Re: [ccp4bb] Coot label on symmetric residue not working consistent

[B.Lohkamp]

On 10/04/2017 20:14, Xiao Lei wrote:

Thanks Paul,

I tried, it failed with a message as below:
Coot>> set-symmetry-shift-search-size 2
BL Warning:: Python syntax error!
   (or you attempted to use an invalid guile command..)
Python error:
invalid, syntax (, line1)

coot>>


You are mixing python and scheme commands. If you use python it should be:

set_symmetry_shift_search_size(2)

... and in scheme there should be parenthesis around the command (see 
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Python_to_Scheme_and_return).


HTH,

Bernhard



On Mon, Apr 10, 2017 at 11:05 AM, Paul Emsley > wrote:

On 10/04/17 18:39, Xiao Lei wrote:

Hi All,

I am using Coot 0.8.3 EL on Mac OS X 10.10.  After I generate
symmetric molecule by Draw---> Cell & Symmetry.  I found double
click a residue in symmetric molecules will give me a label
sometime but not always. I do not know if anyone has similar
experience.



Try applying the solution described for Missing Symmetry in the
manual (4.11.1).

Paul.

[ccp4bb] Some problems in data processing

[高艺娜]

Dear all,
For my crystal, I have to merge 3-4 sets of diffraction data using HKL2000 
program to meet requirements for data completeness, but the problem is the 
Rmerge value was too high to go on every time.
Did anyone have met the same problem and how to solve it? or some tips for 
solve this problem？

All comments will be appreciated!

Best Regards,

[ccp4bb] off topic: MacPymol and macOS Sierra

[Peter Hsu]

Hi all, 

Sorry for the very off topic message, but I recently upgraded my OS to Sierra 
and all of a sudden MacPymol has stopped working for me. Clicking on the 
program just gives the appearance of it about to start by showing the icon on 
the dock, and then just blinks out, without ever starting. My xcode and xquartz 
is up to date, so I'm not sure where the problem is. Any help is much 
appreciated!

Thanks,
Peter

Re: [ccp4bb] Fwd: Re: [ccp4bb] Structure comparison

[Dmytro Guzenko]

Gert,

There is nothing wrong with suggesting 45 softwares, as one of those may 
do exactly what a person needs and save loads of time.


Besides, comparing protein structures locally need not involve any 
superposition method. I would say comparing torsion angles/distances 
between atoms is a more common solution to this problem. There are still 
cutoffs and weights to consider of course. Approaches vary on how to 
handle those (e.g. theoretical or through validation), but I seriously 
doubt your response constitutes 'case closed'.


Kind regards,

Dmytro.


On 10/04/17 12:06, Gert Vriend wrote:

Rather then now start mentioning yet 45 other 3D superposition
softwares, I think a pointer to the Wikipedia should suffice:

https://en.wikipedia.org/wiki/Structural_alignment

The Russian Doll effect (if you align more residues the comparison stats
get worse) is best explained (my opinion) by the CATH people (Orengo
group), and Arthur Lest is the only one (still, I think) who has been
thinking extensively about the cutoff question.

Greetings
Gert


From: Reza Khayat
Sent: Sunday, April 9, 2017 6:07 PM
To: CCP4 bulletin board
Subject: Structure comparison

Hi,

I have refined several structures of a protein from different space 
groups and would like to compare them to one another. Is there a 
program/software suite that would provide an objective comparison 
of the structures and identify regions where the structures are 
sufficiently different from one another to warrant a closer look? I 
think the most important aspect of the analysis would be defining a 
threshold (possibly based on resolution and structure statistics) 
that would identify sufficient difference between structures. Thanks.


Best wishes,
Reza

Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031


Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het 
handelsregister onder nummer 41055629.
The Radboud university medical center is listed in the Commercial 
Register of the Chamber of Commerce under file number 41055629.

Re: [ccp4bb] Structure comparison

[Naima Sharaf]

Hi Reza,

Maybe Dr. karplus's program ensemblator might be of some help.

https://github.com/Karplus-Lab-OSU/ensemblator

Naima G Sharaf

*

Postdoctoral Scholar-Division of Biology and Biological Engineering
California Institute of Technology
1200 E. California Blvd
Pasadena, CA 91125
email: ngsha...@caltech.edu


On Sun, Apr 9, 2017 at 4:39 PM Reza Khayat  wrote:

Hi,

My initial e-mail may have been a bit vague so I'll try to be more
specific. Superposing the structures and comparing them against one
another, while appropriate, is a subjective way to do the analysis as I
would have to subjectively define a threshold that would indicate a
difference between the structures. My threshold may be grossly different
than someone else's threshold. I am interested in an objective criterion.
One where strong emphasis has been put on error analysis and error modeling
in terms of both the refined structure and the underlying data. I realize
that defining such criterion is by no means trivial. Thanks again for the
help.

