Re: [ccp4bb] Program to find the center of mass

[Nian Huang]

WOW. There are so many ways to do it. Thank you all for replying.

Nian Huang
Department of Biochemistry
Univ of Texas Southwestern Medical Center

On 5/10/07, Charlie Bond <[EMAIL PROTECTED]> wrote:

Just to complete the set, in pdb-mode for emacs, if you do
pdb-increment-centroid 0 0 0 (e.g. to move a molecule to the origin), it
reports the original centroid.

Cheers,
Charlie

--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310
35 Stirling Highway
Crawley WA 6009
Australia
[EMAIL PROTECTED]
+61 8 6488 4406

[ccp4bb] Laue for heavy atoms, etc.

[Bryan W. Lepore]

does anyone know of any reports where heavy atom positions were identified 
by any method (or mol. rep.) in a Laue data set (or sets)?


also - i thought there was some Laue work out there on watching virus 
nucleic acids move around in a crystal, so again, if anyone knows any 
references (or names, etc.)...


thx

-bryan

Re: [ccp4bb] rmsd calculation

[Douglas L. Theobald]

Jenny,

I of course would suggest that you follow Olve's advice, and use  
theseus to do a maximum likelihood, simultaneous superposition of all  
your structures ( http://www.theseus3d.org ).  The variable bits,  
like your loop, will be naturally down-weighted in a rigorous  
statistical manner.  Then you can look at the average structure file  
that is output (_ave.pdb at the end of the filename), and the B- 
factor column has the overall RMSD for each atom in there.  You can  
look at the full superposition (the _sup.pdb file) in rasmol or in  
pymol with the 'set all_states, on' command.


However, if you really need to do the very analysis that you asked  
about, the following bash script will do exactly that with theseus  
(you need both awk and theseus in your executable path).  It prints  
out the average RMSD for the atoms you specify in the loop, after  
pairwise least-squares superpositioning on all atoms other than the  
loop, for all possible pairwise combinations of your pdb files. (Note  
that in this script all backslashes '\' must have a carriage return  
immediately after them.)  You will need to change the lower and upper  
values at the top of the script (inclusive for the loop you want  
excluded).  You invoke the script something like "karen.sh pdb1.pdb  
pdb2.pdb pdb3.pdb" or "karen.sh *.pdb" to do all the .pdbs in one  
directory.  If you have any problems or have other specific  
superpositioning issues I'm glad to help out.


Cheers,

Douglas


karen.sh
#

#!/bin/bash

# everything including and between lower and upper
# is excluded from the superposition
lower=40;
upper=60;

pdbs=($*);

for (( i = 0; i < [EMAIL PROTECTED]; ++i ))
do
  for (( j = 0; j < i; ++j ))
  do
name="${pdbs[i]%.*}_${pdbs[j]%.*}";
theseus -l -r ${name} -S ${lower}-${upper} ${pdbs[i]} ${pdbs[j]}\
> ${name}.log;
rmsd=$(cut -c 7-11,61-67 ${name}_ave.pdb |\
awk '{if ($1 > lo && $1 < up) {sum += $2; n++}}; END {print sum/ 
n}'\

lo=${lower} up=${upper});
echo "${name} rmsd = ${rmsd}";
  done
done





^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`
Douglas L. Theobald
Department of Biochemistry
Brandeis University
Waltham, MA  02454-9110

[EMAIL PROTECTED]

 ^\
   /`  /^.  / /\
  / / /`/  / . /`
 / /  '   '
'


On May 11, 2007, at 1:58 PM, Olve Peersen wrote:

I would highly recommend Doug Theobald's program Theseus for this -  
the pictures at www.theseus3d.org say it all.  Theseus does maximum  
likely hood superimpositions of multiple structures (i.e. NOT  
pairwise against a "master" copy), and the real beauty of it is  
that you don't have to pick which residues you want to  
superimpose.  Places where the whole set of structures show  
divergence are effectively down-weighted and don't contribute much  
to the final solution vs. least squares where every atom position  
has equal weight and the "bad" parts screw up the alignment of the  
"good" parts.  For this, I would do a Theseus superposition of all  
the structures and then analyze the set of superimposed structures  
by whatever method you want (e.g. rmsd of variances in important  
sections of the structures).


- Olve

---
Olve Peersen
Associate Professor
Dept. of Biochemistry & Molecular Biology
1870 Campus Delivery
Colorado State University
Ft. Collins, CO  80523-1870
---
970.491-0433Office  (MRB 279)
970.491-0271Lab (MRB 149)
970.491-0494Fax
[EMAIL PROTECTED]
---

On May 11, 2007, at 11:15 AM, Donnie Berkholz wrote:


Eleanor Dodson wrote:
It is a bit clunky - you can use siperpose molecules - fit  
residues to
fit a selected range (1-40; 60-100 say) and write out a complete  
fitted

pdb file. Then you could use a VERY old program
compar  xyzin1 original.pdb xyzin2 fitted.pdb  (xyzin3 another.pdb)
and it will match all pairs with the same RESIDUE ID and give the  
RMSD

distance

There is documentation for it.


There's a nice (non-CCP4) program called ProFit that does a pretty  
nice

job of superimposing with a lot of flexibility.

Thanks,
Donnie



On May 10, 2007, at 6:45 PM, Jenny wrote:

Hi, All,

I have a question about rmsd calculation.

