Re: [ccp4bb] Shape similarity of ligand binding sites

[Robert Campbell]

Hi Stephen,

I have a python script that does exactly that.  It uses a surface calculated by 
MSMS and calculates the similarity using a function like that of the SC 
program.  You'll need to align the structures first.  There is an equivalent 
script that calculates the complementarity of two surfaces.  I also have a 
script that reads the output of this and draws the surface in PyMOL and colours 
it according to the SC value at each vertex.

You can find the similarity and complementarity scripts here, along with some 
instructions:

  http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/#msms_similarity.py
  
http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/#msms_complementarity.py

The script for drawing the surface is here:

  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/#msms_sim_draw.py


Cheers,
Rob


On Wed, 2017-06-14 11:42  +,  "" 
 wrote:

> Dear ccp4bb,
> 
> I am trying to compare the shape of a ligand binding site in my
> protein with that of some homologues and mutants and was wondering
> how others go about this?  I specifically want to compare the shapes
> of the surface (similar to an sc analysis of an interface) rather
> than the positions of the atoms in the residues that make up the
> site.  I have come across PESDserv, but this doesn't do quite what I
> would like.  Any suggestions would be very welcome.
> 
> Best wishes,
> 
> Steve
> 
> Dr Stephen Carr
> Research Complex at Harwell (RCaH)
> Rutherford Appleton Laboratory
> Harwell Oxford
> Didcot
> Oxon OX11 0FA
> United Kingdom
> Email stephen.c...@rc-harwell.ac.uk
> tel 01235 567717
> 
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-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc

Re: [ccp4bb] Visualize symmetry operations

[Robert Campbell]

Hi Aaron,

I have a PyMOL plugin based on cctbx (i.e. it requires the installation of 
cctbx) that will do this.  This allows one to make images like this:

  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/pymol_symmetry.png


The script is called draw_symops_cctbx.py and is available here:

  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

(this may site may already be listed in the repositories of the PyMOL plugin 
manager).


Cheers,
Rob


On Wed, 2017-01-04 12:38  -0800,  Pavel Afonine  wrote:

> Explore this:
> 
> http://cci.lbl.gov/cctbx/
> 
> Pavel
> 
> On Wed, Jan 4, 2017 at 8:20 AM, Aaron Finke  wrote:
> 
> > Dear CCP4-keteers,
> >
> > Is there a program that can visualize symmetry operation positions
> > (e.g. twofold screws, fourfolds) in protein structures, like CCDC
> > Mercury does for small molecules?
> >
> > Thanks in advance,
> > Aaron
> >
> > --
> > Aaron Finke
> > Staff Scientist, MacCHESS
> > Cornell University
> > e-mail: af...@cornell.edu
> >
> >  




-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

[Robert Campbell]

Hi Nic,

There is no reason that you have to use the Unity desktop at all.  I prefer
using the XFCE4 desktop myself.  It is easily installable from the Ubuntu
repositories and then you just have to select it at login.

Cheers,
Rob

On Tue, 2014-03-11 14:44 EDT, Nic Steussy csteu...@purdue.edu wrote:

 Matic,
 
 I am struggling with Ubuntu on this issue.
 
 The Nvidia driver needs the 'Composite' function disabled in order to
 function in 3D.  This required the use of the Unity-2D package to disable
 the 3D used in the Ubuntu desktop effects.  This worked fine in Ubuntu
 12.04.  Unfortuately the developers have decided that the eye candy is
 essential to their desktop and have deprecated the Unity-2D package(since
 13.04).  So in a more recent release of Ubuntu the 'Composite disable' in
 the xorg.conf with the Nvidia driver will yield a blank screen and a core
 dump.
 
 I'd certainly love it if someone could offer a solution aside from
 stepping back to an older release.
 
 Nic out
 
 On 03/10/2014 05:23 AM, Matic Kisovec wrote:
 Dear everybody,
 
 to my recent experience not everything is good in the stereo world. Since
 I see that others don't have these problems (and I am happy/sad to see
 that the same exact combinations work without problems) I would just like
 to add my experience.
 
 For the past 4 months I have been struggling to configure a stereo setup
 for viewing structures in Pymol. I got the VG278HR and PNY Quadro K600
 connected over the original DVI-D cable. Since then I was unable to get
 anything in stereo on Linux (tried Ubuntu, OpenSUSE, Fedora).
 Unfortunately I get a blank/black screen whenever I use the stereo option
 in xorg.conf. Also tried changing the motherboard and CPU but got the
 same result.
 
