Re: [ccp4bb] rmsd calculation. .

[Miguel Ortiz Lombardia]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Jenny and Iain,

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.

Cheers,


M.

Kerr, Iain escribió:
> Hi Jenny,
> 
>  
> 
> You can do this in LSQMAN (if I’m understanding your question correctly…)
> 
>  
> 
> You’d first superimpose the residues in the “fixed region” to give a
> superimposed core using the ‘EXplicit’ command, eg:
> 
>  
> 
> *LSQMAN > ex m1*
> 
> * Range 1 ? (A1-10) "a4-10 a19-23 a28-36 a44-51 a53-66 a91-97 a106-111 
> a123:126"*
> 
> * Mol 2 ? (M1) m2*
> 
> * Range 2 ? (A1) "a4 a19 a28 a44 a53 a91 a106 a123"*
> 
> * Explicit fit of M1 "A4-10 A19-23 A28-36 A44-51 A53-66 A91-97 A106-111 
> A123:126"*
> 
> * And M2 "A4 A19 A28 A44 A53 A91 A106 A123"*
> 
> * Atom types | CA | N  | C  | O  | CB |*
> 
> * Nr of atoms to match : (295)*
> 
> * The295 atoms have an RMS distance of0.892 A*
> 
> * Rotation:  -0.956932  0.127723 -0.260706*
> 
> * 0.170532 -0.479456 -0.860837*
> 
> *-0.234946 -0.868222  0.437026*
> 
> * Translation : 13.78726.80038.541*
> 
>  
> 
>  
> 
> Then use the “IMProve” command to iteratively improve the fit over all
> CAs…this only works for two molecules at a time though…I guess choose a
> fixed standard to align all the others against. Remember to write out
> the coordinates for the rotated (ie. “m2”) molecules:
> 
>  
> 
> Ø   apply m1 m2
> 
> Ø   wr m2 blah_rotated.pdb
> 
>  
> 
> Then to calculate the RMSDs for just the loop regions compare the
> superimposed molecules to the fixed standard (ie. “m1” is the fixed
> standard, “m2” is your blah_rotated.pdb), explicitly using just the loop
> atoms this time in “m1” and “m2” ranges.
> 
>  
> 
> I’m sure there is an easier way to do this, but works for me.
> 
>  
> 
> HTH,
> 
> Iain
> 
>  
> 
>  
> 
> 
> 
> *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of
> *Jenny
> *Sent:* Thursday, May 10, 2007 5:46 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] rmsd calculation. .
> 
>  
> 
> 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
> 

- --
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)
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JkvZQL9IHdB+ENi92nVVUmI=
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[ccp4bb] Molecular Replacement issues with a WD-40 7-bladed beta propeller

[Scott Coyle]

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

Re: [ccp4bb] rmsd calculation. .

[Kerr, Iain]

Hi Jenny,

 

You can do this in LSQMAN (if I'm understanding your question
correctly...)

 

You'd first superimpose the residues in the "fixed region" to give a
superimposed core using the 'EXplicit' command, eg:

 

LSQMAN > ex m1
 Range 1 ? (A1-10) "a4-10 a19-23 a28-36 a44-51 a53-66 a91-97 a106-111
a123:126"
 Mol 2 ? (M1) m2
 Range 2 ? (A1) "a4 a19 a28 a44 a53 a91 a106 a123"
 Explicit fit of M1 "A4-10 A19-23 A28-36 A44-51 A53-66 A91-97 A106-111
A123:126"
 And M2 "A4 A19 A28 A44 A53 A91 A106 A123"
 Atom types | CA | N  | C  | O  | CB |
 Nr of atoms to match : (295)
 The295 atoms have an RMS distance of0.892 A
 Rotation:  -0.956932  0.127723 -0.260706
 0.170532 -0.479456 -0.860837
-0.234946 -0.868222  0.437026
 Translation : 13.78726.80038.541

 

 

Then use the "IMProve" command to iteratively improve the fit over all
CAs...this only works for two molecules at a time though...I guess
choose a fixed standard to align all the others against. Remember to
write out the coordinates for the rotated (ie. "m2") molecules:

 

*   apply m1 m2

*   wr m2 blah_rotated.pdb

 

Then to calculate the RMSDs for just the loop regions compare the
superimposed molecules to the fixed standard (ie. "m1" is the fixed
standard, "m2" is your blah_rotated.pdb), explicitly using just the loop
atoms this time in "m1" and "m2" ranges.

 

I'm sure there is an easier way to do this, but works for me.

 

HTH,

Iain

 

 



From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Jenny
Sent: Thursday, May 10, 2007 5:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] rmsd calculation. .

 

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 

[ccp4bb] rmsd calculation

[Jenny]

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

[Winn, MD (Martyn)]

That kind of thing has been suggested a few times, and in principle is 
a better way of doing things. 
One problem we face, is that we're a collaboration rather than a single
project, and it is not always possible to adopt neat solutions across the 
suite. Which is partly why ccp4i was designed to be totally separate from
the underlying programs.

I should stress that I'm not offering to do all the ideas raised today ;-)  
(I'm already behind on enough projects). But we'll try to fix a few things soon 
within the current ccp4i design. The other suggestions from today will go into 
the melting pot for longer term development (my plan b from earlier).

But we do appreciate the ideas and feedback.

Cheers
Martyn


-Original Message-
From: CCP4 bulletin board on behalf of Peter Adrian Meyer
Sent: Thu 5/10/2007 5:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4 GUI
 
Hopefully my offhand remark wasn't taken as a criticism of ccp4i (it
wasn't meant as such); but seeing as I don't use it, it's not a place
where I could tell someone how to find an option.

> As developers, we also have to think about long-term maintainability.
> Options, in particular little-used options, can soon become out-of-date.

This is might be a bad idea*, but I'll throw it out there anyhow:  What
about the storing program keywords in a grammer file (something along the
lines of yacc/lex), reading gui options from the grammer, and generating a
parser subroutine from the grammer for the data-processing programs?
This would mean changes to the parser library (and to a large number of
existing programs which already work), but would eliminate the issue of
keeping the gui options in sync with the program options.


Pete

*specifically, bad idea type #2 - probably more trouble than it's worth

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Re: [ccp4bb] CCP4 GUI

[Peter Adrian Meyer]

Hopefully my offhand remark wasn't taken as a criticism of ccp4i (it
wasn't meant as such); but seeing as I don't use it, it's not a place
where I could tell someone how to find an option.

> As developers, we also have to think about long-term maintainability.
> Options, in particular little-used options, can soon become out-of-date.

This is might be a bad idea*, but I'll throw it out there anyhow:  What
about the storing program keywords in a grammer file (something along the
lines of yacc/lex), reading gui options from the grammer, and generating a
parser subroutine from the grammer for the data-processing programs?
This would mean changes to the parser library (and to a large number of
existing programs which already work), but would eliminate the issue of
keeping the gui options in sync with the program options.


Pete

*specifically, bad idea type #2 - probably more trouble than it's worth

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

[ccp4bb] Biophysicist position in crystallography at LBNL, SF Bay Area

[Amy Pagsolingan]

*PROTEIN CRYSTALLOGRAPHER*
Job # 20546

The X-ray Crystallography Team of the Integrated Center for Structure 
and Function Innovation (ISFI), has an immediate opening for a scientist 
level protein crystallographer at the Lawrence Berkeley National 
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PSI-2 specialized technology center, funded through the Protein 
Structure Initiative of the National Institutes of Health (See 
http://www.nigms.nih.gov/psi/)


*Key Responsibilities:* The successful candidate will have the 
opportunity to become the primary contact of the ISFI crystallization 
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will assist PI with training and managing the work flow of other 
technical staff.  The preferred candidate should possess the potential 
to initiate independent projects in the framework of structural biology 
or structural genomics.


*Qualifications:*  Significant experience in protein crystallization and 
x-ray diffraction data collection is required.  The candidate must have 
the ambition and desire to automate procedures for routine tasks.  
Excellent written communication, organizational, and analytical skills, 
and the ability to work in a team environment are required. Experience 
in molecular biology and/or computer system management is a plus.  A 
Ph.D. with 2 or more years of successful postdoctoral experience in 
Biophysics, Chemistry, Biochemistry, Molecular Biology, or a related 
area is preferred.


*Note: *This is a career-track term appointment, renewable based on 
funding availability and employee performance.


Lawrence Berkeley National Laboratory (LBNL) is a world leader in 
science and engineering research, with 11 Nobel Prize recipients over 
the past 75 years, and 59 present members of the National Academy of 
Sciences. LBNL conducts unclassified research across a wide range of 
scientific disciplines and hosts four national user facilities. Learn 
more at www.lbl.gov .

*
**To inquire about this position, please contact Dr. Li-Wei Hung at 
[EMAIL PROTECTED] .*


*Please apply* at 
_http://jobs.lbl.gov/LBNLCareers/details.asp?jid=20546&p=1 
_ in order to 
be considered for this opportunity. Submit a single attachment including 
your résumé or CV and cover letter, using Internet Explorer for best 
compatibility with our system.


Reference "Professional Organization" and "CCP4BB" as your source.

