pymol-users Mailing List for PyMOL Molecular Graphics System

Hi,

This is really for Warren. A while ago there was=20
discussion of the =B1 of updates versus new=20
manuals. The current documentation is now several=20
years out of date. Are their plans to update this?

Thanks to all who have worked on Wiki and posted scripts on web sites.

Mark
-- 

Hi All,

We've acquired a geowall system which will likely be attached to a  
intel Mac tower.  Does anyone know if the OS X drivers for the quadro  
fx 4500 will support the dual monitor clone mode necessary to drive  
quadbuffered stereo on the geowall?  Anyone actually done this?

Everything I've found on geowall and pymol has been linux, and I want  
to try and find out if apple has built in the appropriate support  
before we drop the cash on the quadro.

Thanks!

      ---Stephen

The easiest way I'm aware of to do this would be to use the ccp4 program
pdbset, but there are numerous other ways/programs that will do this (if
pymol has this capacity, I'm not aware of it; but someone else will
correct me).

Pete

<snip>

>> I've been looking through the PyMol reference and wiki page and I can't
find a command for moving a molecule through a matrix, I
>> would like to move one pdb onto the other using the info below. Is
there such a command?
>> ## MATRICES: UX+T is the least-squares superimposition of STRID2 (X)
onto STRID1
>>   NR. STRID1 STRID2           U(.,1)    U(.,2)    U(.,
>> 3)             T(.)
>>    1: 9506-A 1ris    U(1,.)  -0.230692 -0.010007
>> -0.972975           50.701385
>>    1: 9506-A 1ris    U(2,.)   0.443459  0.888979
>> -0.114287           31.716473
>>    1: 9506-A 1ris    U(3,.)   0.866098 -0.457839
>> -0.200643           26.479412



Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Hi Mark:

Most likely there is, but I don't know the answer to your question.  
I'm posting this to the pymol users list (via cc) so hopefully  
someone else will know the answer.

I trust all is going well for you.

Bill


On Jun 30, 2006, at 8:19 AM, Mark Collins wrote:

> Hi Bill,
>
> I've been looking through the PyMol reference and wiki page and I  
> can't find a command for moving a molecule through a matrix, I  
> would like to move one pdb onto the other using the info below. Is  
> there such a command?
>
> ## MATRICES: UX+T is the least-squares superimposition of STRID2  
> (X) onto STRID1
>   NR. STRID1 STRID2           U(.,1)    U(.,2)    U(., 
> 3)             T(.)
>    1: 9506-A 1ris    U(1,.)  -0.230692 -0.010007  
> -0.972975           50.701385
>    1: 9506-A 1ris    U(2,.)   0.443459  0.888979  
> -0.114287           31.716473
>    1: 9506-A 1ris    U(3,.)   0.866098 -0.457839  
> -0.200643           26.479412
>
> Thanks Mark

Hi Michael,

The answer to the second question is: yes

alter selection,vdw=1.0

will change the radius of selected atoms to 1.0 angstrom.

Cheers,

Tsjerk

On 6/30/06, Michael Weber <we...@st...> wrote:
> Hi,
> I have a question concerning the "spheres" representation. According to my
> rough estimation the spheres drawn for individual atoms/ions don't seem not
> match experimental atomic/ionic radii if I compare different elements. Is
> that correct (I quickly checked for oxygen, phosphorus and magnesium2+)?
> Furthermore, is it possible to manually assign radii to selected atoms?
>
> Best regards,
> Michael.
>
>
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

Hi Dong,

My guess is (but ofcourse Warren knows best) that pymol chokes in the
full pathname, including the spaces. Note that under windows the
actual pathname would be D:\DOCUME~1\1LTL.pdb The long pathname is an
alias.