I have some pdbs (100 residues ) and these pdbs differ pretty  
much only the loop region 40-60. Is there any easy way that I can  
superimpose the fixed region ( 1-40,60-100) and then calculate  
the rmsd for the loop?I need to calculate for each pair, so if  
there is any script or program available to do this quickly, that  
would be great.


Thanks.

Jenny

Re: [ccp4bb] rmsd calculation

[Olve Peersen]

I would highly recommend Doug Theobald's program Theseus for this -  
the pictures at www.theseus3d.org say it all.  Theseus does maximum  
likely hood superimpositions of multiple structures (i.e. NOT  
pairwise against a "master" copy), and the real beauty of it is that  
you don't have to pick which residues you want to superimpose.   
Places where the whole set of structures show divergence are  
effectively down-weighted and don't contribute much to the final  
solution vs. least squares where every atom position has equal weight  
and the "bad" parts screw up the alignment of the "good" parts.  For  
this, I would do a Theseus superposition of all the structures and  
then analyze the set of superimposed structures by whatever method  
you want (e.g. rmsd of variances in important sections of the  
structures).


- Olve



---
Olve Peersen
Associate Professor
Dept. of Biochemistry & Molecular Biology
1870 Campus Delivery
Colorado State University
Ft. Collins, CO  80523-1870
---
970.491-0433Office  (MRB 279)
970.491-0271Lab (MRB 149)
970.491-0494Fax
[EMAIL PROTECTED]
---



On May 11, 2007, at 11:15 AM, Donnie Berkholz wrote:


Eleanor Dodson wrote:
It is a bit clunky - you can use siperpose molecules - fit  
residues to
fit a selected range (1-40; 60-100 say) and write out a complete  
fitted

pdb file. Then you could use a VERY old program
compar  xyzin1 original.pdb xyzin2 fitted.pdb  (xyzin3 another.pdb)
and it will match all pairs with the same RESIDUE ID and give the  
RMSD

distance

There is documentation for it.


There's a nice (non-CCP4) program called ProFit that does a pretty  
nice

job of superimposing with a lot of flexibility.

Thanks,
Donnie

Re: [ccp4bb] rmsd calculation

[Donnie Berkholz]

Eleanor Dodson wrote:
> It is a bit clunky - you can use siperpose molecules - fit residues to
> fit a selected range (1-40; 60-100 say) and write out a complete fitted
> pdb file. Then you could use a VERY old program
> compar  xyzin1 original.pdb xyzin2 fitted.pdb  (xyzin3 another.pdb)
> and it will match all pairs with the same RESIDUE ID and give the RMSD
> distance
> 
> There is documentation for it.

There's a nice (non-CCP4) program called ProFit that does a pretty nice
job of superimposing with a lot of flexibility.

Thanks,
Donnie



signature.asc
Description: OpenPGP digital signature

Re: [ccp4bb] quick question.... .

[Kerr, Iain]

Hi Jim,

MAPMAN from the Uppsala software factory will do this.

> re m1 ccp4.map
(FORMAT) CCP4


> wr m1 xplor.map
(FORMAT) X-PLOR


Check the new map is written out on the same scale, just talking to a
colleague I can't recall if any additional commands are required...

Best,
Iain

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
James Pauff
Sent: Friday, May 11, 2007 11:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] quick question .

Good day all,

First off, thank you all so much for your help a
couple days ago!  I just have a quick question
regarding the use of CCP4 to generate density maps. 
Is there a way to generate a map(s) that can be read
into PyMol?  I understand that PyMol can only read CNS
or XPLOR maps, is this correct?  Is there a means by
which I can output maps (on a Windows platform) in a
format that can be read by PyMol?

My only option in CCP4 is to create my FFT map in CCP4
format.

Thank you,
Jim


   

Boardwalk for $500? In 2007? Ha! Play Monopoly Here and Now
(it's updated for today's economy) at Yahoo! Games.
http://get.games.yahoo.com/proddesc?gamekey=monopolyherenow  

[ccp4bb] quick question... thanks

[James Pauff]

Thank you all, that was much easier than I expected.

Best,
Jim


   
Boardwalk
 for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's 
economy) at Yahoo! Games.
http://get.games.yahoo.com/proddesc?gamekey=monopolyherenow  

Re: [ccp4bb] quick question...

[Nicholas Noinaj]

Jim,

i actually think you can read in CCP4 maps, at least i have been doing it for 
some time now.

load *.map, format=ccp4

hope this helps.  best of luck.




cheers,
nick


-Original Message-
From: James Pauff <[EMAIL PROTECTED]>
To: CCP4BB@JISCMAIL.AC.UK
Date: Fri, 11 May 2007 09:06:21 -0700
Subject: [ccp4bb] quick question...

Good day all,

First off, thank you all so much for your help a
couple days ago!  I just have a quick question
regarding the use of CCP4 to generate density maps. 
Is there a way to generate a map(s) that can be read
into PyMol?  I understand that PyMol can only read CNS
or XPLOR maps, is this correct?  Is there a means by
which I can output maps (on a Windows platform) in a
format that can be read by PyMol?

My only option in CCP4 is to create my FFT map in CCP4
format.

Thank you,
Jim


   
Boardwalk
 for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's 
economy) at Yahoo! Games.
http://get.games.yahoo.com/proddesc?gamekey=monopolyherenow

[ccp4bb] quick question...

