Re: [ccp4bb] Characterization of Protein Conformational Changes

[Roberto Mosca]

I version of ESCET working in a pairwise fashion on different conformation
of the same structure or structures of similar proteins with different
sequences is also available as a web-server. The algorithm is called RAPIDO
and you can find it here:

webapps.embl-hamburg.de/rapido

And is described in the two references:

http://www.ncbi.nlm.nih.gov/pubmed/18727838
http://www.ncbi.nlm.nih.gov/pubmed/18460546

Best,
Roberto

-- 
Roberto Mosca, Ph.D.

Structural Bioinformatics Group
Institute for Research in Biomedicine (IRB Barcelona)
Parc Científic de Barcelona
C/ Baldiri Reixac 10-12
08028 Barcelona - Spain

Email: roberto.mo...@irbbarcelona.org
Tel:   +34 93 403 96 89
Web:   http://gatealoy.pcb.ub.es/people/roberto_mosca.html

Re: [ccp4bb] Characterization of Protein Conformational Changes

[Konrad Hinsen]

On 07.01.2009, at 22:54, Jacob Keller wrote:

These cases, however, presuppose that one knows which type of case  
one is dealing with. This could be done by guesswork and trial-and- 
error, but does anybody know of an approach (e.g., a program) to  
define the most reasonable way to think about a given  
conformational change? Variable-size sliding-window least-squares  
superpositions with comparisons of local versus global rmsd's come  
to mind, but I do not know whether this has been implemented  
anywhere, and would not know readily how to set the parameters  
thereof either.


As you say quite correctly, what you want to optimize is the "way to  
think about" a conformational change. Since this is a mental rather  
than a physical criterion, I wouldn't expect any mathematical  
approach to give an answer. I think you will have to choose your  
criteria based on the interpretation you want to make, and only then  
invoke mathematics to do the computation.


For any purpose other than visualization, and in particular for any  
quantitative analysis, I strongly recommend to look only at changes  
in scalar functions of atomic positions, which do not depend on the  
orientation of the whole protein. The probably most widely used  
analysis of this kind is a difference-distance map, but many others  
can be defined. For example, flexibility in a protein can be  
quantified by defining a local deformation energy: imagine a spring  
between each pair of atoms (up to a certain distance), and calculate  
the energy change in the spring network when moving from one  
conformation to another. This deformation energy is high in flexible  
regions and low in nearly rigid domains. This approach is described in


K. Hinsen et al., "Analysis of domain motions in large proteins",
Proteins. 34 (1999): 369-382
	http://dirac.cnrs-orleans.fr/plone/publications/preprints/all- 
preprints/domain_motions.pdf/view


and implemented in the DomainFinder program:

http://dirac.cnrs-orleans.fr/DomainFinder/

as a preliminary step before domain analysis. After all, there is no  
point in looking for domains in flexible regions of a protein.


In a protein with clearly defined domains, you can also look at their  
relative motion (translation, rotation) without any reference to  
absolute orientations. In fact, I suppose that most conformational  
changes in proteins can be described in a useful way without any  
initial superposition.


Konrad.
--
-
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hin...@cnrs-orleans.fr
-

[ccp4bb] Call for abstracts 2009- Young Crystallographers Group

[Arefeh Seyedarabi]

Dear Members,

The YC2009 Satellite will take place in the afternoon of 20th April and 
in the morning of 21st April prior to the BCA Spring Meeting in 
Loughborough. As in previous years we will run three sessions of oral 
presentations, which are a superb opportunity for Young 
Crystallographers (i.e. PhD students or early post docs) to discuss their 
work in a relaxed environment and practise their presentation skills. 
There will also be a poster session on Monday evening together with a 
buffet dinner and drinks. 

Accommodation and registration for the YC2009 will be free for Young 
Crystallographers once more and should be done either by filling in the 
registration form (make sure you tick the little box!) or by registering 
online on the BCA Spring Meeting website, where you can also find 
further information on bursary applications. Of course you don’t have to 
be a YC to attend our meeting! 

So all we need now is your abstracts! 
Deadline for abstracts to be considered for oral contributions is 26th 
January 2009 and deadline for poster abstracts is 2nd February 2009. 
The abstract submission is now open and should be done by logging in 
to the members areas on our webpage www.chem.gla.ac.uk/yc/ (please 
register first if you are a new member or have forgotten your details). 
Note that if you want to submit any poster abstracts to the main 
meeting this has to be done through the 2009 Spring Meeting webpage. 

Like in the years previously there will be a range of prizes for 
outstanding contributions to be awarded at the main conference dinner 
so get in there quick! 


See you all in Loughborough!


Susanne Huth
YCG chair

Re: [ccp4bb] Published derivation of mFo-DFc formula?

[Ian Tickle]

 
All - I didn't get a single response to my posting last week
(https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0812&L=CCP4BB&T=0&O=D
&X=512817322E87355F7F&Y=i.tickle%40astex-therapeutics.com&P=266420)
concerning the formulae that are widely used for the 'minimally-biased'
Fourier and difference Fourier coefficients.  It probably didn't help
that I posted it in the middle of the festive season! - but still
somewhat surprising since I imagine everyone here is involved with maps
at one time or another, and has an interest in getting the density that
shows best what if any further modifications need to be made to the
current model.  Anyway now that people have hopefully returned to work
from the rigours of the CCP4 Study Weekend I thought I'd post it again
and see if I can provoke some discussion this time.  I won't post all my
calculations again, just a summary of my conclusions.

First, I think I can now prove my conjecture that the optimal difference
Fourier coefficient dF is given for both acentrics and centrics by:

dF = Fm - DFc

where Fm is the 'minimally-biased' Fourier coefficient derived by Read
(AC 1986,A42,140):

Fm(acen) = 2mFo - DFc
Fm(cen)  =  mFo

I'm satisfied now that my alternative conjecture, that dF = Fm - Fc, is
probably wrong.  Also I can see that there might be an argument to put
DFc in the FC (FC_ALL) column in place of Fc as appears to be currently
done by REFMAC, but not by SIGMAA (but I'd still like to see some
discussion of that).

So here's a summary comparison of theory with what is my understanding
is actually implemented in software, and with the inconsistencies
highlighted (>...<):

Source   Coefficient   AcentricsCentrics
==   ===   =

THEORY(Read) Fm2mFo - DFc   mFo
  ..  (me)   dF2(mFo-DFc)   mFo - DFc

SIGMAA   Fm2mFo - DFc   mFo
 dF   > mFo - DFc < mFo - DFc
   FcFc  Fc

REFMAC   Fm2mFo - DFc> 2mFo - DFc <
 dF   > mFo - DFc < mFo - DFc
   Fc > DFc < > DFc <

Even if you don't accept my suggestion for the acentric dF coefficient
there are clearly some significant inconsistencies between the
coefficients output by SIGMAA & REFMAC which it would be nice to
resolve!

Cheers

-- Ian


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Re: [ccp4bb] ARP/wARP Solvent

[Matthew Chu]

Thanks Damian, but I have been using my library file for refmac refinement
and it works fine. And I can't find the line "Unrecognized atom type", but
presumably, if it works in refmac refinement, why not in Arp/wArp?

