Re: [ccp4bb] water at the same exactly position

[Nat Echols]

On Wed, Oct 29, 2014 at 8:53 PM, luzuok  wrote:

> I think it is better for COOT to solve this issue.
>

Coot already can be used to solve this issue - I think the automation is
somewhat lacking, but it's vastly preferable to anything involving a text
editor or shell commands.

1. Load molecule and electron density maps in Coot
2. From the "Validate" menu, select "Check/Delete waters..."
3. Just select for waters with very close distances, for example 0.2Å; I've
attached a screenshot of what it should look like.
4. This will give you a list of overlapping waters - then you just need to
delete one of each pair.  (It doesn't matter which one - the waters will be
renumbered later anyway.)

Alternately, you can set "Action" to "Delete", which is much less effort,
but that will delete both copies.  If you are just going to run a program
(or Coot function) to place more waters automatically (my preference), this
won't matter, but if they're atoms you really care about, you should delete
them manually.

-Nat

[image: Inline image 1]

Re: [ccp4bb] water at the same exactly position

[Ed Pozharski]

Why? Merging waters like that in coot is a user error, and it does not happen 
too often.  I realize you are talking about changeable settings, but it would 
be really annoying if a refinement program kept removing water molecules that 
were placed manually because it does not fit some internal standard. Adding 
waters by default may obscure density that is due to other components.

I just feel one should be careful when changing chemical compositon of a model. 
That is something algorithms do not (yet) do well. 


Sent on a Sprint Samsung Galaxy S® III

 Original message From: Pavel Afonine 
 Date:10/30/2014  12:27 AM  (GMT-05:00) 
To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] water at 
the same exactly position 
This conversation makes me more and more certain that water update 
(add/remove/refine water) done as part of (a default) refinement run is a good 
idea -:)

Pavel

On Wed, Oct 29, 2014 at 5:08 AM, luzuok  wrote:
Dear all,
I found that there are some water molecules in my pdb that share the same 
position. This maybe cause by merging molecules in coot. It seems that I have 
mereged water molecules into my protein for more than one time. 
Does anyone tell me how to fix this problem?

Best regards!
Lu Zuokun




--
卢作焜
南开大学新生物站A202

Re: [ccp4bb] water at the same exactly position

[Edward A. Berry]

That is a different question- I thought you already knew which atoms are 
duplicates.
To identify them, there are programs that will print a list of pairs of atoms 
within
a threshold distance from each other.
But in this case I think plain old "sort" program will be easiest.

1. Get all the waters in one file
  grep HOH mypdb.pdb >waters1.pdb
(or awk '$1~/HETATM/ && $4~/HOH/' mypdb.pdb > waters1.pdb)
   (may need to adjust depending what you call the waters)

2. sort -nk7 waters1.pdb >! waters2.pdb
  This will sort the atoms on the X-coord value, so identically positioned 
water will be adjacent in the file.

3. go through waters2.pdb with a text editor, looking at the 7'th column, find 
pairs or clusters of adjacent lines with the same x,y,z values, and delete all 
but one such line in each group.

4. This is still pdb format, so you can merge the remaining atoms into your pdb 
file with the waters removed by something like
awk '$1!~/HETATM/ || $4!~/HOH/' mypdb.pdb > nowaters.pdb)

The awk and sort commands here assume you have a plain vanilla pdb file with no 
alternate conformations, insertion codes, and less than  atoms, with chain 
letter, so that the X coordinate is the 7th column. And no anisou records for 
the waters. See recent discussion on advisability of using shell commands vs 
custom tools for modifying pdb files.


On 10/29/2014 11:53 PM, luzuok wrote:

Dear Nicolas,
It is really time-consuming! Philip told me to run the structure on PDB 
validation server. It will post error if there is duplicate molecules. Then I 
can directly find them on a text editor.
I think it is better for COOT to solve this issue.

Best reagards!
Lu zuokun



--
卢作焜
南开大学新生物站A202


在 2014-10-29 22:29:35，"FOOS Nicolas"  写道：

Dear Lu,

one simple solution is to remove the water molecules with text editor for 
example. It depend of how-many times you have multiply water molecules and if 
your model have several or more water molecules.
In coot you can remove it graphically, but according to my knowledge not 
automatically, and it maybe time consuming.

Hope to help
Nicolas


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de luzuok 
[luzuo...@126.com]
Envoyé : mercredi 29 octobre 2014 13:08
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] water at the same exactly position

Dear all,
I found that there are some water molecules in my pdb that share the same 
position. This maybe cause by merging molecules in coot. It seems that I have 
mereged water molecules into my protein for more than one time.
Does anyone tell me how to fix this problem?