Best wishes,
Reza

Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031


From: Reza Khayat
Sent: Sunday, April 9, 2017 6:07 PM
To: CCP4 bulletin board
Subject: Structure comparison

Hi,

I have refined several structures of a protein from different space groups
and would like to compare them to one another. Is there a program/software
suite that would provide an objective comparison of the structures and
identify regions where the structures are sufficiently different from one
another to warrant a closer look? I think the most important aspect of the
analysis would be defining a threshold (possibly based on resolution and
structure statistics) that would identify sufficient difference between
structures. Thanks.

Best wishes,
Reza

Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031

Re: [ccp4bb] Structure comparison

[Dmytro Guzenko]

Have a look at local distance difference 
test.https://swissmodel.expasy.org/lddt/
It's superposition-free and compares local atomic environment only. You will be 
able to see unusually different regions from the output.

I am not aware of a similar structure comparison method that would also take 
into account the underlying data, you'll probably need to come up with 
something here. E.g. place one structure instead of another in its crystal and 
evaluate local electron density correlations along the sequence (sfcheck can do 
that I think) at different resolution levels. Then compare changes in local 
correlation (replaced-original) vs. lddt plot. If both plots go down in the 
same region, then it warrants a closer look.

Kind regards,
Dmytro.


On 10/04/17 01:37, Reza Khayat wrote:

Hi,

My initial e-mail may have been a bit vague so I'll try to be more specific. 
Superposing the structures and comparing them against one another, while 
appropriate, is a subjective way to do the analysis as I would have to 
subjectively define a threshold that would indicate a difference between the 
structures. My threshold may be grossly different than someone else's 
threshold. I am interested in an objective criterion. One where strong emphasis 
has been put on error analysis and error modeling in terms of both the refined 
structure and the underlying data. I realize that defining such criterion is by 
no means trivial. Thanks again for the help.

Best wishes,
Reza

Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031


From: Reza Khayat
Sent: Sunday, April 9, 2017 6:07 PM
To: CCP4 bulletin board
Subject: Structure comparison

Hi,

I have refined several structures of a protein from different space groups and 
would like to compare them to one another. Is there a program/software suite 
that would provide an objective comparison of the structures and identify 
regions where the structures are sufficiently different from one another to 
warrant a closer look? I think the most important aspect of the analysis would 
be defining a threshold (possibly based on resolution and structure statistics) 
that would identify sufficient difference between structures. Thanks.

Best wishes,
Reza

Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031

Re: [ccp4bb] suggestion on protein crystallization optimization from phase separation

[Edward Snell]

I would also point out that a key part of the technique described in the 
reference below is to vary the temperature. The Lenhoff group published a nice 
study on protein phase behavior where they talk about liquid-liquid phase 
separation amongst other things. Figure 1 of the paper (Dumetz et al, Biophys 
J. 94, 570-583, 2008, 10.1529/biophysj.107.116152)  can be recast in the 
conventional phase diagram space and shows how temperature affects the gelation 
point and can be used to shift the phase.

Cheers,

Eddie

http://Getacrystal.org

Edward Snell Ph.D.
President and CEO Hauptman-Woodward Medical Research Institute
Assistant Prof. Department of Structural Biology, University at Buffalo
700 Ellicott Street, Buffalo, NY 14203-1102
hwi.buffalo.edu
Phone: (716) 898 8631 Fax: (716) 898 8660
Skype:  eddie.snell Email: esn...@hwi.buffalo.edu
[cid:image001.png@01D2B21A.8EA7C860]
Heisenberg was probably here!

