those 
horrid beady little eyeballs, ditch the Comic Sans, flip Redmond the bird, HTFU 
and learn to use LaTeX equation markup, and ask that our journals do the same.  
It really isn’t any harder than learning basic HTML (and predates it as one of 
the original mark-up languages). Journals and funding agencies should not be 
demanding that we use crappy broken and restrictive proprietary formats for 
submitting papers and proposals.

Ascii text documents provide the ultimate form of universal interchangeability.

The syntax is actually quite straightforward and easy to learn (or look up), eg:

https://urldefense.proofpoint.com/v2/url?u=http-3A__en.wikibooks.org_wiki_LaTeX_Mathematicsd=AwIF-gc=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEkr=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdIIm=U-vNRZjPhftiaADvIzN7HNUo5rnv5-JKR6RwZjW0UDQs=Q3biyCgXkL73q4eLw0MovreIp6p923PLHLrEp3AiuBge=

LaTeX allows you to focus on content rather than document formatting.  Although 
it is definitely more badass to do this in vim, other ascii text editors often 
have very useful LaTeX functionality.  (My favorite on OS X is TextMate, 
version 2 of which is now free. If you code on OS X, you should take a look at 
this.)

Once you make the small investment of time learning LaTeX, it makes other tasks 
easier.  For example, you can use jsMath to embed LaTeX-encoded equations 
(including chemistry symbols) in web pages, eg:

https://urldefense.proofpoint.com/v2/url?u=http-3A__www.math.union.edu_-7Edpvc_jsmath_examples_welcome.htmld=AwIF-gc=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEkr=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdIIm=U-vNRZjPhftiaADvIzN7HNUo5rnv5-JKR6RwZjW0UDQs=UAkZG7nG6yJ1m41HFCqn3Ah_ifo-u-S4N8VwWbtbi3oe=

Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac

2015-05-19 Thread Mooers, Blaine H.M. (HSC)

Hi Randy,

You could use a LyX--LaTeXiT--MS Word workflow to solve the equation editing 
issue without anyone learning LaTeX syntax.

The LyX document with equations can be exported to a LaTeX  *.tex file, and you 
can open this tex file  in any text editor to copy the equations encoded in 
LaTeX syntax for pasting into the LaTeXiT gui.  Alternatively, you can select 
and copy the equation in the LyX document and paste it directly into the 
LaTeXiT gui to get back the LaTeX encoding. 

LyX gui is very easy to start using productively without reading the manual. 
However, I do not know of a way to directly use ENDNOTE with LyX. I use LyX to 
assemble my early drafts, and then I move the draft into MS Word when I need to 
start adding citations. In MS Word 2011 on a Mac, it is painful to scroll 
through a large document (10 pages) with tables and figures, whereas a 1000 
page document in LyX can be scrolled through in a flash. LyX has been used to 
assemble books.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Assistant Professor
Director of the Laboratory of Biomolecular Structure and Function
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466

Shipping address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

Letter address:
P.O. Box 26901, BRC 466
Oklahoma City, OK 73190

office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910
e-mail:  blaine-moo...@ouhsc.edu

Faculty webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-

Small Angle Scattering webpage: 
http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0

X-ray lab webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of George Reeke 
[re...@mail.rockefeller.edu]
Sent: Tuesday, May 19, 2015 10:17 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac

Dear Randy et al,
May I suggest Lyx, an open-source wysiwyg editor that outputs
Latex.  The interface is so much like other word processors that
it is a snap to learn quickly and you get those Latex files with
equations that journals, at least math and physics journals, like.
Maybe you could get your colleagues to try it--I did even though
I was sure I didn't want to learn Latex.  I use it in Linux,
where you do one of those configure-make-install-from-source-
code installs.  Here is the online info for using it on a mac:
https://urldefense.proofpoint.com/v2/url?u=http-3A__wiki.lyx.org_Mac_Macd=AwIFaQc=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEkr=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdIIm=LcTP6vjD81n8gdU8pO7MO0O_G5V4cd6IYIjH5HR5LAQs=ZKNr8DjE1hiSYE6bjdgorDpAUWU_3gUFfRH9urzCZxIe=
George Reeke

On Mon, 2015-05-18 at 09:10 +0100, Randy Read wrote:
 Rather off-topic, but maybe someone on the list has found a way to work 
 around this!