--

Amy Pagsolingan, PHR
Senior Recruiter
Lawrence Berkeley National Laboratory
http://jobs.lbl.gov 
510-486-5277 (phone)

Re: [ccp4bb] CCP4 GUI

[William Scott]

Hi Martyn:

I never use the GUI and it scares me, so I probably should just STFU, but
that sort of thing has never kept me from pontificating. I often get 
emails from people asking how to do something with the GUI and they don't
believe me, because I've developed a reputation as something of a Mac OS X
shill.  The Mac OS X GUI (and newer Linux desktops like Xfce) are nice 
because they are unobtrusive.  The CCP4 GUI, at least back when I decided 
to try it, seemed to always fight me and try to make me do stuff I don't 
want to do, and I already have a wife.

The worst GUI I have seen is the one with Phenix.  Which is odd, because 
it has the best command-line experience. I think the file parsing and IO 
is part of the open-source portion of the project (CCTBX) and since that 
is already an optional distribution with CCP4, may I humbly suggest 
tighter integration with the existing CCP4 suit?  

If that happens, a parsing editor for the def file is really all you would 
probably need for a GUI.


Bill





On Thu, 10 May 2007, Martyn Winn wrote:

 This is timely. We're in the process of a) trying to organise a major
 effort to tidy up the existing ccp4i classic (rather than fire-fighting
 problems), and b) thinking about designing the next generation. Not sure
 which this is. Option b) would be a project over several years. 
 
 Can you elucidate further. As an expert user, would you want a less
 scary free text box (which is essentially what Run&View Com File is), or
 actual widgets for every option. The latter could be done as a hidden
 folder, made visible according to an Expert switch in Preferences. 
 
 As developers, we also have to think about long-term maintainability.
 Options, in particular little-used options, can soon become out-of-date.
 
 m
 
 
 On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote:
 > -BEGIN PGP SIGNED MESSAGE-
 > Hash: SHA1
 > 
 > Dear all,
 > 
 > I'm a well-known luddite as Eleanor says. However, I shamelessly confess
 > that the CCP4 GUI is great. Not that I think this is necessary here, I'm
 > sure most people agree with that.
 > 
 > If I write now is because Martynn's e-mail have reminded me of something
 > I thought once, but forgot to ask for to the ccp4i developpers: perhaps
 > the GUI could have "two faces/modes", a basic one and an expert/advanced
 > one. I understand that they already exist, but the "expert" one is
 > hidden under the "Run&View Com File", while I'm thinking on a real
 > expert GUI-mode. Users should be able to choose one or the other in
 > their defaults, or switch from one to the other on-the-fly.
 > 
 > I don't have a particular problem in editing the scripts as it is done
 > now, but I have found that students tend to get a bit nervous about
 > doing it themselves ;-)
 > 
 > Cheers,
 > 
 > 
 > Miguel
 > 
 > Martyn Winn escribió:
 > > The level of detail in the GUI is a matter of constant debate. The
 > > underlying programs are far far richer, so the question is how much to
 > > expose in the GUI. We try to get a balance between ease-of-use and
 > > coverage, but it won't always work. BTW I don't think we ever claimed
 > > that ccp4i (or anything else in ccp4) is "finished" ;-)
 > > 
 > > Having said that, we're always happy to hear about specific defects in
 > > the GUI. When reporting these to [EMAIL PROTECTED] please give as much
 > > information as possible, in particular knowing the context is always
 > > helpful.
 > > 
 > > Cheers
 > > Martyn
 > > 
 

Re: [ccp4bb] CCP4 GUI

[Juergen Bosch]

Hi Tim,

I just had a conversation with somebody who pointed that out to me, that 
tells you how much I use the GUI :-)

Thanks,

Juergen

Tim Grune wrote:

As long as I have been using the ccp4i (which has been a couple of 
years now), this magic button has been there, and it has even been in 
the 'lower left corner': When you hold your mouse button on the "Run" 
button, a submenu appears, the second item of which is saying 
"Run&View com file". This opens an editable window with the script 
used to run the ccp4-program.


 
This, by the way, is very handy for setting the matrix weight in 
Refmac5 to 'auto', as recommended by the authors of ARP/wARP.
 
Tim


-Original Message-
From: Roger Rowlett <[EMAIL PROTECTED]>
To: CCP4BB@JISCMAIL.AC.UK
Date: Thu, 10 May 2007 10:44:13 -0400
Subject: Re: [ccp4bb] CCP4 GUI

I think a "tweak script" button or option (before running) would
be an excellent idea.

Cheers,

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

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [EMAIL PROTECTED]


-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf
Of Juergen Bosch
Sent: Thursday, May 10, 2007 10:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4 GUI


Hi Martyn,

how about option c:

in each gui window at the lower left corner have a button called
"Display script", or call it "Expert Mode" if people feel better as
"Experts" :-) , before running of course. Then people who would
like to
edit their stuff could do so before running the script. I think it
would
be scary to many if the "Expert Mode" actually would display all
other
options available for that particular program - for this you have
the RTFM*

I tend to use the GUI only for standard stuff and keep migrating my
scripts from directories to directories, which if you run a search on
say e.g. "refmac." spits out a ton of handcrafted scripts for each
project - maybe also not the best thing to do, but that's how it is.

Juergen

* Fine of course, what else !

Martyn Winn wrote:

>This is timely. We're in the process of a) trying to organise a
major
>effort to tidy up the existing ccp4i classic (rather than
fire-fighting
>problems), and b) thinking about designing the next generation. Not
>sure which this is. Option b) would be a project over several years.
>
>Can you elucidate further. As an expert user, would you want a less
>scary free text box (which is essentially what Run&View Com File
is),
>or actual widgets for every option. The latter could be done as a
>hidden folder, made visible according to an Expert switch in
>Preferences.
>
>As developers, we also have to think about long-term
maintainability.
>Options, in particular little-used options, can soon become
>out-of-date.
>
>m
>
>
>On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote:
>  
>

>>-BEGIN PGP SIGNED MESSAGE-
>>Hash: SHA1
>>
>>Dear all,
>>
>>I'm a well-known luddite as Eleanor says. However, I shamelessly
>>confess that the CCP4 GUI is great. Not that I think this is
necessary
>>here, I'm sure most people agree with that.
>>
>>If I write now is because Martynn's e-mail have reminded me of
>>something I thought once, but forgot to ask for to the ccp4i
>>developpers: perhaps the GUI could have "two faces/modes", a
basic one
>>and an expert/advanced one. I understand that they already
exist, but
>>the "expert" one is hidden under the "Run&View Com File", while I'm
>>thinking on a real expert GUI-mode. Users should be able to
choose one
>>or the other in their defaults, or switch from one to the other
>>on-the-fly.
>>
>>I don't have a particular problem in editing the scripts as it
is done
>>now, but I have found that students tend to get a bit nervous about
>>doing it themselves ;-)
>>
>>Cheers,
>>
>>
>>Miguel
>>
>>Martyn Winn escribió:
>>
>>

>>>The level of detail in the GUI is a matter of constant debate. The
>>>underlying programs are far far richer, so the question is how
much
>>>to expose in the GUI. We try to get a balance between
ease-of-use and
>>>coverage, but it won't always work. BTW I don't think we ever
claimed
>>>that ccp4i (or anything else in ccp4) is "finished" ;-)
>>>
>>>Having said that, we're always happy to hear about specific
defects
>>>in the GUI. When reporting these to [EMAIL PROTECTED] please give
as much
>>>information as possible, in particular knowing the context is
always

Re: [ccp4bb] CCP4 GUI

[Tim Grune]

As long as I have been using the ccp4i (which has been a couple of years 
now), this magic button has been there, and it has even been in the 'lower 
left corner': When you hold your mouse button on the "Run" button, a submenu 
appears, the second item of which is saying "Run&View com file". This opens 
an editable window with the script used to run the ccp4-program.

This, by the way, is very handy for setting the matrix weight in Refmac5 to 
'auto', as recommended by the authors of ARP/wARP.

Tim


-Original Message-

From: Roger Rowlett <[EMAIL PROTECTED]>

To: CCP4BB@JISCMAIL.AC.UK

Date: Thu, 10 May 2007 10:44:13 -0400

Subject: Re: [ccp4bb] CCP4 GUI




I think a "tweak script" button or option (before running) would be an 
excellent idea.



Cheers,



___

Roger S. Rowlett

Professor

Department of Chemistry

Colgate University

13 Oak Drive

Hamilton, NY 13346



tel: (315)-228-7245

ofc: (315)-228-7395

fax: (315)-228-7935

email: [EMAIL PROTECTED]





-Original Message-

From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of 
Juergen Bosch

Sent: Thursday, May 10, 2007 10:40 AM

To: CCP4BB@JISCMAIL.AC.UK

Subject: Re: [ccp4bb] CCP4 GUI





Hi Martyn,



how about option c:



in each gui window at the lower left corner have a button called 

"Display script", or call it "Expert Mode" if people feel better as 

"Experts" :-) , before running of course. Then people who would like to 

edit their stuff could do so before running the script. I think it would 

be scary to many if the "Expert Mode" actually would display all other 

options available for that particular program - for this you have the RTFM*



I tend to use the GUI only for standard stuff and keep migrating my 

scripts from directories to directories, which if you run a search on 

say e.g. "refmac." spits out a ton of handcrafted scripts for each 

project - maybe also not the best thing to do, but that's how it is.



Juergen



* Fine of course, what else !



Martyn Winn wrote:



>This is timely. We're in the process of a) trying to organise a major 

>effort to tidy up the existing ccp4i classic (rather than fire-fighting 

>problems), and b) thinking about designing the next generation. Not 

>sure which this is. Option b) would be a project over several years.