Cheers,

Tsjerk

On 6/29/06, LIU Changdong <cd...@us...> wrote:
> Dear all:
>  After I install pymol successfully,I load a pdb file,but the progroam
> give me a error message below.Can you give me any suggestions?My operate
> system is windows xp sp2.
>
> excecutiveprocessPDBfile-error:unableto open file'D:/Documents and
> settings/1LTL.pdb
> Function:<bound method Normal.file_open of < pmg_tk.skins.normal.Normal
> instance at 0x09477F30>>(type: < type `instancemethod~>)
>
> Arg:
> ()Traceback=A3=A8inner most last):
>
> File"D\Program files\Delano
> scientific\PyMOL/modules\pmw_1_2\lib\PmwBase.py", line 1747,in _call_
> return apply (self.func,args)
> File"D\Program files\Delano
> scientific\PyMOL/modules\pmw_1_2\lib\PmwBase.py", line438, in file_open
> self.cmd.load=A3=A8ofile,quiet=3D0)
> File"D\Program files\Delano
> scientific\PyMOL/modules\pmw_1_2\lib\PmwBase.py", line585,in load
> if_raising(r):raise pymol.cmdexpception
> cmdexception:<pymol.cmdexception instance at 0x0961e620
>
>
>
>
> Many thanks!
> Best
>  Dong
>
>
>
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job ea=
sier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronim=
o
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=
=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


--=20

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

Hi,
I have a question concerning the "spheres" representation. According to my 
rough estimation the spheres drawn for individual atoms/ions don't seem not 
match experimental atomic/ionic radii if I compare different elements. Is 
that correct (I quickly checked for oxygen, phosphorus and magnesium2+)? 
Furthermore, is it possible to manually assign radii to selected atoms?

Best regards,
Michael. 

Dear all:
 After I install pymol successfully,I load a pdb file,but the progroam
give me a error message below.Can you give me any suggestions?My operate
system is windows xp sp2.

excecutiveprocessPDBfile-error:unableto open file'D:/Documents and
settings/1LTL.pdb
Function:<bound method Normal.file_open of < pmg_tk.skins.normal.Normal
instance at 0x09477F30>>(type: < type `instancemethod~>)

Arg:
()Traceback=A3=A8inner most last):

File"D\Program files\Delano
scientific\PyMOL/modules\pmw_1_2\lib\PmwBase.py", line 1747,in _call_
return apply (self.func,args)
File"D\Program files\Delano
scientific\PyMOL/modules\pmw_1_2\lib\PmwBase.py", line438, in file_open
self.cmd.load=A3=A8ofile,quiet=3D0)
File"D\Program files\Delano
scientific\PyMOL/modules\pmw_1_2\lib\PmwBase.py", line585,in load
if_raising(r):raise pymol.cmdexpception
cmdexception:<pymol.cmdexception instance at 0x0961e620




Many thanks!
Best
 Dong

On Mon, Jun 26, 2006 at 02:25:31PM +0200, Martin Weisel wrote:
> 
> i would like to re-implement the mesh-generating algorithm in Java.
> Is there a reference paper? If not, how does the algorithm works?
> I`m particulary interested in generation of nice, nearly equidistant points.
> 

There are two typical algorithms for this purpose, the "O" method:

@incollection{diamond:82,
  AUTHOR = {Diamond, R.},
  EDITOR = {Sayre, D.},
  TITLE = {Two Contouring Algorithms},
  BOOKTITLE = {Computational Crystallography},
  YEAR = {1982},
  PAGES = {267-272},
  PUBLISHER = {Oxford University Press},
  ADDRESS = {New York},
  KEYWORDS = {}
}

and any one of the permutations on the marching cubes/tetrahedra
algorithms, partly described here:

@inproceedings{lorensen:87,
  AUTHOR = {Lorensen, W. E. and Cline, H. E.},
  TITLE = {Marching cubes: A high resolution 3D surface construction
                  algorithm.},
  BOOKTITLE = {SIGGRAPH 1987 Conference Proceedings},
  EDITOR = {Stone, M. C.},
  MONTH = {July},
  YEAR = {1987},
  VOLUME = {21},
  PAGES = {163-169},
  PUBLISHER = {ACM Press},
  ADDRESS = {New York},
  KEYWORDS = {}
}

The latter algorithms are part of GTS, if you're looking for some
code and more references:

http://gts.sourceforge.net/

along with other sources (google for Paul Bourke's websites for some
more goodies).