 In Windows the demo stuff from Nvidia works just fine but again I have
 problems with Pymol. So far the only way to see anything connected to
 molecular structures in Windows was via DVI-to-HDMI cable but due to HDMI
 restrictions the quality isn't as good as it would be over DVI-D. If I
 use DVI-D that was shipped with the monitor the quadro card is detected
 in Pymol but the monitor doesn't switch to stereo.
 
 I have been in contact with the company that makes Quadro cards (PNY) but
 they were unable to help me. I also contacted some very kind users of
 CCP4BB and they kindly answered a bunch of question regarding specific
 setup options. Thanks again! Still there was no success so far.
 
 I am slowly giving up on the stereo so if anybody has any ideas/thoughts
 what could be wrong/done I would greatly appreciate any insight.
 
 Kind regards,
 Matic
  
 
 
 On 06. 03. 2014 19:32, White, Mark wrote:
 Alexy
 
 I have the ASUS 27 stereo LCD monitors with built in emitter connected
 to Linux WS with the cheaper Quadro cards. The monitor comes with a
 special DVI cable that caries the sync signal and thus it does not need
 the 3-pin connector. 
 
 The new LCD stereo monitors produce superb 3D images that are much
 crisper than we used to get with CRT displays. 
 
 Best regards
 Mark
 
 Sent from my iPhone
 
 On Mar 6, 2014, at 12:01 PM, Alexey Rozov alexey.ro...@gmail.com
 wrote:
 
 Hello,
 
 Sorry, if this question somewhat off-top to the actual discussion, but to
 my understanding one does need the 3-pin connector to operate 3D under
 Linux even for the monitors with the built-in emitter. It appears to be
 necessary to guide the emitter, or am I wrong about it? I'd be thankful
 if anyone can advise me on that since it looks like a big problem to
 acquire the commercial connectors and cables.
 
 I think I have seen an older discussion on CCP4BB where the importance of
 the 3-pin connector was emphasized...
 
 Alexey
 
 
 On 6 March 2014 18:30, mesters mest...@biochem.uni-luebeck.de wrote:
 Hello Moutse,
 
 as you noted correctly, the ASUS VG278H (HR or HE) comes in two flavours,
 one with build in emitter (120 Hz, HR model) and one without (144 Hz, HE
 model).
 
 The VG278HR (ships with one pair of shutter glasses) with build in
 emitter can be used under windows and linux with a cheap nvidia quadro
 card (the ones without a 3-pin stereo connector).
 
 With the VG278HE under windows and a cheap nvidia quadro, you will need
 the nvidia emitter that uses a usb port for driving the emitter. To
 operate the VG278HE under linux requires a truely expensive quadro card
 (k4000 and upwards) with an optional (!) 3-pin connector or, purchase an
 old refurbished quadro card with 3-pin.
 
 Have a look at the following link
 http://www.nvidia.com/object/3d-vision-pro-requirements.html, especially
 the table at the end with the small print explanation 2 and 3
 
 - J. -
 
 
 Am 06.03.14 17:41, schrieb Mouts Ranaivoson:
 Hi, 
 
 I am currently also looking for a 3D monitor, and I am particularly
 attentive to this particular discussion. My interrogation is that does
 the  Asus VG278HE model work under linux ? From previous ccp4bb
 discussions I understood that only built-in emmitter (like the  Asus
 

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

[Robert Campbell]

Hi Nic,

There is no reason that you have to use the Unity desktop at all.  I prefer
using the XFCE4 desktop myself.  It is easily installable from the Ubuntu
repositories and then you just have to select it at login.  In one of the
xfce4 settings options (Window Manager Tweaks) you can disable display
compositing.

Cheers,
Rob

On Tue, 2014-03-11 14:44 EDT, Nic Steussy csteu...@purdue.edu wrote:

 Matic,
 
 I am struggling with Ubuntu on this issue.
 
 The Nvidia driver needs the 'Composite' function disabled in order to
 function in 3D.  This required the use of the Unity-2D package to disable
 the 3D used in the Ubuntu desktop effects.  This worked fine in Ubuntu
 12.04.  Unfortuately the developers have decided that the eye candy is
 essential to their desktop and have deprecated the Unity-2D package(since
 13.04).  So in a more recent release of Ubuntu the 'Composite disable' in
 the xorg.conf with the Nvidia driver will yield a blank screen and a core
 dump.
 