[James Pauff]

Good day all,

First off, thank you all so much for your help a
couple days ago!  I just have a quick question
regarding the use of CCP4 to generate density maps. 
Is there a way to generate a map(s) that can be read
into PyMol?  I understand that PyMol can only read CNS
or XPLOR maps, is this correct?  Is there a means by
which I can output maps (on a Windows platform) in a
format that can be read by PyMol?

My only option in CCP4 is to create my FFT map in CCP4
format.

Thank you,
Jim


   
Boardwalk
 for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's 
economy) at Yahoo! Games.
http://get.games.yahoo.com/proddesc?gamekey=monopolyherenow  

Re: [ccp4bb] xsect.dat=cossec.lib?

[Ethan Merritt]

On Friday 11 May 2007 00:57, Bernhard Rupp wrote:
> Dear Coders,
> 
> Do I see this correctly that crossec.lib
> is the XSECT.DAT file from Don Cromer's FPRIME
> program? If so, has there ever been an update? 

I do not know the history of crossec.lib, but the X-ray scattering
server
http://skuld.bmsc.washington.edu/scatter/AS_form.html

uses values from the Brennan & Cowen (1992) library that
are updated versions of the original Cromer work.

-- 
Ethan A MerrittCourier Deliveries: 1959 NE Pacific
Dept of Biochemistry
Health Sciences Building
University of Washington - Seattle WA 98195-7742

Re: [ccp4bb] . .

[Kerr, Iain]

Hi Emmanuel,

Perhaps a little more information ? 

What was the Z-score and LLG in PHASER ? I take it the translation
function solution is fairly well separated from the rest ? Are you sure
the spacegroup is correct ? How complete is the model before refinement
?
 
Not to be paranoid, but Hexagonal/Trigonal settings support merohedral
twinning...

best,
Iain

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Emmanuel Prata
Sent: Friday, May 11, 2007 10:27 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb]. .

Dear all,

I have a structure  (with 6 dissulphide bridges) at fairly low
resolution (3A) that I am trying to refine with Refmac. I've used
phaser with a template with 72% sequence identity. RFZ was 3.4 and TFZ
6.6, without clashes, with 80.7% of completeness. Space group was
p3121 (pointless) and Rmerge 0.12. When i tried refmac, Rfac drop to
24%, but Rfree only drop to 41%.
Can anybody explain this fact?

Thanks in advance,

Emmanuel Prata de Souza

[ccp4bb]

[Emmanuel Prata]

Dear all,

I have a structure  (with 6 dissulphide bridges) at fairly low
resolution (3A) that I am trying to refine with Refmac. I've used
phaser with a template with 72% sequence identity. RFZ was 3.4 and TFZ
6.6, without clashes, with 80.7% of completeness. Space group was
p3121 (pointless) and Rmerge 0.12. When i tried refmac, Rfac drop to
24%, but Rfree only drop to 41%.
Can anybody explain this fact?

Thanks in advance,

Emmanuel Prata de Souza

Re: [ccp4bb] Program to evaluate RNA torsion angles?

[Robert Immormino]

Forwarded from Jane Richardson:

Yuan Lin,

The sources you've been given (esp. the reduced-variable ones)
are excellent for identifying RNA structural motifs but not very good
for crystallographic validation, and the PDB tools are still primitive
for nucleic acids.  Fortunately, a suitable system is pretty far along
in development and partly available now.
The backbone committee of the RNA Ontology Consortium (our Duke
group, Helen Berman, Bohdan Schneider, Loren Williams, and Anna Marie
Pyle) has agreed on a nomenclature and a consensus set of valid
all-angle conformers for RNA backbone (soon to be published in RNA).
As part of that, we developed a program Suitename that will assign
those conformer names or declare an outlier for each suite
(sugar-to-sugar unit) in an RNA structure.  It will soon be part of
our MolProbity validation site (http://molprobity.biochem.duke.edu),
but we'd be glad to send it to you now in advance.  Already on
MolProbity you can get a quick and easy analysis of all-atom steric
clashes and probable bad sugar puckers (Davis 2007 NAR web issue, now
on-line), which can locate most of the backbone fitting errors.

Jane Richardson



- Show quoted text -



On Tue, 8 May 2007 19:41:13 -0400
"Robert Immormino" <[EMAIL PROTECTED]> wrote:

Forwarded Conversation
Subject: [ccp4bb] Program to evaluate RNA torsion angles?


From: Yuan Lin <[EMAIL PROTECTED]>
Reply-To: Yuan Lin <[EMAIL PROTECTED]>
To: CCP4BB@jiscmail.ac.uk
Date: Tue, May 8, 2007 at 5:08 PM

Dear All,
  I was wonder if anyone knows of a program for evaluating the
quality of
nucleic acid torsion angles in a manner comparable to a Ramachandran
plot
for proteins? I am working on an A-form dsRNA structure and there
are some
deviations from the average torsion angles for A-RNA, due to the
incorporation of an A-bulge. This might be silly, but how could I
know
whether those deviations are outrageous or not?

 Thanks very much!


Yuan



Yuan Lin
Biochemistry and Molecular Biology
Johns Hopkins University
Rm. W8702 BSPH
615 N. Wolfe St.
Baltimore, MD 21205
Ph. 443-287-4988


From: Das, Debanu <[EMAIL PROTECTED]>
Reply-To: "Das, Debanu" <[EMAIL PROTECTED]>
To: CCP4BB@jiscmail.ac.uk
Date: Tue, May 8, 2007 at 5:51 PM

This might be silly, but how could I know
whether those deviations are outrageous or not?