HTH,
Tim

-- 
---------------------------------------------------------

        Tim Fenn
        fe...@st...
        Stanford University, School of Medicine
        James H. Clark Center
        318 Campus Drive, Room E300
        Stanford, CA  94305-5432
        Phone:  (650) 736-1714
        FAX:  (650) 736-1961

---------------------------------------------------------

Hi all,

I am trying to represent the CA trace of a protein using cone frustum (each
frustum is defined by two vertices and a radius at each vertex).

I was initially thinking that
    cartoon putty
with
   cartoon_trace,1
would work but unfortunately (for me) PyMol uses a smoothed CA trace as soon
as I have >2 points. I have also tried to define each pair of
residues/ca-atoms as a separate object but again these are automatically
joined by a spline curve.

A second idea was to use cgos (lines and spheres) to define cone segments
but this would most likely not turn out nice.

Would anybody out there be able to help me out? Either by telling me how to
turn of the spline interpolation or how to define new (nice) cgos.

Thanks a million,
Mikael

Ronald,

You can try the yale morph server:

http://molmovdb.mbb.yale.edu/molmovdb/morph/

There are probably other tools that will perform linear interpolation
of structures and output "intermeditate" .pdb files, which could be
cleaned up and used in pymol to create a similar, but more user
controlled movie.

Hope this helps,

-bob



On 6/27/06, Ronald Chiu <rcc...@gm...> wrote:
>
> Hello All,
>
> Is there a way to show the three dimesional (x, y, z) coordinates for a
> selected alpha carbon?
>
> Lets say that you have two homologous structures aligned; one crystal
> structure  in unbound state and the other in agonist bound state.  How would
> you show the movement (change in positon of a residue) between the two
> states.
>
> Thanks for your help.
>
> Ron
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>

Hi,

I am trying to create a surface representation of a cryo-em density, =
which is a brix file, but all I can do is create a mesh representation.  =
Is there a way to create the surface representation of cryo-em density =
in pymol?  Any help or advice would be greatly appreciated.

Thank you,
Jen Pfingsten

Hello All,

Is there a way to show the three dimesional (x, y, z) coordinates for a
selected alpha carbon?

Lets say that you have two homologous structures aligned; one crystal
structure  in unbound state and the other in agonist bound state.  How would
you show the movement (change in positon of a residue) between the two
states.

Thanks for your help.

Ron

Hello everybody,

i would like to re-implement the mesh-generating algorithm in Java.
Is there a reference paper? If not, how does the algorithm works?
I`m particulary interested in generation of nice, nearly equidistant points.

Cheers

Martin

The fix on SuSE is to download the readline4.3 compatibility patch, and
after installing that the install seems to go just fine:

The file is attached, or find at 

http://rpmfind.net/linux/rpm2html/search.php?query=libreadline.so.4

Make sure to get the compat-readline4-4.3-3.i586.rpm for SuSE 9.3

Steve

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Sabuj
Pattanayek
Sent: Friday, June 23, 2006 12:23 PM
To: pym...@li...
Subject: Re: [PyMOL] FW: APBS - libreadline

I have these versions installed on i686 RH boxes:

readline-4.3-13
readline-devel-4.3-13

At 
http://rpmfind.net/linux/rpm2html/search.php?query=readline&submit=Search+..
. 
it shows that SuSE 9.3 uses readline-5.0-7.2.i586.rpm . I don't know if 
that is going to be a problem. You may have to re-compile.

venkataraman kabaleeswaran wrote:
> Hi
> 
> I had the same problem while installing the apbs, 
> 
> I contacted the apbs-users mailing list   , they
> adviced me to install readline, I did but still didnot
> work , after installation I got the same error. 
> 
> check and see if your system as readline library if
> not install that and try againg, good luck.
> Try post your problem at
> apb...@li....
> 
> cheers
> vk

Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job
easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users



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I have these versions installed on i686 RH boxes:

readline-4.3-13
readline-devel-4.3-13

At 
http://rpmfind.net/linux/rpm2html/search.php?query=readline&submit=Search+... 
it shows that SuSE 9.3 uses readline-5.0-7.2.i586.rpm . I don't know if 
that is going to be a problem. You may have to re-compile.

venkataraman kabaleeswaran wrote:
> Hi
> 
> I had the same problem while installing the apbs, 
> 
> I contacted the apbs-users mailing list   , they
> adviced me to install readline, I did but still didnot
> work , after installation I got the same error. 
> 
> check and see if your system as readline library if
> not install that and try againg, good luck.
> Try post your problem at
> apb...@li....
> 
> cheers
> vk

Hi

I had the same problem while installing the apbs, 

I contacted the apbs-users mailing list   , they
adviced me to install readline, I did but still didnot
work , after installation I got the same error. 

check and see if your system as readline library if
not install that and try againg, good luck.
Try post your problem at
apb...@li....

cheers
vk



--- "Becker, Joseph W" <jos...@me...>
wrote:

> Yes, apbs-0.4.0-1.i386.rpm
> Joe
> 
> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...]
> On Behalf Of Sabuj
> Pattanayek
> Sent: Friday, June 23, 2006 11:02 AM
> To: pym...@li...
> Subject: Re: [PyMOL] APBS - libreadline
> 
> This is using the binary distributions of APBS?
> 
> Becker, Joseph W wrote:
> > I'm trying to install APBS on a LINUX (IBM T43P)
> box running SuSE 9.3 
> > Professional.  I've successfully installed maloc,
> but the apbs install
> > gives:
> > 
> > error: Failed dependencies
> >             libreadline.so.4 is needed by
> apbs-0.4.0-1
> > 
> > What to do?
> > 
> > Thanks,
> > 
> > Joe Becker
> > Merck Research Labs
> 
> Using Tomcat but need to do more? Need to support
> web services, security?
> Get stuff done quickly with pre-integrated
> technology to make your job
> easier Download IBM WebSphere Application Server
> v.1.0.1 based on Apache
> Geronimo
>
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
>
https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 
>
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> Notice:  This e-mail message, together with any
> attachments, contains information of Merck & Co.,
> Inc. (One Merck Drive, Whitehouse Station, New
> Jersey, USA 08889), and/or its affiliates (which may
> be known outside the United States as Merck Frosst,
> Merck Sharp & Dohme or MSD and in Japan, as Banyu)
> that may be confidential, proprietary copyrighted
> and/or legally privileged. It is intended solely for
> the use of the individual or entity named on this
> message.  If you are not the intended recipient, and
> have received this message in error, please notify
> us immediately by reply e-mail and then delete it
> from your system.
>
------------------------------------------------------------------------------
> 
> Using Tomcat but need to do more? Need to support
> web services, security?
> Get stuff done quickly with pre-integrated
> technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1
> based on Apache Geronimo
>
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
>
https://lists.sourceforge.net/lists/listinfo/pymol-users
> 


Kabaleeswaran Venkataraman

Arise, Awake and stop not until goal is Reached 
                           -  Swami Vivekanand

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 

I just installed the binary -i686 (not -i386), x86_64, and ia64 versions 
of apbs and apbs tools for some redhat machines and tested them all 
yesterday. None of the machines return anything when I do rpm -qa | grep 
maloc . Do you actually need maloc if you're not compiling from source?


Becker, Joseph W wrote:
> Yes, apbs-0.4.0-1.i386.rpm
> Joe
> 

Yes, apbs-0.4.0-1.i386.rpm
Joe

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Sabuj
Pattanayek
Sent: Friday, June 23, 2006 11:02 AM
To: pym...@li...
Subject: Re: [PyMOL] APBS - libreadline

This is using the binary distributions of APBS?