 There’s a problem with the Equation Editor in Office 2011 for Mac (i.e. the 
 one that is based on a stripped-down version of MathType, which you get with 
 Insert-Object-Microsoft Equation).  You can insert an equation, re-open it 
 and edit it several times, and then suddenly (and seemingly randomly) the 
 equation object will be replaced by a picture showing the equation, which can 
 no longer be edited.  I’m writing a rather equation-heavy paper at the 
 moment, and this is driving me crazy.

 This seems to be a known bug, which has existed from the release of Office 
 2011.  Apparently it happens, unpredictably, when an AutoSave copy of the 
 document is saved, so you can avoid it by turning off the AutoSave feature.  
 The last time this drove me crazy, several years ago, I did try turning off 
 AutoSave.  For a while, I was very good about manually saving frequently, but 
 I got into bad habits and eventually Word crashed after I had worked for 
 several hours on a grant proposal without manually saving.  So I turned 
 AutoSave back on.

 At the moment, the least-bad solution seems to be to turn off AutoSave while 
 I’m working on a document with lots of equations and then (hopefully) 
 remember to turn it back on after that document is finished.  But it would be 
 great if someone has come up with a better cure for this problem.

 No doubt someone will suggest switching from Word to LaTeX, but I need to be 
 able to collaborate on paper-writing, and even though I might be willing to 
 invest the effort in learning LaTeX, I can’t really expect that of my 
 collaborators.  Most people in our field do use Microsoft Word, regardless of 
 its failings.  I’ve also tried using the professional version of MathType, 
 but that requires your collaborators to install it as well — and I don’t 
 think that

Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac

2015-05-18 Thread Mooers, Blaine H.M. (HSC)

Hi Randy,

I too suggest LaTeXiT. To add to what has already been suggested, LaTeXiT 
allows the assembly of a custom library of equations. You can send your 
collaborators this library as a file, and they could make minor edits to the 
equations in LaTexit gui editor without having to learn the full syntax of 
LaTeX. Minor edits would be self-explanatory to implement. Then they could 
export the edited equations for insertion into the current draft in MS Word. If 
they can't install LaTeXiT, you can send them the equations in the LaTeX format 
in a plain text file, and they could edit the equations in the LaTeXiT syntax, 
which can be deduced by comparing the syntax to the final equation. They could 
then return the edited plain text file to you for you to copy and paste into 
LaTeXiT.  If that is too hard for them, they could always write out the edited 
equation on paper with a pen or pencil, scan it into a pdf, and e-mail it back 
to you for typesetting in LaTeXiT. 

An alternative would be to move the document into RMarkdown via RStudio (a gui 
interface to R) which is much easier to master than LaTeX while still having 
access to the LaTeX equation syntax. This document can be quickly converted (by 
knitting) to doc, pdf and html within the RStudio gui. The exported document 
might require additional editing if the conversion does not go well. If you are 
using ENDNOTE and not BibTeX for managing citations, the workflow may become 
more complicated. 

Best regards,

Blaine

Blaine Mooers, Ph.D.
Assistant Professor
Director of the Laboratory of Biomolecular Structure and Function
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466

Shipping address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

Letter address:
P.O. Box 26901, BRC 466
Oklahoma City, OK 73190

office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910
e-mail:  blaine-moo...@ouhsc.edu

Faculty webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-

Small Angle Scattering webpage: 
http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0

X-ray lab webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy Read 
[rj...@cam.ac.uk]
Sent: Monday, May 18, 2015 3:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Equation Editor woes with Office 2011 for Mac

Rather off-topic, but maybe someone on the list has found a way to work around 
this!

There’s a problem with the Equation Editor in Office 2011 for Mac (i.e. the one 
that is based on a stripped-down version of MathType, which you get with 
Insert-Object-Microsoft Equation).  You can insert an equation, re-open it 
and edit it several times, and then suddenly (and seemingly randomly) the 
equation object will be replaced by a picture showing the equation, which can 
no longer be edited.  I’m writing a rather equation-heavy paper at the moment, 
and this is driving me crazy.

