[ccp4bb] Putting ligand in the protein structure

2008-09-30 Thread Anshul Awasthi
Hi all the crystallographers,

I am trying to solve a structure of a protein with some inhibitor. I want to
know how I can put in my inhibitor in the density map of the data i got. I
can see some density in the active site where the  inhibitor should be. I
generated the topoly file of the inhibitor (in both pdba nd refmac5 top
formats) from the Dundee PRODRG server. Now do i need to incorporate the
structure of the inhibitor in ccp4 or can i do in coot?? I am not sure of
how to do it. 

ANy sugegstion will be very valuable for me.


[ccp4bb] PhD Position at Structural Biology Brussels

2008-09-30 Thread Wim Versees
A PhD Position in Structural Biology is available at Structural Biology 
Brussels, 
Vrije Universiteit Brussel, Belgium.


We are looking for a highly motivated PhD student interested in biochemical 
and structural studies on tRNA modifying enzymes and enzyme complexes. The 
Structural Biology Brussels laboratory (for more info: 
http://www.structuralbiology.be/) is located at the Free University of Brussels 
and is affiliated with the Flanders Institute for Biotechnology (VIB). 

Project description:

Transfer RNA (tRNA) molecules are pivotal in the translation of the genetic 
code into protein sequences. In this process, the recognition of the mRNA 
codon by the correct tRNA does not solely dependent on the primary sequence 
of the tRNA molecule. Rather, around 100 different posttranscriptional 
nucleoside modifications have been described, particularly in the anticodon 
loop, that can modify cognate codon recognition, stabilize the codon-
anticodon wobble base pairing and/or affect aminoacylation properties. The 
current project will deal with the study of the structure/function relationship 
of tRNA modifying enzymes from both prokaryotic and eukaryotic origin. To 
study these often multi-subunit complexes and the interaction with their tRNA 
substrates, an integrated approach of X-ray crystallography, enzyme kinetics 
and different biophysical methods to study the protein-protein and protein-
nucleic acid interactions, will be used.


The position is available immediately

Candidates should have a recent Masters degree in Biochemistry, Biology, 
Chemistry or related. Skills in either molecular biology or protein chemistry  
purification or protein crystallography would be an asset. 
Please send applications (including CV, research experience, and at least two 
names and contact information for references) to:

Wim Versées, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 
2, 
1050 Brussel - [EMAIL PROTECTED]


Re: [ccp4bb] Putting ligand in the protein structure

2008-09-30 Thread George Kontopidis
You need protein structure, a different e. density map (1Fo-1Fc) and your
ligand structure. Then from COOT menu select Other Modelling Tools and click
Find Ligand. You can also  move manually the ligand into the density map.

George 

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Anshul
Awasthi
Sent: Tuesday, September 30, 2008 10:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Putting ligand in the protein structure

Hi all the crystallographers,

I am trying to solve a structure of a protein with some inhibitor. I want to
know how I can put in my inhibitor in the density map of the data i got. I
can see some density in the active site where the  inhibitor should be. I
generated the topoly file of the inhibitor (in both pdba nd refmac5 top
formats) from the Dundee PRODRG server. Now do i need to incorporate the
structure of the inhibitor in ccp4 or can i do in coot?? I am not sure of
how to do it. 

ANy sugegstion will be very valuable for me.

No virus found in this incoming message.
Checked by AVG - http://www.avg.com 
Version: 8.0.173 / Virus Database: 270.7.5/1697 - Release Date: 29/9/2008
7:25 ìì


Re: [ccp4bb] Putting ligand in the protein structure

2008-09-30 Thread Eleanor Dodson

Yes:
 There are details in the coot manual

1) Get a dictionary for your ligand from PRODRG or somewhere. - you have 
obviously done this..


2) CHECK IT IS CORRECT!!! Right chirality, planar groups, etc..

3) Import dictionary into coot, and a set of coordinates.

4) Import 2mFo-Dfc and mFo-Dfc maps ( auto mtz from REFMAC will do this)

5) Hit find ligand.

6) Real space refine it - you might need to do some brutal gradding and 
shoving of bits..

Eleanor

George Kontopidis wrote:

You need protein structure, a different e. density map (1Fo-1Fc) and your
ligand structure. Then from COOT menu select Other Modelling Tools and click
Find Ligand. You can also  move manually the ligand into the density map.

