pymol-users Mailing List for PyMOL Molecular Graphics System

Dear pymol users,

I'm trying to understand how align command measures the RMSD between 2  
homologues and explain the discrepancy between that value and the one  
obtained from ProFit. The sequence alignments produced by both  
programs are continuous and match, but the RMS values are 1.781 and  
4.615 for Pymol and Profit respectively. The RMS corresponds to Ca  
atoms only (pymol command line: "align 3G5U_A and name CA and chain A,  
H_ABCB1_NBD1 and name CA, cycles=0, object=ao"). Does pymol consider  
only Ca atoms that are closer than a default cutoff distance only  
(e.g. 5 A) when calculating the RMSD?

As usual, the answer presented itself minutes after I posted the message. Everything is working fine again after the NVidia driver was upgraded to the latest version (190.53).

> Dear Pymol users,
> 
> I checked out the last source code via subversion (rev. 3881), 
> compiled the code and PyMol launched fine. Then I upgraded the 
> packages on the system (Red Hat Enterprise v5, 64 bit) and PyMol 
> does not launch anymore (please see output below). I have 
> uninstalled the program and re-compiled the code (no errors), but 
> the result is still the same. If it helps, my freeglut version is 
> 2.4.0-7.1.
> 
> freeglut (pymol): Unable to create direct context rendering for 
> window 'PyMOL Viewer'
> This may hurt performance.
> X Error of failed request:  BadMatch (invalid parameter attributes)
>  Major opcode of failed request:  143 (GLX)
>  Minor opcode of failed request:  5 (X_GLXMakeCurrent)
>  Serial number of failed request:  37
>  Current serial number in output stream:  37
> PyMOL: abrupt program termination.
> 
> Thank you in advance.
> 
> --------------------------------------------------------------------
> ----------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
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> and easy
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> _______________________________________________
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-
> us...@li...

Dear Pymol users,

I checked out the last source code via subversion (rev. 3881), compiled the code and PyMol launched fine. Then I upgraded the packages on the system (Red Hat Enterprise v5, 64 bit) and PyMol does not launch anymore (please see output below). I have uninstalled the program and re-compiled the code (no errors), but the result is still the same. If it helps, my freeglut version is 2.4.0-7.1.

freeglut (pymol): Unable to create direct context rendering for window 'PyMOL Viewer'
This may hurt performance.
X Error of failed request:  BadMatch (invalid parameter attributes)
  Major opcode of failed request:  143 (GLX)
  Minor opcode of failed request:  5 (X_GLXMakeCurrent)
  Serial number of failed request:  37
  Current serial number in output stream:  37
 PyMOL: abrupt program termination.

Thank you in advance.

Mike,

Lots of info here: http://pymolwiki.org/index.php/Cartoon_smooth_loops

Hope this helps,

-- Jason

--
Jason Vertrees, PhD

PyMOLWiki -- http://www.pymolwiki.org



On Thu, Dec 24, 2009 at 2:22 PM, Mirek Cygler <mi...@br...> wrote:
> Dear Pymolers,
>        Which parameter controls the smoothing of the loops in cartoon mode?
> I am trying to make the loops passing through the Calpha atoms of explicitly
> displayed residues. Can not remember how to set this up.
>        Thanks,
>
>                                Mirek
>
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and easy
> Join now and get one step closer to millions of Verizon customers
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> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Dear Pymolers,
	Which parameter controls the smoothing of the loops in cartoon mode?
I am trying to make the loops passing through the Calpha atoms of explicitly
displayed residues. Can not remember how to set this up.
	Thanks,

                                Mirek

Hi all!
Thanks for the link and the tutorial.
We also have been using PyMOL and Blender for some scientific 
animations. Indeed, during the Blender Conference in Amsterdam 
last october, we witnessed several presentations of people 
using Blender in academics/research setting, and have recently 
started a new forum for such users in 
http://www.blender.org/forum/viewforum.php?f=21&sid=c4bebca2b3c6253663fc663aa2eb0b75.
Shiven, would you like to post your work there as well?

Our work at present is mostly done via scripting,  but the 
preparation of a human-friendly interface and of some tutorial 
is on the top of our todo list.In the meantime, if you wish to 
use/test our scripts, please ask, we will be glad to send 
them.
  An idea of our progress can be found on our website 
www.scivis.ifc.cnr.it You 'll find some movies, biological 
explanatory notes and papers describing the work.

Comments are welcome!!

Raluca

Thank you for the nice tutorial.

On Tue, Dec 22, 2009 at 8:17 PM, Shiven Shandilya <
shi...@gm...> wrote:

> Hello List,
>
> An initial attempt at a  PyMOL + Blender  tutorial is now on the pymolwiki:
>
> http://pymolwiki.org/index.php/Blender
>
> Hope some of you will find it useful.
>
> Fellow Blenderheads, crits are welcome.
> Also, please help improve/add to the tutorial.
>
> Best,
> Shiven
>
>
> ----------------------------------------------------
> Shivender Shandilya,
> Graduate Student,
> Schiffer Lab,
> Dept. of Biochemistry & Molecular Pharmacology,
> University of Massachusetts Medical School,
> Worcester, MA 01604.
>
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and
> easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hello List,

An initial attempt at a  PyMOL + Blender  tutorial is now on the pymolwiki:

http://pymolwiki.org/index.php/Blender

Hope some of you will find it useful.