 I'd certainly love it if someone could offer a solution aside from
 stepping back to an older release.
 
 Nic out
 
 On 03/10/2014 05:23 AM, Matic Kisovec wrote:
 Dear everybody,
 
 to my recent experience not everything is good in the stereo world. Since
 I see that others don't have these problems (and I am happy/sad to see
 that the same exact combinations work without problems) I would just like
 to add my experience.
 
 For the past 4 months I have been struggling to configure a stereo setup
 for viewing structures in Pymol. I got the VG278HR and PNY Quadro K600
 connected over the original DVI-D cable. Since then I was unable to get
 anything in stereo on Linux (tried Ubuntu, OpenSUSE, Fedora).
 Unfortunately I get a blank/black screen whenever I use the stereo option
 in xorg.conf. Also tried changing the motherboard and CPU but got the
 same result.
 
 In Windows the demo stuff from Nvidia works just fine but again I have
 problems with Pymol. So far the only way to see anything connected to
 molecular structures in Windows was via DVI-to-HDMI cable but due to HDMI
 restrictions the quality isn't as good as it would be over DVI-D. If I
 use DVI-D that was shipped with the monitor the quadro card is detected
 in Pymol but the monitor doesn't switch to stereo.
 
 I have been in contact with the company that makes Quadro cards (PNY) but
 they were unable to help me. I also contacted some very kind users of
 CCP4BB and they kindly answered a bunch of question regarding specific
 setup options. Thanks again! Still there was no success so far.
 
 I am slowly giving up on the stereo so if anybody has any ideas/thoughts
 what could be wrong/done I would greatly appreciate any insight.
 
 Kind regards,
 Matic
  
 
 
 On 06. 03. 2014 19:32, White, Mark wrote:
 Alexy
 
 I have the ASUS 27 stereo LCD monitors with built in emitter connected
 to Linux WS with the cheaper Quadro cards. The monitor comes with a
 special DVI cable that caries the sync signal and thus it does not need
 the 3-pin connector. 
 
 The new LCD stereo monitors produce superb 3D images that are much
 crisper than we used to get with CRT displays. 
 
 Best regards
 Mark
 
 Sent from my iPhone
 
 On Mar 6, 2014, at 12:01 PM, Alexey Rozov alexey.ro...@gmail.com
 wrote:
 
 Hello,
 
 Sorry, if this question somewhat off-top to the actual discussion, but to
 my understanding one does need the 3-pin connector to operate 3D under
 Linux even for the monitors with the built-in emitter. It appears to be
 necessary to guide the emitter, or am I wrong about it? I'd be thankful
 if anyone can advise me on that since it looks like a big problem to
 acquire the commercial connectors and cables.
 
 I think I have seen an older discussion on CCP4BB where the importance of
 the 3-pin connector was emphasized...
 
 Alexey
 
 
 On 6 March 2014 18:30, mesters mest...@biochem.uni-luebeck.de wrote:
 Hello Moutse,
 
 as you noted correctly, the ASUS VG278H (HR or HE) comes in two flavours,
 one with build in emitter (120 Hz, HR model) and one without (144 Hz, HE
 model).
 
 The VG278HR (ships with one pair of shutter glasses) with build in
 emitter can be used under windows and linux with a cheap nvidia quadro
 card (the ones without a 3-pin stereo connector).
 
 With the VG278HE under windows and a cheap nvidia quadro, you will need
 the nvidia emitter that uses a usb port for driving the emitter. To
 operate the VG278HE under linux requires a truely expensive quadro card
 (k4000 and upwards) with an optional (!) 3-pin connector or, purchase an
 old refurbished quadro card with 3-pin.
 
 Have a look at the following link
 http://www.nvidia.com/object/3d-vision-pro-requirements.html, especially
 the table at the end with the small print explanation 2 and 3
 
 - J. -
 
 
 Am 06.03.14 17:41, schrieb Mouts Ranaivoson:
 Hi, 
 
 I am currently also looking for a 3D monitor, and I am particularly
 attentive to this particular discussion. My interrogation is that does
 the  Asus VG278HE model work under 

Re: [ccp4bb] Any tool to calculate surface accessible by ... another protein?