This seems to be a known bug, which has existed from the release of Office 
2011.  Apparently it happens, unpredictably, when an AutoSave copy of the 
document is saved, so you can avoid it by turning off the AutoSave feature.  
The last time this drove me crazy, several years ago, I did try turning off 
AutoSave.  For a while, I was very good about manually saving frequently, but I 
got into bad habits and eventually Word crashed after I had worked for several 
hours on a grant proposal without manually saving.  So I turned AutoSave back 
on.

At the moment, the least-bad solution seems to be to turn off AutoSave while 
I’m working on a document with lots of equations and then (hopefully) remember 
to turn it back on after that document is finished.  But it would be great if 
someone has come up with a better cure for this problem.

No doubt someone will suggest switching from Word to LaTeX, but I need to be 
able to collaborate on paper-writing, and even though I might be willing to 
invest the effort in learning LaTeX, I can’t really expect that of my 
collaborators.  Most people in our field do use Microsoft Word, regardless of 
its failings.  I’ve also tried using the professional version of MathType, but 
that requires your collaborators to install it as well — and I don’t think that 
cured the equation to picture problem anyway.

Thanks!

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.

Re: [ccp4bb] Graphic for rotation about axis

2015-05-08 Thread Mooers, Blaine H.M. (HSC)

Hi Nick,

These symmetry element fonts at the IUCr website might be useful or at least 
inspirational:

http://www.iucr.org/resources/symmetry-font

Best regards,

Blaine

Blaine Mooers, Ph.D.
Assistant Professor
Director of the Laboratory of Biomolecular Structure and Function
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466

Shipping address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

Letter address:
P.O. Box 26901, BRC 466
Oklahoma City, OK 73190

office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910
e-mail:  blaine-moo...@ouhsc.edu

Faculty webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-

Small Angle Scattering webpage: 
http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0

X-ray lab webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Nicholas Keep 
[n.k...@mail.cryst.bbk.ac.uk]
Sent: Friday, May 08, 2015 9:37 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Graphic for rotation about axis

Where can you get hold of a graphic that indicates a rotation around the
horizontal or vertical axis
These occur in a lot of papers to indicate the relation between two
views but I don't seem to easily be able to google how to get hold of them
best wishes
Nick

--
Prof Nicholas H. Keep
Executive Dean of School of Science
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

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
   020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

Re: [ccp4bb] [ot]: nedit on Mac 10.10 yosemite

2014-10-29 Thread Mooers, Blaine H.M. (HSC)

nedit is available in macports.

sudo port install nedit

Best regards,

Blaine

Blaine Mooers, Ph.D.
Assistant Professor
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466

Shipping address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

Letter address:
P.O. Box 26901, BRC 466
Oklahoma City, OK 73190

office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910
e-mail:  blaine-moo...@ouhsc.edu

Faculty webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-

Small Angle Scattering webpage: 
http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0

X-ray lab webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Anindito Sen 
[andysen.to...@gmail.com]
Sent: Wednesday, October 29, 2014 10:50 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [ot]: nedit on Mac 10.10 yosemite

Thanks for the note guys. I really love nedit on my Linux boxes but never knew 
that nedit is available for Mac. Can you have the URL for downloading the nedit 
for Mac.

Andy


Anindito Sen. Ph.D

Scientist and Application Specialist in Biological Sciences

JEOL LTD.

13F, Ohtemachi Nomura Bldg.UrlBlockedError.aspx

2-1-1 Ohtemachi, Chiyoda-ku, Tokyo

100-0004tel:100-0004

Tel: +81-3-62623563tel:%2B81-3-62623563

Fax: +81-3-6262-3577tel:%2B81-3-6262-3577



www.jeol.comhttps://urldefense.proofpoint.com/v1/url?u=http://www.jeol.com/k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=5Bb%2FSfjw8o69utS64QapE0bxR3%2BfN9SV65K3vmqh49s%3D%0As=b307047fa8ceb5fb0fb5714aa957ca26179915f8dd70df5d9473c101fb130d79

Sent from my iPad

On 2014/10/30, at 午前12:36, Thomas, Leonard M. 
lmtho...@ou.edumailto:lmtho...@ou.edu wrote:

My guess you might just have to reinstall with the latest version of nedit.  
That is what I had to do when I went from 10.5 to 10.9.  Have yet to jump to 
10.10 yet.