George 


-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Anshul
Awasthi
Sent: Tuesday, September 30, 2008 10:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Putting ligand in the protein structure

Hi all the crystallographers,

I am trying to solve a structure of a protein with some inhibitor. I want to
know how I can put in my inhibitor in the density map of the data i got. I
can see some density in the active site where the  inhibitor should be. I
generated the topoly file of the inhibitor (in both pdba nd refmac5 top
formats) from the Dundee PRODRG server. Now do i need to incorporate the
structure of the inhibitor in ccp4 or can i do in coot?? I am not sure of
how to do it. 


ANy sugegstion will be very valuable for me.

No virus found in this incoming message.
Checked by AVG - http://www.avg.com 
Version: 8.0.173 / Virus Database: 270.7.5/1697 - Release Date: 29/9/2008

7:25 ìì



  


Re: [ccp4bb] CCP4i can NOT run

2008-09-30 Thread Yingjie Peng
Hi Iain,

Thanks for your reply. The path for tclsh is /usr/local/tcltkblt/bin/.
There are six files: bltsh, bltwish, tclsh, tclsh8.4, wish and wish8.4. The
tclsh
and wish are symbolic links for tclsh8.4 and wish8.4, respectively. For the
permission reason you mentioned, I have also tried this change:
sudo chown yjpeng:yjpeng -R /usr/local/tcltkblt
It does NOT work!

For better analysis, I paste my ccp4.setup file as following:
### THIS SECTION MUST BE EDITED #

# CCP4_MASTER is the location of the top-level directory containing
`ccp4-version'
# This is usually the directory in which you ran the tar command to unpack
the
# code, and is assumed to be shared between machines at a multi-machine
site.

setenv CCP4_MASTER/home/prog/ccp4-6.0.2
setenv CCP4$CCP4_MASTER/ccp4-6.0.2

# Check for existence of CCP4_MASTER
if (! -e $CCP4_MASTER) then
echo * WARNING **
echo The directory $CCP4_MASTER
echo (assigned to CCP4_MASTER) does not exist.
echo The CCP4 programs will not run correctly, and any
echo installation attempt will have errors or will fail.
echo * WARNING **
endif

# CCP4_SCR: a per-user directory for run-time-generated scratch
# files. A dedicated scratch filesystem is probably better than (/usr)/tmp
# BINSORT_SCR: a scratch directory for binsort's use; normally same as
CCP4_SCR

setenv CCP4_SCR  /data/tmp
# check to see if this exists and if not try to make it
if (! -e $CCP4_SCR) mkdir $CCP4_SCR
if (! -e $CCP4_SCR) \
echo Unable to make CCP4_SCR. CCP4 progs will not run correctly.

setenv BINSORT_SCR   $CCP4_SCR

### CCP4i setup - you may need to edit CCP4I_TCLTK ###
# CCP4I_TOP - the top directory of the interface
setenv CCP4I_TOP ${CCP4}/ccp4i
# CCP4I_TCLTK - directory containing tclsh,wish and bltwish executables
#   as used in $CCP4I_TOP/bin/ccp4i,ccp4ish,loggraph
#   For 'standard' installations this is /usr/local/bin
#   but note the SGI distributed version of Tcl/Tk is not
#   appropriate version
setenv CCP4I_TCLTK /usr/local/tcltkblt/bin
# CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help
setenv CCP4I_HELP ${CCP4I_TOP}/help

### Optional - setting http_proxy environment
# The commented out 'setenv' line below may have to be declared to download
# and edit protein sequences using the new Import/Edit Protein Sequences
# (This may also be required for remote job submission in arp/warp.)
# task. If so, uncomment this line and replace the example proxy URL with
your
# relevant URL

#setenv HTTP_PROXY wwwblah.blah.ac.uk:/blah.blah

### NOVICE USERS STOP HERE #

### OPTIONS TO CUSTOMISE CCP4 #

# By default, CCP4 directories are appended to the end of paths (PATH,
# LD_LIBRARY_PATH, and DYLD_LIBRARY_PATH). If ccp4_first_in_path is set
# to 1, then they will be prepended to the beginning of paths.
# When deciding local policy, bear in mind the possible existence of
# other CCP4 installations, and the possibility of non-CCP4 programs
# with conflicting names.
set ccp4_first_in_path = 1