Fellow Blenderheads, crits are welcome.
Also, please help improve/add to the tutorial.

Best,
Shiven


----------------------------------------------------
Shivender Shandilya,
Graduate Student,
Schiffer Lab,
Dept. of Biochemistry & Molecular Pharmacology,
University of Massachusetts Medical School,
Worcester, MA 01604.

Hi,
I apologize for this weird email for the PyMOL users.
Is there any PyMOL user out there happen to have a some old dusty Q-Plates (NOT Q-II) somewhere in  their lab and you were tried and still trying to get rid of them? 
Or if you know where I can still purchase them ?
Please let me know.
 
"PyMOL rocks"
 
Best regards.
 
 
 
Hasan DeMirci, Ph.D.
Postdoctoral Fellow
Department of Molecular Biology, Cellular Biology & Biochemistry
Brown University
185 Meeting Street
Providence, RI    02912

(401) 863-3652 lab (SFH)
(401) 863-6124 lab (ship st)
(401) 226-7852 cell

Has...@Br...
dem...@gm...

Hi all,

Just wanted to mention that I've updated some of the info on the wiki here:

http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options#LCD_Displays_.28120_Hz.29

to note that quad buffered stereo (QBS) on the 120Hz Samsung 2233RZ
LCD monitor works on Linux. It's nowhere as cheap as the Zalman
solution but will work with any other visualization apps out there
that have QBS support which don't support the Zalman.

HTH,
Sabuj Pattanayek

David,

I think groups are treated like objects (see "help group").  So, one can type
    print cmd.get_names("objects")
and all the objects (proteins, groups, etc) will be returned.

For example:
  group a
  group b
  group c
  print cmd.get_names("objects")

The problem is that other objects will be returned, too.  So, if you
don't use special naming for your groups, they will run together with
other objects.

-- Jason

--
Jason Vertrees, PhD

PyMOLWiki -- http://www.pymolwiki.org



On Mon, Dec 21, 2009 at 6:45 PM, David Hall <dwa...@ya...> wrote:
> How would someone get the list of groups in a pymol session?  get_object_list doesn't have them and the only commands I can find in cmd that have the word "group" in them seems to be group and ungroup (if my quick regex search worked right).
>
> Thanks,
> David
>
>
>
>
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

How would someone get the list of groups in a pymol session?  get_object_list doesn't have them and the only commands I can find in cmd that have the word "group" in them seems to be group and ungroup (if my quick regex search worked right).

Thanks,
David



      

Hi Raluca,

So I am guessing this something like the surface being in fragments,
with small vertices floating within the larger object?

Unfortunately there is no easy way to do this from within PyMOL,
unless you can "separate" out the residues/atoms that are contributing
the disjointed meshes into new objects and then turn them off before
export.

Right now the best thing I can think of going into edit mode in
Blender and deleting those vertices by hand.  :-(

Best,
Shiven


On Mon, Dec 21, 2009 at 12:11 PM, Raluca Mihaela ANDREI <r.a...@sn...> wrote:
> Thank you Shiven,
> I know how to remove the double vertices in Blender but I would like to
> remove them directly from PyMOL. By disjoint meshes I mean non-connected
> meshes, inside my mesh I have some smaller meshes that are non connected to
> the big mesh. I would like to know how to remove these meshes before saving.
> Thank you,
> Raluca
>
>
> On Mon, 21 Dec 2009 11:24:11 -0500
>  Shiven Shandilya <shi...@gm...> wrote:
>>
>> Raluca,
>>
>> Something that helps is: tabbing into edit mode, selecting all
>> vertices (ctrl-a) and removing doubles (Mesh >Vertices
>>>
>>> Remove
>>
>> Doubles).
>> Turning on smooth display also helps.
>>
>> What exactly are you having problems with?   In what way are things
>> "disjointed" ?
>>
>> Best,
>> Shiven
>>
>>
>> On Mon, Dec 21, 2009 at 6:51 AM, Raluca Mihaela ANDREI <r.a...@sn...>
>> wrote:
>>>
>>> Hi,
>>> I imported into Blender (a 3D modelling and animation
>>> software) a surface created in PyMOL and I realized that there
>>> are some disjoint surfaces inside. Is it possible to remove
>>> these surfaces in PyMOL?
>>> Thank you,
>>> Raluca
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> This SF.Net email is sponsored by the Verizon Developer Community
>>> Take advantage of Verizon's best-in-class app development support
>>> A streamlined, 14 day to market process makes app distribution fast and
>>> easy
>>> Join now and get one step closer to millions of Verizon customers
>>> http://p.sf.net/sfu/verizon-dev2dev
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>>
>> --
>> ~^v^~ the cgull ...
>
>



-- 
~^v^~ the cgull ...