Yes Gerrit, the "[" and "]" should not be there.so auto_solvent.sh can
recognize my mtz fp, etc. BUT
I did check the box 'input a user-defined library file' in GUI and the
command 'extralibrary' in the script, and again, it fails to read my library
file or the one refmac just created, but obviously the extralibrary command
works fine?
Here is the log:

 Working directory/home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/
 Job ID is set to 20090108_114504
 X-ray data file  /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//L1.mtz
 Protein file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//L1.pdb
 Extralibrary file
/home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//refmac5_temp1.10491_lib.cif
 TLS input file   /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent//L1_TLS.tls
 Creating directory
/home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504
 Output solvent file
/home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504/L1_solvent.pdb
 mtz labels taken: F_New SIGF_New FreeR_flag
 Parameter file
/home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504/arp_warp_solvent.par
 Job launched in
/home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504
 The log file is
/home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/20090108_114504/L1_warp_solvent_details.log

But ERROR:
Important, Important, Important!
Your coordinate file has a ligand which has either minimum or no description
in the library
A new ligand description has been added to
/tmp/mchu/refmac5_temp1.11125_lib.cif
Picture of the new ligand can be viewed using postscript file. See above
Check description in this file and, if satisfied, use it as the input
library
Otherwise either edit bond orders manually or use CCP4i Sketcher to view and
edit the ligand
and create a library entry by running libcheck
It is strongly recommended that dictionary  entry should be checked
carefully before using it
If you are happy with the library description then use the keyword (MAKE
CHECK NONE)
I.e. do not check correctness of the coordinates
===> Error: New ligand has been encountered. Stopping now

I really have no idea what is the problem?
Any suggestion would be greatly appreciated!

Kind regards,
Matt




2009/1/8 Damian Ekiert 
Matt,

I had a similar sounding problem once, but it may or may the problem in your
case.  Do you have any ligands or glycans on your protein that you just
added in?  I was working on a protein with glycosylations and hadn't yet
removed the oxygens from my sugars that would be lost after condensation
(e.g., the oxygen that would be lost as water when the first residue was
attached to Asn).  My suggestion would be to look a little bit higher up in
the log file and see if you see any lines saying something like
"Unrecognized atom type".  I think when there is a discrepancy between the
residue name and the names of the atoms in the residue, you can have this
problem.

Hope that helps.

Best,

Damian Ekiert


2009/1/8 Gerrit Langer 

> Dear Matt,
>
> have you tried the 'input a user-defined library file' check box under
> 'refmac parameters' in the gui? Else try the keyword 'extralibrary' when
> using the 'auto_solvent.sh' script from the command line. Both options
> define a string 'LIB_IN mylib.cif' that is passed on to refmac.
>
> When using the auto_solvent.sh script, please omit the '[' and ']'
> characters. Type e.g.: auto_solvent.sh datafile L1.mtz protein L1.pdb fp
> F_New sigfp SIGF_New extralibrary refmac5_templ.03957_lib.cif
>
> I hope this will help.
> Regards,
> Gerrit.
>
>
> Matthew Chu wrote:
>
>  Dear all,
>>
>> I tried to use ARP/wARP 7.0.1 GUI for solvent building, however it
>> couldn't
>> recognize my ligand library file (.cif), which works fine in refmac
>> refinement.
>> Apparently, the error message is:
>>
>> ===> Error: New ligand has been encountered. Stopping now
>> Refmac_5.2.0019:  New ligand has been encountered. Stopping now
>> Your coordinate file has a ligand which has either minimum or no
>> description
>> in the library
>> A new ligand description has been added to
>> /tmp/mchu/refmac5_temp1.03957_lib.cif
>>
>> Even if I use the one refmac created after the error,  it still can't
>> recognize this new cif file...
>>
>> I also tried to run it from command line, another problem was raised. It
>> couldn't recognize the FP label in my mtz when I used the keyword [fp
>> F_New]
>> [sigfp SIGF_New] [freer FreeR_flag]
>>
>> Error message:
>> Label FP does not match the content of the datafile
>> /home/mchu/ARP_wARP/solvent/L1.mtz
>> Possible mtz labels are: F_New FC FWT DELFWT
>>
>> Does anyone have any idea why and how I can fix it? Thank you so much in
>> advance!
>>
>> Kind regards,
>> Matt
>>
>>
>>
>>
>
>


-- 

[ccp4bb] NCS restraints of domains

[Nicholas Keep]

I am refining a low (3A) resolution structure of a 3 domain protein. 
There are 4 copies in the ASU.  I have been applying tight NCS 
restraints by domain in refmac and have pulled the weak MR solution down 
to Rfree below 30 (just).


However my question is that in 2 of the 4 copies one of the domains is 
very poorly resolved.  I can lower Rfree by around 0.5% by omitting the 
domains from the PDB entirely or not applying the NCS restraints to 
these copies of the domain.  Clearly they are there and should resemble 
the moderately well resolved copies by coordinates but the way Bfactor 
restraints are applied between NCS copies seems to be the issue.  If 
tight restraints are included the B factors are much lower (30-40) 
rather than 60-80 for the poor domains.


I was wondering if there is a theoretically correct way to treat this?

Would applying TLS scaling to each domain lead to the residual B factors 
being more balanced?
Can a B factor offset be applied to the NCS restraints or could I only 
apply a coordinate restraint not a B factor restraint between certain 
copies?


Comments welcomed especially from Garib.

Happy New Year
Nick





--

Dr Nicholas H. Keep
Dean of Faculty of Science
Reader in Structural Biology
School of Crystallography,
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6868  (Rosalind Franklin Laboratory)
  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] NCS restraints of domains

[Eleanor Dodson]

It is worth doing sme rounds of non-NCS restrainded refinement then 
sending it to the Ethan Merrit server to get TLS groups suggested..


Eleanor

Frank von Delft wrote:

Two points:

1. B-factors tend to differ lots between NCS copies, so you want to 
set those restraints rather low (at least, I always do, by default)


2. NCS groups tend to need a far more fine-grained description than 
just plonking in the whole domain.  For structures in my lab, we often 
see that tight NCS "does not work" -- until the group definitions are 
selected more carefully.


Cheers
phx



Nicholas Keep wrote:
I am refining a low (3A) resolution structure of a 3 domain protein. 
There are 4 copies in the ASU.  I have been applying tight NCS 
restraints by domain in refmac and have pulled the weak MR solution 
down to Rfree below 30 (just).


However my question is that in 2 of the 4 copies one of the domains 
is very poorly resolved.  I can lower Rfree by around 0.5% by 
omitting the domains from the PDB entirely or not applying the NCS 
restraints to these copies of the domain.  Clearly they are there and 
should resemble the moderately well resolved copies by coordinates 
but the way Bfactor restraints are applied between NCS copies seems 
to be the issue.  If tight restraints are included the B factors are 
much lower (30-40) rather than 60-80 for the poor domains.


I was wondering if there is a theoretically correct way to treat this?

Would applying TLS scaling to each domain lead to the residual B 
factors being more balanced?
Can a B factor offset be applied to the NCS restraints or could I 
only apply a coordinate restraint not a B factor restraint between 
certain copies?


Comments welcomed especially from Garib.