Leonard M. Thomas Ph.D.
Macromolecular Crystallography Laboratory Manager
University of Oklahoma
Department of Chemistry and Biochemistry
Stephenson Life Sciences Research Center
101 Stephenson Parkway
Norman, OK 73019
405-325-1126
lmtho...@ou.edumailto:lmtho...@ou.edu
http://barlywine.chem.ou.eduhttps://urldefense.proofpoint.com/v1/url?u=http://barlywine.chem.ou.eduk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=5Bb%2FSfjw8o69utS64QapE0bxR3%2BfN9SV65K3vmqh49s%3D%0As=7339994e5583e1ca8bfb8b0cfdc5392797d440b26126254b8bc94e2343cfd8ec
http://structuralbiology.ou.eduhttps://urldefense.proofpoint.com/v1/url?u=http://structuralbiology.ou.eduk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=5Bb%2FSfjw8o69utS64QapE0bxR3%2BfN9SV65K3vmqh49s%3D%0As=5ed4bf3a917c795469cf455d26a63103e99ffe84f393043d13bc5467ab6a4151

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] 
on behalf of Ioan Vancea 
[ivan...@embl-hamburg.demailto:ivan...@embl-hamburg.de]
Sent: Wednesday, October 29, 2014 10:00 AM
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [ot]: nedit on Mac 10.10 yosemite

Hi,

I think that's a standard X11 library, do you have X11 (XQuartz) installed?

Regards,
Ioan

--
Dr. Ioan Vancea
European Molecular Biology Laboratory c/o DESY
Notkestrasse 85, 22607 Hamburg, Germany
Tel: +49 (0)40 89902-340
Email: ivan...@embl-hamburg.demailto:ivan...@embl-hamburg.de


On Oct 29, 2014, at 3:45 PM, Sebastiano Pasqualato wrote:


Hi folks,
sorry for the off-topic and slightly ‘demodée’ question, but, since I updated 
to Yosemite on my Mac, nedit does not work any more.
Here’s the error message:

Seba@host041:~ nedit
dyld: Library not loaded: /usr/X11R6/lib/libXp.6.dylib
 Referenced from: /Applications/nedit/nedit
 Reason: image not found
Trace/BPT trap: 5
Seba@host041:~

Anybody knows if there is a fix for that?
Thanks in advance,
S



--
Sebastiano Pasqualato, PhD
Crystallography Unit
Department of Experimental Oncology
European Institute of Oncology
IFOM-IEO Campus
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990
web 
http://is.gd/IEO_XtalUnithttps://urldefense.proofpoint.com/v1/url?u=http://is.gd/IEO_XtalUnitk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=5Bb%2FSfjw8o69utS64QapE0bxR3%2BfN9SV65K3vmqh49s%3D%0As=25085272fc46477bf97b36ff9278158b6eb446a8d69460123480f93d165ce280

Re: [ccp4bb] Calculating over all bend in a DNA

2014-10-22 Thread Mooers, Blaine H.M. (HSC)

Hi Sasha,

You can also use Richard Lavery's webservice for Curves+ ( 
http://gbio-pbil.ibcp.fr/cgi/Curves_plus/  ) and visualize the curve of the 
helical axis in 3D in a molecular graphics program.

In addition, you can do a normal vector analysis similar to the one suggested 
by Tim Gruene by running FREEHELIX by Richard Dickerson which has been 
available through the fink depository and which could be found this morning at 
the Nucleic Acid Databank via 
http://ndbserver.rutgers.edu/files/ftp/NDB/programs/freehelix98.
Linux binaries and the source code are available. I was able to compile from 
source code on a Mac several years ago.

