Re: [ccp4bb] mac pro configuration for crystallographic computing

[mesters]

Hi,

the FX4500 is what Mac likes to sell to us but in principle the driver 
should be able to work with any Nvidia card of the same family (quadro 
FX). These type of cards have hardware openGL implemented on a chip, 
instead of partly emulating the commands by software. This makes the 
quadro card work fast with O and coot etc. but slow with most of the 
games as they require other graphic gadgets.


We also do not use stereo much, mostly for public relation purposes. 
However, I can highly recommended the students to use it especially for 
writing a manuscript: It minimizes the chances of having important 
features overlooked!!


Quadro's have two clock frequency chips allowing to connect two screens 
(CRT and LCD) that run at different frequencies.  Two screens are very 
helpful and I can highly recommend it: on the 20" CRT, coot can run in 
stereo (120 Hz) and on the 19" LCD (60 Hz), the coot menus can be 
operated without having to minimize etc. the window all the time!! 
However, the setup under linux is not easy with two DIFFERENT screens. 
If somebody is interested, just send me an email and I can forward you 
the XF86config file for you to study.


- J.-



Gretchen Meinke wrote:

Hi--
I last saw some entries on the Mac Pro Xeon dated ~ April 2007.  Were 
they purchased? Are you happy with them?


Does ccp4, mosflm, hkl2000, coot run seamlessly on them?

If so, what was the final cost and configuration (we would like stereo).
How much memory should one get?
Assuming Nuvision glasses for stereo, A CRT monitor (either NEC or 
Viewsonic)


Based on previous readings, it still looks like the FX4500 is the only 
graphics card to support stereo for macs, correct?


Thanks for any and all input.
Gretchen Meinke



--
Jeroen Raymundus Mesters, Ph.D.
Institut fuer Biochemie, Universitaet zu Luebeck
Zentrum fuer Medizinische Struktur und Zellbiologie
Ratzeburger Allee 160, D-23538 Luebeck
Tel: +49-451-5004070, Fax: +49-451-5004068
E-mail: [EMAIL PROTECTED]
Http://www.biochem.uni-luebeck.de
Http://www.iobcr.org
Http://www.opticryst.org
--
If you can look into the seeds of time and say
which grain will grow and which will not - speak then to me  (Macbeth)
--

Re: [ccp4bb] Save image in Postscript format from PYMOL

[Julie Bouckaert]

Pymol version 0.99 has the option to set the label position, similar to 
eg. molscript.


Go to Select - Edit all - scroll down to label-offset - edit the x,y,z 
parameters. Pymol version 0.98 does not have this option.


Julie.

shi jiahai wrote:


Hi, all

I am drawing some stereo images with label by PYMOL. But the label 
interfere with protein. I try to output to Postscript  format so that I 
can change the position of label. However, I can't output the image to 
Postscript  format in Pymol.


Is there anyboy know how to save image in Postscript format from PYMOL?

Your help would be appreciated.

Thank you very much!

Shi Jiahai
Dept of Biological Sciences
National University of Singapore



--

Julie Bouckaert, PhD[EMAIL PROTECTED]   
VIB Project leader

VIB Department of Molecular and Cellular Interactions, Vrije 
Universiteit Brussel


Tel. 32-2-629-1988  Fax 32-2-6291963

ULTR, Building E 4.18   
Vrije Universiteit Brussel
Pleinlaan 2
1050 Brussel
Belgium 

[ccp4bb] Open position at the crystallography platform, Heidelberg University Biochemistry Center

[Klemens Wild]

Institution: Heidelberg University Biochemistry Center (BZH) and Cluster 
of Excellence (CellNetworks)

Location: Heidelberg, Germany
URL: www.uni-heidelberg.de/zentral/bzh/
Start: As soon as possible
Duration: 4 years
Salary: According to the German public service tariff scale TV-L.

Description: We are establishing a medium-throughput crystallization 
facility for biological macromolecules as a central technology platform. 
We are looking for a scientific leader of the facility, to both run the 
platform and organize the user support. The successful candidate is an 
expert in protein biochemistry with a profound knowledge in recombinant 
protein expression, purification, and crystallization. Experience in 
X-ray crystallography and/or automation would be an advantage.


Prerequisites: PhD or equivalent, basic knowledge in German
Please submit: CV, 2 letters of reference until July 20
Contact: Prof. Dr. Irmgard Sinning
Address: Heidelberg University Biochemistry Center (BZH), INF328, 
D-69120 Heidelberg, Germany.

Email: irmi.sinning(at)bzh.uni-heidelberg.de, Phone: +49 6221 544780

Re: [ccp4bb] Ligand fitting in COOT and SHELX refinement

[Dale Tronrud]

U Sam wrote:

Hi
I would like to know following issue for a ligand.
A ligand of a long alkyl chain can have multiple conformation.
In coot in order to fit any protein residues into "difference Density", we can select a 
specific "rotamer" conformation and refine.
For fitting ligand of above kind, how does it work out.


   For amino acids there are tens of thousands of examples from which
one can derive rotomer libraries.  There is no such luck with most
other compounds.  This is why Coot has special case code for handling
amino acids that does not understand your (or my) favorite molecules.

   Fortunately, Coot does not require such information to run its real
space refinement.  You do need a cif definition that includes, amongst
other things, the ideal bond lengths and bond angles.  You can work
with Coot to build the conformation of your molecule that fits your
density.  All conformations will be consistent with the same bonds
and angles, unless you have a very strange molecule.

Taking the PDB with ligand when we go to refine in SHELX, how restraints like (DFIX, DANG etc) are mentioned for such kind of ligand which can have multiple conformation (particularly for the long alkyl chain) and during refinement values can deviate a lot from a particular value taken from the literature. 


SHELXL will take whatever conformation you build and come up with a
model that is consistent with the values on the DFIX and DANG statements.
It should never produce a model that deviates from the literature values,
if you put those values on your DFIX and DANG statements.  The final
model will have a configuration similar to what you built in Coot.
Use Coot to make the big changes and SHELXL to fine tune.

   I have been refining some long chain hydrocarbons along with my
protein and have had no problems, once I was able to create the proper
definitions for Coot and SHELXL.  SHELXL is certainly easier to create
a library for, but you need both if you want to model build and refine.

   Building a cif with ideal geometry for Coot/Refmac is not an easy
task.  You need to understand your chemistry and the file format,
which is not well documented.

   You have several options:

1) You can sit down and figure out how to create a cif definition.
   This is hard to do but a valuable skill to acquire.