Happy New Year
Nick

Re: [ccp4bb] NCS restraints of domains

[Frank von Delft]

Two points:

1. B-factors tend to differ lots between NCS copies, so you want to set 
those restraints rather low (at least, I always do, by default)


2. NCS groups tend to need a far more fine-grained description than just 
plonking in the whole domain.  For structures in my lab, we often see 
that tight NCS "does not work" -- until the group definitions are 
selected more carefully.


Cheers
phx



Nicholas Keep wrote:
I am refining a low (3A) resolution structure of a 3 domain protein. 
There are 4 copies in the ASU.  I have been applying tight NCS 
restraints by domain in refmac and have pulled the weak MR solution 
down to Rfree below 30 (just).


However my question is that in 2 of the 4 copies one of the domains is 
very poorly resolved.  I can lower Rfree by around 0.5% by omitting 
the domains from the PDB entirely or not applying the NCS restraints 
to these copies of the domain.  Clearly they are there and should 
resemble the moderately well resolved copies by coordinates but the 
way Bfactor restraints are applied between NCS copies seems to be the 
issue.  If tight restraints are included the B factors are much lower 
(30-40) rather than 60-80 for the poor domains.


I was wondering if there is a theoretically correct way to treat this?

Would applying TLS scaling to each domain lead to the residual B 
factors being more balanced?
Can a B factor offset be applied to the NCS restraints or could I only 
apply a coordinate restraint not a B factor restraint between certain 
copies?


Comments welcomed especially from Garib.

Happy New Year
Nick

Re: [ccp4bb] ARP/wARP Solvent

[Anastassis Perrakis]

Hi -

Its a bug in version 7.0.1 that went (almost) unnoticed  ... there was  
one more complaint a year ago and I had fixed it but there was no  
release in between. Sorry.


Apart from simply doing the solvent building from the REFMAC interface  
instead (either with arp_warp as since now or with Coot as since CCP4  
6.1) I will mail you the fixed file (which might work). Anyone else  
interested ask me ; the fix will be in the imminent 7.1 release.


A.



On Jan 8, 2009, at 12:59, Matthew Chu wrote:

Thanks Damian, but I have been using my library file for refmac  
refinement and it works fine. And I can't find the line  
"Unrecognized atom type", but presumably, if it works in refmac  
refinement, why not in Arp/wArp?


Yes Gerrit, the "[" and "]" should not be there.so  
auto_solvent.sh can recognize my mtz fp, etc. BUT
I did check the box 'input a user-defined library file' in GUI and  
the command 'extralibrary' in the script, and again, it fails to  
read my library file or the one refmac just created, but obviously  
the extralibrary command works fine?

Here is the log:

 Working directory/home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/
 Job ID is set to 20090108_114504
 X-ray data file  /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent// 
L1.mtz
 Protein file /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent// 
L1.pdb
 Extralibrary file   /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent// 
refmac5_temp1.10491_lib.cif
 TLS input file   /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent// 
L1_TLS.tls
 Creating directory   /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/ 
20090108_114504
 Output solvent file  /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/ 
20090108_114504/L1_solvent.pdb

 mtz labels taken: F_New SIGF_New FreeR_flag
 Parameter file   /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/ 
20090108_114504/arp_warp_solvent.par
 Job launched in  /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/ 
20090108_114504
 The log file is  /home/mchu/ArpwARP/l1/ArpwARP_070109/solvent/ 
20090108_114504/L1_warp_solvent_details.log


But ERROR:
Important, Important, Important!
Your coordinate file has a ligand which has either minimum or no  
description in the library
A new ligand description has been added to /tmp/mchu/ 
refmac5_temp1.11125_lib.cif
Picture of the new ligand can be viewed using postscript file. See  
above
Check description in this file and, if satisfied, use it as the  
input library
Otherwise either edit bond orders manually or use CCP4i Sketcher to  
view and edit the ligand

and create a library entry by running libcheck
It is strongly recommended that dictionary  entry should be checked  
carefully before using it
If you are happy with the library description then use the keyword  
(MAKE CHECK NONE)

I.e. do not check correctness of the coordinates
===> Error: New ligand has been encountered. Stopping now

I really have no idea what is the problem?
Any suggestion would be greatly appreciated!

Kind regards,
Matt




2009/1/8 Damian Ekiert 
Matt,

I had a similar sounding problem once, but it may or may the problem  
in your case.  Do you have any ligands or glycans on your protein  
that you just added in?  I was working on a protein with  
glycosylations and hadn't yet removed the oxygens from my sugars  
that would be lost after condensation (e.g., the oxygen that would  
be lost as water when the first residue was attached to Asn).  My  
suggestion would be to look a little bit higher up in the log file  
and see if you see any lines saying something like "Unrecognized  
atom type".  I think when there is a discrepancy between the residue  
name and the names of the atoms in the residue, you can have this  
problem.


Hope that helps.

Best,

Damian Ekiert


2009/1/8 Gerrit Langer 
Dear Matt,

have you tried the 'input a user-defined library file' check box  
under 'refmac parameters' in the gui? Else try the keyword  
'extralibrary' when using the 'auto_solvent.sh' script from the  
command line. Both options define a string 'LIB_IN mylib.cif' that  
is passed on to refmac.


When using the auto_solvent.sh script, please omit the '[' and ']'  
characters. Type e.g.: auto_solvent.sh datafile L1.mtz protein  
L1.pdb fp F_New sigfp SIGF_New extralibrary refmac5_templ. 
03957_lib.cif


I hope this will help.
Regards,
Gerrit.


Matthew Chu wrote:

Dear all,

I tried to use ARP/wARP 7.0.1 GUI for solvent building, however it  
couldn't

recognize my ligand library file (.cif), which works fine in refmac
refinement.
Apparently, the error message is:

===> Error: New ligand has been encountered. Stopping now
Refmac_5.2.0019:  New ligand has been encountered. Stopping now
Your coordinate file has a ligand which has either minimum or no  
description

in the library
A new ligand description has been added to
/tmp/mchu/refmac5_temp1.03957_lib.cif

Even if I use the one refmac created after the error,  it still can't
recognize this new cif file...

I also tried to run it from comman

[ccp4bb] dog slow ccp4i on 64 OpenSUSE and home is on NFS

[Joachim Reichelt]

Dear all,

we have a real slow performance of ccp4i, if:
- homedir is on NFS, here /nero is on a i586 Linux system
- actual system is 64 bit, here OpenSUSE 10.3 on core2quad with 8GB ram

from entering ccp4i to see the gui it takes ~2 minutes.
and any popup/dialogue take the same time
This is 6.1, was the same with 6.02

Same user, same system, home dir shifted to a local disk or
same home, user, but i586 (P4, 1GB) some seconds