[Robert Campbell]

Hi Emmanuel,

On Wed, 2013-02-13 16:30  EST,  Sampson, Jared jared.samp...@nyumc.org
wrote:

 You might consider using MSMS.  If you wish to visualize it, there is a
 PyMOL script available: http://pymolwiki.org/index.php/Msms.
 
 Relatedly, one should keep in mind that, while a 10 or 50 Angstrom probe
 will give you a general idea of accessible surface, if there is any shape
 complimentarity between two interacting proteins, it won't provide the
 whole picture.

I would second Jared's suggestion of MSMS.  It is straightforward to set up
a script to calculate the areas for each atom at many different probe
radii.  Note that when run with a very large probe size, the calculation
takes substantially longer -- total run times on a protein of 185
residues takes less than a second for radii up to 15 A, but increases to
5 minutes for a 20 A probe radius.  I didn't bother trying a 50 A probe.

MSMS when run with the -af option will generate a file containing the
accessible areas for each atom. I have several python scripts that will
calculate total areas for various atom classes (hydrophobic, charged, etc.)
and also save an output file with areas for each atom and/or residue. These
can be run from within PyMOL or as standalone scripts. Similar to the script
Jared mentions, my msms_pymol.py script will also allow visualization of the
MSMS surface in PyMOL.
 
My various python scripts can be found here:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Cheers,
Rob

 On Feb 12, 2013, at 2:51 PM, Emmanuel Levy
 emmanuel.l...@gmail.commailto:emmanuel.l...@gmail.com wrote:
 
 Hello,
 
 I have been looking for a tool to measure the Protein accessible
 surface area, which could be defined exactly as the solvent ASA
 except with a probe of larger radius.
 
 Most tools that calculate ASA however do not work with a probe radius
 of a size equal to 10 or 50 Angstroms. Plus, ideally one would like to
 know the largest probe size that can access each atom or residue. So
 using classic ASA programs means one would have to run it ~30 times,
 each time with different probe radius for each protein.
 
 So my question is, do you know of a tool that could help us in
 obtaining this type of information?
 
 Thanks in advance for any hint,
 All the best,
 
 Emmanuel

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical  Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [ccp4bb] Software for Conserved Solvent

[Robert Campbell]

Hi Jacob,

On Wed, 2011-05-25 11:58  EDT,  Jacob Keller
j-kell...@fsm.northwestern.edu wrote:

 Dear Crystallographers,
 
 does anyone know of a program to compare multiple structures and
 identify which solvent molecules (water, ions, etc.) are conserved
 between the structures? I guess it would be nice also if it could
 identify when, for example, a Cl- in structure A was re-occupied by an
 HOH in B, or even some atom in a ligand being replaced by a water.

PyMOL's selection routines can allow something like this.  To find all
waters and ions in one structure that are within 0.5 Angstroms (for
example) of the waters and ions in another structure you can type:

select conserved_waters, structure1 ! polymer ! organic within 0.5
of structure 2 ! polymer ! organic

You can then either save that selection to a file or iterate through it to
look at the details:

iterate conserved_waters, print chain,resn,resi,name


To search for an ion (or ligand atom) that replaces a water you could do:

select structure1  r. hoh within 0.5 of structure1 ! polymer ! r. hoh

If you wanted to do this sort of thing on a large set of structures, then
it could be scripted in a more user-friendly way.

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [ccp4bb] pymol python and cctbx

[Robert Campbell]

On Wed, 23 Jun 2010 09:07:36 -0400 Schubert, Carsten [PRDUS]
cschu...@its.jnj.com wrote:

 Tim,
 
 I'm shooting from the hip here, but I think the problem is that cctbx
 comes with its own python, which you would need to run both pymol and
 numpy under. According to Ralf it is at least not trivial to utilize the
 system python to run cctbx. So I think you need to compile/install pymol
 against cctbx.python and install it as a module under cctbx.python.
 Similar deal for numpy, which may already be available in cctbx, if not
 installation should be straightforward.
 
 These broad steps may work (again shooting from the hip...)
 -Install cctbx
 -link cctbx.python to python and make sure its first in your path (may
 be optional)
 -install numpy under cctbx.python (if not already present)
 -compile and install open.pymol against the cctbx.python, either via the
 renaming trick 
  above or calling cctbx.python setup.py (build/install)
 
 Good luck, let us know how it works...