2) You can find a compound similar to yours for which there is a
   definition built into Coot and modify it for your needs.  You
   still need to understand the file format, but you can get away
   with less understanding because you are starting with something
   that works.

3) You can use web resources to find/create a file for you.  A number
   of options are available, none of which I would trust completely.
   The HIC-UP website is perhaps the most popular, but the values
   are quite unreliable.  These files can be used as a starting point
   but always verify...  The Elbow builder in Phenix is quite
   reasonable, but takes a bit of study to understand, and again,
   don't trust it.

   Remember the quote from the Harry Potter books: "Never trust
anything you can't see where it keeps its brains."


I appreciate suggestion and comments.
Many Thanks
Sam
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Re: [ccp4bb] Save image in Postscript format from PYMOL

[shi jiahai]

Hi, Julie,

Thank you very much for your kindly reply!

But it seems this function  can not set the individual label position. For
example, one label is set at ( 2, 1,-0.5) while another label is set at (1,
2, 3).
Is there a way to set the label position one by one?

Your help is highly appreciated

Thank you very much!

Jiahai

On 6/22/07, Julie Bouckaert <[EMAIL PROTECTED]> wrote:


Pymol version 0.99 has the option to set the label position, similar to
eg. molscript.

Go to Select - Edit all - scroll down to label-offset - edit the x,y,z
parameters. Pymol version 0.98 does not have this option.

Julie.

shi jiahai wrote:

> Hi, all
>
> I am drawing some stereo images with label by PYMOL. But the label
> interfere with protein. I try to output to Postscript  format so that I
> can change the position of label. However, I can't output the image to
> Postscript  format in Pymol.
>
> Is there anyboy know how to save image in Postscript format from PYMOL?
>
> Your help would be appreciated.
>
> Thank you very much!
>
> Shi Jiahai
> Dept of Biological Sciences
> National University of Singapore


--

Julie Bouckaert, PhD[EMAIL PROTECTED]
VIB Project leader

VIB Department of Molecular and Cellular Interactions, Vrije
Universiteit Brussel

Tel. 32-2-629-1988  Fax 32-2-6291963

ULTR, Building E 4.18
Vrije Universiteit Brussel
Pleinlaan 2
1050 Brussel
Belgium





--
Best Regards,
Shi Jiahai

Re: [ccp4bb] Open position at the crystallography platform, Heidelberg University Biochemistry Center

[Frank von Delft]

Whereas I am young, cheap and very very easy -- phwooaaarrr!!


Gebhard Schertler wrote:

Sorry Irmi, I am too old and expensive.

All the best.

good luck

Gebhard
On 22 Jun 2007, at 09:17, Klemens Wild wrote:

Institution: Heidelberg University Biochemistry Center (BZH) and 
Cluster of Excellence (CellNetworks)

Location: Heidelberg, Germany
URL: www.uni-heidelberg.de/zentral/bzh/ 


Start: As soon as possible
Duration: 4 years
Salary: According to the German public service tariff scale TV-L.

Description: We are establishing a medium-throughput crystallization 
facility for biological macromolecules as a central technology 
platform. We are looking for a scientific leader of the facility, to 
both run the platform and organize the user support. The successful 
candidate is an expert in protein biochemistry with a profound 
knowledge in recombinant protein expression, purification, and 
crystallization. Experience in X-ray crystallography and/or automation 
would be an advantage.


Prerequisites: PhD or equivalent, basic knowledge in German
Please submit: CV, 2 letters of reference until July 20
Contact: Prof. Dr. Irmgard Sinning
Address: Heidelberg University Biochemistry Center (BZH), INF328, 
D-69120 Heidelberg, Germany.

Email: irmi.sinning(at)bzh.uni-heidelberg.de, Phone: +49 6221 544780






Dr. Gebhard F. X. Schertler

Senior Scientist and Group Leader
MRC
Laboratory of Molecular Biology
Cambridge CB2 2QH
 
tel  0044 1223 402328

e-mail   [EMAIL PROTECTED] 
web   http://www2.mrc-lmb.cam.ac.uk/SS/Schertler_G/
 

Re: [ccp4bb] Open position at the crystallography platform, Heidelberg University Biochemistry Center

[Gebhard Schertler]

Sorry Irmi, I am too old and expensive.

All the best.

good luck

Gebhard
On 22 Jun 2007, at 09:17, Klemens Wild wrote:

Institution: Heidelberg University Biochemistry Center (BZH) and  
Cluster of Excellence (CellNetworks)

Location: Heidelberg, Germany
URL: www.uni-heidelberg.de/zentral/bzh/
Start: As soon as possible
Duration: 4 years
Salary: According to the German public service tariff scale TV-L.

Description: We are establishing a medium-throughput  
crystallization facility for biological macromolecules as a central  
technology platform. We are looking for a scientific leader of the  
facility, to both run the platform and organize the user support.  
The successful candidate is an expert in protein biochemistry with  
a profound knowledge in recombinant protein expression,  
purification, and crystallization. Experience in X-ray  
crystallography and/or automation would be an advantage.


Prerequisites: PhD or equivalent, basic knowledge in German
Please submit: CV, 2 letters of reference until July 20
Contact: Prof. Dr. Irmgard Sinning
Address: Heidelberg University Biochemistry Center (BZH), INF328,  
D-69120 Heidelberg, Germany.

Email: irmi.sinning(at)bzh.uni-heidelberg.de, Phone: +49 6221 544780






Dr. Gebhard F. X. Schertler

Senior Scientist and Group Leader
MRC
Laboratory of Molecular Biology
Cambridge CB2 2QH

tel  0044 1223 402328
e-mail   [EMAIL PROTECTED]
web   http://www2.mrc-lmb.cam.ac.uk/SS/Schertler_G/

Re: [ccp4bb] Save image in Postscript format from PYMOL

[shi jiahai]

Hi, Stefan

Your advice is wonderful! This is the easiest way!!

Thank you very much!!!

Jiahai

On 6/22/07, Stefan schmelz <[EMAIL PROTECTED]> wrote:


Hi Jiahai,

there is an easy way to move labels in pymol. You have to change your
Mouse Mode from "3-Button Viewing" to "3-Button Editing". Than your able
to drag the labels by pressing "CTRL" and using your left mouse button
(both has to be pressed). But be careful not changing your molecule :-)!!