The following references may answer your questions:

1)

Sims GE, Kim SH.

Global mapping of nucleic acid conformational space: dinucleoside
monophosphate conformations and transition pathways among
conformational classes.
Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):618-21. Epub 2005 Jan
7.


2) Nucleic Acids Res.   2004 Mar 11;32(5):1666-77. RNA conformational classes,
Schneider B

, Moravek Z

, Berman HM

.


-Debanu.


From: William Scott <[EMAIL PROTECTED]>
Reply-To: William Scott <[EMAIL PROTECTED]>
To: CCP4BB@jiscmail.ac.uk
Date: Tue, May 8, 2007 at 5:54 PM

One option is to just use the tools available from the pdb (the
nucleic
acid database).

http://ndbserver.rutgers.edu

Another is Anna Marie Pyle's program Amigos.

http://www.csb.yale.edu/people/pyle/software

There are a lot of combinations consistent with A and B form
helices, so
this might be worth doing even if you use the first option.
[Quoted text hidden]



Richardson Lab
211 Nanaline Duke Bldg.
Duke U Med Ctr
Durham NC 27710-3711 USA
1-919-684-6010; fax 684-8885

On 5/8/07, Yuan Lin <[EMAIL PROTECTED]> wrote:

Dear All,
   I was wonder if anyone knows of a program for evaluating the quality of
nucleic acid torsion angles in a manner comparable to a Ramachandran plot
for proteins? I am working on an A-form dsRNA structure and there are some
deviations from the average torsion angles for A-RNA, due to the
incorporation of an A-bulge. This might be silly, but how could I know
whether those deviations are outrageous or not?

  Thanks very much!


Yuan



Yuan Lin
Biochemistry and Molecular Biology
Johns Hopkins University
Rm. W8702 BSPH
615 N. Wolfe St.
Baltimore, MD 21205
Ph. 443-287-4988

[ccp4bb] Filament Lifetime

[Mark Agacan]

I think the filament from one of our x-ray generators must be a record
breaker.  Yesterday it clocked up its 6000th  hour or 250th day on the
job, not counting down / holiday time.

The intensity had only dropped by around 25 % of the value it was when I
put it in, eight-and-a-half months ago...

Really, this filament is like the horror-movie bad guy who just won't
die - it survived countless power drop-outs and  surges, the rough
treatment of everyone from undergraduates to postdocs, and still it kept
on and on...

So, I decided to give it a break, as it has already smashed the Guinness
world record for filament lifetimes (I checked) - I removed and replaced
this beauty today, even though it's still working.

I thought about framing it and keeping it on display in the generator
lab for future generations to marvel at, but I got greedy - It will be
up on eBay soon.  Discounts available for academic institutions, etc

Have a nice weekend (it's my birthday!)

Cheers Rigaku!

Mark



_
Dr Mark Agacan
Scientific Officer,
Division of Biological Chemistry 
and Molecular Microbiology,
Wellcome Trust Biocentre,
College of Life Sciences,
Dow St., 
University of Dundee,
Dundee, DD1 5EH
Tel: +44 1382 388751
Fax: +44 1382 345764
_

Re: [ccp4bb] Molecular Replacement issues with a WD-40 7-bladed beta propeller

[Eleanor Dodson]

You dont say how close your sequence ID is for your new protein and the 
model.  It is often very hard to kick start refinement with low homology


And what about internal symmetry
Is there a Non crystallographic translation?
Does the self rotation function show a relationship between the two 
molecules?

Does it show the 7 fold symetry?
Maybe you can verify your solutions fit with anv NCS. ( This is often 
not easy!)

I use superpose molecules to a
) fit copy 1 to copy 2, and then
b) propellor blade 1 to 2 3 4 etc..

Then verify the rotation angles given are consistent with those in the 
self rotation function.
MOLREP and POLARRFN both give a complete list of symmetry equivalents 
for angles.


Then if the answer is right the struggle to refine begins..
 Eleanor




Scott Coyle wrote:

Hello,
I'm an undergraduate and recently crystallized and obtained 2.9A 
diffraction data for a protein which is predicted to fold into a WD40 
7-bladed beta-propeller structure (which has been crudely verified by 
cryo-EM by another lab). The space group appears to be I4(1) with unit 
cell parameters 118.936   118.93685.45690.00090.000
90.000. Using a number of different search models (which I trimmed and 
aligned to my protein's sequence using Chainsaw) I have obtained a 
number of MR solutions placing 2 molecules in the AU with Phaser with 
high Z-scores (ranging from Z=9 to 12) that seem to pack together 
nicely, so I was hoping to use this technique to solve my structure. 
However, the initial Rfree for my best solution is relatively high 
(0.49) and all attempts to refine the structure result in the Rfree 
blowing up almost immediately. This makes me worry that the maps I'm 
generating may be too model-biased to use to generate a solution. I've 
tried using Prime and Switch to remove model bias but the resulting 
map looks worse than the starting map. As the predicted structure 
possesses so much radial symmetry (7-fold), I'm worried that my MR 
solutions will never be oriented correctly enough for me to be able to 
build a model. If anyone has any suggestions for tackling this kind of 
molecular replacement woe, I would greatly appreciate it. Otherwise I 
guess I'll just plan to collect experimental phasing information 
sometime in the near future.