# The commented-out switch statement below provides an example of how
# to use this file for several machines/architectures sharing $CCP4_MASTER.
# If necessary, uncomment and edit this.  Otherwise, if you're only
supporting
# a single system alter the uncommented part as necessary.
#
# The significance of the environment variables is as follows:
#   CBIN: location of the executables -- must be on your path (see below);
#   CLIB: location of (binary) library files such as libccp4.a and
libccp4.so;
#   MANPATH: set this if your system's `man' looks at such an environment
#  variable to determine where to look for man pages.  By adding
#  $CCP4/man to the normal path you get the CCP4 man pages
#  with keyword searching as system ones.
#   MCTYPE: used for LAUE make -- see LAUE documentation
#   CCP4_BROWSER: set this if you intend to use the html documentation
#  (recommended).  It should have the path and name of a html browser eg
#  /usr/bin/X11/netscape or /usr/local/bin/lynx. The browser will be
#  started with the alias ccp4help and will open the file
#  $CHTML/INDEX.html.

#   switch (`hostname`)# edit this switch statement if used
#   # for multiple systems
#   case 'foo':
setenv CBIN  $CCP4/bin
setenv CLIB  $CCP4/lib

setenv CCP4_BROWSER  firefox

if (${?MANPATH}) then
  if ($ccp4_first_in_path) then
setenv MANPATH ${CCP4}/man:${MANPATH}
  else
setenv MANPATH ${MANPATH}:${CCP4}/man
  endif
else
  if ($ccp4_first_in_path) then
setenv MANPATH ${CCP4}/man:/usr/share/man
  else
setenv MANPATH /usr/share/man:${CCP4}/man
  endif
endif
setenv MCTYPE

Re: [ccp4bb] cryo-protection for crystals grown in ethanol

2008-09-30 Thread Mark J. van Raaij

Dear Rongjin,

I would:
-prepare different cryosolutions, adding glycerol, replacing water  
with glycerol, replacing ethanol with other more cryogenic alcohols:  
if you have enough crystals, see how these behave when transferred to  
these solutions, if they crack, decrease precipitant, if they  
dissolve, increase.

once you have measurement time:
-first measure a couple of crystals in a capillary or mitegen loop  
and sleeve at room temperature to get a best case diffraction. On a  
home source you might even get a dataset, but surely you'll get good  
estimates of mosaic spread, spacegroup, and other crystallographic  
parameters, like for instance an idea about if the crystals may be  
twinned.
-then measure a couple of crystals directly frozen from the drop (i.e.  
worst-case scenario).
-then go for complete cryoprotected datasets, using the combined  
knowledge of previous experiments.
Even if the upcoming beamtime is not enough for all of this and you  
have to book more time in the coming weeks, I would go through all  
these steps and resist the temptation to go for quick and dirty. If  
you only ever measure at 100K you never know how good the crystals  
were before freezing.


Mark

Quoting Rongjin Guan [EMAIL PROTECTED]


Dear All

I got crystals from 20% Ethanol with 0.1M Tris pH 8.5. This is my first
time to have crystals in Ethanol and want to get some suggestions of
cryo-protection from those who have done this before.

I am waiting for my time on home X-ray facility, and hope I can get
some suggestions before that.

Thanks,

Rongjin Guan



[ccp4bb] precipitates

2008-09-30 Thread amit sharma
Dear CCP4bbers,
I am trying to crystallize a protein with a peptide attached to it via a 9aa
linker. I am mostly getting precipitates in conditions carrying salts. I
have tried optimization screens by varying the pH and salt concentrations,
but in vain. Can anyone please suggest ways by which I could optimize the
conditions further?

thanks in advance,

-- 
Amit Sharma


Re: [ccp4bb] CCP4i can NOT run

2008-09-30 Thread Ben Eisenbraun
On Tue, Sep 30, 2008 at 10:48:27AM +0800, Yingjie Peng wrote:
 I have installed the latest version of CCP4i under Fedora 9 on my laptop
 HP Compaq 6515b (two processors). The system setup was done and the CCP4i
 interface can run normally. But if I submit a job, it displayes
 STARTING the job in the job window and will NOT actually run the job.
 Also I can NOT kill the job with its status as STARTING.