Becker, Joseph W wrote:
> I'm trying to install APBS on a LINUX (IBM T43P) box running SuSE 9.3 
> Professional.  I've successfully installed maloc, but the apbs install
> gives:
> 
> error: Failed dependencies
>             libreadline.so.4 is needed by apbs-0.4.0-1
> 
> What to do?
> 
> Thanks,
> 
> Joe Becker
> Merck Research Labs

Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job
easier Download IBM WebSphere Application Server v.1.0.1 based on Apache
Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users



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This is using the binary distributions of APBS?

Becker, Joseph W wrote:
> I'm trying to install APBS on a LINUX (IBM T43P) box running SuSE 9.3
> Professional.  I've successfully installed maloc, but the apbs install
> gives:
> 
> error: Failed dependencies
>             libreadline.so.4 is needed by apbs-0.4.0-1
> 
> What to do?
> 
> Thanks,
> 
> Joe Becker
> Merck Research Labs

I'm trying to install APBS on a LINUX (IBM T43P) box running SuSE 9.3
Professional.  I've successfully installed maloc, but the apbs install
gives:

error: Failed dependencies
            libreadline.so.4 is needed by apbs-0.4.0-1

What to do?

Thanks,

Joe Becker
Merck Research Labs


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Dear Folmer,
Thanks a lot for your comment. Thats exactly what I was looking for and 
works perfectly. Thank you heaps.
Regards
Nagesh

Folmer Fredslund wrote:

> Dear Nagesh
>
> Just a short comment.
>
> If you want the orientation you can write
> get_view
> and the orientation will be printed to the GUI.
> Then all you have to do is put it at the end of your script
>
> Best regards,
> Folmer
>
> Nagesh Chakka wrote:
>
>> Dear Joel,
>> Thanks for you email. I now installed version 0.99 and my problem is 
>> solved.
>> Regards
>> Nagesh
>>
>>
>> Joel Tyndall wrote:
>>
>>  
>>
>>> Dear Nagesh,
>>>
>>> If you upgrade to the latest version (0.99) there is an option do 
>>> display the disulfides under the show menu
>>>
>>> J
>>>
>>> Nagesh Chakka wrote:
>>>
>>>    
>>>
>>>> Hi Jerome,
>>>> Thanks for the mail. The web address you gave is about obtaining 
>>>> information about Cys involved in bond formation. In my case, I do 
>>>> know which pair of Cys are involved in it and this information is 
>>>> also provided in the PDB file but I am unable to display the bridge 
>>>> in the PyMOL viewer.
>>>> Also I need to display the structure in a particular orientation. 
>>>> Can this information be be added in my script.
>>>> Thanks
>>>> Nagesh
>>>>
>>>> Jerome Pansanel wrote:
>>>>
>>>>  
>>>>
>>>>      
>>>>
>>>>> Hello,
>>>>>
>>>>> You can find some documentation about sulfur bonds on this page:
>>>>> http://www.pymolwiki.org/index.php/Process_All_Files_In_Directory
>>>>>
>>>>> If you are not successfull by using this resource, don't hesitate 
>>>>> to post
>>>>> again.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Jerome Pansanel
>>>>>
>>>>> Selon Nagesh Chakka <nag...@an...>:
>>>>>
>>>>>  
>>>>>
>>>>>   
>>>>>        
>>>>>
>>>>>> Hello everyone,
>>>>>> I am unable to display disulphide bonds using PyMOL (version 
>>>>>> 0.97). My understanding is that PyMOL can connect Cys that are 
>>>>>> within bonding distance. The PDB file (ID 1AG2) defines residues 
>>>>>> involved in the SSBond
>>>>>>
>>>>>> formation. I  also tried to  use the command "bond" to connect 
>>>>>> the residues but without any success. I am not sure if I am doing 
>>>>>> anything wrong. Any suggestion in this regard is appreciated.
>>>>>> Thanks
>>>>>> Nagesh
>>>>>>
>>>>>>
>>>>>> Using Tomcat but need to do more? Need to support web services,
>>>>>> security?
>>>>>> Get stuff done quickly with pre-integrated technology to make 
>>>>>> your job
>>>>>> easier
>>>>>> Download IBM WebSphere Application Server v.1.0.1 based on Apache
>>>>>> Geronimo
>>>>>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 
>>>>>>
>>>>>> _______________________________________________
>>>>>> PyMOL-users mailing list
>>>>>> PyM...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>>>
>>>>>>                   
>>>>>
>>>>>
>>>>> --------------------------------------------
>>>>> Mail sent through IMP: http://horde.org/imp/
>>>>>  
>>>>>
>>>>>             
>>>>
>>>>
>>>> Using Tomcat but need to do more? Need to support web services, 
>>>> security?
>>>> Get stuff done quickly with pre-integrated technology to make your 
>>>> job easier
>>>> Download IBM WebSphere Application Server v.1.0.1 based on Apache 
>>>> Geronimo
>>>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 
>>>>
>>>> _______________________________________________
>>>> PyMOL-users mailing list
>>>> PyM...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>
>>>>         
>>>
>>>     
>>
>>
>>
>> Using Tomcat but need to do more? Need to support web services, 
>> security?
>> Get stuff done quickly with pre-integrated technology to make your 
>> job easier
>> Download IBM WebSphere Application Server v.1.0.1 based on Apache 
>> Geronimo
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>   
>
>

