[ccp4bb] ccp4-7.0 for windows

2018-02-01 Thread Andrey Lebedev 
Dear CCP4 users

A new ccp4-7.0 installer for Windows is now available:
http://www.ccp4.ac.uk/download/index.php#os=windows
- consolidates updates 1-50
- includes Coot and SHELX as optional components (do not forget to
register at SHELX web site).

Best wishes
Andrey

Re: [ccp4bb] definition of "apo" and alternatives?

2018-02-01 Thread Roman Fedorov 
Dear Colleagues,

   I wish to apologise for any offence that may have been caused by the 
inappropriate content of the email from Johannes Cramer, which does not 
represent the views of the rest of our research group.

With kind regards,

Roman Fedorov

Re: [ccp4bb] cavities in protein structures

2018-02-01 Thread Fulvio Saccoccia 

You can try VOIDOO as well:

http://xray.bmc.uu.se/usf/voidoo.html

a bit dated but still effective

Cheers, Fulvio


Il 01/02/18 09:54, Claudia Binda ha scritto:

Dear All,

thanks everyone for your help.
Below is a summary of all suggestions for calculating and representing 
cavities of protein structures.

Best
Claudia


Caver (https://www.caver.cz/)

3V (http://3vee.molmovdb.org)

ProFunc (https://www.ebi.ac.uk/thornton-srv/databases/profunc/)

Ghecom (http://strcomp.protein.osaka-u.ac.jp/ghecom/)

using pymol with no other plug-ins required

CastP (http://sts.bioe.uic.edu/castp/index.html)

Metapocket (http://projects.biotec.tu-dresden.de/metapocket/)

Hollow (http://hollow.sourceforge.net/)


2018-01-30 14:55 GMT+01:00 Johannes Cramer >:


Hi Claudia,

another program that I used with success is Hollow
(https://www.ncbi.nlm.nih.gov/pubmed/19014592
).
It is really easy to use. You can get is here
http://hollow.sourceforge.net/ 
It finds pockets in a defined area, fills them with water
molecules and generates a pdb with those waters. You can then
import it into pymol and represent it however you think is fitting.

Cheers,
Johannes

2018-01-30 14:20 GMT+01:00 Vipul Panchal >:

Hi Claudia,
For the identification of cavities and residues linning them,
metapocket is one of the preferred choice as it uses
prediction from various program.
Output of the server is pdb file.

I found caver program represent cavities in a best manner.
There is caver plugin available for pymol. Output is tunnel
like representation with different colours. Interestingly, it
also provides tunnel length, radius and list of residues
linning the bottle-neck of each of the cavity. As a input for
the presentation of cavities, you need to provide list of
residues lining cavities. Identified by other programs.

All the best!


On 30-Jan-2018 6:28 PM, "Boaz Shaanan" > wrote:

Hi Claudia,

Another possibility is CastP:
http://sts.bioe.uic.edu/castp/index.html


They also have a Pymol plugin. I have not used this plugin
since I'm displaying the CastP o/p files in UCSF-chimera
which handles them nicely.


Cheers,


            Boaz


/Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il 
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710 /
//
//
/

/




*From:* CCP4 bulletin board > on behalf of Claudia Binda
>
*Sent:* Tuesday, January 30, 2018 1:51 PM
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* [ccp4bb] cavities in protein structures
Hi everyone,

I need suggestions to calculate and represent cavities of
protein structures. For years I have been using Voidoo
that produces maps in ezd format which could be converted
in map format (ccp4) using the online server
http://xray.bmc.uu.se/cgi-bin/gerard/mapman_server.pl
.
However, this does not work anymore. Is there another way
to do it? What is the best tool to calculate cavities and
draw them by Pymol or ccp4mg?