I have done an strace to see what is going on and I see a lot of:

lstat("/nero/jre", {st_mode=S_IFDIR|0755, st_size=6336, ...}) = 0
lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=248, ...}) = 0
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file 
or directory)

select(0, NULL, NULL, NULL, {0, 1}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file 
or directory)

select(0, NULL, NULL, NULL, {0, 1}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file 
or directory)

select(0, NULL, NULL, NULL, {0, 1}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file 
or directory)

select(0, NULL, NULL, NULL, {0, 1}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file 
or directory)

select(0, NULL, NULL, NULL, {0, 1}) = 0 (Timeout)
... (32 times repeated)

open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 4
fcntl(4, F_SETFD, FD_CLOEXEC)   = 0
ioctl(4, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624760) = -1 ENOTTY 
(Inappropriate ioctl for device)

lseek(4, 0, SEEK_END)   = 351
write(4, "db_get_handler_port: opening loc"..., 38) = 38
close(4)= 0
open("/nero/jre/.CCP4/dbccp4i.LOCK", O_RDONLY) = 4
fcntl(4, F_SETFD, FD_CLOEXEC)   = 0
ioctl(4, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d6250f0) = -1 ENOTTY 
(Inappropriate ioctl for device)

read(4, "port number is:4090", 4096)= 19
read(4, "", 4077)   = 0
lstat("/nero", {st_mode=S_IFDIR|0755, st_size=1992, ...}) = 0
lstat("/nero/jre", {st_mode=S_IFDIR|0755, st_size=6336, ...}) = 0
lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=280, ...}) = 0
open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 5
fcntl(5, F_SETFD, FD_CLOEXEC)   = 0
ioctl(5, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624760) = -1 ENOTTY 
(Inappropriate ioctl for device)

lseek(5, 0, SEEK_END)   = 389
write(5, "db_get_handler_port: line from l"..., 63) = 63
...

lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=280, ...}) = 0
open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 6
fcntl(6, F_SETFD, FD_CLOEXEC)   = 0
ioctl(6, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624820) = -1 ENOTTY 
(Inappropriate ioctl for device)

lseek(6, 0, SEEK_END)   = 8764
write(6, "db_handler_processResponse: invo"..., 54) = 54
close(6)= 0
lstat("/nero", {st_mode=S_IFDIR|0755, st_size=1992, ...}) = 0
lstat("/nero/jre", {st_mode=S_IFDIR|0755, st_size=6336, ...}) = 0
lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=280, ...}) = 0
open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 6
fcntl(6, F_SETFD, FD_CLOEXEC)   = 0
ioctl(6, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624820) = -1 ENOTTY 
(Inappropriate ioctl for device)

lseek(6, 0, SEEK_END)   = 8818
write(6, "*** REQUEST_LIST: request#9\n", 28) = 28
close(6)= 0

and I see a lot of:

read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource 
temporarily unavailable)
read

Re: [ccp4bb] dog slow ccp4i on 64 OpenSUSE and home is on NFS

[Roger Rowlett]

I don't know if this is relevant here, but we found that certain CCP4
6.0.2 tasks run under CCP4i suffered poor performance over NFS due to
the frequent writing and reading of temporary files. Starting CCP4i
from a local directory eliminated the problem. (It appeared that the
temporary files were written to the origination directory instead of
/home/user in this case.) We created a directory on our client
workstations called /local-projects just for that purpose. As you, we
have a common /home directory mounted on an NFS share so that all users
will have a portable desktop.

Cheers,

-- 

Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@mail.colgate.edu

Joachim Reichelt wrote:

  Dear all,

we have a real slow performance of ccp4i, if:
- homedir is on NFS, here /nero is on a i586 Linux system
- actual system is 64 bit, here OpenSUSE 10.3 on core2quad with 8GB ram

from entering ccp4i to see the gui it takes ~2 minutes.
and any popup/dialogue take the same time
This is 6.1, was the same with 6.02

Same user, same system, home dir shifted to a local disk or
same home, user, but i586 (P4, 1GB) some seconds

I have done an strace to see what is going on and I see a lot of:

lstat("/nero/jre", {st_mode=S_IFDIR|0755, st_size=6336, ...}) = 0
lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=248, ...}) = 0
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file
or directory)
select(0, NULL, NULL, NULL, {0, 1}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file
or directory)
select(0, NULL, NULL, NULL, {0, 1}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file
or directory)
select(0, NULL, NULL, NULL, {0, 1}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file
or directory)
select(0, NULL, NULL, NULL, {0, 1}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file
or directory)
select(0, NULL, NULL, NULL, {0, 1}) = 0 (Timeout)
... (32 times repeated)

open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 4
fcntl(4, F_SETFD, FD_CLOEXEC)   = 0
ioctl(4, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624760) = -1 ENOTTY
(Inappropriate ioctl for device)
lseek(4, 0, SEEK_END)   = 351
write(4, "db_get_handler_port: opening loc"..., 38) = 38
close(4)= 0
open("/nero/jre/.CCP4/dbccp4i.LOCK", O_RDONLY) = 4
fcntl(4, F_SETFD, FD_CLOEXEC)   = 0
ioctl(4, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d6250f0) = -1 ENOTTY
(Inappropriate ioctl for device)
read(4, "port number is:4090", 4096)= 19
read(4, "", 4077)   = 0
lstat("/nero", {st_mode=S_IFDIR|0755, st_size=1992, ...}) = 0
lstat("/nero/jre", {st_mode=S_IFDIR|0755, st_size=6336, ...}) = 0
lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=280, ...}) = 0
open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 5
fcntl(5, F_SETFD, FD_CLOEXEC)   = 0
ioctl(5, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624760) = -1 ENOTTY
(Inappropriate ioctl for device)
lseek(5, 0, SEEK_END)   = 389
write(5, "db_get_handler_port: line from l"..., 63) = 63
...

lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=280, ...}) = 0
open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 6
fcntl(6, F_SETFD, FD_CLOEXEC)   = 0
ioctl(6, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624820) = -1 ENOTTY
(Inappropriate ioctl for device)
lseek(6, 0, SEEK_END)   = 8764
write(6, "db_handler_processResponse: invo"..., 54) = 54
close(6)= 0
lstat("/nero", {st_mode=S_IFDIR|0755, st_size=1992, ...}) = 0
lstat("/nero/jre", {st_mode=S_IFDIR|0755, st_size=6336, ...}) = 0
lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=280, ...}) = 0
open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 6
fcntl(6, F_SETFD, FD_CLOEXEC)   = 0
ioctl(6, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624820) = -1 ENOTTY
(Inappropriate ioctl for device)
lseek(6, 0, SEEK_END)   = 8818
write(6, "*** REQUEST_LIST: request#9\n", 28) = 28
close(6)= 0

and I see a lot of:

read(3, 0x61df94, 4096) = -1 EAGAIN (Resource
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource
temporarily unavailable)
read(3, 0x61df94, 4096) = -1 EA

[ccp4bb] SLS PX Beamlines: Call for Proposals is Open

[Mueller Stefan]

Dear Colleagues, 

Call is open for proposals for the PX (Protein Crystallography) beamlines of 
the Swiss Light Source, SLS.