Dear Joel,
Thanks for you email. I now installed version 0.99 and my problem is 
solved.
Regards
Nagesh


Joel Tyndall wrote:

> Dear Nagesh,
>
> If you upgrade to the latest version (0.99) there is an option do 
> display the disulfides under the show menu
>
> J
>
> Nagesh Chakka wrote:
>
>> Hi Jerome,
>> Thanks for the mail. The web address you gave is about obtaining 
>> information about Cys involved in bond formation. In my case, I do 
>> know which pair of Cys are involved in it and this information is 
>> also provided in the PDB file but I am unable to display the bridge 
>> in the PyMOL viewer.
>> Also I need to display the structure in a particular orientation. Can 
>> this information be be added in my script.
>> Thanks
>> Nagesh
>>
>> Jerome Pansanel wrote:
>>
>>  
>>
>>> Hello,
>>>
>>> You can find some documentation about sulfur bonds on this page:
>>> http://www.pymolwiki.org/index.php/Process_All_Files_In_Directory
>>>
>>> If you are not successfull by using this resource, don't hesitate to 
>>> post
>>> again.
>>>
>>> Cheers,
>>>
>>> Jerome Pansanel
>>>
>>> Selon Nagesh Chakka <nag...@an...>:
>>>
>>>  
>>>
>>>    
>>>
>>>> Hello everyone,
>>>> I am unable to display disulphide bonds using PyMOL (version 0.97). 
>>>> My understanding is that PyMOL can connect Cys that are within 
>>>> bonding distance. The PDB file (ID 1AG2) defines residues involved 
>>>> in the SSBond
>>>>
>>>> formation. I  also tried to  use the command "bond" to connect the 
>>>> residues but without any success. I am not sure if I am doing 
>>>> anything wrong. Any suggestion in this regard is appreciated.
>>>> Thanks
>>>> Nagesh
>>>>
>>>>
>>>> Using Tomcat but need to do more? Need to support web services,
>>>> security?
>>>> Get stuff done quickly with pre-integrated technology to make your job
>>>> easier
>>>> Download IBM WebSphere Application Server v.1.0.1 based on Apache
>>>> Geronimo
>>>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 
>>>>
>>>> _______________________________________________
>>>> PyMOL-users mailing list
>>>> PyM...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>
>>>>   
>>>>       
>>>
>>>
>>>
>>> --------------------------------------------
>>> Mail sent through IMP: http://horde.org/imp/
>>>  
>>>
>>>     
>>
>>
>>
>> Using Tomcat but need to do more? Need to support web services, 
>> security?
>> Get stuff done quickly with pre-integrated technology to make your 
>> job easier
>> Download IBM WebSphere Application Server v.1.0.1 based on Apache 
>> Geronimo
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>   
>
>