Best regards!
Lu Zuokun




--
卢作焜
南开大学新生物站A202

Re: [ccp4bb] water at the same exactly position

[Pavel Afonine]

This conversation makes me more and more certain that water update
(add/remove/refine water) done as part of (a default) refinement run is a
good idea -:)

Pavel

On Wed, Oct 29, 2014 at 5:08 AM, luzuok  wrote:

> Dear all,
> I found that there are some water molecules in my pdb that share the
> same position. This maybe cause by merging molecules in coot. It seems that
> I have mereged water molecules into my protein for more than one time.
> Does anyone tell me how to fix this problem?
>
> Best regards!
> Lu Zuokun
>
>
>
>
> --
> 卢作焜
> 南开大学新生物站A202
>
>
>

Re: [ccp4bb] water at the same exactly position

[luzuok]

Dear Nicolas,
It is really time-consuming!  Philip told me to run the structure on PDB 
validation server. It will post error if there is duplicate molecules. Then I 
can directly find them on a text editor.
I think it is better for COOT to solve this issue.


Best reagards!
Lu zuokun




--
卢作焜
南开大学新生物站A202



在 2014-10-29 22:29:35，"FOOS Nicolas"  写道：
>Dear Lu,
>
>one simple solution is to remove the water molecules with text editor for 
>example. It depend of how-many times you have multiply water molecules and if 
>your model have several or more water molecules.
>In coot you can remove it graphically, but according to my knowledge not 
>automatically, and it maybe time consuming.
>
>Hope to help
>Nicolas
>
>
>De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de luzuok 
>[luzuo...@126.com]
>Envoyé : mercredi 29 octobre 2014 13:08
>À : CCP4BB@JISCMAIL.AC.UK
>Objet : [ccp4bb] water at the same exactly position
>
>Dear all,
>I found that there are some water molecules in my pdb that share the same 
> position. This maybe cause by merging molecules in coot. It seems that I have 
> mereged water molecules into my protein for more than one time.
>Does anyone tell me how to fix this problem?
>
>Best regards!
>Lu Zuokun
>
>
>
>
>--
>卢作焜
>南开大学新生物站A202
>

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

[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.

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

100-0004

Tel: +81-3-62623563

Fax: +81-3-6262-3577



www.jeol.com

Sent from my iPad

On 2014/10/30, at 午前12:36, "Thomas, Leonard M." 
mailto: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.edu
http://barlywine.chem.ou.edu
http://structuralbiology.ou.edu

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] 
on behalf of Ioan Vancea 
[ivan...@embl-hamburg.de]
Sent: Wednesday, October 29, 2014 10:00 AM
To: 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.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_XtalUnit

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

[Anindito Sen]

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.
>> 2-1-1 Ohtemachi, Chiyoda-ku, Tokyo
>> 100-0004
>> Tel: +81-3-62623563
>> Fax: +81-3-6262-3577
>> 
>> 
>> www.jeol.com


Sent from my iPad

On 2014/10/30, at 午前12:36, "Thomas, Leonard M."  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.edu
> http://barlywine.chem.ou.edu
> http://structuralbiology.ou.edu
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Ioan Vancea 
> [ivan...@embl-hamburg.de]
> Sent: Wednesday, October 29, 2014 10:00 AM
> To: 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.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_XtalUnit

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

[Thomas, Leonard M.]

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.edu
http://barlywine.chem.ou.edu
http://structuralbiology.ou.edu

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Ioan Vancea 
[ivan...@embl-hamburg.de]
Sent: Wednesday, October 29, 2014 10:00 AM
To: 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.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_XtalUnit

Re: [ccp4bb] XDS

[Almudena Ponce Salvatierra]

Thank you all for the suggestions.

What worked better for me was to run XDS with different batches of images
and to merge them later with XSCALE.