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kevin Jude
Sent: Monday, April 10, 2017 4:41 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] suggestion on protein crystallization optimization from 
phase separation

I had success once by varying the drop volume ratios as described here:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2203341/
although we ended up getting data from a different crystal form.
~1 M LiSO4 is a surprising condition for cocrystallizing protein and DNA if 
they aren't covalently or topologically linked. Best of luck to you.
kmj

On Thu, Apr 6, 2017 at 8:16 AM, Joseph Ho 
> wrote:
Dear all:

I would like to seek your suggestion on protein crystallization from
phase separation.
We recently observed many small round droplets shown in our
protein/DNA crystallization. Condition are 0.8M-1.6M LiSO4; 20mM
MgCl2; pH 5-8;  protein conc. ~15mg/ml). The UV microscope confirms
those are protein-rich phase separation.
We have tried to change conc. of LiSO4 and pH. Still we got different
size and amount of small round droplets. At 20 degree, those droplets
appear within one day and at 4 degree, it takes two-three days.  We
also tried additive and silver bullet screen. So far, we have not
found a condition to have protein crystals. The protein is already
truncated. Several DNA constructs are on-going.
At this point, I would like to seek your advice on the method to
optimize the condition. Based on


PS. Any people have luck with protein crystallization by streaking the
Gelationous protein to new drop as shown in
http://xray.bmc.uu.se/terese/tutorial3.html . Can you please share
your experience with us?

Thanks for your help.

Joseph Ho



--
Kevin Jude, PhD
Research Specialist, Garcia Lab
Departments of Molecular & Cellular Physiology and Structural Biology
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431

Re: [ccp4bb] suggestion on protein crystallization optimization from phase separation

[Kevin Jude]

I had success once by varying the drop volume ratios as described here:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2203341/
although we ended up getting data from a different crystal form.

~1 M LiSO4 is a surprising condition for cocrystallizing protein and DNA if
they aren't covalently or topologically linked. Best of luck to you.

kmj

On Thu, Apr 6, 2017 at 8:16 AM, Joseph Ho  wrote:

> Dear all:
>
> I would like to seek your suggestion on protein crystallization from
> phase separation.
> We recently observed many small round droplets shown in our
> protein/DNA crystallization. Condition are 0.8M-1.6M LiSO4; 20mM
> MgCl2; pH 5-8;  protein conc. ~15mg/ml). The UV microscope confirms
> those are protein-rich phase separation.
> We have tried to change conc. of LiSO4 and pH. Still we got different
> size and amount of small round droplets. At 20 degree, those droplets
> appear within one day and at 4 degree, it takes two-three days.  We
> also tried additive and silver bullet screen. So far, we have not
> found a condition to have protein crystals. The protein is already
> truncated. Several DNA constructs are on-going.
> At this point, I would like to seek your advice on the method to
> optimize the condition. Based on
>
>
> PS. Any people have luck with protein crystallization by streaking the
> Gelationous protein to new drop as shown in
> http://xray.bmc.uu.se/terese/tutorial3.html . Can you please share
> your experience with us?
>
> Thanks for your help.
>
> Joseph Ho
>



-- 
Kevin Jude, PhD
Research Specialist, Garcia Lab
Departments of Molecular & Cellular Physiology and Structural Biology
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431

Re: [ccp4bb] Coot label on symmetric residue not working consistent

[Xiao Lei]

Thanks Paul,

I tried, it failed with a message as below:
Coot>> set-symmetry-shift-search-size 2
BL Warning:: Python syntax error!
   (or you attempted to use an invalid guile command..)
Python error:
invalid, syntax (, line1)

coot>>

On Mon, Apr 10, 2017 at 11:05 AM, Paul Emsley 
wrote:

> On 10/04/17 18:39, Xiao Lei wrote:
>
>> Hi All,
>>
>> I am using Coot 0.8.3 EL on Mac OS X 10.10.  After I generate symmetric
>> molecule by Draw---> Cell & Symmetry.  I found double click a residue in
>> symmetric molecules will give me a label sometime but not always. I do not
>> know if anyone has similar experience.
>>
>>
>>
> Try applying the solution described for Missing Symmetry in the manual
> (4.11.1).
>
> Paul.
>
>

Re: [ccp4bb] Coot label on symmetric residue not working consistent

[Paul Emsley]

On 10/04/17 18:39, Xiao Lei wrote:

Hi All,

I am using Coot 0.8.3 EL on Mac OS X 10.10.  After I generate 
symmetric molecule by Draw---> Cell & Symmetry.  I found double click 
a residue in symmetric molecules will give me a label sometime but not 
always. I do not know if anyone has similar experience.





Try applying the solution described for Missing Symmetry in the manual 
(4.11.1).


Paul.

[ccp4bb] Coot label on symmetric residue not working consistent

[Xiao Lei]

Hi All,

I am using Coot 0.8.3 EL on Mac OS X 10.10.  After I generate symmetric
molecule by Draw---> Cell & Symmetry.  I found double click a residue in
symmetric molecules will give me a label sometime but not always. I do not
know if anyone has similar experience.