Examples of our use of these programs as applied to two RNAs are found in
PMID:
21878548.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Assistant Professor
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466

Shipping address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

Letter address:
P.O. Box 26901, BRC 466
Oklahoma City, OK 73190

office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910
e-mail:  blaine-moo...@ouhsc.edu

Faculty webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-

Small Angle Scattering webpage: 
http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0

X-ray lab webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Valerie Pye 
[val...@googlemail.com]
Sent: Wednesday, October 22, 2014 6:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Calculating over all bend in a DNA

Hi Sasha - you can use 3DNA:  
http://x3dna.org/https://urldefense.proofpoint.com/v1/url?u=http://x3dna.org/k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=W0wpHNp%2B8HgFTfPnP6qooGcmzdq8AE7MNR43ZgeBMfQ%3D%0As=af3103f233522fb093353110ed7e13d1eed31bf25752556b48cba4b59d77da85;
 
http://w3dna.rutgers.edu/https://urldefense.proofpoint.com/v1/url?u=http://w3dna.rutgers.edu/k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=W0wpHNp%2B8HgFTfPnP6qooGcmzdq8AE7MNR43ZgeBMfQ%3D%0As=cbdb78f021cd77670fe306d17f761286b2f1c9550d9e296f664f0dac18f60b2e
HTH, val

On 21 October 2014 20:53, Sasha Pausch 
sashapau...@gmail.commailto:sashapau...@gmail.com wrote:
Hello CCP4bb,

May I know how can we calculate or use any server which can calculate the 
overall bend in a DNA (crystal structure)?

Re: [ccp4bb] High Salt Cryo

2014-02-19 Thread Mooers, Blaine H.M. (HSC)

For crystals grown out of a 2 uL drop of 1.2-1.8 M LiSO4 or 1.6-2.4 M AmmSO4, 
we do in situ cryoprotection with sodium malonate. We add 2-4 uL of 1.9 M Na 
malonate to the crystallization drop, wait 10 seconds and add 2-4 uL of 2.4 M 
sodium malonate, repeat with 2.8 M and then 3.4 M. We do not bother withdrawing 
aliquots to maintain a fixed volume. You may need to tweak the volumes to 
optimize the resulting diffraction. You can also break the additions at given 
concentration into smaller aliquots to reduce the osmotic shock. This approach 
is much gentler than transferring the crystal directly to 3 M sodium malonate. 
Do not leave the drop exposed to the air for more than 3 minutes or so because 
salt crystals will start to grow. When there are multiple crystals in a drop, 
often the unused crystals in the very high salt solution will still diffract 
well up to a year later if the crystallization chamber is resealed well; their 
diffraction might even improve with the prolonged exposure to high salt.  


Blaine Mooers
Assistant Professor
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466

Shipping address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

Letter address:
P.O. Box 26901, BRC 466
Oklahoma City, OK 73190

office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910
e-mail:  blaine-moo...@ouhsc.edu

Faculty webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-

X-ray lab webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory

Small Angle Scattering webpage: 
http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links.html?sfvrsn=0

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Katherine Sippel 
[katherine.sip...@gmail.com]
Sent: Tuesday, February 18, 2014 12:08 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] High Salt Cryo

Hi all,

I'm looking for a cryo condition for high NaCl (3+ M) crystallization 
condition. I would do it the proper way, but our beam/cryostream is down.

I've tried a bunch of things at the moment. Ethylene glycol and PEG 400 nuke 
the crystals immediately even at low concentrations. Prolonged exposure to 
glycerol and sucrose starts to break them down so I'm thinking that the 
diffraction will probably suffer. I can't find any reports of NaCl's viability 
as a cryosalt. I've got Paratone/Paraffin oil/Mitegen's LV cryo oil on tap but 
I was hoping to not put all my eggs in one basket.

I tried the ISRDB database through 
archive.comhttps://urldefense.proofpoint.com/v1/url?u=http://archive.comk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=Vjr4m%2Fds%2FdLGOVQoQ0x8PApF%2FzyGkSwsbIoq92CSnOk%3D%0As=3cfbf18821b5b59934971bf583cf3dd6e2ded91923c614e670857e10916c687e
 without any luck (no search function). I've gone to the PDB searching for 
similar crystallization conditions and looked up the papers for their cryos, 
but they are all glycerol. Google gives me the same.

I thought I'd see if anyone on the bb has an anecdotal this worked for us 
story. I would love to hear it.

Thank you for your time,
Katherine

--
Nil illegitimo carborundum - Didactylos

[ccp4bb] create a lower resolution data set by truncating a high resolution data

2014-02-13 Thread Mooers, Blaine H.M. (HSC)

For some simulated phasing experiments, I want to create a lower resolution 
diffraction data set by truncating a high resolution data set. I would like to 
avoid Fourier ripples due to the truncation of the high resolution data by 
downscaling the data  such that I/sigma=2.0 in the highest resolution shell 
of the truncated data. What is the best way to do this?