Stefan

shi jiahai wrote:
> Hi, Julie,
>
> Thank you very much for your kindly reply!
>
> But it seems this function  can not set the individual label position.
> For example, one label is set at ( 2, 1,-0.5) while another label is
> set at (1, 2, 3).
> Is there a way to set the label position one by one?
>
> Your help is highly appreciated
>
> Thank you very much!
>
> Jiahai
>
> On 6/22/07, *Julie Bouckaert * <[EMAIL PROTECTED]
> > wrote:
>
> Pymol version 0.99 has the option to set the label position,
> similar to
> eg. molscript.
>
> Go to Select - Edit all - scroll down to label-offset - edit the
x,y,z
> parameters. Pymol version 0.98 does not have this option.
>
> Julie.
>
> shi jiahai wrote:
>
> > Hi, all
> >
> > I am drawing some stereo images with label by PYMOL. But the label
> > interfere with protein. I try to output to Postscript  format so
> that I
> > can change the position of label. However, I can't output the
> image to
> > Postscript  format in Pymol.
> >
> > Is there anyboy know how to save image in Postscript format from
> PYMOL?
> >
> > Your help would be appreciated.
> >
> > Thank you very much!
> >
> > Shi Jiahai
> > Dept of Biological Sciences
> > National University of Singapore
>
>
> --
>
> Julie Bouckaert, PhD[EMAIL PROTECTED]
> 
> VIB Project leader
>
> VIB Department of Molecular and Cellular Interactions, Vrije
> Universiteit Brussel
>
> Tel. 32-2-629-1988  Fax 32-2-6291963
>
> ULTR, Building E 4.18
> Vrije Universiteit Brussel
> Pleinlaan 2
> 1050 Brussel
> Belgium
>
>
>
>
> --
> Best Regards,
> Shi Jiahai





--
Best Regards,
Shi Jiahai

[ccp4bb] How to replace 2.45M K/Na phosphate buffer

[Claudia Scotti]

Dear list,

I've crystals in a condition including 2,45 M K/Na phosphate buffer for the 
well condition, and 1 microl protein + 0.8 microl Na/K phosphate buffer + 0.25 
microl 30% 1,6-hexanediol in the drop condition.

These crystals dissolve in several cryoprotectant solutions and survive only in 
malonic acid, with which they give diffraction at 7-8 A.

Among the several different possibilities, I'd like to try to optimize the 
crystals, and one possiblity among others would be to change the buffer. 

Any suggestions, please, about how to replace K/Na phosphate? At these 
concentrations it is acting as a buffer but also as a precipitant and I was 
wondering if anybody has experienced nice buffer-salt combinations that proved 
to be useful starting from a similar condition.

Thanks a lot,

Claudia



   



  







Claudia Scotti
Dipartimento di Medicina Sperimentale
Sezione di Patologia Generale
Universita' di Pavia
Piazza Botta, 10
27100 Pavia
Italia
Tel.   0039 0382 986335/8/1
Facs 0039 0382 303673
_
Make every IM count. Download Windows Live Messenger and join the i’m 
Initiative now. It’s free. 
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[ccp4bb] How to replace 2.45M K/Na phosphate buffer - 2

[Claudia Scotti]

Sorry: forgotten the pH: the crystals grow between pH 6.5 and 6.7.

Claudia


Claudia Scotti
Dipartimento di Medicina Sperimentale
Sezione di Patologia Generale
Universita' di Pavia
Piazza Botta, 10
27100 Pavia
Italia
Tel.   0039 0382 986335/8/1
Facs 0039 0382 303673


> Date: Fri, 22 Jun 2007 14:15:47 +0200
> From: [EMAIL PROTECTED]
> Subject: [ccp4bb] How to replace 2.45M K/Na phosphate buffer
> To: CCP4BB@JISCMAIL.AC.UK
> 
> Dear list,
> 
> I've crystals in a condition including 2,45 M K/Na phosphate buffer for the 
> well condition, and 1 microl protein + 0.8 microl Na/K phosphate buffer + 
> 0.25 microl 30% 1,6-hexanediol in the drop condition.
> 
> These crystals dissolve in several cryoprotectant solutions and survive only 
> in malonic acid, with which they give diffraction at 7-8 A.
> 
> Among the several different possibilities, I'd like to try to optimize the 
> crystals, and one possiblity among others would be to change the buffer. 
> 
> Any suggestions, please, about how to replace K/Na phosphate? At these 
> concentrations it is acting as a buffer but also as a precipitant and I was 
> wondering if anybody has experienced nice buffer-salt combinations that 
> proved to be useful starting from a similar condition.
> 
> Thanks a lot,
> 
> Claudia
> 
> 
> 
>
> 
> 
> 
>   
> 
> 
> 
> 
> 
> 
> 
> Claudia Scotti
> Dipartimento di Medicina Sperimentale
> Sezione di Patologia Generale
> Universita' di Pavia
> Piazza Botta, 10
> 27100 Pavia
> Italia
> Tel.   0039 0382 986335/8/1
> Facs 0039 0382 303673
> _
> Make every IM count. Download Windows Live Messenger and join the i’m 
> Initiative now. It’s free. 
> http://im.live.com/messenger/im/home/?source=TAGWL_June07

_
Make every IM count. Download Windows Live Messenger and join the i’m 
Initiative now. It’s free. 
http://im.live.com/messenger/im/home/?source=TAGWL_June07

Re: [ccp4bb] How to replace 2.45M K/Na phosphate buffer - 2

[Murray, James W]

Dear Claudia, 

>These crystals dissolve in several cryoprotectant solutions and survive only 
>in malonic acid, with which they give diffraction at 7-8 A.

You do not mention what the room temperature diffraction is like. If you have 
not tested it already, you should do so - even without malonate, you might only 
get 7-8A diffraction. Assuming the room-temp diffraction is OK, you could just 
try increasing the concentration of phosphate buffer - high salt can also act 
as a cryoprotectant.


James

Dr. James Murray
Biochemistry Building
Department of Biological Sciences
Imperial College London
London, SW7 2AZ
Tel: +44 (0)20 7594 5276





-Original Message-
From: CCP4 bulletin board on behalf of Claudia Scotti
Sent: Fri 22/06/2007 13:42
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] How to replace 2.45M K/Na phosphate buffer - 2
 
Sorry: forgotten the pH: the crystals grow between pH 6.5 and 6.7.