Deadline for proposal submission:   Sunday, February 15, 2009.
Submission: All submissions will be handled by the SLS Digital Users Office 
(DUO) /contact: sl...@psi.ch

 

Please consult the following website to obtain information about the status of 
the different beamlines and the procedure to set-up the proposal:

http://sls.web.psi.ch/view.php/users/experiments/proposals/opencalls/PX/index.html

 

In case of questions related to the experiments at the PX beamlines, please 
contact one of the beamline scientists:  
 
http://sls.web.psi.ch/view.php/beamlines/px/staff/index.html

With kind regards

Stefan Müller
On behalf of the SLS Team 

- 
SLS Science Coordinator 
Paul Scherrer Institut 
CH-5232 Villigen PSI  
  stefan.muel...@psi.ch 
http://sls.web.psi.ch/ 

 

 

Re: [ccp4bb] Affordable 3D LCD Arriving Soon

[Christopher Bahl]

The 3D LCDs have been out for about a year now.  They started at around 
$700, but you can find them for about $350 now.

http://computershopper.com/lcd-monitors/reviews/iz3d-lcd-monitor

It's a different technology than the shutter glasses- If I understand it 
correctly, it basically uses the same principle as a 3D movie...

http://iz3d.com/t-3dproductex.aspx

Does anyone have an idea as to how long it will be until this is 
supported by coot/chimera/ccp4mg/VMD, etc.?


-Chris



James M. Vergis wrote:
I came across an article about Samsung's  $400 3D LCD monitor coming 
out in April so I thought I'd pass it on for those who may be 
interested. 
http://www.engadget.com/2009/01/07/samsung-officially-introduces-2233rz-the-22-inch-3d-panel-for-g/ 



I'm pretty sure their 3D implementation is different than the current 
shutter-glasses active 3D.  Hopefully it will be supported by coot and 
other 3D programs.

Re: [ccp4bb] Affordable 3D LCD Arriving Soon

[Jim Fairman]

The problem with the iZ3D monitor is its requirement for Windows and its
related API DirectX.  This rules out alot of the crystallography community
becuase of their affinity for Linux and Mac.

On Thu, Jan 8, 2009 at 11:38 AM, Christopher Bahl wrote:

> The 3D LCDs have been out for about a year now.  They started at around
> $700, but you can find them for about $350 now.
> http://computershopper.com/lcd-monitors/reviews/iz3d-lcd-monitor
>
> It's a different technology than the shutter glasses- If I understand it
> correctly, it basically uses the same principle as a 3D movie...
> http://iz3d.com/t-3dproductex.aspx
>
> Does anyone have an idea as to how long it will be until this is supported
> by coot/chimera/ccp4mg/VMD, etc.?
>
> -Chris
>
>
>
>
> James M. Vergis wrote:
>
>> I came across an article about Samsung's  $400 3D LCD monitor coming out
>> in April so I thought I'd pass it on for those who may be interested.
>> http://www.engadget.com/2009/01/07/samsung-officially-introduces-2233rz-the-22-inch-3d-panel-for-g/
>>
>> I'm pretty sure their 3D implementation is different than the current
>> shutter-glasses active 3D.  Hopefully it will be supported by coot and other
>> 3D programs.
>>
>


-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfair...@utk.edu james.fair...@case.edu

[ccp4bb] SLS PX Beamlines: Call for Proposals is Open

[Stefan Mueller]

Dear SLS users, 



Call is open for proposals for the PX (Protein Crystallography) beamlines of 
the Swiss Light Source, SLS.

Deadline for proposal submission:   Sunday, February 15, 2009.

Submission: All submissions will be handled by the SLS Digital Users Office 
(DUO) /contact: sl...@psi.ch

 

Please consult the following website to obtain information about the status of 
the different beamlines and the procedure to set-up the proposal:

http://sls.web.psi.ch/view.php/users/experiments/proposals/opencalls/PX/index.html

 

In case of questions related to the experiments at the PX beamlines, please 
contact one of the beamline scientists: 
http://sls.web.psi.ch/view.php/beamlines/px/staff/index.html





With kind regards

Stefan Müller

- 

SLS Science Coordinator 

Paul Scherrer Institut 

WSLA 116 

CH-5232 Villigen PSI 

+41 56 310 54 27 

stefan.muel...@psi.ch 

http://sls.web.psi.ch/ 


-
To unsubscribe from this mailing list, please click the following link:
https://duo.psi.ch/duo/change_mailing.php?CMD=UkVNOjIwNzQ6MTY%3D
-

[ccp4bb] Secondary structure restraints

[Phil Evans]

Does anyone have a good way of imposing secondary structure restraints  
in a low resolution refinement?


I've done this in the past as hydrogen bond distance restraints within  
helices, input to refmac as "LINK"s , with the list generated with a  
little program and certain amount of pain


refmac now accepts an explicit list of external restraints, as does  
phenix.refine, but I'm looking for a way of generating these lists for  
quite a large structure without too much hackery, perhaps from a  
hydrogen-bond or secondary structure assignment program. Helices are  
reasonably straightforward (I can see how to do them from eg DSSP),  
but sheets are more complicated.


Any suggestions? I'm sure that someone must have done this

Phil

Re: [ccp4bb] Secondary structure restraints

[Eckhard Hofmann]

XPLO2D from the USF-Suite does this:


You feed it a PDB file of the model to which you want to restrain your 
refinement model (e.g., that high-resolution native structure you 
already have, even though it may be in a different spacegroup or with 
different domain orientations). The program generates an X-PLOR include 
file which contains DIHEdral statements for the PHI, PSI, CHI-1 and 
CHI-2 torsions of the protein. If you protein contains a hinge region, 
simply remove or comment-out the relevant PHI and PSI restraints. If you 
don't want to impose restraints on CHI-1 and/or CHI-2, set the 
corresponding weights to zero (at the top of the X-PLOR include file).


I never tried, but this will be compatible with phenix as well.
Cheers
Eckhard


Phil Evans schrieb:
Does anyone have a good way of imposing secondary structure restraints 
in a low resolution refinement?


I've done this in the past as hydrogen bond distance restraints within 
helices, input to refmac as "LINK"s , with the list generated with a 
little program and certain amount of pain


refmac now accepts an explicit list of external restraints, as does 
phenix.refine, but I'm looking for a way of generating these lists for 
quite a large structure without too much hackery, perhaps from a 
hydrogen-bond or secondary structure assignment program. Helices are 
reasonably straightforward (I can see how to do them from eg DSSP), but 
sheets are more complicated.


Any suggestions? I'm sure that someone must have done this

Phil



--
Eckhard Hofmann 
Ruhr-Uni Bochum
AG Proteinkristallographie, LS Biophysik, ND04/316
44780 Bochum
Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762

Re: [ccp4bb] NCS restraints of domains

[Winn, MD (Martyn)]

Sounds like a good candidate for (domain-level) TLS to me.

Cheers
Martyn

-Original Message-
From: CCP4 bulletin board on behalf of Nicholas Keep
Sent: Thu 1/8/2009 10:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] NCS restraints of domains
 
I am refining a low (3A) resolution structure of a 3 domain protein. 
There are 4 copies in the ASU.  I have been applying tight NCS 
restraints by domain in refmac and have pulled the weak MR solution down 
to Rfree below 30 (just).

However my question is that in 2 of the 4 copies one of the domains is 
very poorly resolved.  I can lower Rfree by around 0.5% by omitting the 
domains from the PDB entirely or not applying the NCS restraints to 
these copies of the domain.  Clearly they are there and should resemble 
the moderately well resolved copies by coordinates but the way Bfactor 
restraints are applied between NCS copies seems to be the issue.  If 
tight restraints are included the B factors are much lower (30-40) 
rather than 60-80 for the poor domains.