I have no trouble running cctbx with pymol using the system python for both.
I also use Debian testing and various Ubuntu versions.  To do so I
install cctbx from the sources. I have a web page with instructions for using
pymol and cctbx together at:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/cctbx/

In short, I install cctbx using the self-extracting *source* not a
precompiled version.  Go to http://cci.lbl.gov/cctbx_build/ and scroll down to
Self-extracting cctbx sources for Unix.

Once that installation is done, I go to where the cctbx.python script is (in
the install/cctbx_build/bin directory). I then make a link to that called
python:  (i.e. ln -s cctbx.python python).

Then to make sure that pymol sees the cctbx modules, I make sure
that the command in the startup script for pymol has just python, not
/usr/bin/python in it so then it ends up running cctbx.python.  (The setup
scripts for cctbx will place its directory and the *beginning* of the PATH
environment variable).

I hope this helps,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [ccp4bb] programmatic symmetry mate generation

[Robert Campbell]

Hi James,

On Sun, 25 Apr 2010 15:41:32 -0700, James Stroud xtald...@gmail.com wrote:

 cctbx is cool in principle, but I would be very happy to know how to  
 use it with a pre-existing python like most other packages are capable  
 of. I'm starting to lose patience reverse-engineering the install  
 scripts to figure out how to do it. I can't seem to find instructions  
 on the web page.
 
 What am I missing? Is it that I must migrate my entire python  
 environment to cctbx.python? Isn't it better to add cctbx to a current  
 environment rather than the other way around? If every package  
 required the user's migrating his python environment to the package's  
 environment, then we wouldn't be able to use more than one package  
 with a given python install.
 
 It seems ridiculous.

I don't have a problem doing this (at least with Linux).  I simply download
the Self-extracting cctbx sources for Unix and put it somewhere appropriate
and run the installation command perl cctbx_bundle.selfx.  After it finishes
installing I modify my login shell script according to the installers
instructions.  Actually I modify a large setup script that allows me and all
the users to set up any particular program. This will add the
cctbx/cctbx_build/bin directory to the beginning of the PATH variable.  In
order for cctbx to work with any python script then I simply add a link in the
cctbx/cctbx_build/bin directory so that python points at cctbx.python: i.e.

cd cctbx_build/bin
ln -s cctbx.python python


Any other python scripts that call cctbx then start with 

#! /usr/bin/env python

rather than

#! /usr/bin/python

In order to have cctbx play nice with PyMOL, then I also install PyMOL
from the SVN sources (also not too difficult).  Then I make sure that my PyMOL
start up script uses python and not /usr/bin/python and then I can use
both PyMOL and cctbx with the system's python. Perhaps this still sounds
ridiculous to you, but I don't have a problem with it.  Once the initial set
up is done there isn't much to it.  Of course I have left myself little
instruction files in my installation directories to remind myself what I need
to do.

 It doesn't make sense, so I must be missing something fundamental. I  
 think this is the reason I have never used cctbx before. I last tried  
 about 4 years and I thought that it was because the package was  
 immature.

There is also a new PyMOL script in the PyMOL wiki called supercell 
http://pymolwiki.org/index.php/Supercell
that will build a unit cell, or a block of multiple unit cells.  I think this
should work in a script to PyMOL, hence not needing the graphics nor any
interactive work.  I haven't tried it that way, though.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [ccp4bb] program to display space group symmetry in three dimensions

[Robert Campbell]

Hi Karthik,

On Tue, 16 Mar 2010 20:11:29 -0400 Karthik S biokart...@gmail.com wrote:

 Hi, I was looking around for programs that display space group symmetry
 information and could not find any but perhaps i am lost for valuable or
 relevant keywords.
 I found two references TABLES and CRYST, but are there other alternatives
 that are more recent, or that can run on more common hardware?
 TABLES:
 http://scripts.iucr.org/cgi-bin/paper?S0021889887086060
 CRYST:
 http://scripts.iucr.org/cgi-bin/paper?S0021889889007168

This may not be exactly what you are looking for, but I have a python script
for drawing symmetry operators in PyMOL.  It uses cctbx to do the
crystallographic calculations and PyMOL to display them.  One can either use
it with a PDB file and have PyMOL pull the necessary symmetry information
from the PDB file, or one can simply enter the space group information and
have the program draw the symmetry axes.  Of course PyMOL can also display
the symmetry-related molecules as well.

This script (draw_symop_cctbx.py) can be found on my PyMOL scripts page:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

An example image can be seen here:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/pymol_symmetry.png
(The unit cell in that image is drawn with my draw_cell.py script.)