Claudia


Claudia Scotti
Dipartimento di Medicina Sperimentale
Sezione di Patologia Generale
Universita' di Pavia
Piazza Botta, 10
27100 Pavia
Italia
Tel.   0039 0382 986335/8/1
Facs 0039 0382 303673


> Date: Fri, 22 Jun 2007 14:15:47 +0200
> From: [EMAIL PROTECTED]
> Subject: [ccp4bb] How to replace 2.45M K/Na phosphate buffer
> To: CCP4BB@JISCMAIL.AC.UK
> 
> Dear list,
> 
> I've crystals in a condition including 2,45 M K/Na phosphate buffer for the 
> well condition, and 1 microl protein + 0.8 microl Na/K phosphate buffer + 
> 0.25 microl 30% 1,6-hexanediol in the drop condition.
> 
> These crystals dissolve in several cryoprotectant solutions and survive only 
> in malonic acid, with which they give diffraction at 7-8 A.
> 
> Among the several different possibilities, I'd like to try to optimize the 
> crystals, and one possiblity among others would be to change the buffer. 
> 
> Any suggestions, please, about how to replace K/Na phosphate? At these 
> concentrations it is acting as a buffer but also as a precipitant and I was 
> wondering if anybody has experienced nice buffer-salt combinations that 
> proved to be useful starting from a similar condition.
> 
> Thanks a lot,
> 
> Claudia
> 
> 
> 
>
> 
> 
> 
>   
> 
> 
> 
> 
> 
> 
> 
> Claudia Scotti
> Dipartimento di Medicina Sperimentale
> Sezione di Patologia Generale
> Universita' di Pavia
> Piazza Botta, 10
> 27100 Pavia
> Italia
> Tel.   0039 0382 986335/8/1
> Facs 0039 0382 303673
> _
> Make every IM count. Download Windows Live Messenger and join the i'm 
> Initiative now. It's free. 
> http://im.live.com/messenger/im/home/?source=TAGWL_June07

_
Make every IM count. Download Windows Live Messenger and join the i'm 
Initiative now. It's free. 
http://im.live.com/messenger/im/home/?source=TAGWL_June07

Re: [ccp4bb] How to replace 2.45M K/Na phosphate buffer - 2

[Kornelius Zeth]

at around 4 molar P-buffer freezes clean.

Best wishes

Kornelius

On Fri, 22 Jun 2007 14:42:00 +0200
 Claudia Scotti <[EMAIL PROTECTED]> wrote:
> Sorry: forgotten the pH: the crystals grow between pH 6.5
> and 6.7.
> 
> Claudia
> 
> 
> Claudia Scotti
> Dipartimento di Medicina Sperimentale
> Sezione di Patologia Generale
> Universita' di Pavia
> Piazza Botta, 10
> 27100 Pavia
> Italia
> Tel.   0039 0382 986335/8/1
> Facs 0039 0382 303673
> 
> 
> > Date: Fri, 22 Jun 2007 14:15:47 +0200
> > From: [EMAIL PROTECTED]
> > Subject: [ccp4bb] How to replace 2.45M K/Na phosphate
> buffer
> > To: CCP4BB@JISCMAIL.AC.UK
> > 
> > Dear list,
> > 
> > I've crystals in a condition including 2,45 M K/Na
> phosphate buffer for the well condition, and 1 microl
> protein + 0.8 microl Na/K phosphate buffer + 0.25 microl
> 30% 1,6-hexanediol in the drop condition.
> > 
> > These crystals dissolve in several cryoprotectant
> solutions and survive only in malonic acid, with which
> they give diffraction at 7-8 A.
> > 
> > Among the several different possibilities, I'd like to
> try to optimize the crystals, and one possiblity among
> others would be to change the buffer. 
> > 
> > Any suggestions, please, about how to replace K/Na
> phosphate? At these concentrations it is acting as a
> buffer but also as a precipitant and I was wondering if
> anybody has experienced nice buffer-salt combinations
> that proved to be useful starting from a similar
> condition.
> > 
> > Thanks a lot,
> > 
> > Claudia
> > 
> > 
> > 
> >
> > 
> > 
> > 
> >   
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > Claudia Scotti
> > Dipartimento di Medicina Sperimentale
> > Sezione di Patologia Generale
> > Universita' di Pavia
> > Piazza Botta, 10
> > 27100 Pavia
> > Italia
> > Tel.   0039 0382 986335/8/1
> > Facs 0039 0382 303673
> >
>
_
> > Make every IM count. Download Windows Live Messenger
> and join the i’m Initiative now. It’s free. 
> >
> http://im.live.com/messenger/im/home/?source=TAGWL_June07
> 
>
_
> Make every IM count. Download Windows Live Messenger and
> join the i’m Initiative now. It’s free. 
> http://im.live.com/messenger/im/home/?source=TAGWL_June07
> 

 --
 Kornelius Zeth
 Max Planck Institute for Developmental Biology
 Dept. Protein Evolution
 Spemannstr. 35
 72076 Tuebingen, Germany
 [EMAIL PROTECTED]
 Tel -49 7071 601 323
 Fax -49 7071 601 349

[ccp4bb] Molscript and symbolic label

[U Sam]

Hi 
I would appreciate knowing how to make label of symbolic letters like alpha, 
beta, pi etc. using molscript.
Thanks.
Sam
_
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[ccp4bb] Flat Screen and Stereo

[Zach Powers]

Hello,

I have been having a problem getting stereo to work on the lab's new
flatsceeen ( i know, i know. CRTs = much better but i think the
purchaser was overcome with flatscreen lust). 

I am using a Dell 3007WFP (2560x 1600, refresh rate = 60hz) attached to
nVidia Quadro FX 4500 graphics card with the eDimensional stereo glasses. I
am using the current drivers from livna (100.14.09-2lvn7) on a Fedora7 box 
with the 2.6.21_1.3228 kernel.

When I try to get Pymol or Coot to use stereo, no luck: Coot tells me that
the hardware does not support quad buffered stereo. To the best of my
knowledge I have the xorg.conf file correctly configured (see below) and I
am wondering if anyone has run into these problems before or if somehow the
livna driver can detect a refresh rate that is suboptimal and therefore
refuse to start stereo. Perhaps there is also the issue of the kernel? I
don't know, but I would appreciate any help. 

Below is my xorg.conf file and you can see I have 'Option "Stereo"' set to
"3". I have fiddled around with many of the options in the xorg.conf file -
basically trying every variation that i found other people had used.
However, still no luck, which makes me think there may be some driver or
kernel issue.