Dear Nagesh,

If you upgrade to the latest version (0.99) there is an option do 
display the disulfides under the show menu

J

Nagesh Chakka wrote:
> Hi Jerome,
> Thanks for the mail. The web address you gave is about obtaining 
> information about Cys involved in bond formation. In my case, I do know 
> which pair of Cys are involved in it and this information is also 
> provided in the PDB file but I am unable to display the bridge in the 
> PyMOL viewer.
> Also I need to display the structure in a particular orientation. Can 
> this information be be added in my script.
> Thanks
> Nagesh
>
> Jerome Pansanel wrote:
>
>   
>> Hello,
>>
>> You can find some documentation about sulfur bonds on this page:
>> http://www.pymolwiki.org/index.php/Process_All_Files_In_Directory
>>
>> If you are not successfull by using this resource, don't hesitate to post
>> again.
>>
>> Cheers,
>>
>> Jerome Pansanel
>>
>> Selon Nagesh Chakka <nag...@an...>:
>>
>>  
>>
>>     
>>> Hello everyone,
>>> I am unable to display disulphide bonds using PyMOL (version 0.97). My 
>>> understanding is that PyMOL can connect Cys that are within bonding 
>>> distance. The PDB file (ID 1AG2) defines residues involved in the SSBond
>>>
>>> formation. I  also tried to  use the command "bond" to connect the 
>>> residues but without any success. I am not sure if I am doing anything 
>>> wrong. Any suggestion in this regard is appreciated.
>>> Thanks
>>> Nagesh
>>>
>>>
>>> Using Tomcat but need to do more? Need to support web services,
>>> security?
>>> Get stuff done quickly with pre-integrated technology to make your job
>>> easier
>>> Download IBM WebSphere Application Server v.1.0.1 based on Apache
>>> Geronimo
>>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> PyM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>
>>>    
>>>
>>>       
>>
>>
>> --------------------------------------------
>> Mail sent through IMP: http://horde.org/imp/
>>  
>>
>>     
>
>
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>   

-- 
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                     

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293 
Fax / Waeawhakaahua     +64 3 4797034

Hi Jerome,
Thanks for the mail. The web address you gave is about obtaining 
information about Cys involved in bond formation. In my case, I do know 
which pair of Cys are involved in it and this information is also 
provided in the PDB file but I am unable to display the bridge in the 
PyMOL viewer.
Also I need to display the structure in a particular orientation. Can 
this information be be added in my script.
Thanks
Nagesh

Jerome Pansanel wrote:

>Hello,
>
>You can find some documentation about sulfur bonds on this page:
>http://www.pymolwiki.org/index.php/Process_All_Files_In_Directory
>
>If you are not successfull by using this resource, don't hesitate to post
>again.
>
>Cheers,
>
>Jerome Pansanel
>
>Selon Nagesh Chakka <nag...@an...>:
>
>  
>
>>Hello everyone,
>>I am unable to display disulphide bonds using PyMOL (version 0.97). My 
>>understanding is that PyMOL can connect Cys that are within bonding 
>>distance. The PDB file (ID 1AG2) defines residues involved in the SSBond
>>
>>formation. I  also tried to  use the command "bond" to connect the 
>>residues but without any success. I am not sure if I am doing anything 
>>wrong. Any suggestion in this regard is appreciated.
>>Thanks
>>Nagesh
>>
>>
>>Using Tomcat but need to do more? Need to support web services,
>>security?
>>Get stuff done quickly with pre-integrated technology to make your job
>>easier
>>Download IBM WebSphere Application Server v.1.0.1 based on Apache
>>Geronimo
>>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>_______________________________________________
>>PyMOL-users mailing list
>>PyM...@li...
>>https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>    
>>
>
>
>
>
>--------------------------------------------
>Mail sent through IMP: http://horde.org/imp/
>  
>