I'm not sure if this is the right place to be asking this question, 
perhaps you guys could direct me elsewhere.


Thanks!
-Scott

Re: [ccp4bb] Molecular Replacement issues with a WD-40 7-bladed beta propeller

[Matthew . Franklin]

CCP4 bulletin board  wrote on 05/10/2007 09:31:59
PM:

> Hello,
> I'm an undergraduate and recently crystallized and obtained 2.9A
> diffraction data for a protein which is predicted to fold into a WD40
> 7-bladed beta-propeller structure (which has been crudely verified by
> cryo-EM by another lab). The space group appears to be I4(1) with
> unit cell parameters 118.936   118.93685.45690.000
> 90.00090.000. Using a number of different search models (which I
> trimmed and aligned to my protein's sequence using Chainsaw) I have
> obtained a number of MR solutions placing 2 molecules in the AU with
> Phaser with high Z-scores (ranging from Z=9 to 12) that seem to pack
> together nicely, so I was hoping to use this technique to solve my
> structure. However, the initial Rfree for my best solution is
> relatively high (0.49) and all attempts to refine the structure
> result in the Rfree blowing up almost immediately. This makes me
> worry that the maps I'm generating may be too model-biased to use to
> generate a solution. I've tried using Prime and Switch to remove
> model bias but the resulting map looks worse than the starting map.
> As the predicted structure possesses so much radial symmetry (7-
> fold), I'm worried that my MR solutions will never be oriented
> correctly enough for me to be able to build a model. If anyone has
> any suggestions for tackling this kind of molecular replacement woe,
> I would greatly appreciate it. Otherwise I guess I'll just plan to
> collect experimental phasing information sometime in the near future.
>
> I'm not sure if this is the right place to be asking this question,
> perhaps you guys could direct me elsewhere.
>
> Thanks!
> -Scott


Hi Scott -

You can probably overcome the 7-fold symmetry problem manually.  I suggest
the following:

- Take a few of your search models that give the best solutions (are all
the solutions roughly superimposed?)

- Generate copies of the search model in each of the 7 orientations
corresponding to the 7-fold symmetry.  You might be able to generate a
symmetry operator to do this, but I'd probably just do it by eye using O or
something similar.

- Submit the rotated models to optimization using Phaser.  You'll use the
"Refinement and phasing" option in the GUI, or the "MODE MR_RNP" keyword in
the script file.  You'll feed Phaser a fake solution file (the .sol file)
with all Euler angles and fractional translations set to zero.

- Compare the resulting LLGs of the seven symmetry-related models.  With
luck, one of them will stand out from the others.  (Z-scores may not be
meaningful here - I forget whether Phaser calculates Z-score using a random
set of orientations, or just takes the mean and std. deviation of the
ensemble of solutions.)

- Take the best orientation (or all of them if one doesn't stand out) and
try Refmac refinement.  Again, one will hopefully look better than the
others.

Hope this works for you - it's certainly something to try while you're
trying to get derivatives...
And feel free to contact me if this wasn't clear enough for you to try it.

- Matt

--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116   fax:(212)645-2054


Confidentiality Note:  This e-mail, and any attachment to it, contains
privileged and confidential information intended only for the use of the
individual(s) or entity named on the e-mail.  If the reader of this e-mail
is not the intended recipient, or the employee or agent responsible for
delivering it to the intended recipient, you are hereby notified that
reading it is strictly prohibited.  If you have received this e-mail in
error, please immediately return it to the sender and delete it from your
system.  Thank you.

[ccp4bb] CNS problem: anneal.inp segmentation fault

[jean]

Hi all

 

Apologies for the non-ccp4 question - hopefully some of you who use CNS can
help me - I have a problem with anneal.inp in CNS:

 

When I run the anneal script for my structure containing novel ligand, the
program fails before the start of the torsion dynamics with no error message
- except SEGMENTATION FAULT at the bash commandline.

 

With "quiet" output, the last lines in the output file are:

 

 ASSFIL: file /usr/local/CNS/cns_solve_1.1/libraries/toppar/torsionmdmods
opened.

 MESSage=NORM

 EVALUATE: symbol $MESSAGE_OLD_TMOD set to "NORM" (string)

 ECHO=FALSe {OFF}

 EVALUATE: symbol $ECHO_OLD_TMOD set to FALSE (logical)

 NEXTCD: condition evaluated as false

 Program version= 1.1 File version= 1.1

 SELRPN:  0 atoms have been selected out of   4883

 

so the torsionmods routine (and everything before it) ran fine but the
torsion dynamics never started.

 

My pdb, mtf, top and par files all work fine for minimization so I don't
think there's anything wrong with them.

 

I have been using CNSv1.1 on this Linux machine for some time so it's not a
compile problem.

 

I can run the same routine on the same PC, from the same script, with the
same protein but with a different ligand and there's no fault.

 

Can anyone suggest a solution?  I've tried just about everything short of
running the whole script manually from the command line!

 

Sincerely

Jean Watermeyer

 

 

Re: [ccp4bb] rmsd calculation. .