Anyhow, any suggestions would be greatly appreciated (I would like to get
this monitor work before falling back on a CRT - if the flicker is terrible,
there will be no choice but it seems others have been using these monitors
for stereo).


thank you,
zach charlop-powers
PhD Candidate
Graduate School of Biological Sciences
Mount Sinai School of Medicine
New York, NY

### Xorg configuration created by livna-config-display

Section "ServerLayout"
Identifier "single head configuration"
Screen  0  "Screen0" 0 0
InputDevice"Keyboard0" "CoreKeyboard"
EndSection

Section "Files"
ModulePath   "/usr/lib64/xorg/modules/extensions/nvidia"
ModulePath   "/usr/lib64/xorg/modules"
EndSection

Section "Module"
Load  "dbe"
Load  "extmod"
Load  "glx"
Load  "dbe"
Load  "extmod"
EndSection

Section "InputDevice"
Identifier  "Keyboard0"
Driver  "kbd"
Option  "XkbModel" "pc105"
Option  "XkbLayout" "us"
EndSection

Section "Monitor"
Identifier   "Monitor0"
ModelName"Dell 3007WFP"
HorizSync30.0 - 100.0
VertRefresh  56.0 - 76.0
Option  "dpms"
EndSection

Section "Device"
Identifier  "Videocard0"
Driver  "nvidia"
Option  "Stereo" "3"
Option  "AllowDFPStereo" "1"
Option  "UBB" "True"
Option  "AddARGBGLXVisuals" "True"
Option  "DisableGLXRootClipping" "True"
EndSection

Section "Screen"
Identifier "Screen0"
Device "Videocard0"
Monitor"Monitor0"
DefaultDepth 24
SubSection "Display"
Viewport   0 0
Depth 24
Modes"2560x1600" "1600x1200" "1600x1024" "1440x900" 
"1400x1050"
"1280x1024" "1280x960" "1280x800" "1152x864" "1024x768" "800x600" "640x480"
"640x400"
EndSubSection
EndSection

Re: [ccp4bb] Flat Screen and Stereo

[P Hubbard]

Hi,

The following web page should answer your question:

http://pymol.sourceforge.net/stereo3d.html

On a related note, I recently came across a new 22" LCD stereo system which 
is below $1000 and requires polarized glasses ($10 each). It doesn't seem to 
be set up for OpenGL yet, so isn't suitable for Linux. I am curious as to 
whether anyone has it running on some DirectX molecular visualization 
software in Windows:


http://www.iz3d.com/

Paul



From: Zach Powers <[EMAIL PROTECTED]>
Reply-To: Zach Powers <[EMAIL PROTECTED]>
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Flat Screen and Stereo
Date: Fri, 22 Jun 2007 16:38:21 +0100

Hello,

I have been having a problem getting stereo to work on the lab's new
flatsceeen ( i know, i know. CRTs = much better but i think the
purchaser was overcome with flatscreen lust).

I am using a Dell 3007WFP (2560x 1600, refresh rate = 60hz) attached to
nVidia Quadro FX 4500 graphics card with the eDimensional stereo glasses. I
am using the current drivers from livna (100.14.09-2lvn7) on a Fedora7 box
with the 2.6.21_1.3228 kernel.

When I try to get Pymol or Coot to use stereo, no luck: Coot tells me that
the hardware does not support quad buffered stereo. To the best of my
knowledge I have the xorg.conf file correctly configured (see below) and I
am wondering if anyone has run into these problems before or if somehow the
livna driver can detect a refresh rate that is suboptimal and therefore
refuse to start stereo. Perhaps there is also the issue of the kernel? I
don't know, but I would appreciate any help.

Below is my xorg.conf file and you can see I have 'Option "Stereo"' set to
"3". I have fiddled around with many of the options in the xorg.conf file -
basically trying every variation that i found other people had used.
However, still no luck, which makes me think there may be some driver or
kernel issue.

Anyhow, any suggestions would be greatly appreciated (I would like to get
this monitor work before falling back on a CRT - if the flicker is 
terrible,

there will be no choice but it seems others have been using these monitors
for stereo).


thank you,
zach charlop-powers
PhD Candidate
Graduate School of Biological Sciences
Mount Sinai School of Medicine
New York, NY

### Xorg configuration created by livna-config-display

Section "ServerLayout"
Identifier "single head configuration"
Screen  0  "Screen0" 0 0
InputDevice"Keyboard0" "CoreKeyboard"
EndSection

Section "Files"
ModulePath   "/usr/lib64/xorg/modules/extensions/nvidia"
ModulePath   "/usr/lib64/xorg/modules"
EndSection

Section "Module"
Load  "dbe"
Load  "extmod"
Load  "glx"
Load  "dbe"
Load  "extmod"
EndSection

Section "InputDevice"
Identifier  "Keyboard0"
Driver  "kbd"
Option  "XkbModel" "pc105"
Option  "XkbLayout" "us"
EndSection

Section "Monitor"
Identifier   "Monitor0"
ModelName"Dell 3007WFP"
HorizSync30.0 - 100.0
VertRefresh  56.0 - 76.0
Option  "dpms"
EndSection

Section "Device"
Identifier  "Videocard0"
Driver  "nvidia"
Option  "Stereo" "3"
Option  "AllowDFPStereo" "1"
Option  "UBB" "True"
Option  "AddARGBGLXVisuals" "True"
Option  "DisableGLXRootClipping" "True"
EndSection

Section "Screen"
Identifier "Screen0"
Device "Videocard0"
Monitor"Monitor0"
DefaultDepth 24
SubSection "Display"
Viewport   0 0
Depth 24
Modes"2560x1600" "1600x1200" "1600x1024" "1440x900" 
"1400x1050"
"1280x1024" "1280x960" "1280x800" "1152x864" "1024x768" "800x600" "640x480"
"640x400"
EndSubSection
EndSection







_
Picture this – share your photos and you could win big!  
http://www.GETREALPhotoContest.com?ocid=TXT_TAGHM&loc=us

[ccp4bb] [Fwd: Re: [ccp4bb] Flat Screen and Stereo]

[zach powers]

Adding the following commands to my xorg.conf file "fixed" my problem:

Section "Extensions"
  Option  "Composite" "Disable"
EndSection


The screen now makes an attempt to run stereo: it will draw two sets of 
lines and the eDimensional glasses now work. But the flickering is 
unbearable to look at for any length of time even though the 3D effect 
is noticeable.  It seems that there are several possible sources of this 
new problem:

1) asynchrony between the glasses and the monitor refresh rate [unlikely]
2) problems due to the way flat screens adjust (not all-at-once, as 
pointed out to me by another respondent)
3) simply too slow of a refresh rate. ( i can try to force maximum 
refresh rate)


I am going to tool around with numbers 1 and 3 to see if I can get a 
halfway decent stereo effect. If i get anything to work I will post 
again. In the meantime, I'll try to avoid the slightly nauseating 
effects of the flickering.


thank you for the many (and prompt!) responses to my problem,
best
zach cp
--- Begin Message ---

Hi Zach,

I think you need to add:

Section "Extensions"
   Option  "Composite" "Disable"
EndSection

to your xorg.conf file.  The driver cannot do stereo with the composite 
extensions enabled.