Best,

Almudena

2014-09-29 11:56 GMT+02:00 Almudena Ponce Salvatierra 
:

> Dear all,
>
> I would like to ask something regarding XDS. Is it possible, without
> changing the Name of the Frames, to leave some out while processing?
>
> i.e. something like defining twice the data range
> DATA_RANGE= 1 900
> !DATA_RANGE= 901 1000
> DATA_RANGE= 1001 1200
>
> Is there a way to do so? to leave out wedges like this? I have tried like
> so, but I have the Impression it only takes then the last number of Frames,
> in this example it would only take 1001 to 1200.
>
> Thanks a lot.
>
> Best wishes,
>
> Almudena
> --
> Almudena Ponce-Salvatierra
> Macromolecular crystallography and Nucleic acid chemistry
> Max Planck Institute for Biophysical Chemistry
> Am Fassberg 11 37077 Göttingen
> Germany
>
>


-- 
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany

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

[Sebastiano Pasqualato]

Thanks Mark,
that solved the problem.

Thanks also to Ioan, Engin and Jochen, who replied with similar solutions.

Best,
ciao,
S


> On 29 Oct 2014, at 15:56, Mark Brooks  wrote:
> 
> Try reinstalling X-quartz.
>  
> IIRC, /usr/X11R6 is deleted during MacOS upgrades.
>  
> Mark
> 
> On 29 October 2014 14:45, Sebastiano Pasqualato 
> mailto:sebastiano.pasqual...@gmail.com>> 
> 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_XtalUnit 
> 
> 
> 
> 
> 
> 
> 
> ___
> phenixbb mailing list
> pheni...@phenix-online.org 
> http://phenix-online.org/mailman/listinfo/phenixbb 
> 
> 
> 

-- 
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_XtalUnit

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

[Ioan Vancea]

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.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_XtalUnit

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

[Mark Brooks]

Try reinstalling X-quartz.

IIRC, /usr/X11R6 is deleted during MacOS upgrades.

Mark

On 29 October 2014 14:45, Sebastiano Pasqualato <
sebastiano.pasqual...@gmail.com> 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_XtalUnit
>
>
>
>
>
>
>
> ___
> phenixbb mailing list
> pheni...@phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>

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

[Sebastiano Pasqualato]

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_XtalUnit

Re: [ccp4bb] water at the same exactly position

[FOOS Nicolas]

Dear Lu,

one simple solution is to remove the water molecules with text editor for 
example. It depend of how-many times you have multiply water molecules and if 
your model have several or more water molecules.
In coot you can remove it graphically, but according to my knowledge not 
automatically, and it maybe time consuming.

Hope to help
Nicolas


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de luzuok 
[luzuo...@126.com]
Envoyé : mercredi 29 octobre 2014 13:08
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] water at the same exactly position

Dear all,
I found that there are some water molecules in my pdb that share the same 
position. This maybe cause by merging molecules in coot. It seems that I have 
mereged water molecules into my protein for more than one time.
Does anyone tell me how to fix this problem?

Best regards!
Lu Zuokun




--
卢作焜
南开大学新生物站A202

[ccp4bb] water at the same exactly position

[luzuok]

Dear all,
I found that there are some water molecules in my pdb that share the same 
position. This maybe cause by merging molecules in coot. It seems that I have 
mereged water molecules into my protein for more than one time. 
Does anyone tell me how to fix this problem?


Best regards!
Lu Zuokun





--
卢作焜
南开大学新生物站A202

Re: [ccp4bb] "modeling" flexible ends on proteins

[Tommi Kajander]

Hi, thanks for all the answers, i will try to wrap up some conclustion once i 
have tested things.

Best
Tommi


On Oct 24, 2014, at 7:09 PM, Tim Gruene wrote:

> Hi Tommi,
> 
> I used Molscript to place a dotted line in the gap. This shows clearly
> from where to where the gap goes and that the data don't show
> interpretable density in that region.
> 
> I would call everything else 'tabloid science'.
> 
> Cheers,
> Tim
> 
> On 10/24/2014 04:11 PM, Michal Jamroz wrote:
>> Dnia 2014-10-22, o godz. 15:43:18
>> Tommi Kajander  napisał(a):
>> 
>>> Would anyone know a software to model (just with some kind of random
>>> coil) the amino acid chain for the assumed flexible disorderd regions
>>> between domains, or at one end of protein? just for illustrative
>>> purposes.
>> 
>> Hi Tommi,
>> 
>> check CABSflex: http://biocomp.chem.uw.edu.pl/CABSflex
>> You can simply put there PDB code of considered structure and get info
>> about flexibility, native-state dynamics movie, etc.
>> 
>> Michał
>> 
> 
> -- 
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A
> 


Tommi Kajander, Ph.D.
Team Leader
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1 (P.O. Box 65)
00014 Helsinki
Finland
p. +358-50-4480991
tommi.kajan...@helsinki.fi
http://www.biocenter.helsinki.fi/bi/kajander/