>

>Can you elucidate further. As an expert user, would you want a less 

>scary free text box (which is essentially what Run&View Com File is), 

>or actual widgets for every option. The latter could be done as a 

>hidden folder, made visible according to an Expert switch in 

>Preferences.

>

>As developers, we also have to think about long-term maintainability. 

>Options, in particular little-used options, can soon become 

>out-of-date.

>

>m

>

>

>On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote:

>  

>

>>-BEGIN PGP SIGNED MESSAGE-

>>Hash: SHA1

>>

>>Dear all,

>>

>>I'm a well-known luddite as Eleanor says. However, I shamelessly 

>>confess that the CCP4 GUI is great. Not that I think this is necessary 

>>here, I'm sure most people agree with that.

>>

>>If I write now is because Martynn's e-mail have reminded me of 

>>something I thought once, but forgot to ask for to the ccp4i 

>>developpers: perhaps the GUI could have "two faces/modes", a basic one 

>>and an expert/advanced one. I understand that they already exist, but 

>>the "expert" one is hidden under the "Run&View Com File", while I'm 

>>thinking on a real expert GUI-mode. Users should be able to choose one 

>>or the other in their defaults, or switch from one to the other 

>>on-the-fly.

>>

>>I don't have a particular problem in editing the scripts as it is done 

>>now, but I have found that students tend to get a bit nervous about 

>>doing it themselves ;-)

>>

>>Cheers,

>>

>>

>>Miguel

>>

>>Martyn Winn escribió:

>>

>>

>>>The level of detail in the GUI is a matter of constant debate. The 

>>>underlying programs are far far richer, so the question is how much 

>>>to expose in the GUI. We try to get a balance between ease-of-use and 

>>>coverage, but it won't always work. BTW I don't think we ever claimed 

>>>that ccp4i (or anything else in ccp4) is "finished" ;-)

>>>

>>>Having said that, we're always happy to hear about specific defects 

>>>in the GUI. When reporting these to [EMAIL PROTECTED] please give as much 

>>>information as possible, in particular knowing the context is always 

>>>helpful.

>>>

>>>Cheers

>>>Martyn

>>>  

>>>

>

>

>  

>





-- 

Jürgen Bosch

University of Washington

Dept. of Biochemistry, K-426

1705 NE Pacific Street

Seattle, WA 98195

Box 357742

Phone: +1-206-616-4510

FAX:+1-206-685-7002

Re: [ccp4bb] CCP4 GUI

[Roger Rowlett]

I think a "tweak script" button or option (before running) would be an 
excellent idea.

Cheers,

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

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [EMAIL PROTECTED]


-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Juergen Bosch
Sent: Thursday, May 10, 2007 10:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4 GUI


Hi Martyn,

how about option c:

in each gui window at the lower left corner have a button called 
"Display script", or call it "Expert Mode" if people feel better as 
"Experts" :-) , before running of course. Then people who would like to 
edit their stuff could do so before running the script. I think it would 
be scary to many if the "Expert Mode" actually would display all other 
options available for that particular program - for this you have the RTFM*

I tend to use the GUI only for standard stuff and keep migrating my 
scripts from directories to directories, which if you run a search on 
say e.g. "refmac." spits out a ton of handcrafted scripts for each 
project - maybe also not the best thing to do, but that's how it is.

Juergen

* Fine of course, what else !

Martyn Winn wrote:

>This is timely. We're in the process of a) trying to organise a major 
>effort to tidy up the existing ccp4i classic (rather than fire-fighting 
>problems), and b) thinking about designing the next generation. Not 
>sure which this is. Option b) would be a project over several years.
>
>Can you elucidate further. As an expert user, would you want a less 
>scary free text box (which is essentially what Run&View Com File is), 
>or actual widgets for every option. The latter could be done as a 
>hidden folder, made visible according to an Expert switch in 
>Preferences.
>
>As developers, we also have to think about long-term maintainability. 
>Options, in particular little-used options, can soon become 
>out-of-date.
>
>m
>
>
>On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote:
>  
>
>>-BEGIN PGP SIGNED MESSAGE-
>>Hash: SHA1
>>
>>Dear all,
>>
>>I'm a well-known luddite as Eleanor says. However, I shamelessly 
>>confess that the CCP4 GUI is great. Not that I think this is necessary 
>>here, I'm sure most people agree with that.
>>
>>If I write now is because Martynn's e-mail have reminded me of 
>>something I thought once, but forgot to ask for to the ccp4i 
>>developpers: perhaps the GUI could have "two faces/modes", a basic one 
>>and an expert/advanced one. I understand that they already exist, but 
>>the "expert" one is hidden under the "Run&View Com File", while I'm 
>>thinking on a real expert GUI-mode. Users should be able to choose one 
>>or the other in their defaults, or switch from one to the other 
>>on-the-fly.
>>
>>I don't have a particular problem in editing the scripts as it is done 
>>now, but I have found that students tend to get a bit nervous about 
>>doing it themselves ;-)
>>
>>Cheers,
>>
>>
>>Miguel
>>
>>Martyn Winn escribió:
>>
>>
>>>The level of detail in the GUI is a matter of constant debate. The 
>>>underlying programs are far far richer, so the question is how much 
>>>to expose in the GUI. We try to get a balance between ease-of-use and 
>>>coverage, but it won't always work. BTW I don't think we ever claimed 
>>>that ccp4i (or anything else in ccp4) is "finished" ;-)
>>>
>>>Having said that, we're always happy to hear about specific defects 
>>>in the GUI. When reporting these to [EMAIL PROTECTED] please give as much 
>>>information as possible, in particular knowing the context is always 
>>>helpful.
>>>
>>>Cheers
>>>Martyn
>>>  
>>>
>
>
>  
>


-- 
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone:   +1-206-616-4510
FAX: +1-206-685-7002

Re: [ccp4bb] CCP4 GUI

[Juergen Bosch]

Hi Martyn,

how about option c:

in each gui window at the lower left corner have a button called 
"Display script", or call it "Expert Mode" if people feel better as 
"Experts" :-) , before running of course. Then people who would like to 
edit their stuff could do so before running the script. I think it would 
be scary to many if the "Expert Mode" actually would display all other 
options available for that particular program - for this you have the RTFM*


I tend to use the GUI only for standard stuff and keep migrating my 
scripts from directories to directories, which if you run a search on 
say e.g. "refmac." spits out a ton of handcrafted scripts for each 
project - maybe also not the best thing to do, but that's how it is.


Juergen

* Fine of course, what else !

Martyn Winn wrote:


This is timely. We're in the process of a) trying to organise a major
effort to tidy up the existing ccp4i classic (rather than fire-fighting
problems), and b) thinking about designing the next generation. Not sure
which this is. Option b) would be a project over several years. 


Can you elucidate further. As an expert user, would you want a less
scary free text box (which is essentially what Run&View Com File is), or
actual widgets for every option. The latter could be done as a hidden
folder, made visible according to an Expert switch in Preferences. 


As developers, we also have to think about long-term maintainability.
Options, in particular little-used options, can soon become out-of-date.

m


On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote:
 


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear all,

I'm a well-known luddite as Eleanor says. However, I shamelessly confess
that the CCP4 GUI is great. Not that I think this is necessary here, I'm
sure most people agree with that.

If I write now is because Martynn's e-mail have reminded me of something
I thought once, but forgot to ask for to the ccp4i developpers: perhaps
the GUI could have "two faces/modes", a basic one and an expert/advanced
one. I understand that they already exist, but the "expert" one is
hidden under the "Run&View Com File", while I'm thinking on a real
expert GUI-mode. Users should be able to choose one or the other in
their defaults, or switch from one to the other on-the-fly.

I don't have a particular problem in editing the scripts as it is done
now, but I have found that students tend to get a bit nervous about
doing it themselves ;-)

Cheers,


Miguel

Martyn Winn escribió:
   


The level of detail in the GUI is a matter of constant debate. The
underlying programs are far far richer, so the question is how much to
expose in the GUI. We try to get a balance between ease-of-use and
coverage, but it won't always work. BTW I don't think we ever claimed
that ccp4i (or anything else in ccp4) is "finished" ;-)

Having said that, we're always happy to hear about specific defects in
the GUI. When reporting these to [EMAIL PROTECTED] please give as much
information as possible, in particular knowing the context is always
helpful.

Cheers
Martyn
 




 




--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone:   +1-206-616-4510
FAX: +1-206-685-7002

Re: [ccp4bb] Refmac and B factors

[Roger Rowlett]

IMO, the GUI is a lifesaver for getting undergraduates involved in
crystallography in an efficient way. While it is possible to teach my
undergraduates to write scripts for CNS, CCP4, and O, it is much, much
easier for them to learn the CCP4 GUI. Sooner or later, real problems
require you to look under the hood to some degree or other, so it is not
so much a black box as one would think, but to the extent that it is, it
has made crystallography accessible to many more investigators and
students than otherwise. (If you had asked me a decade ago if my
undergraduates would be solving protein X-ray structures I may have
laughed.) Personally, I would like to see as many options as possible
included in the GUI, just for consistency and ease of use, although I
realize that this requires a lot more work on the developers' part. But
when all else fails, there is always RTFM...or CCP4BB.
 
Cheers,
___ 
Roger S. Rowlett 
Professor 
Department of Chemistry 
Colgate University 
13 Oak Drive 
Hamilton, NY 13346 

tel: (315)-228-7245 
ofc: (315)-228-7395 
fax: (315)-228-7935 
email: [EMAIL PROTECTED] 

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On
Behalf Of Kolstoe S.E.
Sent: Thursday, May 10, 2007 5:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and B factors


Thanks very much for the replies, and especially for the link to
the previous thread on this topic (Eva).
 