[Miguel Ortiz Lombardia]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Excellent!
Thank you Gerard,


Miguel

Gerard DVD Kleywegt escribió:
>> But my understanding is that Iain's procedure gives the rmsds of the
>> _aligned_ C-alphas, whereas Jenny actually seems to be more interested
>> in those that she excludes from the alignment. I may be wrong, but in
>> these cases, I use lsqman (from DVD) or lsqkab (from ccp4) to superpose
>> the proteins (using one as reference) according to a particular scheme
>> (Jenny's 1-40,60-100) and then write a script to calculate the rmsds for
>> the "interesting" 41-59 residues. There may be an easier way, which I'll
>> be interested to learn about.
> 
> hola miguel,
> 
> i would use the rmsd command in lsqman, like so:
> 
>   read m1 m1.pdb
>   read m2 m2.pdb
>   expl m1 "a1-40 a60-100" m2 "a1 a60"
>   rmsd m1 a41-59 m2 a41
> 
> --gerard
> 
> **
> Gerard J.  Kleywegt
> [Research Fellow of the Royal  Swedish Academy of Sciences]
> Dept. of Cell & Molecular Biology  University of Uppsala
> Biomedical Centre  Box 596
> SE-751 24 Uppsala  SWEDEN
> 
> http://xray.bmc.uu.se/gerard/  mailto:[EMAIL PROTECTED]
> **
>The opinions in this message are fictional.  Any similarity
>to actual opinions, living or dead, is purely coincidental.
> **
> 
> 