Re: [ccp4bb] ccp4/coot on macOSSierra

[Sankar N. Manicka]

xquartz 2.7.11 (currently the newest version) running on MacOS 10.12.4
(upto date) has no problem either.



On Thu, Apr 6, 2017 at 3:26 PM, Didier Spittler 
wrote:

> Hello Nikos,
>
> I use Zquartz 2.7.9 too and it works fine for me.
>
> Best,
>
> Didier
>
> 2017-04-06 11:52 GMT+02:00 Nikos Pinotsis  >:
>
>> Hi Ehmke,
>>
>> for sierra 10.12.3 try with the Xquartz 2.7.9 (xorg-server 1.17.4). This
>> set up works for me (including pymol etc)
>>
>> good luck
>>
>> Nikos
>>
>> Dr. Nikos Pinotsis
>> Institute of Structural and Molecular Biology
>> Department of Biological Sciences, 3rd Floor, R313
>> Birkbeck College
>> Malet Street
>> London WC1E 7HX
>> T: +44 (0)207 631 6827 <+44%2020%207631%206827>
>> F: +44 (0)207 631 6803 <+44%2020%207631%206803>
>> M: +44 (0)792 384 3593 <+44%207923%20843593>
>>
>> On 06/04/2017 09:59, POHL, EHMKE wrote:
>>
>> Dear ccp4 community,
>>
>>I would appreciate any suggestions how to get the ccp4 interfaces
>> (ccp4 and ccp4i2) and coot running on the new MacBook Pro under macOS
>> Sierra 10.12.3. control. I have already tried different Xquartz version
>> with no success
>>
>> thanks so much
>>
>> Ehmke
>>
>>
>>
>
>
> --
> Didier Spittler, PhD
> Phone number : +33658576481 <+33%206%2058%2057%2064%2081>
>

Re: [ccp4bb] Ligand building in real space

[Paul Emsley]

To answer your question...

On 10/04/17 08:44, Mohamed Noor wrote:


Is it possible to directly build a ligand in real space (in Coot?) and then 
generate a SMILES string for restraint generation.


I think that you are describing a 3D editor. It is not possible to do 
this in Coot (Coot's molecular editor is 2D).  If you want to use Coot I 
would do as Johannes says, use File -> Get Monomer.


PG4 (first choice), PGE, PEG, PE8. These are fun to refine in Coot, they 
wriggle around.


I think that SMILES is a bit of side-issue.



I am already using Polder and omit maps that confirm these are not noise.



:-)

Paul.

[ccp4bb] 4th ReNaFoBiS Integrated Structural Biology School. Oléron, June 16-23

[VIE]

 
4th ReNaFoBiS Integrated Structural Biology School. Oléron, June 16-23There are 
still some limited places available for this school that will take place on the 
Oléron island (France), from June 16 to June 23, 2017. The main objective of 
this workshop is to offer a theoretical and practical training in the different 
techniques used in integrative structural biology (X-ray diffraction, Small 
angle X-ray scattering, NMR, cryo-electron microscopy, biophysical methods and 
macromolecular interactions.) The goals are to explain and illustrate, to an 
audience mainly composed of doctoral students and young researchers, the 
contributions and limitations of each method with a strong emphasis on their 
complementarity and future developments. The school include theoretical 
sessions in the morning and practical training in the afternoon.The official 
language of the workshop is French but presentations may be given in English, 
depending on the overall profile of the students. For practical’s, English and 
French speaking groups may be organized.

Deadline for registration: April 17, 2017 (maximum number of participants: 25)
https://ecolebios2017.sciencesconf.org/
More information on the French Initiative ReNaFoBiS : http://www.renafobis.fr/

 
4ème École de Biologie Structurale Intégrative
Oléron – du 16 au 23 juin 2017
Il reste quelques places pour la 4ème École de Biologie Structurale 
Intégrative. Cette quatrième école propose une formation théorique et appliquée 
aux différentes approches utilisées en biologie structurale (diffraction et 
diffusion des rayons X, RMN, cryo-microscopie, méthodes d'études et de 
caractérisations des interactions macromoléculaires).
Elle mettra l’accent sur l’intégration de plusieurs de ces méthodes pour 
répondre aux grandes questions de la biologie fonctionnelle à l’échelle 
cellulaire.Pour un public de doctorants ou de jeunes chercheurs, cette 
formation montrera les apports et les limites de chaque méthode et leur 
complémentarité. Elle inclura des sessions théoriques le matin et des travaux 
pratiques en groupes l’après-midi. Les conférences seront données 
principalement en français. Les supports des présentations seront en anglais, 
afin de permettre aux participants non-francophones de suivre plus facilement. 
Lors des sessions pratiques (TP), des groupes anglophones pourront être 
proposés si besoin.