Blaine Mooers
Assistant Professor
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466

Shipping address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

Letter address:  
P.O. Box 26901, BRC 466  
Oklahoma City, OK 73190 

office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910
e-mail:  blaine-moo...@ouhsc.edu

Faculty webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-

X-ray lab webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory

Small Angle Scattering webpage: 
http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links.html?sfvrsn=0

Re: [ccp4bb] anomalous scattering server down?

2013-06-01 Thread Mooers, Blaine H.M. (HSC)

Bernhard Rupp has a calculator of Bijvoet ratios:

http://www.ruppweb.org/new_comp/anomalous_scattering.htm



Blaine Mooers
Assistant Professor
Director Macromolecular Crystallography Lab
Member Stephenson Cancer Center
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466

Letter address:
P.O. Box 26901, BRC 466
Oklahoma City, OK 73190

 Shipping address:
 975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910

e-mail:  blaine-moo...@ouhsc.edu

Faculty webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-
X-ray lab webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory
SAXS Links webpage: 
http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-x-ray-scattering-links.html?sfvrsn=0


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A. Berry 
[ber...@upstate.edu]
Sent: Saturday, June 01, 2013 6:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] anomalous scattering server down?

Hmm- looks like crosssec calculates F' and F (and cros-section).
I guess you're thinking of the x-ray edge page on the same server.
Ive got local copies and graphs of that in an excel spreadsheet.

I was thinking about the page where you enter your protein's
molecular weight, number and type of anomalous scatterers, and
it tells you how accurate your data has to be to make the
anomalous signal significant.

Thanks,
eab

Bosch, Juergen wrote:
 seems to be down sorry.
 you should be able to use crossec from ccp4
 Jürgen

 On Jun 1, 2013, at 6:47 PM, Edward A. Berry wrote:

 Is Ethan Merritt's anomalous scattering page at:
 https://urldefense.proofpoint.com/v1/url?u=http://www.bmsc.washington.edu/scatter/k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=vriAf%2FYLAE3OBEruPk8rCrKni5F1ZSfZwaGrrX0lwuk%3D%0As=57fb37f57cec12f6c778c53c6bfbdd04afc795f050605681dca25305998c6af0
 down or moved, or  the firewall I'm behind is blocking it?

 I want to check feasibility of a native-iron MAD experiment,
 and I'm not very good at math.

 thanks,
 eab

 ..
 Jürgen Bosch
 Johns Hopkins University
 Bloomberg School of Public Health
 Department of Biochemistry  Molecular Biology
 Johns Hopkins Malaria Research Institute
 615 North Wolfe Street, W8708
 Baltimore, MD 21205
 Office: +1-410-614-4742
 Lab:  +1-410-614-4894
 Fax:  +1-410-955-2926
 https://urldefense.proofpoint.com/v1/url?u=http://lupo.jhsph.edu/k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=vriAf%2FYLAE3OBEruPk8rCrKni5F1ZSfZwaGrrX0lwuk%3D%0As=d80576bcb5bffce1fe3f7ffe04c9ec7a4b3338c452e984d4efcbd8036ce5b83c

Re: [ccp4bb] cc1/2

2012-11-29 Thread Mooers, Blaine H.M. (HSC)

In the output file from xscale XSCALE.LP

Look in the middle of the file for the table

STATISTICS OF SCALED OUTPUT DATA SET :



Blaine Mooers
Assistant Professor
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466

Letter address:  Shipping address:
P.O. Box 26901, BRC 466  975 NE 10th Street, BRC 466
Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419

office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910
e-mail:  blaine-moo...@ouhsc.edu

webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of So Jay 
[scjay2...@hotmail.com]
Sent: Thursday, November 29, 2012 9:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] cc1/2

Dear All,

Where exactly I can find cc 1/2 of Karplus and Diederichs, 2012 in XDS?  Can I 
find a similar thing in HKL2000 processed data?

Thanks
Jay

Re: [ccp4bb] usefulness of cacodylate?