One important point about using this is that one cannot use pre-compiled
versions of PyMOL and cctbx as each then has its own python executable that
will not be able to import the modules of the other.

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [ccp4bb] In PYMOL looks different from that in O

[Robert Campbell]

Hi Raja,

On Wed, 16 Sep 2009 16:57:18 -0700, Raja Dey deyra...@yahoo.co.in wrote:

 Hi,
 I am getting a problem to prepare a figure in PYMOL. I have 4 nearly
 identical monomers in the AU sitting at the corners of a rectangle. The 2
 front monomers almost perfectly superimpose on the back 2 when I am looking
 along the plane. I can see this view in O program. For some reason I could
 not make this view in PYMOL. It looks off in PYMOL. Front 2 looks widely
 separated and back 2 looks colser at this orientation in PYMOL. Does anyone
 have any idea? I tried centering at many position, but the problem remains.
 Looking forward to your suggestion.

It sounds like you are seeing the effects of perspective.  Try setting the
display mode to Orthoscopic (under the Display main menu).

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [ccp4bb] Calculating shape complementarity parameter using Sc

[Robert Campbell]

Dear Jae,

On Thu, 23 Oct 2008 17:05:32 +0100, Jae Hyun [EMAIL PROTECTED] wrote:

  I tried to calculate the shape complementarity parameter using Sc in CCP4.
 But, this gave me error message as follows:
 
 BFONT COLOR=#FF!--SUMMARY_BEGIN--
  
  $TEXT:Warning: $$ comment $$ 
  WARNING:  No Space group given on PDB CRYST1 line
  $$
 !--SUMMARY_END--/FONT/B

This is just a warning.  The real error is below.

 UNFORMATTEDSCRATCH file opened on unit   7
 BFONT COLOR=#FF!--SUMMARY_BEGIN--
 Logical name: SCTEMP, Filename: /tmp/jhbae/sc_tmp.02978
 !--SUMMARY_END--/FONT/B
 
 
  Number of atoms read from PDB file:  4144

  
  GRASP mode disabled - no Grasp output will be produced
  
  Selection commands:
  ---
 
   Molecule 1
   Number of atoms selected in chain A =   2372
 
   Molecule 2
   Number of atoms selected in chain B =   1772
 
  Parameter values
  
  Dot density  :15.00 per square Angstrom
  Interface separation : 8.00 Angstroms
  Trim width   : 1.50 Angstroms
  Probe radius : 1.70 Angstroms
  Weight factor:  .50 per square Angstrom
  No radius found for
  Residue PTR Atom CG  

This is the real error.  You have an atom called CG in a residue called
PTR which does not exist in the radii file.  You can copy the radii file
and add your own entries to it and use that with the command line option:

SCRADII radii.lib 

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
[EMAIL PROTECTED]http://pldserver1.biochem.queensu.ca/~rlc

Re: [ccp4bb] HKL2000 and gcc4

[Robert Campbell]

On Mon, 05 May 2008 13:48:00 -0600, James Stroud [EMAIL PROTECTED] wrote:

 Get a new sys-admin. He is getting in the way of your research. There  
 is no good reason to be paranoid about this particular shared library  
 sitting in /usr/lib.
 
 James
 
 On May 5, 2008, at 1:32 PM, Chris Waddling wrote:
  I have tried an experiment
  of putting the library into the /usr/lib/ folder, and HKl2000 runs,  
  but our
  sys-admin refuses to let it stay there.

I'd echo James, but to say that there is no reason that you cannot have both
gcc3 and gcc4 installed.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
[EMAIL PROTECTED]http://pldserver1.biochem.queensu.ca/~rlc

Re: [ccp4bb] HKL2000 and gcc4

[Robert Campbell]

Hi Chris,

On Mon, 05 May 2008 12:57:17 -0700, Chris Waddling
[EMAIL PROTECTED] wrote:

 Robert,
 
 that's exactly what I keep asking him to do maybe I 
 should take James Stroud's advice...

Yes, maybe you should, if you cannot convince him of the error of his ways. :)

 BTW, nice to hear from my M.Sc. alma mater... I worked in 
 Donal Macarntney's Chemistry lab from '91-93.

I haven't crossed paths with Donal, just with a couple of others like Victor
Snieckus and David Zechel in the Chemistry department here.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
[EMAIL PROTECTED]http://pldserver1.biochem.queensu.ca/~rlc