Steve

Zach Powers wrote:

Hello,

I have been having a problem getting stereo to work on the lab's new
flatsceeen ( i know, i know. CRTs = much better but i think the
purchaser was overcome with flatscreen lust). 


I am using a Dell 3007WFP (2560x 1600, refresh rate = 60hz) attached to
nVidia Quadro FX 4500 graphics card with the eDimensional stereo glasses. I
am using the current drivers from livna (100.14.09-2lvn7) on a Fedora7 box 
with the 2.6.21_1.3228 kernel.


When I try to get Pymol or Coot to use stereo, no luck: Coot tells me that
the hardware does not support quad buffered stereo. To the best of my
knowledge I have the xorg.conf file correctly configured (see below) and I
am wondering if anyone has run into these problems before or if somehow the
livna driver can detect a refresh rate that is suboptimal and therefore
refuse to start stereo. Perhaps there is also the issue of the kernel? I
don't know, but I would appreciate any help. 


Below is my xorg.conf file and you can see I have 'Option "Stereo"' set to
"3". I have fiddled around with many of the options in the xorg.conf file -
basically trying every variation that i found other people had used.
However, still no luck, which makes me think there may be some driver or
kernel issue.

Anyhow, any suggestions would be greatly appreciated (I would like to get
this monitor work before falling back on a CRT - if the flicker is terrible,
there will be no choice but it seems others have been using these monitors
for stereo).


thank you,
zach charlop-powers
PhD Candidate
Graduate School of Biological Sciences
Mount Sinai School of Medicine
New York, NY

### Xorg configuration created by livna-config-display

Section "ServerLayout"
Identifier "single head configuration"
Screen  0  "Screen0" 0 0
InputDevice"Keyboard0" "CoreKeyboard"
EndSection

Section "Files"
ModulePath   "/usr/lib64/xorg/modules/extensions/nvidia"
ModulePath   "/usr/lib64/xorg/modules"
EndSection

Section "Module"
Load  "dbe"
Load  "extmod"
Load  "glx"
Load  "dbe"
Load  "extmod"
EndSection

Section "InputDevice"
Identifier  "Keyboard0"
Driver  "kbd"
Option  "XkbModel" "pc105"
Option  "XkbLayout" "us"
EndSection

Section "Monitor"
Identifier   "Monitor0"
ModelName"Dell 3007WFP"
HorizSync30.0 - 100.0
VertRefresh  56.0 - 76.0
Option  "dpms"
EndSection

Section "Device"
Identifier  "Videocard0"
Driver  "nvidia"
Option  "Stereo" "3"
Option  "AllowDFPStereo" "1"
Option  "UBB" "True"
Option  "AddARGBGLXVisuals" "True"
Option  "DisableGLXRootClipping" "True"
EndSection

Section "Screen"
Identifier "Screen0"
Device "Videocard0"
Monitor"Monitor0"
DefaultDepth 24
SubSection "Display"
Viewport   0 0
Depth 24
Modes"2560x1600" "1600x1200" "1600x1024" "1440x900" 
"1400x1050"
"1280x1024" "1280x960" "1280x800" "1152x864" "1024x768" "800x600" "640x480"
"640x400"
EndSubSection
EndSection




 

  


--
Steven Stayrook, Ph.D.
Assistant Director Johnson Research Foundation
Senior Research Investigator
Department of Biochemistry and Biophysics
423 Guardian Blvd.
G11 Blockley Hall
University of Pennsylvania School of Medicine
Philadelphia, Pa.  19104

e-mail:  [EMAIL PROTECTED]
Phone:  215-573-9968
fax:215-573-2503

--- End Message ---

Re: [ccp4bb] Flat Screen and Stereo

[Latchem, MJ (Mike)]

Rather strangely my stereo set uses the following

Option "AllowDFPStereo" "on"

I look forward to hearing how you get on as all my past experience with stereo 
and LCD screens was less than positive

Hope this helps

Mike

-Original Message-
From: CCP4 bulletin board on behalf of James M. Vergis
Sent: Fri 22/06/2007 17:10
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Flat Screen and Stereo
 
I don't know if this will help but the NVIDIA readme says it should be a
BOOLEAN after ALLOWDFPSTEREO.

You have: Option"AllowDFPStereo" "1"
Change to:Option"AllowDFPStereo" "true"

Hope that helps.  I'd be curious as to how an LCD works for stereo.

Good luck,
James




James M. Vergis, Ph.D.
University of Virginia Molecular Physiology and Biological Physics
MKWEINR 438 Jordan Hall
1340 Jefferson Park Ave
Charlottesville, VA 22908-0736
phone: 434-243-2730   FAX: 434-982-1616
[EMAIL PROTECTED]

 