Just a comment about the ccp4i GUI in general - pretty much all
the students in my department are slowly becoming dependant on the GUI
because it is so much easier to use for those brought up using MS
windows. However, is it really fair to be distributing the GUI as a
"finished" product when it has so many limitations, and in this
particular case is just plain misleading? Although I applaud the idea of
making crystallography more user friendly, is it not just asking for
trouble (and bad science) when software is written that gives the
illusion that things are more straight forward than they actually are?
 
Simon
 




From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On
Behalf Of Eva Kirchner
Sent: 09 May 2007 17:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and B factors


Hi Simon,

you can't stop it - I asked the same question (with some more
questions) some weeks ago. 

You can find the original email and the tips I got for
not-so-good resolution B-factor refinement here:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html

Good luck,
Eva



2007/5/9, Kolstoe S.E. <[EMAIL PROTECTED]>: 


Dear all,

I have a structure at fairly low resolution that I am
trying to refine
with Refmac. I do not want to refine B factors so have
arbitrarily set
them all to 20 and then run refmac in the ccp4i GUI
after deselecting 
the "refine temperature factors" box. However, when I
look at the
resulting pdb file my B factors vary from 2 to 90.

Is Refmac just calculating my B factors or is it still
refining them,
and if the latter how can I stop it? 

Thanks,

Simon

Re: [ccp4bb] CCP4 GUI

[Dima Klenchin]

The level of detail in the GUI is a matter of constant debate. The
underlying programs are far far richer, so the question is how much to
expose in the GUI.


How about the simple and elegant way it is done in Refmac?
Tacked under "Developers Options" is "specify an external
keyword script file for Refmac". I frequently use this and
always wished that *all* CCP4i GUIs had this.

Sounds like something that lets user enjoy the simplicity
GUI yet allowing flexibility of using complete functionality
of the programs. This should be very easy to implement.

Dima

Re: [ccp4bb] CCP4 GUI

[Kolstoe S.E.]

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. It would also be nice to see how
different options are changing the .com file (something similar to the
way dreamweaver shows you the updated html in a split-screen with the
WYSIWYG editor).

Something else that might be useful could be log files suggesting extra
keywords/parameters in much the same way as mosflm does already.

Finally, if a function does not work (such as the shelx conversion in
mtz2various mentioned last month or the temperature factor check box I
mentioned in Refmac) then these functions should definitely not be
included in the GUI. Better a spartan GUI where everything works than a
complete GUI with questionable parts.

Simon




-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Phil Evans
Sent: 10 May 2007 13:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4 GUI

I always liked Kevin's comments on little-used options in the DM  
documentation

"Don't use these unless you really know what you are doing. In which  
case you'd better have a better idea of what you
  are doing than I do."

Phil

On 10 May 2007, at 13:07, Kevin Cowtan wrote:

> Miguel Ortiz Lombardia wrote:
>> I was thinking in the "less scary" widgets-based interface for
>> not-so-used options. If possible, I think that all options should be
>> available to the interface.
>
> My programs at least have a load of options which I put in for the  
> purposes of testing out ideas, which didn't work but may be useful  
> at some point in the future. Generally these options are not error  
> checked. They should not be made available to the user.

Re: [ccp4bb] A different idea

[Martyn Winn]

Thanks Pierre. Its good to have more than one idea.

I'd had a similar private idea - basically to have a pull-down menu of
all keywords (there's a slight issue that ccp4i tasks tend to include
several programs).

My feeling is that segregating the expert options into folder(s) under
global control is less work for us. You, Dear User, shouldn't care about
that, but it means that it is more likely to get done.

m

On Thu, 2007-05-10 at 13:31 +0100, Rizkallah, PJ (Pierre) wrote:
> Dear Martyn et al.,
> 
> How about putting all the keywords of any program into its GUI, then the
> user can click on the ones he/she thinks are needed, to open up the
> subkeywords for editing. It might be a case of one horizontal bar for
> each and every keyword, and could quickly become tedious when programs
> have many keywords. But it could also be a radio button, which, when
> clicked, would present the extra options in a temporary box at the
> bottom, as appears when you click a horizontal bar in the current GUI.
> Not too different from the present, but would be more compact while at
> the same time offering all the keywords.
> 
> I hope you can make sense out of my suggestion. And, thanks for the
> effort made by the CC4 staff and programmers over the years.
> 
> Pierre
> 
> ***
> Pierre Rizkallah, Daresbury Laboratory, Warrington, Cheshire WA4 4AD,
> U.K.
> Phone:  (+)44 1925 603808  Fax:  (+)44 1925 603124
> e-mail: [EMAIL PROTECTED] html: http://www.srs.ac.uk/px/pjr/

Re: [ccp4bb] CCP4 GUI

[Phil Evans]

I always liked Kevin's comments on little-used options in the DM  
documentation


"Don't use these unless you really know what you are doing. In which  
case you'd better have a better idea of what you

 are doing than I do."

Phil

On 10 May 2007, at 13:07, Kevin Cowtan wrote:


Miguel Ortiz Lombardia wrote:

I was thinking in the "less scary" widgets-based interface for
not-so-used options. If possible, I think that all options should be
available to the interface.


My programs at least have a load of options which I put in for the  
purposes of testing out ideas, which didn't work but may be useful  
at some point in the future. Generally these options are not error  
checked. They should not be made available to the user.

[ccp4bb] A different idea

[Rizkallah, PJ (Pierre)]

Dear Martyn et al.,

How about putting all the keywords of any program into its GUI, then the
user can click on the ones he/she thinks are needed, to open up the
subkeywords for editing. It might be a case of one horizontal bar for
each and every keyword, and could quickly become tedious when programs
have many keywords. But it could also be a radio button, which, when
clicked, would present the extra options in a temporary box at the
bottom, as appears when you click a horizontal bar in the current GUI.
Not too different from the present, but would be more compact while at
the same time offering all the keywords.

I hope you can make sense out of my suggestion. And, thanks for the
effort made by the CC4 staff and programmers over the years.

Pierre

***
Pierre Rizkallah, Daresbury Laboratory, Warrington, Cheshire WA4 4AD,
U.K.
Phone:  (+)44 1925 603808  Fax:  (+)44 1925 603124
e-mail: [EMAIL PROTECTED] html: http://www.srs.ac.uk/px/pjr/

Re: [ccp4bb] CCP4 GUI

[Martyn Winn]

Many interfaces already have an other parameters folder, see e.g. the
folder "Infrequently Used Parameters" in the Molrep GUI. The request
seems to be to:

a) complete this with more parameters for more programs (taking due note
of Kevin's comment)

b) have a Preferences switch that globally hides these folders (i.e. not
just close them) for the basic GUI

Provided you're happy for the advanced options to be segregated into
their own folders, then we already have the means (I think) to do this.
Actually going through all interfaces will take time though. 

Maintainability means options disappearing from programs, new options
appearing, keyword arguments changing and defaults changing. For one
person looking after one program with one interface, its not a problem.
For 15 developers looking after 200 programs, it becomes a problem. It
is "only" a management problem, but nevertheless a real issue (some
people make a living out of telling you how to deal with such issues).

Cheers
Martyn


On Thu, 2007-05-10 at 14:18 +0200, Dirk Kostrewa wrote:
> Hi Martyn,
> 
> 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.
> 
> Best regards,
> 
> Dirk.
> 
> Miguel Ortiz Lombardia wrote:
> > -BEGIN PGP SIGNED MESSAGE-
> > Hash: SHA1
> > 
> > Hi Martyn,
> > 
> > I was thinking in the "less scary" widgets-based interface for
> > not-so-used options. If possible, I think that all options should be
> > available to the interface. This would make the GUI more consistent, in
> > a way. I know is a lot more work, but I think that this will be
> > especially appreciated by people newly approaching CCP4 (students or
> > not). Those of us who worked with these programs from scripts (and rtfm)
> > know that there are more options than those exported to the GUI. Others
> > find this situation confusing.
> > 
> > The Expert switch in Preferences would be excellent.
> > 
> > I'm not sure to have understood the maintainability issue... unless you
> > mean that it can happen that options that become outdated disappear from
> > the program, so there would be a risk of having their "ghosts" in the
> > GUI. But normally programs complain when an option is not available,
> > don't they?
> > 
> > Cheers,
> > 
> > 
> > Miguel
> > 
> > Martyn Winn escribió:
> >> This is timely. We're in the process of a) trying to organise a major
> >> effort to tidy up the existing ccp4i classic (rather than fire-fighting
> >> problems), and b) thinking about designing the next generation. Not sure
> >> which this is. Option b) would be a project over several years. 
> >>
> >> Can you elucidate further. As an expert user, would you want a less
> >> scary free text box (which is essentially what Run&View Com File is), or
> >> actual widgets for every option. The latter could be done as a hidden
> >> folder, made visible according to an Expert switch in Preferences. 
> >>
> >> As developers, we also have to think about long-term maintainability.
> >> Options, in particular little-used options, can soon become out-of-date.
> >>
> >> m
> >>
> >>
> >> On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote:
> >>> -BEGIN PGP SIGNED MESSAGE-
> >>> Hash: SHA1
> >>>
> >>> Dear all,
> >>>
> >>> I'm a well-known luddite as Eleanor says. However, I shamelessly confess
> >>> that the CCP4 GUI is great. Not that I think this is necessary here, I'm
> >>> sure most people agree with that.
> >>>
> >>> If I write now is because Martynn's e-mail have reminded me of something
> >>> I thought once, but forgot to ask for to the ccp4i developpers: perhaps
> >>> the GUI could have "two faces/modes", a basic one and an expert/advanced
> >>> one. I understand that they already exist, but the "expert" one is
> >>> hidden under the "Run&View Com File", while I'm thinking on a real
> >>> expert GUI-mode. Users should be able to choose one or the other in
> >>> their defaults, or switch from one to the other on-the-fly.
> >>>
> >>> I don't have a particular problem in editing the scripts as it is done
> >>> now, but I have found that students tend to get a bit nervous about
> >>> doing it themselves ;-)
> >>>
> >>> Cheers,
> >>>
> >>>
> >>> Miguel
> >>>
> >>> Martyn Winn escribió:
>  The level of detail in the GUI is a matter of constant debate. The
>  underlying programs are far far richer, so the question is how much to
>  expose in the GUI. We try to get a balance between ease-of-use and
>  coverage, but it won't always work. BTW I don't thin

Re: [ccp4bb] CCP4 GUI

[Dirk Kostrewa]

Hi Martyn,

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.