I was wondering if there is a theoretically correct way to treat this?

Would applying TLS scaling to each domain lead to the residual B factors 
being more balanced?
Can a B factor offset be applied to the NCS restraints or could I only 
apply a coordinate restraint not a B factor restraint between certain 
copies?

Comments welcomed especially from Garib.

Happy New Year
Nick





-- 

Dr Nicholas H. Keep
Dean of Faculty of Science
Reader in Structural Biology
School of Crystallography,
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
   020-7631-6868  (Rosalind Franklin Laboratory)
   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] Secondary structure restraints: Oops

[Eckhard Hofmann]

Hi Phil,
sorry, haven't read you question properly. No idea how to get easily 
from top/par to cif for refmac.
Probably would need a little scripting, but that's been exactly your 
question ...

Eckhard



XPLO2D from the USF-Suite does this:


You feed it a PDB file of the model to which you want to restrain your
refinement model (e.g., that high-resolution native structure you
already have, even though it may be in a different spacegroup or with
different domain orientations). The program generates an X-PLOR include
file which contains DIHEdral statements for the PHI, PSI, CHI-1 and
CHI-2 torsions of the protein. If you protein contains a hinge region,
simply remove or comment-out the relevant PHI and PSI restraints. If you
don't want to impose restraints on CHI-1 and/or CHI-2, set the
corresponding weights to zero (at the top of the X-PLOR include file).

I never tried, but this will be compatible with phenix as well.
Cheers
Eckhard


Phil Evans schrieb:
Does anyone have a good way of imposing secondary structure restraints 
in a low resolution refinement?


I've done this in the past as hydrogen bond distance restraints within 
helices, input to refmac as "LINK"s , with the list generated with a 
little program and certain amount of pain


refmac now accepts an explicit list of external restraints, as does 
phenix.refine, but I'm looking for a way of generating these lists for 
quite a large structure without too much hackery, perhaps from a 
hydrogen-bond or secondary structure assignment program. Helices are 
reasonably straightforward (I can see how to do them from eg DSSP), but 
sheets are more complicated.


Any suggestions? I'm sure that someone must have done this

Phil



--
Eckhard Hofmann 
Ruhr-Uni Bochum
AG Proteinkristallographie, LS Biophysik, ND04/316
44780 Bochum
Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762

Re: [ccp4bb] Secondary structure restraints: Oops

[Garib Murshudov]

If top/par file could be converted to the following type of  
instructions then you do not need to define everything in cif file  
(these are for torsion angles, all other restraints can be defined  
similarly)


General torsion angle restraints for any quartet of atoms:

external torsion first chain [ch] residue [res] insertion [ins]  atom  
[n] [altecode [a]] next chain [ch] residue [res] insertion [ins]  atom  
[n] [altecode [a] ] [symm y/n] next chain [ch] residue [res] insertion  
[ins] atom [n] [altecode [a] ] next chain [ch] residue [res] insertion  
[ins] atom [n] [altecode [a] ]

 [symm y/n] value  sigma  period> 

Exampl

external torsion first chain A residue 220 atom C next chain A residue  
220 atom CA next chain A residue 220 atom C next chain A residue 221  
atom N value -60 sigma 10 period 1


regards
Garib



On 8 Jan 2009, at 18:14, Eckhard Hofmann wrote:


Hi Phil,
sorry, haven't read you question properly. No idea how to get easily  
from top/par to cif for refmac.
Probably would need a little scripting, but that's been exactly your  
question ...

Eckhard



XPLO2D from the USF-Suite does this:


You feed it a PDB file of the model to which you want to restrain your
refinement model (e.g., that high-resolution native structure you
already have, even though it may be in a different spacegroup or with
different domain orientations). The program generates an X-PLOR  
include

file which contains DIHEdral statements for the PHI, PSI, CHI-1 and
CHI-2 torsions of the protein. If you protein contains a hinge region,
simply remove or comment-out the relevant PHI and PSI restraints. If  
you

don't want to impose restraints on CHI-1 and/or CHI-2, set the
corresponding weights to zero (at the top of the X-PLOR include file).

I never tried, but this will be compatible with phenix as well.
Cheers
Eckhard


Phil Evans schrieb:
Does anyone have a good way of imposing secondary structure  
restraints in a low resolution refinement?
I've done this in the past as hydrogen bond distance restraints  
within helices, input to refmac as "LINK"s , with the list  
generated with a little program and certain amount of pain
refmac now accepts an explicit list of external restraints, as does  
phenix.refine, but I'm looking for a way of generating these lists  
for quite a large structure without too much hackery, perhaps from  
a hydrogen-bond or secondary structure assignment program. Helices  
are reasonably straightforward (I can see how to do them from eg  
DSSP), but sheets are more complicated.

Any suggestions? I'm sure that someone must have done this
Phil



--
Eckhard Hofmann 
Ruhr-Uni Bochum
AG Proteinkristallographie, LS Biophysik, ND04/316
44780 Bochum
Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762

[ccp4bb] application for synchrotron beam time 2009 at EMBL Hamburg

[Victor Lamzin]

Dear Colleagues,

This is just a gentle reminder that the deadline for applications
for synchrotron beam time 2009 at the EMBL Hamburg is on January 13.

With best regards,
Victor Lamzin


Call for access to Synchrotron Beamline Facilities 2009 


 EMBL Hamburg, Germany

We announce a call for synchrotron beam time applications in biological 
small-angle scattering (SAXS) and X-ray crystallography (PX). Up to 32 
weeks of beam time will be available at the DORIS storage ring (DESY) 
from March 2009 to February 2010.


EMBL Hamburg will operate the following beamlines:

Beamline  New featuresScientist responsible

X33SAXS   Automated and remote operation  Dmitri Svergun
X11PX MAR555 Flat Panel detector  Paul Tucker
X12PX MAD, S-SAD, fluorescence analysis   Manfred Weiss
X13PX Microspec, expert data collection   Matthew Groves
BW7A*  PX High flux, multilayer opticsAndrea Schmidt
BW7B*  PX Automated sample changer MARVIN Santosh Panjikar

*These beamlines are used as Petra-III test facilities and therefore will 
be only temporarily available.


The deadline for submission of proposals is January 13, 2009.
An external Priorities Committee will assess the proposals.

Electronic beam proposal forms and a detailed description of the beamline 
facilities are available at www.embl-hamburg.de and 
www.embl-hamburg.de/facilities


Access to the EMBL Hamburg high-throughput crystallisation facility is 
available via www.embl-hamburg.de/services/crystallisation


EMBL is constructing three new beamlines for applications in biological 
X-ray crystallography (PX) and small-angle scattering (SAXS) at the Petra-III 
synchrotron storage ring, which are scheduled to be available from 2010/11. 
See www.embl-hamburg.de/services/petra for further information.


For further information 
tel. +49-40-89902-110, 
s...@embl-hamburg.de (SAXS)

b...@embl-hamburg.de (PX).

Access to the EMBL Hamburg facilities will be supported by the European 
Commission, Research Infrastructure Action under the FP7 "ELISA (European 
Light Sources Activities)".