I have seen similar behavior before.  Is your /etc/hosts correct?  The
localhost line should look like this:

127.0.0.1 localhost

Some of the CCP4 utilities act as miniature servers and bind to localhost
to communicate between the GUI and the process.  If this is actually the 
problem, you should see output in the shell that started ccp4i similar 
to this:

ERROR running script can not connect to server port (RunNotification)
SERVER_HOST  localhost SERVER_PORT 4441

-ben

--
Ben Eisenbraun
Structural Biology Grid   Harvard Medical School
http://sbgrid.org http://hms.harvard.edu


Re: [ccp4bb] CCP4i can NOT run

2008-09-30 Thread Yingjie Peng
I have checked /etc/hosts, it is similar to what you say. I also tried to
set it exactly the same as
yours. But it did NOT work. Thanks!

On Tue, Sep 30, 2008 at 10:24 PM, Ben Eisenbraun
[EMAIL PROTECTED]wrote:

 On Tue, Sep 30, 2008 at 10:48:27AM +0800, Yingjie Peng wrote:
  I have installed the latest version of CCP4i under Fedora 9 on my laptop
  HP Compaq 6515b (two processors). The system setup was done and the CCP4i
  interface can run normally. But if I submit a job, it displayes
  STARTING the job in the job window and will NOT actually run the job.
  Also I can NOT kill the job with its status as STARTING.

 I have seen similar behavior before.  Is your /etc/hosts correct?  The
 localhost line should look like this:

 127.0.0.1 localhost

 Some of the CCP4 utilities act as miniature servers and bind to localhost
 to communicate between the GUI and the process.  If this is actually the
 problem, you should see output in the shell that started ccp4i similar
 to this:

 ERROR running script can not connect to server port (RunNotification)
 SERVER_HOST  localhost SERVER_PORT 4441

 -ben

 --
 Ben Eisenbraun
 Structural Biology Grid   Harvard Medical School
 http://sbgrid.org http://hms.harvard.edu



Re: [ccp4bb] CCP4i can NOT run

2008-09-30 Thread Yingjie Peng
Hi Boaz,

Thanks for your suggestion. I have tried as you suggested. In my case,
CCP4_MASTER
can NOT set to be /home/prog.
The ccp4i did not launched because it can not locate the ccp4i.tcl file.



On Tue, Sep 30, 2008 at 8:53 PM, Boaz Shaanan [EMAIL PROTECTED] wrote:

 Your setup in ccp4.setup seems to be incorrect.
 You should have:
 setenv CCP4_MASTER/home/prog

 and then you would have:

 echo $CCP4  /home/prog/ccp4-6.0.2

  I don´t think your problem has anything to do with tcl setup.

Boaz

 - Original Message -
 From: Yingjie Peng [EMAIL PROTECTED]
 Date: Tuesday, September 30, 2008 15:45
 Subject: Re: [ccp4bb] CCP4i can NOT run
 To: CCP4BB@JISCMAIL.AC.UK

  Hi Iain,
 
  Thanks for your reply. The path for tclsh is
  /usr/local/tcltkblt/bin/.There are six files: bltsh, bltwish,
  tclsh, tclsh8.4, wish and wish8.4. The
  tclsh
  and wish are symbolic links for tclsh8.4 and wish8.4,
  respectively. For the
  permission reason you mentioned, I have also tried this change:
  sudo chown yjpeng:yjpeng -R /usr/local/tcltkblt
  It does NOT work!
 