Best regards,

Dirk.

Miguel Ortiz Lombardia wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Martyn,

I was thinking in the "less scary" widgets-based interface for
not-so-used options. If possible, I think that all options should be
available to the interface. This would make the GUI more consistent, in
a way. I know is a lot more work, but I think that this will be
especially appreciated by people newly approaching CCP4 (students or
not). Those of us who worked with these programs from scripts (and rtfm)
know that there are more options than those exported to the GUI. Others
find this situation confusing.

The Expert switch in Preferences would be excellent.

I'm not sure to have understood the maintainability issue... unless you
mean that it can happen that options that become outdated disappear from
the program, so there would be a risk of having their "ghosts" in the
GUI. But normally programs complain when an option is not available,
don't they?

Cheers,


Miguel

Martyn Winn escribió:

This is timely. We're in the process of a) trying to organise a major
effort to tidy up the existing ccp4i classic (rather than fire-fighting
problems), and b) thinking about designing the next generation. Not sure
which this is. Option b) would be a project over several years. 


Can you elucidate further. As an expert user, would you want a less
scary free text box (which is essentially what Run&View Com File is), or
actual widgets for every option. The latter could be done as a hidden
folder, made visible according to an Expert switch in Preferences. 


As developers, we also have to think about long-term maintainability.
Options, in particular little-used options, can soon become out-of-date.

m


On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear all,

I'm a well-known luddite as Eleanor says. However, I shamelessly confess
that the CCP4 GUI is great. Not that I think this is necessary here, I'm
sure most people agree with that.

If I write now is because Martynn's e-mail have reminded me of something
I thought once, but forgot to ask for to the ccp4i developpers: perhaps
the GUI could have "two faces/modes", a basic one and an expert/advanced
one. I understand that they already exist, but the "expert" one is
hidden under the "Run&View Com File", while I'm thinking on a real
expert GUI-mode. Users should be able to choose one or the other in
their defaults, or switch from one to the other on-the-fly.

I don't have a particular problem in editing the scripts as it is done
now, but I have found that students tend to get a bit nervous about
doing it themselves ;-)

Cheers,


Miguel

Martyn Winn escribió:

The level of detail in the GUI is a matter of constant debate. The
underlying programs are far far richer, so the question is how much to
expose in the GUI. We try to get a balance between ease-of-use and
coverage, but it won't always work. BTW I don't think we ever claimed
that ccp4i (or anything else in ccp4) is "finished" ;-)

Having said that, we're always happy to hear about specific defects in
the GUI. When reporting these to [EMAIL PROTECTED] please give as much
information as possible, in particular knowing the context is always
helpful.

Cheers
Martyn



- --
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)

iD8DBQFGQwV9F6oOrDvhbQIRAvgxAJ4jJXkpU4pandgQKIZJeFooO/0FtACgl+FL
KnxYHozGPko/tOAkcxawNYI=
=TiHW
-END PGP SIGNATURE-



--


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

[Kevin Cowtan]

Miguel Ortiz Lombardia wrote:

I was thinking in the "less scary" widgets-based interface for
not-so-used options. If possible, I think that all options should be
available to the interface.


My programs at least have a load of options which I put in for the 
purposes of testing out ideas, which didn't work but may be useful at 
some point in the future. Generally these options are not error checked. 
They should not be made available to the user.

[ccp4bb] Fellowships available at EMBL Hamburg

[Margret Fischer]

PH.D. AND POSTDOCTORAL FELLOWSHIPS ON STRUCTURAL/FUNCTIONAL 
CHARACTERISATION OF PROTEIN INTERACTION NETWORKS IN YEAST


Two Ph.D. fellowships and one postdoctoral fellowship are available in 
the research group of Matthias Wilmanns at EMBL-Hamburg, Hamburg, Germany.


Src Homology 3 (SH3) domains are modular protein domains which are found 
in hundreds of multifunctional proteins from the human genome and tens 
of similar proteins in eukaryotic model organisms such as S. cerevisiae. 
Many of these proteins are involved in signalling and the organisation 
of the cytoskeleton, for instance. Although the structure and canonical 
binding site for proline-rich ligands has been well studied over more 
than a decade it remains largely unknown by what kind of mechanism many 
of known SH3-domains containing proteins are sorted to correct protein 
ligands within complex cellular networks, to allow their proper function 
in living systems.


The key aim of our future research will be to identify the molecular 
structural basis of cellular protein networks that are mediated by SH3 
domain containing proteins, using four yeast species (S. cerevisiae, S. 
pombe, A. gossypii, C. albicans) as models:


1) We are planning to determine structures of SH3 domain containing 
multifunctional proteins, to unravel their domain organisation, which 
may be important for correct folding and regulation of SH3 domain 
mediated protein/protein interactions.


2) We are aiming to determine structures of SH3 domain mediated 
protein/protein complexes, to provide insight into the molecular 
organisation of SH3 domains within complex protein networks in living 
systems.


3) We will exploit our structural data to explore the use of SH3 domains 
for drug discovery approaches, using both computational and experimental 
screening methods (a large depository of structures from S. cerevisiae 
is already available).


4) We will probe structure-based function by in vitro and in vivo 
approaches, by employing genetics, imaging techniques, and cell biology 
approaches.


Ph.D. fellowship candidates: Please apply at our central web pages: 
http://www.embl.org/training/phdprogramme/intro.html

The deadline for the next selection is: May 31, 2007.

Postdoctoral candidates: Please send your complete CV, including a list 
of publications, a statement of your present achievements and expertise, 
a list at least three addresses, from where letters of reference can be 
obtained. Previous experience in molecular biology, biochemistry, 
biophysical methods and X-ray crystallography is essential. The approach 
of our group is to integrate structural data into functional 
investigations. Please apply directly to Dr. Matthias Wilmanns, 
Notkestrasse 85, D-22603 Hamburg, Germany. Email: [EMAIL PROTECTED]


Further information about group activities: 
www.embl-hamburg.de/~wilmanns/home.html


The projects are supported by two EU networks, 3D Repertoire 
(www.3drepertoire.org/) and Penelope (penelope.crg.es), and EMBL.

Re: [ccp4bb] CCP4 GUI

[Miguel Ortiz Lombardia]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Martyn,

I was thinking in the "less scary" widgets-based interface for
not-so-used options. If possible, I think that all options should be
available to the interface. This would make the GUI more consistent, in
a way. I know is a lot more work, but I think that this will be
especially appreciated by people newly approaching CCP4 (students or
not). Those of us who worked with these programs from scripts (and rtfm)
know that there are more options than those exported to the GUI. Others
find this situation confusing.

The Expert switch in Preferences would be excellent.

I'm not sure to have understood the maintainability issue... unless you
mean that it can happen that options that become outdated disappear from
the program, so there would be a risk of having their "ghosts" in the
GUI. But normally programs complain when an option is not available,
don't they?

Cheers,


Miguel

Martyn Winn escribió:
> This is timely. We're in the process of a) trying to organise a major
> effort to tidy up the existing ccp4i classic (rather than fire-fighting
> problems), and b) thinking about designing the next generation. Not sure
> which this is. Option b) would be a project over several years. 
> 
> Can you elucidate further. As an expert user, would you want a less
> scary free text box (which is essentially what Run&View Com File is), or
> actual widgets for every option. The latter could be done as a hidden
> folder, made visible according to an Expert switch in Preferences. 
> 
> As developers, we also have to think about long-term maintainability.
> Options, in particular little-used options, can soon become out-of-date.
> 
> m
> 
> 
> On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote:
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>>
>> Dear all,
>>
>> I'm a well-known luddite as Eleanor says. However, I shamelessly confess
>> that the CCP4 GUI is great. Not that I think this is necessary here, I'm
>> sure most people agree with that.
>>
>> If I write now is because Martynn's e-mail have reminded me of something
>> I thought once, but forgot to ask for to the ccp4i developpers: perhaps
>> the GUI could have "two faces/modes", a basic one and an expert/advanced
>> one. I understand that they already exist, but the "expert" one is
>> hidden under the "Run&View Com File", while I'm thinking on a real
>> expert GUI-mode. Users should be able to choose one or the other in
>> their defaults, or switch from one to the other on-the-fly.
>>
>> I don't have a particular problem in editing the scripts as it is done
>> now, but I have found that students tend to get a bit nervous about
>> doing it themselves ;-)
>>
>> Cheers,
>>
>>
>> Miguel
>>
>> Martyn Winn escribió:
>>> The level of detail in the GUI is a matter of constant debate. The
>>> underlying programs are far far richer, so the question is how much to
>>> expose in the GUI. We try to get a balance between ease-of-use and
>>> coverage, but it won't always work. BTW I don't think we ever claimed
>>> that ccp4i (or anything else in ccp4) is "finished" ;-)
>>>
>>> Having said that, we're always happy to hear about specific defects in
>>> the GUI. When reporting these to [EMAIL PROTECTED] please give as much
>>> information as possible, in particular knowing the context is always
>>> helpful.
>>>
>>> Cheers
>>> Martyn
>>>
> 

- --
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)
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KnxYHozGPko/tOAkcxawNYI=
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[ccp4bb] RE : [ccp4bb] CCP4 GUI suggestion

[Nicolet Stefan]

Dear all,

As somebody already thought about an user-personalized interface, eg. a CCP4
menu where people could drag & drop their favorite (or mostly used)
programs?