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: [EMAIL PROTECTED]
www: http://www.pangea.org/mol/spip.php?rubrique2
~~~
Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie.  (Raoul Vaneigem)
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.6 (GNU/Linux)

iD8DBQFGRDtWF6oOrDvhbQIRAiYIAJ9Zsh5KNyqzfWhz2WaaRYlRUfKXTwCeLQOK
YtSKkl+Q4N3TF8MganziUDs=
=TWIp
-END PGP SIGNATURE-

Re: [ccp4bb] CCP4 GUI

[Liz Potterton]

Dear CCP4bb,

The intention with CCP4i GUIs is that those folders which are open by 
default (after you have chosen the mode of action from the top protocol 
folder) are for everyone and those that are closed by default are for 
experts OR difficult cases. Unfortunately that is an OR not an AND; the 
crystal fairies are not especially kind to students. I usually suggest 
that newcomers to a particular program should at least make sure they 
understand the options in the open folders before running the program.  
Even within individual folders we try to put the regular stuff at the top.


Ideally, I think program developers, rather than users or CCP4i 
maintainers, should suggest which options to put on the GUI and which 
'advanced' options to leave off.  Then when you say you are using 
non-GUI options we will be sure that you are boasting and not 
complaining (-;.


Liz



Clemens Vonrhein wrote:

On Thu, May 10, 2007 at 02:46:44PM +0100, Kolstoe S.E. wrote:
  

The most useful aspect of the ccp4i GUI is its automatic generation of
com files. However, I would prefer the GUI to output a .com file into my
working directory (rather than the obscure location they are saved to
now) every time I run a program so that I can then tinker with it and
add any extra keywords I want to.



I often use the GUI to get a 'second opinion' about good default
values and options for a given CCP4 program - especially if the
documentation is a bit confusing. Kind of double-checking if I
understood the documentation correctly.

One thing I found very confusing though, is that the com-files created
by the CCP4i will often have (nearly) all possible keywords set, even
if I haven't changed any of the defaults in the gui. Often, a CCP4
program has defaults itself and only requires keywords if one wants to
change things - which is nice, since it leads e.g. to a very short
SCALA comand-file. I'm not always convinced that the settings done by
the CCP4i interface (when keeping all edfaults) correspond to the
defaults as implemented in the program itself.

Maybe any parameter setting unchanged from the values in the
$CCP4/ccp4i/tasks/*.def file should be internally flagged as being at
the 'default value' - resulting in them _not_ being written to the
com-file? This way any potential change in defaults inside the actual
program would have immediate effect, even if the CCP4i hasn't been
updated yet.

Cheers

Clemens

  

Re: [ccp4bb] CCP4 GUI

[Phil Evans]

I would agree with Clemens that the Scala GUI task generates far too  
many keyworded commands, for things which have sensible defaults in  
the program.


One problem conundrum for the GUI  (because it works by generating a  
script without actually running the program) is that the GUI has no  
way of knowing what defaults are set in the program (particularly if  
they are dynamic depending on the data). But this could be managed  
better than it is in all cases.


Phil

On 11 May 2007, at 08:31, Clemens Vonrhein wrote:


On Thu, May 10, 2007 at 02:46:44PM +0100, Kolstoe S.E. wrote:
The most useful aspect of the ccp4i GUI is its automatic  
generation of
com files. However, I would prefer the GUI to output a .com file  
into my

working directory (rather than the obscure location they are saved to
now) every time I run a program so that I can then tinker with it and
add any extra keywords I want to.


I often use the GUI to get a 'second opinion' about good default
values and options for a given CCP4 program - especially if the
documentation is a bit confusing. Kind of double-checking if I
understood the documentation correctly.

One thing I found very confusing though, is that the com-files created
by the CCP4i will often have (nearly) all possible keywords set, even
if I haven't changed any of the defaults in the gui. Often, a CCP4
program has defaults itself and only requires keywords if one wants to
change things - which is nice, since it leads e.g. to a very short
SCALA comand-file. I'm not always convinced that the settings done by
the CCP4i interface (when keeping all edfaults) correspond to the
defaults as implemented in the program itself.

Maybe any parameter setting unchanged from the values in the
$CCP4/ccp4i/tasks/*.def file should be internally flagged as being at
the 'default value' - resulting in them _not_ being written to the
com-file? This way any potential change in defaults inside the actual
program would have immediate effect, even if the CCP4i hasn't been
updated yet.

Cheers

Clemens

--

***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park
*  Cambridge CB3 0AX, UK
*--
* BUSTER Development Group  (http://www.globalphasing.com)
***

Re: [ccp4bb] xsect.dat=cossec.lib?

[Eleanor Dodson]

Bernhard Rupp wrote:

Dear Coders,

Do I see this correctly that crossec.lib
is the XSECT.DAT file from Don Cromer's FPRIME
program? If so, has there ever been an update? 
Mine is from some reel tape I got from him long ago

when I ported the code...seems to be the same.

Thx, br

Bernhard Rupp
www.ruppweb.org  




  

I believe that is so - Eleanor

Re: [ccp4bb] rmsd calculation

[Eleanor Dodson]

It is a bit clunky - you can use siperpose molecules - fit residues to 
fit a selected range (1-40; 60-100 say) and write out a complete fitted 
pdb file. Then you could use a VERY old program

compar  xyzin1 original.pdb xyzin2 fitted.pdb  (xyzin3 another.pdb)
and it will match all pairs with the same RESIDUE ID and give the RMSD 
distance


There is documentation for it.
Eleanor


Jenny wrote:

Hi, All,

I have a question about rmsd calculation.

I have some pdbs (100 residues ) and these pdbs differ pretty much 
only the loop region 40-60. Is there any easy way that I can 
superimpose the fixed region ( 1-40,60-100) and then calculate the 
rmsd for the loop?I need to calculate for each pair, so if there is 
any script or program available to do this quickly, that would be great.


Thanks.

Jenny 

Re: [ccp4bb] CCP4 GUI

[Kevin Cowtan]

Clemens Vonrhein wrote:

One thing I found very confusing though, is that the com-files created
by the CCP4i will often have (nearly) all possible keywords set, even
if I haven't changed any of the defaults in the gui. Often, a CCP4
program has defaults itself and only requires keywords if one wants to
change things - which is nice, since it leads e.g. to a very short
SCALA comand-file. I'm not always convinced that the settings done by
the CCP4i interface (when keeping all edfaults) correspond to the
defaults as implemented in the program itself.


This of course depends on whether the program author wrote their best 
set of defaults into the GUI or the program, which in turn depends on 
whether the program author wrote the GUI or not.


I tend to assume that everyone is running through the GUI these days, 
and make sure that the GUI defaults are the sensible ones (although I 
try and keep the program source in step). If someone asks me how best to 
run one of my programs, the answer is therefore to use the GUI to 
generate a command script and start from there.


Kevin

Re: [ccp4bb] CCP4 GUI

[Harry Powell]

Hi

> Maybe any parameter setting unchanged from the values in the
> $CCP4/ccp4i/tasks/*.def file should be internally flagged as being at
> the 'default value' - resulting in them _not_ being written to the
> com-file? This way any potential change in defaults inside the actual
> program would have immediate effect, even if the CCP4i hasn't been
> updated yet.

This is a _really_ good idea for another reason. There are programs which
determine processing parameter values dyamically, based on what they have