Thank you
Claudia







-- 
Claudia Binda

University of Pavia
Dept. Biology and Biotechnology
via Ferrata 1, 27100 Pavia - Italy
Phone: +39-0382-985535 
Fax: +39-0382-528496 
E-mail: claudia.bi...@unipv.it 
Web: http://www.unipv.it/biocr 





--
Claudia Binda
University of Pavia
Dept. Biology and Biotechnology
via Ferrata 1, 27100 Pavia - Italy
Phone: +39-0382-985535
Fax: +39-0382-528496
E-mail: claudia.bi...@unipv.it 
Web: http://www.unipv.it/biocry

Re: [ccp4bb] cavities in protein structures

2018-02-01 Thread Claudia Binda 
Dear All,

thanks everyone for your help.
Below is a summary of all suggestions for calculating and representing
cavities of protein structures.
Best
Claudia


Caver (https://www.caver.cz/)

3V (http://3vee.molmovdb.org)

ProFunc (https://www.ebi.ac.uk/thornton-srv/databases/profunc/)

Ghecom (http://strcomp.protein.osaka-u.ac.jp/ghecom/)

using pymol with no other plug-ins required

CastP (http://sts.bioe.uic.edu/castp/index.html)

Metapocket (http://projects.biotec.tu-dresden.de/metapocket/)

Hollow (http://hollow.sourceforge.net/)


2018-01-30 14:55 GMT+01:00 Johannes Cramer :

> Hi Claudia,
>
> another program that I used with success is Hollow (
> https://www.ncbi.nlm.nih.gov/pubmed/19014592).
> It is really easy to use. You can get is here http://hollow.
> sourceforge.net/
> It finds pockets in a defined area, fills them with water molecules and
> generates a pdb with those waters. You can then import it into pymol and
> represent it however you think is fitting.
>
> Cheers,
> Johannes
>
> 2018-01-30 14:20 GMT+01:00 Vipul Panchal :
>
>> Hi Claudia,
>> For the identification of cavities and residues linning them, metapocket
>> is one of the preferred choice as it uses prediction from various program.
>> Output of the server is pdb file.
>>
>> I found caver program represent cavities in a best manner. There is caver
>> plugin available for pymol. Output is tunnel like representation with
>> different colours. Interestingly, it also provides tunnel length, radius
>> and list of residues linning the bottle-neck of each of the cavity. As a
>> input for the presentation of cavities, you need to provide list of
>> residues lining cavities. Identified by other programs.
>>
>> All the best!
>>
>>
>> On 30-Jan-2018 6:28 PM, "Boaz Shaanan"  wrote:
>>
>> Hi Claudia,
>>
>> Another possibility is CastP: http://sts.bioe.uic.edu/castp/index.html
>>
>> They also have a Pymol plugin. I have not used this plugin since I'm
>> displaying the CastP o/p files in UCSF-chimera which handles them nicely.
>>
>>
>> Cheers,
>>
>>
>> Boaz
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *Boaz Shaanan, Ph.D. Dept. of
>> Life Sciences  Ben-Gurion University of
>> the Negev  Beer-Sheva
>> 84105
>> Israel
>> E-mail:
>> bshaa...@bgu.ac.il  Phone: 972-8-647-2220  Skype:
>> boaz.shaanan  Fax:   972-8-647-2992 or 972-8-646-1710*
>>
>>
>>
>>
>>
>>
>>
>> --
>> *From:* CCP4 bulletin board  on behalf of Claudia
>> Binda 
>> *Sent:* Tuesday, January 30, 2018 1:51 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [ccp4bb] cavities in protein structures
>>
>> Hi everyone,
>>
>> I need suggestions to calculate and represent cavities of protein
>> structures. For years I have been using Voidoo that produces maps in ezd
>> format which could be converted in map format (ccp4) using the online
>> server http://xray.bmc.uu.se/cgi-bin/gerard/mapman_server.pl. However,
>> this does not work anymore. Is there another way to do it? What is the best
>> tool to calculate cavities and draw them by Pymol or ccp4mg?
>>
>> Thank you
>> Claudia
>>
>>
>>
>>
>>
>>
>>
>> --
>> Claudia Binda
>> University of Pavia
>> Dept. Biology and Biotechnology
>> via Ferrata 1, 27100 Pavia - Italy
>> Phone: +39-0382-985535 <+39%200382%20985535>
>> Fax: +39-0382-528496 <+39%200382%20528496>
>> E-mail: claudia.bi...@unipv.it
>> Web: http://www.unipv.it/biocr 
>>
>>
>


-- 
Claudia Binda
University of Pavia
Dept. Biology and Biotechnology
via Ferrata 1, 27100 Pavia - Italy
Phone: +39-0382-985535
Fax: +39-0382-528496
E-mail: claudia.bi...@unipv.it
Web: http://www.unipv.it/biocry