Cheers,

Stefan

-Message d'origine-
De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] De la part de Martyn
Winn
Envoyé : jeudi, 10. mai 2007 13:05
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] CCP4 GUI

This is timely. We're in the process of a) trying to organise a major
effort to tidy up the existing ccp4i classic (rather than fire-fighting
problems), and b) thinking about designing the next generation. Not sure
which this is. Option b) would be a project over several years. 

Can you elucidate further. As an expert user, would you want a less
scary free text box (which is essentially what Run&View Com File is), or
actual widgets for every option. The latter could be done as a hidden
folder, made visible according to an Expert switch in Preferences. 

As developers, we also have to think about long-term maintainability.
Options, in particular little-used options, can soon become out-of-date.

m


On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Dear all,
> 
> I'm a well-known luddite as Eleanor says. However, I shamelessly confess
> that the CCP4 GUI is great. Not that I think this is necessary here, I'm
> sure most people agree with that.
> 
> If I write now is because Martynn's e-mail have reminded me of something
> I thought once, but forgot to ask for to the ccp4i developpers: perhaps
> the GUI could have "two faces/modes", a basic one and an expert/advanced
> one. I understand that they already exist, but the "expert" one is
> hidden under the "Run&View Com File", while I'm thinking on a real
> expert GUI-mode. Users should be able to choose one or the other in
> their defaults, or switch from one to the other on-the-fly.
> 
> I don't have a particular problem in editing the scripts as it is done
> now, but I have found that students tend to get a bit nervous about
> doing it themselves ;-)
> 
> Cheers,
> 
> 
> Miguel
> 
> Martyn Winn escribió:
> > The level of detail in the GUI is a matter of constant debate. The
> > underlying programs are far far richer, so the question is how much to
> > expose in the GUI. We try to get a balance between ease-of-use and
> > coverage, but it won't always work. BTW I don't think we ever claimed
> > that ccp4i (or anything else in ccp4) is "finished" ;-)
> > 
> > Having said that, we're always happy to hear about specific defects in
> > the GUI. When reporting these to [EMAIL PROTECTED] please give as much
> > information as possible, in particular knowing the context is always
> > helpful.
> > 
> > Cheers
> > Martyn
> > 

Re: [ccp4bb] CCP4 GUI

[Martyn Winn]

This is timely. We're in the process of a) trying to organise a major
effort to tidy up the existing ccp4i classic (rather than fire-fighting
problems), and b) thinking about designing the next generation. Not sure
which this is. Option b) would be a project over several years. 

Can you elucidate further. As an expert user, would you want a less
scary free text box (which is essentially what Run&View Com File is), or
actual widgets for every option. The latter could be done as a hidden
folder, made visible according to an Expert switch in Preferences. 

As developers, we also have to think about long-term maintainability.
Options, in particular little-used options, can soon become out-of-date.

m


On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Dear all,
> 
> I'm a well-known luddite as Eleanor says. However, I shamelessly confess
> that the CCP4 GUI is great. Not that I think this is necessary here, I'm
> sure most people agree with that.
> 
> If I write now is because Martynn's e-mail have reminded me of something
> I thought once, but forgot to ask for to the ccp4i developpers: perhaps
> the GUI could have "two faces/modes", a basic one and an expert/advanced
> one. I understand that they already exist, but the "expert" one is
> hidden under the "Run&View Com File", while I'm thinking on a real
> expert GUI-mode. Users should be able to choose one or the other in
> their defaults, or switch from one to the other on-the-fly.
> 
> I don't have a particular problem in editing the scripts as it is done
> now, but I have found that students tend to get a bit nervous about
> doing it themselves ;-)
> 
> Cheers,
> 
> 
> Miguel
> 
> Martyn Winn escribió:
> > The level of detail in the GUI is a matter of constant debate. The
> > underlying programs are far far richer, so the question is how much to
> > expose in the GUI. We try to get a balance between ease-of-use and
> > coverage, but it won't always work. BTW I don't think we ever claimed
> > that ccp4i (or anything else in ccp4) is "finished" ;-)
> > 
> > Having said that, we're always happy to hear about specific defects in
> > the GUI. When reporting these to [EMAIL PROTECTED] please give as much
> > information as possible, in particular knowing the context is always
> > helpful.
> > 
> > Cheers
> > Martyn
> > 

Re: [ccp4bb] CCP4 GUI

[Miguel Ortiz Lombardia]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear all,

I'm a well-known luddite as Eleanor says. However, I shamelessly confess
that the CCP4 GUI is great. Not that I think this is necessary here, I'm
sure most people agree with that.

If I write now is because Martynn's e-mail have reminded me of something
I thought once, but forgot to ask for to the ccp4i developpers: perhaps
the GUI could have "two faces/modes", a basic one and an expert/advanced
one. I understand that they already exist, but the "expert" one is
hidden under the "Run&View Com File", while I'm thinking on a real
expert GUI-mode. Users should be able to choose one or the other in
their defaults, or switch from one to the other on-the-fly.

I don't have a particular problem in editing the scripts as it is done
now, but I have found that students tend to get a bit nervous about
doing it themselves ;-)

Cheers,


Miguel

Martyn Winn escribió:
> The level of detail in the GUI is a matter of constant debate. The
> underlying programs are far far richer, so the question is how much to
> expose in the GUI. We try to get a balance between ease-of-use and
> coverage, but it won't always work. BTW I don't think we ever claimed
> that ccp4i (or anything else in ccp4) is "finished" ;-)
> 
> Having said that, we're always happy to hear about specific defects in
> the GUI. When reporting these to [EMAIL PROTECTED] please give as much
> information as possible, in particular knowing the context is always
> helpful.
> 
> Cheers
> Martyn
> 
> On Thu, 2007-05-10 at 17:39 +0800, Charlie Bond wrote:
>> I would add that I have found the CCP4 development team very receptive 
>> to being informed about specific improvements which could be made, and 
>> even more so to fixes implemented by users themselves.
>>
>> Perhaps an explicit list of the many limitations which need attention 
>> would be useful to the development team.
>>
>> Cheers,
>> Charlie
>>
>>
>> Flip Hoedemaeker wrote:
>>> Hi Simon,
>>>  
>>> Well, X-ray crystallography nowadays often, but certainly not 
>>> always, amounts to running a set of programs with default settings with 
>>> a few mouse clicks in the GUI. The fun part is knowing when you have to 
>>> deviate from default, leave the well travelled paths etc.
>>>  
>>> The GUI is excellent with the straightforward stuff, if this fails you 
>>> actually have the option of editing the generated scripts (run and view 
>>> com file option), or leave the GUI altogether and go to old fashioned 
>>> command mode or your own scripts. Think of the GUI as a welcome 
>>> addition, but not as a panacea for all your crystallography problems, 
>>> and certainly train new crystallographers in such away that they at 
>>> least have an idea what is going on in the "black box"
>>>  
>>> Flip
>>>
>>> 
>>> *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of 
>>> *Kolstoe S.E.
>>> *Sent:* Thursday, May 10, 2007 11:09
>>> *To:* CCP4BB@JISCMAIL.AC.UK
>>> *Subject:* Re: [ccp4bb] Refmac and B factors
>>>
>>> Thanks very much for the replies, and especially for the link to the 
>>> previous thread on this topic (Eva).
>>>  
>>> Just a comment about the ccp4i GUI in general - pretty much all the 
>>> students in my department are slowly becoming dependant on the GUI 
>>> because it is so much easier to use for those brought up using MS 
>>> windows. However, is it really fair to be distributing the GUI as a 
>>> "finished" product when it has so many limitations, and in this 
>>> particular case is just plain misleading? Although I applaud the idea of 
>>> making crystallography more user friendly, is it not just asking for 
>>> trouble (and bad science) when software is written that gives the 
>>> illusion that things are more straight forward than they actually are?
>>>  
>>> Simon
>>>  
>>>
>>> 
>>> *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of 
>>> *Eva Kirchner
>>> *Sent:* 09 May 2007 17:37
>>> *To:* CCP4BB@JISCMAIL.AC.UK
>>> *Subject:* Re: [ccp4bb] Refmac and B factors
>>>
>>> Hi Simon,
>>>
>>> you can't stop it - I asked the same question (with some more questions) 
>>> some weeks ago.
>>>
>>> You can find the original email and the tips I got for not-so-good 
>>> resolution B-factor refinement here:
>>> http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html
>>>
>>> Good luck,
>>> Eva
>>>
>>>
>>> 2007/5/9, Kolstoe S.E. <[EMAIL PROTECTED] 
>>> >:
>>>
>>>
>>> Dear all,
>>>
>>> I have a structure at fairly low resolution that I am trying to refine
>>> with Refmac. I do not want to refine B factors so have arbitrarily set
>>> them all to 20 and then run refmac in the ccp4i GUI after deselecting
>>> the "refine temperature factors" box. However, when I look at the
>>> resulting pdb file my B factors vary from 2 to 90.
>>>
>>> 

Re: [ccp4bb] CCP4 GUI

[Martyn Winn]

The level of detail in the GUI is a matter of constant debate. The
underlying programs are far far richer, so the question is how much to
expose in the GUI. We try to get a balance between ease-of-use and
coverage, but it won't always work. BTW I don't think we ever claimed
that ccp4i (or anything else in ccp4) is "finished" ;-)

Having said that, we're always happy to hear about specific defects in
the GUI. When reporting these to [EMAIL PROTECTED] please give as much
information as possible, in particular knowing the context is always
helpful.