actually been presented with - UNLESS those values have been input by the
user, who is assumed to "know better". If an interface (e.g. ccp4i) sets
the value to a default, the program really has no way of knowing that it
was the interface and not a user who knows their data which has input the
value.

Just my two ha'porth...

Harry
-- 
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH

[ccp4bb] xsect.dat=cossec.lib?

[Bernhard Rupp]

Dear Coders,

Do I see this correctly that crossec.lib
is the XSECT.DAT file from Don Cromer's FPRIME
program? If so, has there ever been an update? 
Mine is from some reel tape I got from him long ago
when I ported the code...seems to be the same.

Thx, br

Bernhard Rupp
www.ruppweb.org  

Re: [ccp4bb] Molecular Replacement issues with a WD-40 7-bladed beta propeller

[Dirk Kostrewa]

Hello Scott,

hmmm - it is quite difficult to do a good analysis of your problem, 
remotely. You've tried the enantiomorphic space group I4(3), just to be 
sure? In principle, the molecular replacement solution given by Phaser 
sounds good, but this is no proof of whether it's correct. What sounds 
good is, that you have high Z-scores, the packing looks good to you and 
the starting R-factor is quite low, not high! For a first model, the 
working-R and Free-R are usually very close (the initial unrefined model 
explains the whole set and a random subset equally well), and it is 
normal, that the Free-R rises in the first xyzB refinement cycles (the 
free set "decouples" from the working set, so to say). You don't say how 
much it rises, but make sure that you use _very_ tight geometry 
restraints at this resolution to reduce overfitting. I suggest a 
starting weight of 0.01 or even 0.005 for the X-ray term, resulting in 
final RMSD values for the bonds of ~0.010-0.012 (there is no exact 
rule). Your could also use tight NCS restraints for the two molecules to 
even further reduce any potential overfitting. In contrast, you can 
leave the B-factor restraints as they are, or even loosen their 
restraints (I use always values of 2.0, 3.0, 4.5, 6.0 - you can find 
them in REFMAC under the Geometrical Parameters tab)! On one hand, this 
gives the model more freedom which could potentially result in more 
overfitting, on the other hand, however, this additional freedom, at 
least in my experience, effectively _reduces_ model bias by allowing 
wrongly placed atoms to vanish. In general, for molecular replacement, 
never believe any "solution" until you see the resulting electron 
density maps. For a true solution, the electron densities should tell 
you, which parts are wrong and which are missing. At 2.9 A, resolution, 
this might be difficult. I would suggest that you look at the 
NCS-averaged electron density map in Coot.

However, there could be a lot of other problems ...
I would suggest that you could find a local crystallographer at Berkeley 
that helps you on site.


I hope that helps a little bit.

Good luck,

Dirk.

Scott Coyle wrote:

Hello,
I'm an undergraduate and recently crystallized and obtained 2.9A 
diffraction data for a protein which is predicted to fold into a WD40 
7-bladed beta-propeller structure (which has been crudely verified by 
cryo-EM by another lab). The space group appears to be I4(1) with unit 
cell parameters 118.936   118.93685.45690.00090.000
90.000. Using a number of different search models (which I trimmed and 
aligned to my protein's sequence using Chainsaw) I have obtained a 
number of MR solutions placing 2 molecules in the AU with Phaser with 
high Z-scores (ranging from Z=9 to 12) that seem to pack together 
nicely, so I was hoping to use this technique to solve my structure. 
However, the initial Rfree for my best solution is relatively high 
(0.49) and all attempts to refine the structure result in the Rfree 
blowing up almost immediately. This makes me worry that the maps I'm 
generating may be too model-biased to use to generate a solution. I've 
tried using Prime and Switch to remove model bias but the resulting map 
looks worse than the starting map. As the predicted structure possesses 
so much radial symmetry (7-fold), I'm worried that my MR solutions will 
never be oriented correctly enough for me to be able to build a model. 
If anyone has any suggestions for tackling this kind of molecular 
replacement woe, I would greatly appreciate it. Otherwise I guess I'll 
just plan to collect experimental phasing information sometime in the 
near future.


I'm not sure if this is the right place to be asking this question, 
perhaps you guys could direct me elsewhere.


Thanks!
-Scott



--


Dirk Kostrewa
Paul Scherrer Institut
Biomolecular Research, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone:  +41-56-310-4722
Fax:+41-56-310-5288
E-mail: [EMAIL PROTECTED]
http://sb.web.psi.ch

Re: [ccp4bb] CCP4 GUI

[Clemens Vonrhein]

On Thu, May 10, 2007 at 02:46:44PM +0100, Kolstoe S.E. wrote:
> The most useful aspect of the ccp4i GUI is its automatic generation of
> com files. However, I would prefer the GUI to output a .com file into my
> working directory (rather than the obscure location they are saved to
> now) every time I run a program so that I can then tinker with it and
> add any extra keywords I want to.

I often use the GUI to get a 'second opinion' about good default
values and options for a given CCP4 program - especially if the
documentation is a bit confusing. Kind of double-checking if I
understood the documentation correctly.

One thing I found very confusing though, is that the com-files created
by the CCP4i will often have (nearly) all possible keywords set, even
if I haven't changed any of the defaults in the gui. Often, a CCP4
program has defaults itself and only requires keywords if one wants to
change things - which is nice, since it leads e.g. to a very short
SCALA comand-file. I'm not always convinced that the settings done by
the CCP4i interface (when keeping all edfaults) correspond to the
defaults as implemented in the program itself.

Maybe any parameter setting unchanged from the values in the
$CCP4/ccp4i/tasks/*.def file should be internally flagged as being at
the 'default value' - resulting in them _not_ being written to the
com-file? This way any potential change in defaults inside the actual
program would have immediate effect, even if the CCP4i hasn't been
updated yet.

Cheers

Clemens

-- 

***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--
* BUSTER Development Group  (http://www.globalphasing.com)
***

Re: [ccp4bb] CCP4 GUI

[Clemens Vonrhein]

Hi Martyn & Dirk,

On Thu, May 10, 2007 at 02:18:14PM +0200, Dirk Kostrewa wrote:
> I want to second Miguel: a switch between a "basic" GUI (could be with 
> even less options) and an  "advanced" and "expert" GUI that allows 
> access to most and all options that can be used in scripts would be 
> absolutely great! It would allow novice users to do a good job on 
> "standard" problems, and gives experienced users the freedom to use any 
> option of a program in more difficult cases. A similar idea is 
> implemented in the SUSHI GUI of SHARP, where such a switch allows you to 
> change less or more phase refinement and improvement parameters.

What we do there is to always present all options: but depending on
the level (beginner, advanced, expert) a user has declared him/herself
some might be greyed out. This way even a beginner will see that there
are more options - and (most importantly) gets the help messages and
explanations for those advanced options. But only a few items can be
changed by a beginner.

So if the CCP4i would get a beginner/advanced/expert mode I think it
would be best to try and adopt this idea (greying out boxes) if
possible. If expert options are just collected and placed into a
spearate 'folder' widget they would loose their position within some
logical, crystallographic context, making it possibly more confusing
to understand what they mean.

Cheers

Clemens

-- 

***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--
* BUSTER Development Group  (http://www.globalphasing.com)
***