> -Original Message-
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On 
> Behalf Of Zach Powers
> Sent: Friday, June 22, 2007 11:38 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Flat Screen and Stereo
> 
> Hello,
> 
> I have been having a problem getting stereo to work on the 
> lab's new flatsceeen ( i know, i know. CRTs = much better 
> but i think the purchaser was overcome with flatscreen lust). 
> 
> I am using a Dell 3007WFP (2560x 1600, refresh rate = 60hz) 
> attached to nVidia Quadro FX 4500 graphics card with the 
> eDimensional stereo glasses. I am using the current drivers 
> from livna (100.14.09-2lvn7) on a Fedora7 box with the 
> 2.6.21_1.3228 kernel.
> 
> When I try to get Pymol or Coot to use stereo, no luck: Coot 
> tells me that the hardware does not support quad buffered 
> stereo. To the best of my knowledge I have the xorg.conf file 
> correctly configured (see below) and I am wondering if anyone 
> has run into these problems before or if somehow the livna 
> driver can detect a refresh rate that is suboptimal and 
> therefore refuse to start stereo. Perhaps there is also the 
> issue of the kernel? I don't know, but I would appreciate any help. 
> 
> Below is my xorg.conf file and you can see I have 'Option 
> "Stereo"' set to "3". I have fiddled around with many of the 
> options in the xorg.conf file - basically trying every 
> variation that i found other people had used.
> However, still no luck, which makes me think there may be 
> some driver or kernel issue.
> 
> Anyhow, any suggestions would be greatly appreciated (I would 
> like to get this monitor work before falling back on a CRT - 
> if the flicker is terrible, there will be no choice but it 
> seems others have been using these monitors for stereo).
> 
> 
> thank you,
> zach charlop-powers
> PhD Candidate
> Graduate School of Biological Sciences
> Mount Sinai School of Medicine
> New York, NY
> 
> ### Xorg configuration created by livna-config-display
> 
> Section "ServerLayout"
>   Identifier "single head configuration"
>   Screen  0  "Screen0" 0 0
>   InputDevice"Keyboard0" "CoreKeyboard"
> EndSection
> 
> Section "Files"
>   ModulePath   "/usr/lib64/xorg/modules/extensions/nvidia"
>   ModulePath   "/usr/lib64/xorg/modules"
> EndSection
> 
> Section "Module"
>   Load  "dbe"
>   Load  "extmod"
>   Load  "glx"
>   Load  "dbe"
>   Load  "extmod"
> EndSection
> 
> Section "InputDevice"
>   Identifier  "Keyboard0"
>   Driver  "kbd"
>   Option  "XkbModel" "pc105"
>   Option  "XkbLayout" "us"
> EndSection
> 
> Section "Monitor"
>   Identifier   "Monitor0"
>   ModelName"Dell 3007WFP"
>   HorizSync30.0 - 100.0
>   VertRefresh  56.0 - 76.0
>   Option  "dpms"
> EndSection
> 
> Section "Device"
>   Identifier  "Videocard0"
>   Driver  "nvidia"
>   Option  "Stereo" "3"
>   Option  "AllowDFPStereo" "1"
>   Option  "UBB" "True"
>   Option  "AddARGBGLXVisuals" "True"
>   Option  "DisableGLXRootClipping" "True"
> EndSection
> 
> Section "Screen"
>   Identifier "Screen0"
>   Device "Videocard0"
>   Monitor"Monitor0"
>   DefaultDepth 24
>   SubSection "Display"
>   Viewport   0 0
>   Depth 24
>   Modes"2560x1600" "1600x1200" "1600x1024" 
> "1440x900" "1400x1050"
> "1280x1024" "1280x960" "1280x800" "1152x864" "1024x768" 
> "800x600" "640x480"
> "640x400"
>   EndSubSection
> EndSection
> 
> 
> 
> 
>  
> 

This e-mail and any attachments may contain 
confidential, copyright and or privileged material, and are for the use of the 
intended addressee only. If you are not the intended addressee or an authorised 
recipient of the addressee please notify us of receipt by returning the e-mail 
and do not use, copy, retain, distribute or disclose the information in o

[ccp4bb] model building and hardware (tangent)

[Bryan W. Lepore]

this post is is tangential to the model building/hardware thread - 
anything useful presented here is purely coincidental:


tangible model building action shot:
http://puffer.tamu.edu/cs_computer.htm
[slide all the way to the right]

http://www.bassictech.com/blogs/bassictech_news_blog/archive/2007/01/20/remapping-the-universe-using-this-gui.aspx
[a protein model makes an appearance around 2:26]

articulated model project :
http://mgl.scripps.edu/projects

the sensetable - for good measure:
http://tangible.media.mit.edu/projects/sensetable/

-bryan

Re: [ccp4bb] Flat Screen and Stereo

[James M. Vergis]

I don't know if this will help but the NVIDIA readme says it should be a
BOOLEAN after ALLOWDFPSTEREO.

You have: Option"AllowDFPStereo" "1"
Change to:Option"AllowDFPStereo" "true"

Hope that helps.  I'd be curious as to how an LCD works for stereo.

Good luck,
James




James M. Vergis, Ph.D.
University of Virginia Molecular Physiology and Biological Physics
MKWEINR 438 Jordan Hall
1340 Jefferson Park Ave
Charlottesville, VA 22908-0736
phone: 434-243-2730   FAX: 434-982-1616
[EMAIL PROTECTED]

 

> -Original Message-
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On 
> Behalf Of Zach Powers
> Sent: Friday, June 22, 2007 11:38 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Flat Screen and Stereo
> 
> Hello,
> 
> I have been having a problem getting stereo to work on the 
> lab's new flatsceeen ( i know, i know. CRTs = much better 
> but i think the purchaser was overcome with flatscreen lust). 
> 
> I am using a Dell 3007WFP (2560x 1600, refresh rate = 60hz) 
> attached to nVidia Quadro FX 4500 graphics card with the 
> eDimensional stereo glasses. I am using the current drivers 
> from livna (100.14.09-2lvn7) on a Fedora7 box with the 
> 2.6.21_1.3228 kernel.
> 
> When I try to get Pymol or Coot to use stereo, no luck: Coot 
> tells me that the hardware does not support quad buffered 
> stereo. To the best of my knowledge I have the xorg.conf file 
> correctly configured (see below) and I am wondering if anyone 
> has run into these problems before or if somehow the livna 
> driver can detect a refresh rate that is suboptimal and 
> therefore refuse to start stereo. Perhaps there is also the 
> issue of the kernel? I don't know, but I would appreciate any help. 
> 
> Below is my xorg.conf file and you can see I have 'Option 
> "Stereo"' set to "3". I have fiddled around with many of the 
> options in the xorg.conf file - basically trying every 
> variation that i found other people had used.
> However, still no luck, which makes me think there may be 
> some driver or kernel issue.
> 
> Anyhow, any suggestions would be greatly appreciated (I would 
> like to get this monitor work before falling back on a CRT - 
> if the flicker is terrible, there will be no choice but it 
> seems others have been using these monitors for stereo).
> 
> 
> thank you,
> zach charlop-powers
> PhD Candidate
> Graduate School of Biological Sciences
> Mount Sinai School of Medicine
> New York, NY
> 
> ### Xorg configuration created by livna-config-display
> 
> Section "ServerLayout"
>   Identifier "single head configuration"
>   Screen  0  "Screen0" 0 0
>   InputDevice"Keyboard0" "CoreKeyboard"
> EndSection
> 
> Section "Files"
>   ModulePath   "/usr/lib64/xorg/modules/extensions/nvidia"
>   ModulePath   "/usr/lib64/xorg/modules"
> EndSection
> 
> Section "Module"
>   Load  "dbe"
>   Load  "extmod"
>   Load  "glx"
>   Load  "dbe"
>   Load  "extmod"
> EndSection
> 
> Section "InputDevice"
>   Identifier  "Keyboard0"
>   Driver  "kbd"
>   Option  "XkbModel" "pc105"
>   Option  "XkbLayout" "us"
> EndSection
> 
> Section "Monitor"
>   Identifier   "Monitor0"
>   ModelName"Dell 3007WFP"
>   HorizSync30.0 - 100.0
>   VertRefresh  56.0 - 76.0
>   Option  "dpms"
> EndSection
> 
> Section "Device"
>   Identifier  "Videocard0"
>   Driver  "nvidia"
>   Option  "Stereo" "3"
>   Option  "AllowDFPStereo" "1"
>   Option  "UBB" "True"
>   Option  "AddARGBGLXVisuals" "True"
>   Option  "DisableGLXRootClipping" "True"
> EndSection
> 
> Section "Screen"
>   Identifier "Screen0"
>   Device "Videocard0"
>   Monitor"Monitor0"
>   DefaultDepth 24
>   SubSection "Display"
>   Viewport   0 0
>   Depth 24
>   Modes"2560x1600" "1600x1200" "1600x1024" 
> "1440x900" "1400x1050"
> "1280x1024" "1280x960" "1280x800" "1152x864" "1024x768" 
> "800x600" "640x480"
> "640x400"
>   EndSubSection
> EndSection
> 
> 
> 
> 
>  
> 