Cheers
Martyn

On Thu, 2007-05-10 at 17:39 +0800, Charlie Bond wrote:
> I would add that I have found the CCP4 development team very receptive 
> to being informed about specific improvements which could be made, and 
> even more so to fixes implemented by users themselves.
> 
> Perhaps an explicit list of the many limitations which need attention 
> would be useful to the development team.
> 
> Cheers,
> Charlie
> 
> 
> Flip Hoedemaeker wrote:
> > Hi Simon,
> >  
> > Well, X-ray crystallography nowadays often, but certainly not 
> > always, amounts to running a set of programs with default settings with 
> > a few mouse clicks in the GUI. The fun part is knowing when you have to 
> > deviate from default, leave the well travelled paths etc.
> >  
> > The GUI is excellent with the straightforward stuff, if this fails you 
> > actually have the option of editing the generated scripts (run and view 
> > com file option), or leave the GUI altogether and go to old fashioned 
> > command mode or your own scripts. Think of the GUI as a welcome 
> > addition, but not as a panacea for all your crystallography problems, 
> > and certainly train new crystallographers in such away that they at 
> > least have an idea what is going on in the "black box"
> >  
> > Flip
> > 
> > 
> > *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of 
> > *Kolstoe S.E.
> > *Sent:* Thursday, May 10, 2007 11:09
> > *To:* CCP4BB@JISCMAIL.AC.UK
> > *Subject:* Re: [ccp4bb] Refmac and B factors
> > 
> > Thanks very much for the replies, and especially for the link to the 
> > previous thread on this topic (Eva).
> >  
> > Just a comment about the ccp4i GUI in general - pretty much all the 
> > students in my department are slowly becoming dependant on the GUI 
> > because it is so much easier to use for those brought up using MS 
> > windows. However, is it really fair to be distributing the GUI as a 
> > "finished" product when it has so many limitations, and in this 
> > particular case is just plain misleading? Although I applaud the idea of 
> > making crystallography more user friendly, is it not just asking for 
> > trouble (and bad science) when software is written that gives the 
> > illusion that things are more straight forward than they actually are?
> >  
> > Simon
> >  
> > 
> > 
> > *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of 
> > *Eva Kirchner
> > *Sent:* 09 May 2007 17:37
> > *To:* CCP4BB@JISCMAIL.AC.UK
> > *Subject:* Re: [ccp4bb] Refmac and B factors
> > 
> > Hi Simon,
> > 
> > you can't stop it - I asked the same question (with some more questions) 
> > some weeks ago.
> > 
> > You can find the original email and the tips I got for not-so-good 
> > resolution B-factor refinement here:
> > http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html
> > 
> > Good luck,
> > Eva
> > 
> > 
> > 2007/5/9, Kolstoe S.E. <[EMAIL PROTECTED] 
> > >:
> > 
> > 
> > Dear all,
> > 
> > I have a structure at fairly low resolution that I am trying to refine
> > with Refmac. I do not want to refine B factors so have arbitrarily set
> > them all to 20 and then run refmac in the ccp4i GUI after deselecting
> > the "refine temperature factors" box. However, when I look at the
> > resulting pdb file my B factors vary from 2 to 90.
> > 
> > Is Refmac just calculating my B factors or is it still refining them,
> > and if the latter how can I stop it?
> > 
> > Thanks,
> > 
> > Simon
> > 
> > 
> 

Re: [ccp4bb] CCP4 GUI

[Flip Hoedemaeker]

 ... Forgot to say that Simon obviously is right in that the check box
before "refine B factors" should not be there.

Flip

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Charlie Bond
Sent: Thursday, May 10, 2007 11:40
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4 GUI

I would add that I have found the CCP4 development team very receptive 
to being informed about specific improvements which could be made, and 
even more so to fixes implemented by users themselves.

Perhaps an explicit list of the many limitations which need attention 
would be useful to the development team.

Cheers,
Charlie


Flip Hoedemaeker wrote:
> Hi Simon,
>  
> Well, X-ray crystallography nowadays often, but certainly not 
> always, amounts to running a set of programs with default settings with 
> a few mouse clicks in the GUI. The fun part is knowing when you have to 
> deviate from default, leave the well travelled paths etc.
>  
> The GUI is excellent with the straightforward stuff, if this fails you 
> actually have the option of editing the generated scripts (run and view 
> com file option), or leave the GUI altogether and go to old fashioned 
> command mode or your own scripts. Think of the GUI as a welcome 
> addition, but not as a panacea for all your crystallography problems, 
> and certainly train new crystallographers in such away that they at 
> least have an idea what is going on in the "black box"
>  
> Flip
> 
> 
> *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of 
> *Kolstoe S.E.
> *Sent:* Thursday, May 10, 2007 11:09
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Refmac and B factors
> 
> Thanks very much for the replies, and especially for the link to the 
> previous thread on this topic (Eva).
>  
> Just a comment about the ccp4i GUI in general - pretty much all the 
> students in my department are slowly becoming dependant on the GUI 
> because it is so much easier to use for those brought up using MS 
> windows. However, is it really fair to be distributing the GUI as a 
> "finished" product when it has so many limitations, and in this 
> particular case is just plain misleading? Although I applaud the idea of 
> making crystallography more user friendly, is it not just asking for 
> trouble (and bad science) when software is written that gives the 
> illusion that things are more straight forward than they actually are?
>  
> Simon
>  
> 
> 
> *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of 
> *Eva Kirchner
> *Sent:* 09 May 2007 17:37
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Refmac and B factors
> 
> Hi Simon,
> 
> you can't stop it - I asked the same question (with some more questions) 
> some weeks ago.
> 
> You can find the original email and the tips I got for not-so-good 
> resolution B-factor refinement here:
> http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html
> 
> Good luck,
> Eva
> 
> 
> 2007/5/9, Kolstoe S.E. <[EMAIL PROTECTED] 
> >:
> 
> 
> Dear all,
> 
> I have a structure at fairly low resolution that I am trying to refine
> with Refmac. I do not want to refine B factors so have arbitrarily set
> them all to 20 and then run refmac in the ccp4i GUI after deselecting
> the "refine temperature factors" box. However, when I look at the
> resulting pdb file my B factors vary from 2 to 90.
> 
> Is Refmac just calculating my B factors or is it still refining them,
> and if the latter how can I stop it?
> 
> Thanks,
> 
> Simon
> 
> 

-- 
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

Re: [ccp4bb] CCP4 GUI

[Charlie Bond]

I would add that I have found the CCP4 development team very receptive 
to being informed about specific improvements which could be made, and 
even more so to fixes implemented by users themselves.


Perhaps an explicit list of the many limitations which need attention 
would be useful to the development team.


Cheers,
Charlie


Flip Hoedemaeker wrote:

Hi Simon,
 
Well, X-ray crystallography nowadays often, but certainly not 
always, amounts to running a set of programs with default settings with 
a few mouse clicks in the GUI. The fun part is knowing when you have to 
deviate from default, leave the well travelled paths etc.
 
The GUI is excellent with the straightforward stuff, if this fails you 
actually have the option of editing the generated scripts (run and view 
com file option), or leave the GUI altogether and go to old fashioned 
command mode or your own scripts. Think of the GUI as a welcome 
addition, but not as a panacea for all your crystallography problems, 
and certainly train new crystallographers in such away that they at 
least have an idea what is going on in the "black box"
 
Flip



*From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of 
*Kolstoe S.E.

*Sent:* Thursday, May 10, 2007 11:09
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Refmac and B factors

Thanks very much for the replies, and especially for the link to the 
previous thread on this topic (Eva).
 
Just a comment about the ccp4i GUI in general - pretty much all the 
students in my department are slowly becoming dependant on the GUI 
because it is so much easier to use for those brought up using MS 
windows. However, is it really fair to be distributing the GUI as a 
"finished" product when it has so many limitations, and in this 
particular case is just plain misleading? Although I applaud the idea of 
making crystallography more user friendly, is it not just asking for 
trouble (and bad science) when software is written that gives the 
illusion that things are more straight forward than they actually are?
 
Simon
 



*From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of 
*Eva Kirchner

*Sent:* 09 May 2007 17:37
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Refmac and B factors

Hi Simon,

you can't stop it - I asked the same question (with some more questions) 
some weeks ago.