2012-11-09 Thread Mooers, Blaine H.M. (HSC)

Hi Frank,

In our hands, some RNAs only crystallize out of cacodylate buffers. We would
otherwise stop using it out of health and safety concerns.

Blaine


Blaine Mooers
Assistant Professor
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466

Letter address:  Shipping address:
P.O. Box 26901, BRC 466  975 NE 10th Street, BRC 466
Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419

office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910
e-mail:  blaine-moo...@ouhsc.edu

webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft 
[frank.vonde...@sgc.ox.ac.uk]
Sent: Friday, November 09, 2012 6:26 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] usefulness of cacodylate?

Hi all -

Anybody know
 a) how hazardous is cacodylate?
 b) does it really matter for crystallization screens?

It seems by far the most hazardous component of the standard screens;
this 2011 paper seems to think so (bizarrely, I can't access it from
Oxford):
http://onlinelibrary.wiley.com/doi/10./j.1365-2818.1977.tb01136.x/abstract

and this is site says lethal dose is 0.5-5g/kg:
http://cameochemicals.noaa.gov/chemical/4468
meaning 2ml of a 0.1M solution contains 1/10th lethal dose...? (Someone
should check my maths...)  [Coarse screens come mixed 2ml per condition.]


Has anybody done careful experiments that showed it really mattered for
a given crystal -- or even an entire screen?

So I'm inclined to toss it out entirely rather than make crystallization
screening a hazardous activity.  (We're being subjected to a safety
review.)


Thoughts welcome.
phx

[ccp4bb] Postdoctoral Fellow in Mooers Laboratory

2012-10-05 Thread Mooers, Blaine H.M. (HSC)

Postdoctoral Fellow in Mooers Laboratory
Dept. of Biochemistry  Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center (OUHSC)
Oklahoma City, OK, USA

A post-doctoral fellow position is available in structural (X-ray diffraction 
and SAXS) and biophysical studies of RNA. The projects are NIH funded.
Previous experience in RNA biochemistry and thermal stability studies would be 
advantageous. Recent graduates with a strong background in protein 
purification,  RNA purification, or both  and an interest in learning 
crystallography are also encouraged to apply.

Job Requirements:
---
The position requires a Ph.D. at time of hire with prior experience in RNA or 
protein biochemistry, molecular biology, and/or biophysical methods.

The candidate must have clear oral and written communication skills in the 
English language and the desire to work as part of a highly motivated team.

Applications should be received by December 1, 2012 for full consideration.  
Interested individuals send to blaine-moo...@ouhsc.edu  (1) a cover letter that 
includes research interests and future goals, (2) a CV that includes a list of 
publications and presentations and a list of experimental expertise and skills 
relevant to this position, and (3) contact information (including e-mail 
addresses) for three references able to assess your scientific abilities, 
experience, and potential. 

OUHSC is an Equal Opportunity/Affirmative Action Employer. OUHSC does 
background checks on all final candidates.

[ccp4bb] FACULTY POSITION IN STRUCTURAL BIOLOGY

2009-08-31 Thread Mooers, Blaine H.M. (HSC)

FACULTY POSITION IN STRUCTURAL BIOLOGY
08-24-2009
Department of Biochemistry  Molecular Biology, University of Oklahoma Health 
Sciences Center, Oklahoma City
 
The Department of Biochemistry  Molecular Biology in the College of Medicine 
at the University of Oklahoma Health Sciences Center (OUHSC) is seeking tenure 
track/tenured faculty, with the current open position for an individual with 
research interests that involve crystallography or other aspects of structural 
biology.
 
Current faculty members (http://www.oumedicine.com/body.cfm?id=3851) have 
diverse research programs that all converge with the common goal of developing 
a mechanistic understanding of cellular functions. We are seeking new 
colleagues who have, or will develop, independent research programs in 
biomedical research and who will participate in graduate training and 
professional student education. We are especially interested in individuals 
whose research interests mesh with the OUHSC Strategic Plan, which has emphasis 
in cancer, diabetes, and infectious diseases.
 
Candidates must hold a doctoral or equivalent degree in Biochemistry, 
Chemistry, Molecular Cell Biology or a related field and have a strong record 
of research accomplishment. We also seek evidence of excellence in 
teaching/presentation skills.
 