[ccp4bb] POST DOCTORAL POSITION IN STRUCTURAL ENZYMOLOGY AND INHIBITOR DESIGN

[Steve Almo]

** POST DOCTORAL POSITION IN STRUCTURAL ENZYMOLOGY AND INHIBITOR DESIGN **

A post doctoral position is available immediately in the laboratories of
Vern Schramm and Steve Almo in the Department of Biochemistry at the
Albert Einstein College of Medicine. This program utilizes high resolution
crystallographic analysis and kinetic isotope effects to define the
fundamental chemical and physical determinants of enzymatic rate
enhancement, and to design highly specific transition state analogs with
affinities in the nM and pM ranges. These efforts are focused on the
enzymes involved in nucleotide metabolism in bacterial, fungal and
mammalian organisms and have produced a number of therapeutic leads that
are currently being utilized in animal studies and clinical trials for
malaria, T cell lymphoma and autoimmunity.

The successful applicant must have extensive experience in all aspects of
high resolution protein crystallography and a strong desire to complement
these skills with mechanistic enzymology and state-of-the-art transition
state analysis, with an overall goal of developing new therapeutic
approaches.

Representative publications describing this program include:
Fedorov, et al. (2001) “Transition state structure of purine nucleoside
phosphorylase and principles of atomic motion in enzymatic catalysis.
Biochemistry 40(4):853-60.

Lewandowicz, et al. (2003) Over-the-barrier transition state analogues and
crystal structure with Mycobacterium tuberculosis purine nucleoside
phosphorylase. Biochemistry 42(20):6057-66.

Singh, et al. (2004) Picomolar transition state analogue inhibitors of
human 5'-methylthioadenosine phosphorylase and X-ray structure with
MT-immucillin-A. Biochemistry 43(1):9-18.

Kim, et al. (2006) Structural and kinetic characterization of Escherichia
coli TadA, the wobble-specific tRNA deaminase. Biochemistry
45(20):6407-16.

Singh, et al. (2006) Structure and inhibition of a quorum sensing target
from Streptococcus pneumoniae. Biochemistry 45(43):12929-41.

Murkin, et al. (2007) Neighboring group participation in the transition
state of human purine nucleoside phosphorylase. Biochemistry
46(17):5038-49.


Albert Einstein provides an outstanding scientific environment that
includes considerable strengths in microbiology, immunology, cancer
biology, mechanistic enzymology, biophysics, computational biology and
structural genomics. Close proximity to the National Synchrotron Light
Source at Brookhaven National Laboratory ensures extensive and sustained
access to several bending magnet and insertion device beamlines. This
position affords the successful applicant with the opportunity to exploit
their expertise in structural biology within the context of a strong
biological program focused on inhibitor and therapeutic development.

Interested applicants should provide a CV and arrange for three letter of
reference to be sent directly to [EMAIL PROTECTED]

Re: [ccp4bb] Ligand fitting in COOT and SHELX refinement

[George M. Sheldrick]

You can use SHELXPRO to generate ligand restraints, reading in the ligand 
from the CSD or as a SHELX file (which if necessary can be generated from 
a PDB file using SHELXPRO). You may have to add some extra restraints by 
hand (e.g. FLAT, CHIV).

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


On Fri, 22 Jun 2007, U Sam wrote:

> Hi
> I would like to know following issue for a ligand.
> A ligand of a long alkyl chain can have multiple conformation.
> In coot in order to fit any protein residues into "difference Density", we 
> can select a specific "rotamer" conformation and refine.
> For fitting ligand of above kind, how does it work out.
> Taking the PDB with ligand when we go to refine in SHELX, how restraints like 
> (DFIX, DANG etc) are mentioned for such kind of ligand which can have 
> multiple conformation (particularly for the long alkyl chain) and during 
> refinement values can deviate a lot from a particular value taken from the 
> literature. 
> I appreciate suggestion and comments.
> Many Thanks
> Sam
> _
> With Windows Live Hotmail, you can personalize your inbox with your favorite 
> color.
> www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TXT_TAGLM_HMWL_reten_addcolor_0607

[ccp4bb] Suse 10.2 install problem

[John Bruning]

Hi,
 
I installed ccp4 (along with others such as coot) on Suse 10.2.  Everything 
seemed to go well at first.  The gui pops up normally.  But when I try to run a 
process the gui shows the process as "starting" and it hangs there never 
switching to "running".  And there is no log file available in the gui as well. 
 Any ideas?
 
Thanks,
John Bruning

Re: [ccp4bb] Molscript and symbolic label

[Tim Grune]

Before providing the label with the 'label' command, you must set the 
'labelmask' to contain a '%g' at the Position of your greek letter, e.g.
set labelmask '.%g'
label  "Ca"
should produce an 'alpha' for the second letter.

As far as I remember, this does not work with Raster3d-Output, though, 
you'll have to use gimp et al.
Tim


-Original Message-

From: U Sam <[EMAIL PROTECTED]>

To: CCP4BB@JISCMAIL.AC.UK

Date: Fri, 22 Jun 2007 15:42:58 +

Subject: [ccp4bb] Molscript and symbolic label




Hi 

I would appreciate knowing how to make label of symbolic letters like alpha, 
beta, pi etc. using molscript.

Thanks.

Sam

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