You can find the original email and the tips I got for not-so-good 
resolution B-factor refinement here:

http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html

Good luck,
Eva


2007/5/9, Kolstoe S.E. <[EMAIL PROTECTED] 
>:



Dear all,

I have a structure at fairly low resolution that I am trying to refine
with Refmac. I do not want to refine B factors so have arbitrarily set
them all to 20 and then run refmac in the ccp4i GUI after deselecting
the "refine temperature factors" box. However, when I look at the
resulting pdb file my B factors vary from 2 to 90.

Is Refmac just calculating my B factors or is it still refining them,
and if the latter how can I stop it?

Thanks,

Simon




--
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

Re: [ccp4bb] CCP4 GUI (was:RE: [ccp4bb] Refmac and B factors)

[Nave, C (Colin)]

Seems to be a general issue.
Read the editorial in Nature 10 May 2007 Volume 447 Number 7141, pp116.
"Under the microscope - The use of 'black box' techniques carries risks."
Colin
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of Flip Hoedemaeker
Sent: 10 May 2007 10:21
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4 GUI (was:RE: [ccp4bb] Refmac and B factors)


Hi Simon,

Well, X-ray crystallography nowadays often, but certainly not always, amounts 
to running a set of programs with default settings with a few mouse clicks in 
the GUI. The fun part is knowing when you have to deviate from default, leave 
the well travelled paths etc. 

The GUI is excellent with the straightforward stuff, if this fails you actually 
have the option of editing the generated scripts (run and view com file 
option), or leave the GUI altogether and go to old fashioned command mode or 
your own scripts. Think of the GUI as a welcome addition, but not as a panacea 
for all your crystallography problems, and certainly train new 
crystallographers in such away that they at least have an idea what is going on 
in the "black box" 

Flip




From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Kolstoe S.E.
Sent: Thursday, May 10, 2007 11:09
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and B factors


Thanks very much for the replies, and especially for the link to the previous 
thread on this topic (Eva).

Just a comment about the ccp4i GUI in general - pretty much all the students in 
my department are slowly becoming dependant on the GUI because it is so much 
easier to use for those brought up using MS windows. However, is it really fair 
to be distributing the GUI as a "finished" product when it has so many 
limitations, and in this particular case is just plain misleading? Although I 
applaud the idea of making crystallography more user friendly, is it not just 
asking for trouble (and bad science) when software is written that gives the 
illusion that things are more straight forward than they actually are?

Simon





From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Eva Kirchner
Sent: 09 May 2007 17:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and B factors


Hi Simon,

you can't stop it - I asked the same question (with some more questions) some 
weeks ago. 

You can find the original email and the tips I got for not-so-good resolution 
B-factor refinement here:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html

Good luck,
Eva



2007/5/9, Kolstoe S.E. <[EMAIL PROTECTED]>: 

Dear all,

I have a structure at fairly low resolution that I am trying to refine
with Refmac. I do not want to refine B factors so have arbitrarily set
them all to 20 and then run refmac in the ccp4i GUI after deselecting 
the "refine temperature factors" box. However, when I look at the
resulting pdb file my B factors vary from 2 to 90.

Is Refmac just calculating my B factors or is it still refining them,
and if the latter how can I stop it? 

Thanks,

Simon

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

[Charlie Bond]

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] CCP4 GUI (was:RE: [ccp4bb] Refmac and B factors)

[Flip Hoedemaeker]

Hi Simon,
 
Well, X-ray crystallography nowadays often, but certainly not always,
amounts to running a set of programs with default settings with a few mouse
clicks in the GUI. The fun part is knowing when you have to deviate from
default, leave the well travelled paths etc. 
 
The GUI is excellent with the straightforward stuff, if this fails you
actually have the option of editing the generated scripts (run and view com
file option), or leave the GUI altogether and go to old fashioned command
mode or your own scripts. Think of the GUI as a welcome addition, but not as
a panacea for all your crystallography problems, and certainly train new
crystallographers in such away that they at least have an idea what is going
on in the "black box" 
 
Flip

  _  

From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Kolstoe S.E.
Sent: Thursday, May 10, 2007 11:09
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and B factors


Thanks very much for the replies, and especially for the link to the
previous thread on this topic (Eva).
 
Just a comment about the ccp4i GUI in general - pretty much all the students
in my department are slowly becoming dependant on the GUI because it is so
much easier to use for those brought up using MS windows. However, is it
really fair to be distributing the GUI as a "finished" product when it has
so many limitations, and in this particular case is just plain misleading?
Although I applaud the idea of making crystallography more user friendly, is
it not just asking for trouble (and bad science) when software is written
that gives the illusion that things are more straight forward than they
actually are?
 
Simon
 


  _  

From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Eva
Kirchner
Sent: 09 May 2007 17:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and B factors


Hi Simon,

you can't stop it - I asked the same question (with some more questions)
some weeks ago. 

You can find the original email and the tips I got for not-so-good
resolution B-factor refinement here:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html

Good luck,
Eva



2007/5/9, Kolstoe S.E. <[EMAIL PROTECTED]>: 


Dear all,

I have a structure at fairly low resolution that I am trying to refine
with Refmac. I do not want to refine B factors so have arbitrarily set
them all to 20 and then run refmac in the ccp4i GUI after deselecting 
the "refine temperature factors" box. However, when I look at the
resulting pdb file my B factors vary from 2 to 90.

Is Refmac just calculating my B factors or is it still refining them,
and if the latter how can I stop it? 

Thanks,

Simon

Re: [ccp4bb] Refmac and B factors

[Kolstoe S.E.]

Thanks very much for the replies, and especially for the link to the
previous thread on this topic (Eva).
 
Just a comment about the ccp4i GUI in general - pretty much all the
students in my department are slowly becoming dependant on the GUI
because it is so much easier to use for those brought up using MS
windows. However, is it really fair to be distributing the GUI as a
"finished" product when it has so many limitations, and in this
particular case is just plain misleading? Although I applaud the idea of
making crystallography more user friendly, is it not just asking for
trouble (and bad science) when software is written that gives the
illusion that things are more straight forward than they actually are?
 
Simon
 




From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Eva Kirchner
Sent: 09 May 2007 17:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and B factors


Hi Simon,

you can't stop it - I asked the same question (with some more questions)
some weeks ago. 

You can find the original email and the tips I got for not-so-good
resolution B-factor refinement here:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html

Good luck,
Eva



2007/5/9, Kolstoe S.E. <[EMAIL PROTECTED]>: 


Dear all,

I have a structure at fairly low resolution that I am trying to
refine
with Refmac. I do not want to refine B factors so have
arbitrarily set
them all to 20 and then run refmac in the ccp4i GUI after
deselecting 
the "refine temperature factors" box. However, when I look at
the
resulting pdb file my B factors vary from 2 to 90.

Is Refmac just calculating my B factors or is it still refining
them,
and if the latter how can I stop it? 

Thanks,

Simon

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

[Eleanor Dodson]

LSQKAB also tells you the centres of mass of the molecules you are fitting

Look in the log file   (Centroid == centre of mass)
 CENTROID OF "WORKING" MOLECULE  :  -87.717 116.189   1.694
CENTROID OF "WORKING" MOLECULE  :(fractional)   -0.180   1.170   0.010
CENTROID OF "REFERENCE" MOLECULE:   27.449 -14.779  52.855
CENTROID OF "REFERENCE" MOLECULE:(fractional)0.165  -0.149   0.324
Distance between CENTROIDS  :  181.751
Direction cosines of vector between CENTROIDS:  -0.634   0.721  -0.281


Eleanor Dodson

Nian Huang wrote:

Dear all,

I was trying to do a NCS averaging of the map using Resolve. I had a
partial model, which generated a rotation and translation matrix by
program lsqkab. Resolve also requires a center of mass input. Do you
know any program can estimate it either by map or pdb file?
Thanks.

Nian Huang
Department of Biochemistry
Univ of Texas Southwestern Medical Center

Re: [ccp4bb] Refmac and B factors

[Flip Hoedemaeker]

Yes, it is available in the GUI...

Flip 

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Peter
Adrian Meyer
Sent: Wednesday, May 09, 2007 23:28
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and B factors

Simon,

REFI BREF OVERALL should do something close to what you're looking for (it
will refine a single B-factor for the entire model, but there shouldn't be
variation within the model).

Not sure where (or if) this is in the gui, however.

Pete

>
> Dear all,
>
> I have a structure at fairly low resolution that I am trying to refine
> with Refmac. I do not want to refine B factors so have arbitrarily set
> them all to 20 and then run refmac in the ccp4i GUI after deselecting
> the "refine temperature factors" box. However, when I look at the
> resulting pdb file my B factors vary from 2 to 90.
>
> Is Refmac just calculating my B factors or is it still refining them,
> and if the latter how can I stop it?
>
> Thanks,
>
> Simon
>


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

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

[Bernhard C. Lohkamp]

You can use Coot to find the centre of mass. In the scripting window just 
type:

in scheme:

(centre-of-mass yourmoleculenumber)

or in python:

centre_of_mass(yourmoleculenumber)


Bernhard

BTW the American spelling of centre (center) should work too...

> Dear all,
> 
> I was trying to do a NCS averaging of the map using Resolve. I had a
> partial model, which generated a rotation and translation matrix by
> program lsqkab. Resolve also requires a center of mass input. Do you
> know any program can estimate it either by map or pdb file?
> Thanks.
> 
> Nian Huang
> Department of Biochemistry
> Univ of Texas Southwestern Medical Center
> 

*
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