Re: [ccp4bb] NCS restraints of domains

[Garib Murshudov]

Dear Nick

Using TLS sometimes improves behaviour of NCS restraints (it makes  
sense since remaining B values should be similar). However in other  
cases it does not improve. Perhaps removal of B value restraints for  
these domains may improve NCS restrained refinement. I have not done  
tests without B value restraints so I cannot say what would be  
behaviour.


I would do several tests before making decision:

1) TLS (as Martyn suggests - domain level) with NCS restraints
2) TLS with NCS restraints without B value NCS
3) NCS without B value restraints

regards
Garib


On 8 Jan 2009, at 10:54, Nicholas Keep wrote:

I am refining a low (3A) resolution structure of a 3 domain protein.  
There are 4 copies in the ASU.  I have been applying tight NCS  
restraints by domain in refmac and have pulled the weak MR solution  
down to Rfree below 30 (just).


However my question is that in 2 of the 4 copies one of the domains  
is very poorly resolved.  I can lower Rfree by around 0.5% by  
omitting the domains from the PDB entirely or not applying the NCS  
restraints to these copies of the domain.  Clearly they are there  
and should resemble the moderately well resolved copies by  
coordinates but the way Bfactor restraints are applied between NCS  
copies seems to be the issue.  If tight restraints are included the  
B factors are much lower (30-40) rather than 60-80 for the poor  
domains.


I was wondering if there is a theoretically correct way to treat this?

Would applying TLS scaling to each domain lead to the residual B  
factors being more balanced?
Can a B factor offset be applied to the NCS restraints or could I  
only apply a coordinate restraint not a B factor restraint between  
certain copies?


Comments welcomed especially from Garib.

Happy New Year
Nick





--

Dr Nicholas H. Keep
Dean of Faculty of Science
Reader in Structural Biology
School of Crystallography,
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
 020-7631-6868  (Rosalind Franklin Laboratory)
 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] Secondary structure restraints: Oops

[Phil Evans]

I would guess that it would be easier to restrain a helix by hydrogen  
bond lengths rather than by phi/psi torsion angles, and that could  
work for sheets as well.


Phil


On 8 Jan 2009, at 19:05, Garib Murshudov wrote:

If top/par file could be converted to the following type of  
instructions then you do not need to define everything in cif file  
(these are for torsion angles, all other restraints can be defined  
similarly)


General torsion angle restraints for any quartet of atoms:

external torsion first chain [ch] residue [res] insertion [ins]   
atom [n] [altecode [a]] next chain [ch] residue [res] insertion  
[ins]  atom [n] [altecode [a] ] [symm y/n] next chain [ch] residue  
[res] insertion [ins] atom [n] [altecode [a] ] next chain [ch]  
residue [res] insertion [ins] atom [n] [altecode [a] ]

[symm y/n] value  sigma  period> 

Exampl

external torsion first chain A residue 220 atom C next chain A  
residue 220 atom CA next chain A residue 220 atom C next chain A  
residue 221 atom N value -60 sigma 10 period 1


regards
Garib



On 8 Jan 2009, at 18:14, Eckhard Hofmann wrote:


Hi Phil,
sorry, haven't read you question properly. No idea how to get  
easily from top/par to cif for refmac.
Probably would need a little scripting, but that's been exactly  
your question ...

Eckhard



XPLO2D from the USF-Suite does this:


You feed it a PDB file of the model to which you want to restrain  
your

refinement model (e.g., that high-resolution native structure you
already have, even though it may be in a different spacegroup or with
different domain orientations). The program generates an X-PLOR  
include

file which contains DIHEdral statements for the PHI, PSI, CHI-1 and
CHI-2 torsions of the protein. If you protein contains a hinge  
region,
simply remove or comment-out the relevant PHI and PSI restraints.  
If you

don't want to impose restraints on CHI-1 and/or CHI-2, set the
corresponding weights to zero (at the top of the X-PLOR include  
file).


I never tried, but this will be compatible with phenix as well.
Cheers
Eckhard


Phil Evans schrieb:
Does anyone have a good way of imposing secondary structure  
restraints in a low resolution refinement?
I've done this in the past as hydrogen bond distance restraints  
within helices, input to refmac as "LINK"s , with the list  
generated with a little program and certain amount of pain
refmac now accepts an explicit list of external restraints, as  
does phenix.refine, but I'm looking for a way of generating these  
lists for quite a large structure without too much hackery,  
perhaps from a hydrogen-bond or secondary structure assignment  
program. Helices are reasonably straightforward (I can see how to  
do them from eg DSSP), but sheets are more complicated.

Any suggestions? I'm sure that someone must have done this
Phil



--
Eckhard Hofmann 
Ruhr-Uni Bochum
AG Proteinkristallographie, LS Biophysik, ND04/316
44780 Bochum
Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762

Re: [ccp4bb] Secondary structure restraints

[Sean Johnson]

Phil,

I have a student who has been working on a python script that will allow 
the user to manually define hydrogen bonds in pymol (i.e. click on the 
nitrogen and oxygen atoms that you want to restrain). It then outputs a 
restraints definition file for refinement in phenix. It can be tedious 
to define the restraints for a large structure (we are working on a low 
resolution refinement of a large structure right now), but I haven't 
been able to find a better alternative.

If you would like to play with our scripts, let me know.

Sean Johnson


Phil Evans wrote:
Does anyone have a good way of imposing secondary structure restraints  
in a low resolution refinement?


I've done this in the past as hydrogen bond distance restraints within  
helices, input to refmac as "LINK"s , with the list generated with a  
little program and certain amount of pain


refmac now accepts an explicit list of external restraints, as does  
phenix.refine, but I'm looking for a way of generating these lists for  
quite a large structure without too much hackery, perhaps from a  
hydrogen-bond or secondary structure assignment program. Helices are  
reasonably straightforward (I can see how to do them from eg DSSP),  
but sheets are more complicated.


Any suggestions? I'm sure that someone must have done this

Phil
  


--
Sean Johnson, PhD
R. Gaurth Hansen Assistant Professor
Utah State University
Department of Chemistry and Biochemistry
0300 Old Main Hill
Logan, UT 84322-0300
(435) 797-2089
(435) 797-3390 (fax)
sean.john...@usu.edu

Re: [ccp4bb] Secondary structure restraints

[Paul Paukstelis]

I put together a simple perl script to take WHATIF optimal hydrogen 
bonds from a known structure and generate refmac or cns restraints. You 
can limit it to backbone or all h-bonds.


Refmac:
http://hood.icmb.utexas.edu/~paul/ccp4_hbond
CNS:
http://hood.icmb.utexas.edu/~paul/cns_hbond

Phil Evans wrote:
Does anyone have a good way of imposing secondary structure restraints 
in a low resolution refinement?


I've done this in the past as hydrogen bond distance restraints within 
helices, input to refmac as "LINK"s , with the list generated with a 
little program and certain amount of pain


refmac now accepts an explicit list of external restraints, as does 
phenix.refine, but I'm looking for a way of generating these lists for 
quite a large structure without too much hackery, perhaps from a 
hydrogen-bond or secondary structure assignment program. Helices are 
reasonably straightforward (I can see how to do them from eg DSSP), but 
sheets are more complicated.