Date limite pour les inscriptions : 17 avril 2017
https://ecolebios2017.sciencesconf.org/
Plus d’information sur le réseaun RéNaFoBiS
http://www.renafobis.fr/
 
 
 



Jean Cavarelli
Professor of Structural Biology
Tél : +33 (0)3 69 48 52 74
jean.cavare...@unistra.fr
Structural Biology of Epigenetic Targets
Integrated Structural Biology Department
IGBMC. UMR7104 CNRS-UDS, INSERM U964.
F - 67404 Illkirch

[ccp4bb] Post-Doc in RNA-Protein interactions

[Marco Marcia]

Dear all
We are looking for a researcher to explore the druggability of 
RNA-protein interactions with small molecule compounds. The successful 
candidate will identify and characterize novel, disease-implicated 
RNA-protein interactions, establishing and conducting assays to target 
those interactions pharmacologically.
This project is a collaboration between Cellzome-GSK and two leading 
research groups in the field of RNA-protein interaction: the group of 
Matthias Hentze (EMBL-Heidelberg) and the group of Marco Marcia (EMBL 
Grenoble).
This project offers the opportunity to work in multi-disciplinary, 
international teams in Heidelberg-Germany (Cellzome and EMBL) and in 
Grenoble, France (EMBL) and to explore modern drug discovery approaches 
(GSK).
The ideal candidate will possess a PhD-level background in RNA 
biochemistry and an outstanding scientific track record, proven by high 
impact publications in peer-reviewed international journals. Experience 
in genomics or proteomics will be of advantage.
Applicants should send their CV summarizing qualifications and 
experience, including the names and addresses of two referees to:


Dr. Marco Marcia
mmar...@embl.fr


Kind regards,

--
_

Dr. Marco MARCIA
Group Leader
EMBL Grenoble
71 Avenue des Martyrs, room 254
38042 Grenoble Cedex 09
France
phone (lab): 0033-(0)47620-7634/7040
phone (office): 0033-(0)47620-7759
fax: 0033-(0)47620-7199
email: mmar...@embl.fr
web: https://embl.fr/research/unit/marcia/



Project ad druggability RNA-Protein interactions .pdf
Description: application/acrobat

Re: [ccp4bb] Structure comparison

[Tanner, John J.]

TM-align is used in the protein structure prediction community.

-Jack Tanner

Sent from Jack's iPhone

> On Apr 10, 2017, at 8:45 PM, Goldman, Adrian  
> wrote:
> 
> The right people to look at for this are found in the structure prediction 
> community; a series of algorithms were developed to compare different 
> predictions of the same structure.  Look for papers from about CASP-3 (John 
> Mount) or pick up any recent CASP and look at how they compare the different 
> predictions and follow the literature back.
> 
> Adrian
> 
> 
>> On 10 Apr 2017, at 00:44, Gert Vriend  wrote:
>> 
>> Arthur Lesk (at Penn state Univ, I think)m is the only one I know who has 
>> worked on this topic. I suggest you ask him. The topic you elude to is 
>> commonly known as the Russian Doll Effect.
>> 
>> If you want to discuss the topic, feel free to Skype me.
>> 
>> Greetings
>> 
>> Gert Vriend
>> 
>> 
>>> On 10-4-2017 1:37, Reza Khayat wrote:
>>> Hi,
>>> 
>>> My initial e-mail may have been a bit vague so I'll try to be more 
>>> specific. Superposing the structures and comparing them against one 
>>> another, while appropriate, is a subjective way to do the analysis as I 
>>> would have to subjectively define a threshold that would indicate a 
>>> difference between the structures. My threshold may be grossly different 
>>> than someone else's threshold. I am interested in an objective criterion. 
>>> One where strong emphasis has been put on error analysis and error modeling 
>>> in terms of both the refined structure and the underlying data. I realize 
>>> that defining such criterion is by no means trivial. Thanks again for the 
>>> help.
>>> 
>>> Best wishes,
>>> Reza
>>> 
>>> Reza Khayat, PhD
>>> Assistant Professor
>>> City College of New York
>>> Department of Chemistry
>>> New York, NY 10031
>>> 
>>> 
>>> From: Reza Khayat
>>> Sent: Sunday, April 9, 2017 6:07 PM
>>> To: CCP4 bulletin board
>>> Subject: Structure comparison
>>> 
>>> Hi,
>>> 
>>> I have refined several structures of a protein from different space groups 
>>> and would like to compare them to one another. Is there a program/software 
>>> suite that would provide an objective comparison of the structures and 
>>> identify regions where the structures are sufficiently different from one 
>>> another to warrant a closer look? I think the most important aspect of the 
>>> analysis would be defining a threshold (possibly based on resolution and 
>>> structure statistics) that would identify sufficient difference between 
>>> structures. Thanks.
>>> 
>>> Best wishes,
>>> Reza
>>> 
>>> Reza Khayat, PhD
>>> Assistant Professor
>>> City College of New York
>>> Department of Chemistry
>>> New York, NY 10031