The OUHSC campus is highly interactive and provides collaborative opportunities 
with clinical departments, the OU Cancer Institute, the Oklahoma Diabetes 
Center, the Oklahoma Center for Medical Glycobiology, and other researchers in 
a cohort of strong basic science departments. Further collaborative 
opportunities exist at the adjacent Oklahoma Medical Research Foundation 
(OMRF), 20 miles south at the OU Norman campus, and across the six 
macromolecular X-ray facilities and ~20 structural biology research groups in 
Oklahoma. The Department of Biochemistry and Molecular Biology provides 
excellent shared facilities for protein crystallography, mass spectrometry, 
biophysical studies and glycobiology 
(http://www.oumedicine.com/body.cfm?id=3851), while many other Core facilities 
are available on campus and at the OMRF.
 
Review of applications will begin September 15, 2009, and continue until the 
position is filled. Please submit, in electronic form, a curriculum vitae, a 
brief statement of research accomplishments, research interests, future plans, 
and teaching philosophy, 2-3 publications and the names of 3 individuals from 
whom reference letters can be solicited.
 
Applications should be sent by email to
Dr Karla Rodgers, Chair, BMB Faculty Search Committee
biochemsea...@ouhsc.edu.
 
Inquiries can be directed to Karla Rodgers or to any member of the Biochemistry 
 Molecular Biology faculty.
 
OUHSC is an equal opportunity employer

[ccp4bb] off topic: plasmid for high fidelity DNA polymerase

2007-07-05 Thread Mooers, Blaine H.M. (HSC)


This is off topic but probably of great interest to others.

Where can I find an over-expression plasmid for a high fidelity
thermostable DNA polymerase?  I want to make DNA polymerase
to use in a large number of  PCR reactions.  

Many thanks in advance,

Blaine Mooers




*
Blaine Mooers, Ph.D.
Assistant Professor
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center

Letter address:
P.O. Box 26901, BRC 468
Oklahoma City, OK 73190

Shipping address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

office:(405) 271-8300
lab:(405) 271-8313
fax:(405) 271-3910

email:  [EMAIL PROTECTED]

http://w3.ouhsc.edu/biochem/mooers.htm

[ccp4bb] Registration open for the SSRL/LCLS User Meeting

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] ILLUSTRATE in PYMOL

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] ILLUSTRATE in PYMOL

[ccp4bb] Staff scientist position for an experienced biomolecular crystallographer

[ccp4bb] reminder: tomorrow is last day to register for the virtual and free SSRL/LCLS Users Meeting

[ccp4bb] Poster deadline approaching for SSRL/LCLS User's Meeting

[ccp4bb] SSRL/LCLS User's Meeting registration is open

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

Re: [ccp4bb] Phasing a difficult RNA heteroduplex structure

[ccp4bb] Opportunity for experienced crystallographer

[ccp4bb] last day to register for the SSRL/LCLS User Meeting

[ccp4bb] Experienced crystallographer needed

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Contouring Patterson map?

Re: [ccp4bb] Displaying solvent channels in protein crystal

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Macports and Fink - failed building open source pymol on MacOS Catalina

Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies

Re: [ccp4bb] [EXTERNAL] [ccp4bb] cryo suggestions for lithium sulphate xt condition containing 1.8 - 2 M Li2SO4

Re: [ccp4bb] [EXTERNAL] [ccp4bb] suggestions for cryoprotectant

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Python3 and MTZ

Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac

Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac

Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac

Re: [ccp4bb] Graphic for rotation about axis

Re: [ccp4bb] [ot]: nedit on Mac 10.10 yosemite

Re: [ccp4bb] Calculating over all bend in a DNA

Re: [ccp4bb] High Salt Cryo

[ccp4bb] create a lower resolution data set by truncating a high resolution data

Re: [ccp4bb] anomalous scattering server down?

Re: [ccp4bb] cc1/2

Re: [ccp4bb] usefulness of cacodylate?

[ccp4bb] Postdoctoral Fellow in Mooers Laboratory

[ccp4bb] FACULTY POSITION IN STRUCTURAL BIOLOGY

[ccp4bb] off topic: plasmid for high fidelity DNA polymerase

35 matches

Site Navigation

Mail list logo

Footer information