Any suggestions? I'm sure that someone must have done this

Phil



--
Paul Paukstelis, Ph.D.
Research Associate
Institute for Cellular and Molecular Biology
The University of Texas at Austin
P: 512-471-4778, F: 512-232-3420
p...@icmb.utexas.edu

[ccp4bb] Max number of TLS groups in Refmac5 -

[Jonathan Marvin Caruthers]

Hi All:


Longtime listener first time caller.  Does anybody know a relatively simple way 
to increase the maximum number of TLS groups in Refmac5 beyond 70, and if this 
is possible are there any repercussions for doing so?


thanks,


Jon

Jonathan Caruthers
Stowell Lab
University of Colorado
jonathan.caruth...@colorado.edu

[ccp4bb] NonCCP4 - Screening xtals of light sensitive compounds?

[Francis E Reyes]

Non CCP4 related!

If you have experience screening for light sensitive compounds when  
xtals are obtained, can you send me a personal e-mail describing any  
tips,tricks, pitfalls, pointers?


thanks
FR


-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

[ccp4bb] CCP4 Study Weekend 2009

[Paul Swepston]

I guess I will pose this as a question...
 
Can anyone think of a higher quality scientific conference than the CCP4
Study Weekend?  
 
I take my hat off to the scientific organizers of the 2009 meeting - Clemnes
Vonrhein, Elspeth Garman, and Arwen Pearson as well as all of the speakers.
This year's program was very interesting and a great balance between
practical and the theoretical.
 
Good job to all involved.  And if you have never attended a CCP4 Study
Weekend, I highly recommend it (although it can be rather cold).
 
Paul Swepston

Re: [ccp4bb] 2D

[Ho-Leung Ng]

Along the lines of Jeroen's suggestion, we've enjoyed success with
surface entropy reduction mutations to alter crystal contacts. UCLA
has an SER analysis server at:

http://nihserver.mbi.ucla.edu/SER/


Ho
UC Berkeley

-
It mostly means little intermolecular contacts in one direction because=20
of charge repulsion, shape incomplementarity etc etc.

One thing to try is screen for additives that can help to make more=20
contacts between the layers or,  screen for new crystal forms using=20
microseed matrix screening!

- J. -

Re: [ccp4bb] 2D

[Artem Evdokimov]

With respect to the surface entropy reduction method - if you have the
option of sharing your sequence, I can run it through some of my routines
too. Sorry - they're not available as public servers yet because they are
still in development. It significantly helps to have even a very low
resolution structure (just for the packing) or a reasonable degree of
sequence identity with a known structure. But even just from the sequence
alone the stuff works pretty nicely.

Artem

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Vin
Purp
Sent: Wednesday, January 07, 2009 10:20 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] 2D

Sorry for the non ccp4 related post. Can anyone point me in the direction of
a good method, reference or link for improving 2D xtals? They are hexagonal
2D plates, and some have a tendency to stack. Cheers. =v= 

Re: [ccp4bb] dog slow ccp4i on 64 OpenSUSE and home is on NFS

[Tim Gruene]

Hi,

you cut the output of strace a little too late at the top:

find the entry syaing open(") = 3
in order to find out what file cannot be read properly.

You might also check (or send here) the contents of /proc/mounts to see 
what options the nfs-drive was mounted with.


We also often seem to have problems with OpenSuSE through network home 
directories, e.g. it can take ages to log in and start the window manager. 
Unfortunately I have not yet figured out what this is due to.


Tim

--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A


On Thu, 8 Jan 2009, Joachim Reichelt wrote:


Dear all,

we have a real slow performance of ccp4i, if:
- homedir is on NFS, here /nero is on a i586 Linux system
- actual system is 64 bit, here OpenSUSE 10.3 on core2quad with 8GB ram

from entering ccp4i to see the gui it takes ~2 minutes.
and any popup/dialogue take the same time
This is 6.1, was the same with 6.02

Same user, same system, home dir shifted to a local disk or
same home, user, but i586 (P4, 1GB) some seconds

I have done an strace to see what is going on and I see a lot of:

lstat("/nero/jre", {st_mode=S_IFDIR|0755, st_size=6336, ...}) = 0
lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=248, ...}) = 0
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file or 
directory)

select(0, NULL, NULL, NULL, {0, 1}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file or 
directory)

select(0, NULL, NULL, NULL, {0, 1}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file or 
directory)

select(0, NULL, NULL, NULL, {0, 1}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file or 
directory)

select(0, NULL, NULL, NULL, {0, 1}) = 0 (Timeout)
access("/nero/jre/.CCP4/dbccp4i.LOCK", F_OK) = -1 ENOENT (No such file or 
directory)

select(0, NULL, NULL, NULL, {0, 1}) = 0 (Timeout)
... (32 times repeated)

open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 4
fcntl(4, F_SETFD, FD_CLOEXEC)   = 0
ioctl(4, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624760) = -1 ENOTTY 
(Inappropriate ioctl for device)

lseek(4, 0, SEEK_END)   = 351
write(4, "db_get_handler_port: opening loc"..., 38) = 38
close(4)= 0
open("/nero/jre/.CCP4/dbccp4i.LOCK", O_RDONLY) = 4
fcntl(4, F_SETFD, FD_CLOEXEC)   = 0
ioctl(4, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d6250f0) = -1 ENOTTY 
(Inappropriate ioctl for device)

read(4, "port number is:4090", 4096)= 19
read(4, "", 4077)   = 0
lstat("/nero", {st_mode=S_IFDIR|0755, st_size=1992, ...}) = 0
lstat("/nero/jre", {st_mode=S_IFDIR|0755, st_size=6336, ...}) = 0
lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=280, ...}) = 0
open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 5
fcntl(5, F_SETFD, FD_CLOEXEC)   = 0
ioctl(5, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624760) = -1 ENOTTY 
(Inappropriate ioctl for device)

lseek(5, 0, SEEK_END)   = 389
write(5, "db_get_handler_port: line from l"..., 63) = 63
...

lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=280, ...}) = 0
open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 6
fcntl(6, F_SETFD, FD_CLOEXEC)   = 0
ioctl(6, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624820) = -1 ENOTTY 
(Inappropriate ioctl for device)

lseek(6, 0, SEEK_END)   = 8764
write(6, "db_handler_processResponse: invo"..., 54) = 54
close(6)= 0
lstat("/nero", {st_mode=S_IFDIR|0755, st_size=1992, ...}) = 0
lstat("/nero/jre", {st_mode=S_IFDIR|0755, st_size=6336, ...}) = 0
lstat("/nero/jre/.CCP4", {st_mode=S_IFDIR|0755, st_size=280, ...}) = 0
open("/nero/jre/.CCP4/dbclientapi.log", O_WRONLY|O_CREAT|O_APPEND, 0666) = 6
fcntl(6, F_SETFD, FD_CLOEXEC)   = 0
ioctl(6, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1d624820) = -1 ENOTTY 
(Inappropriate ioctl for device)

lseek(6, 0, SEEK_END)   = 8818
write(6, "*** REQUEST_LIST: request#9\n", 28) = 28
close(6)= 0

and I see a lot of:

read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily 
unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily 
unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily 
unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily 
unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily 
unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily 
unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily 
unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resource temporarily 
unavailable)
read(3, 0x61df94, 4096) = -1 EAGAIN (Resour