Re: [ccp4bb] Structure comparison

[Goldman, Adrian]

The right people to look at for this are found in the structure prediction 
community; a series of algorithms were developed to compare different 
predictions of the same structure.  Look for papers from about CASP-3 (John 
Mount) or pick up any recent CASP and look at how they compare the different 
predictions and follow the literature back.

Adrian


> On 10 Apr 2017, at 00:44, Gert Vriend  wrote:
> 
> Arthur Lesk (at Penn state Univ, I think)m is the only one I know who has 
> worked on this topic. I suggest you ask him. The topic you elude to is 
> commonly known as the Russian Doll Effect.
> 
> If you want to discuss the topic, feel free to Skype me.
> 
> Greetings
> 
> Gert Vriend
> 
> 
> On 10-4-2017 1:37, Reza Khayat wrote:
>> Hi,
>> 
>> My initial e-mail may have been a bit vague so I'll try to be more specific. 
>> Superposing the structures and comparing them against one another, while 
>> appropriate, is a subjective way to do the analysis as I would have to 
>> subjectively define a threshold that would indicate a difference between the 
>> structures. My threshold may be grossly different than someone else's 
>> threshold. I am interested in an objective criterion. One where strong 
>> emphasis has been put on error analysis and error modeling in terms of both 
>> the refined structure and the underlying data. I realize that defining such 
>> criterion is by no means trivial. Thanks again for the help.
>> 
>> Best wishes,
>> Reza
>> 
>> Reza Khayat, PhD
>> Assistant Professor
>> City College of New York
>> Department of Chemistry
>> New York, NY 10031
>> 
>> 
>> From: Reza Khayat
>> Sent: Sunday, April 9, 2017 6:07 PM
>> To: CCP4 bulletin board
>> Subject: Structure comparison
>> 
>> Hi,
>> 
>> I have refined several structures of a protein from different space groups 
>> and would like to compare them to one another. Is there a program/software 
>> suite that would provide an objective comparison of the structures and 
>> identify regions where the structures are sufficiently different from one 
>> another to warrant a closer look? I think the most important aspect of the 
>> analysis would be defining a threshold (possibly based on resolution and 
>> structure statistics) that would identify sufficient difference between 
>> structures. Thanks.
>> 
>> Best wishes,
>> Reza
>> 
>> Reza Khayat, PhD
>> Assistant Professor
>> City College of New York
>> Department of Chemistry
>> New York, NY 10031

Re: [ccp4bb] Ligand building in real space

[Johannes Cramer]

Hey Mohamed,

I am not sure, if this is what you want, but you can import different PEG
molecules from coot's "File-> Get monomer". A list of different length PEGs
three letter codes can be found on page 1278 of this paper:

Naschberger et al., (2016) http://doi.org/10.1107/S205979831601723X.

I think you must have ccp4 installed, for this to work, but I am not 100%
sure.

Cheers,
Johannes


2017-04-10 9:44 GMT+02:00 Mohamed Noor :

> Dear all
>
> Is it possible to directly build a ligand in real space (in Coot?) and
> then generate a SMILES string for restraint generation. I have some unknown
> blobs in my density where they look like PEG molecules but these do not
> really fit the density (local CC of 0.7).
>
> I am already using Polder and omit maps that confirm these are not noise.
>
> Thanks.
> Mohamed
>

[ccp4bb] Ligand building in real space

[Mohamed Noor]

Dear all

Is it possible to directly build a ligand in real space (in Coot?) and then 
generate a SMILES string for restraint generation. I have some unknown blobs in 
my density where they look like PEG molecules but these do not really fit the 
density (local CC of 0.7).

I am already using Polder and omit maps that confirm these are not noise.

Thanks.
Mohamed