  For better analysis, I paste my ccp4.setup file as following:
  ### THIS SECTION MUST BE EDITED #
 
  # CCP4_MASTER is the location of the top-level directory containing
  `ccp4-version'
  # This is usually the directory in which you ran the tar command
  to unpack
  the
  # code, and is assumed to be shared between machines at a multi-
  machinesite.
 
  setenv CCP4_MASTER/home/prog/ccp4-6.0.2
  setenv CCP4
  $CCP4_MASTER/ccp4-6.0.2
 
  # Check for existence of CCP4_MASTER
  if (! -e $CCP4_MASTER) then
  echo * WARNING
  **echo The directory
  $CCP4_MASTERecho (assigned to CCP4_MASTER)
  does not exist.
  echo The CCP4 programs will not run
  correctly, and any
  echo installation attempt will have errors
  or will fail.
  echo * WARNING
  **endif
 
  # CCP4_SCR: a per-user directory for run-time-generated scratch
  # files. A dedicated scratch filesystem is probably better than
  (/usr)/tmp# BINSORT_SCR: a scratch directory for binsort's use;
  normally same as
  CCP4_SCR
 
  setenv CCP4_SCR  /data/tmp
  # check to see if this exists and if not try to make it
  if (! -e $CCP4_SCR) mkdir $CCP4_SCR
  if (! -e $CCP4_SCR) \
  echo Unable to make CCP4_SCR. CCP4 progs
  will not run correctly.
 
  setenv BINSORT_SCR   $CCP4_SCR
 
  ### CCP4i setup - you may need to edit CCP4I_TCLTK ###
  # CCP4I_TOP - the top directory of the interface
  setenv CCP4I_TOP ${CCP4}/ccp4i
  # CCP4I_TCLTK - directory containing tclsh,wish and bltwish
  executables#   as used in
 $CCP4I_TOP/bin/ccp4i,ccp4ish,loggraph
  #   For 'standard' installations this is /usr/local/bin
  #   but note the SGI distributed version of Tcl/Tk is not
  #   appropriate version
  setenv CCP4I_TCLTK /usr/local/tcltkblt/bin
  # CCP4I_HELP - directory contain ccp4i help - default is
  $CCP4I_TOP/helpsetenv CCP4I_HELP ${CCP4I_TOP}/help

 
  ### Optional - setting http_proxy environment
  # The commented out 'setenv' line below may have to be declared
  to download
  # and edit protein sequences using the new Import/Edit Protein
  Sequences# (This may also be required for remote job submission
  in arp/warp.)
  # task. If so, uncomment this line and replace the example proxy
  URL with
  your
  # relevant URL
 
  #setenv HTTP_PROXY wwwblah.blah.ac.uk:/blah.blah
 
  ### NOVICE USERS STOP HERE #
 
  ### OPTIONS TO CUSTOMISE CCP4 #
 
  # By default, CCP4 directories are appended to the end of paths (PATH,
  # LD_LIBRARY_PATH, and DYLD_LIBRARY_PATH). If ccp4_first_in_path
  is set
  # to 1, then they will be prepended to the beginning of paths.
  # When deciding local policy, bear in mind the possible
  existence of
  # other CCP4 installations, and the possibility of non-CCP4 programs
  # with conflicting names.
  set ccp4_first_in_path = 1
 
  # The commented-out switch statement below provides an example
  of how
  # to use this file for several machines/architectures sharing
  $CCP4_MASTER.# If necessary, uncomment and edit this.
  Otherwise, if you're only
  supporting
  # a single system alter the uncommented part as necessary.
  #
  # The significance of the environment variables is as follows:
  #   CBIN: location of the executables -- must be on
  your path (see below);
  #   CLIB: location of (binary) library files such as
  libccp4.a and
  libccp4.so;
  #   MANPATH: set this if your system's `man' looks at
  such an environment
  #  variable to determine where to
  look for man pages.  By adding
  #  $CCP4/man to the normal path you
  get the CCP4 man pages
  #  with keyword searching as system ones.
  #   MCTYPE: used for LAUE make -- see LAUE documentation
  #   CCP4_BROWSER: set this if you 

[ccp4bb] mtz library in windows

2008-09-30 Thread Alex XIE
Dear all,

I am using CCP4 mtz library and other libraries to develop a program.
Because
I am using a PC at home, I am actually using the CCP4 in windows.

However, when I link the mtz library(hence libccp4c.lib), it happens that
the
compiler complains

error LNK2001: unresolved external symbol [EMAIL PROTECTED]

and some other functions that should be in libccp4c not found. I checked
the project setting(I am using compaq visual fortran 6.6), I have included
libccp4c, libccp4f in the library, and library path in
/link/input/Additional
Library Path, so I don't understand why the compiler still cannot resolve
the functions.

Can anybody help, please? Your suggestion is greatly appreciated.

Alex