Thank you Shiven,
I know how to remove the double vertices in Blender but I 
would like to remove them directly from PyMOL. By disjoint 
meshes I mean non-connected meshes, inside my mesh I have some 
smaller meshes that are non connected to the big mesh. I would 
like to know how to remove these meshes before saving.
Thank you,
Raluca


On Mon, 21 Dec 2009 11:24:11 -0500
  Shiven Shandilya <shi...@gm...> wrote:
> Raluca,
> 
> Something that helps is: tabbing into edit mode, selecting 
>all
> vertices (ctrl-a) and removing doubles (Mesh >Vertices 
>>Remove
> Doubles).
> Turning on smooth display also helps.
> 
> What exactly are you having problems with?   In what way are 
>things
> "disjointed" ?
> 
> Best,
> Shiven
> 
> 
> On Mon, Dec 21, 2009 at 6:51 AM, Raluca Mihaela ANDREI 
><r.a...@sn...> wrote:
>> Hi,
>> I imported into Blender (a 3D modelling and animation
>> software) a surface created in PyMOL and I realized that 
>>there
>> are some disjoint surfaces inside. Is it possible to remove
>> these surfaces in PyMOL?
>> Thank you,
>> Raluca
>>
>> ------------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Verizon Developer 
>>Community
>> Take advantage of Verizon's best-in-class app development 
>>support
>> A streamlined, 14 day to market process makes app 
>>distribution fast and easy
>> Join now and get one step closer to millions of Verizon 
>>customers
>> http://p.sf.net/sfu/verizon-dev2dev
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: 
>>https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: 
>>http://www.mail-archive.com/pym...@li...
>>
> 
> 
> 
> -- 
> ~^v^~ the cgull ...

Raluca,

Something that helps is: tabbing into edit mode, selecting all
vertices (ctrl-a) and removing doubles (Mesh >Vertices >Remove
Doubles).
Turning on smooth display also helps.

What exactly are you having problems with?   In what way are things
"disjointed" ?

Best,
Shiven


On Mon, Dec 21, 2009 at 6:51 AM, Raluca Mihaela ANDREI <r.a...@sn...> wrote:
> Hi,
> I imported into Blender (a 3D modelling and animation
> software) a surface created in PyMOL and I realized that there
> are some disjoint surfaces inside. Is it possible to remove
> these surfaces in PyMOL?
> Thank you,
> Raluca
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
~^v^~ the cgull ...

Hi,
I imported into Blender (a 3D modelling and animation 
software) a surface created in PyMOL and I realized that there 
are some disjoint surfaces inside. Is it possible to remove 
these surfaces in PyMOL?
Thank you,
Raluca

On Thu, Dec 17, 2009 at 10:54 AM, Jason C Porta <jp...@un...> wrote:

> I have been trying to modify the grid spacing on 2Fo-Fc map that was loaded
> into PyMol directly from phenix.refine. The mesh object is generated from
> the isomesh command. Basically, I would like there to be fewer grid points
> so that the density isn't so thick. If anyone has any advice, it would be
> greatly appreciated.


The grid spacing is built in to XPLOR maps.  The only workaround I can
suggest is to start from the map coefficients in MTZ format, and run CCP4
FFT to output a CCP4 format map with the grid spacing you prefer.
 (0.33*resolution is the default in most programs, but phenix.refine uses
0.25*resolution.)  I'll add a program to the Phenix GUI to do this at some
point.  For now, I'll see if I can make it easier to change the resolution
factor from the GUI.

<FONT face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size=2>Hi everybody,<br><br>I have been trying to modify the grid spacing on 2Fo-Fc map that was loaded into PyMol directly from phenix.refine. The mesh object is generated from the isomesh command. Basically, I would like there to be fewer grid points so that the density isn't so thick. If anyone has any advice, it would be greatly appreciated.<br><br>Regards,<br><br>Jason Porta<br></FONT>

Hi Sing,

You have a few options.

You can try CASTp (either the web service or the PyMOL plugin). I think the .pocinfo file contains information about volumes.

You could also use Voidoo (http://xray.bmc.uu.se/usf/voidoo_man.html). In the distribution, there is a script (cavity.csh) can be used to used to run voidoo to find cavities. The resulting log files have information about volumes. To visualize the cavities, the resulting .ezd files have to bee converted to .ccp4 with mapman.

Hope this helps,

Xavier

Xavier Deupi
Laboratory of Computational Medicine
Biostatistics Unit. School of Medicine
Universitat Autonoma de Barcelona
Bellaterra, 08193 (Barcelona)
Catalunya, EU
lmc.uab.cat

On Dec 17, 2009, at 8:16 AM, Kin Sing Stephen Lee wrote:

> Dear all,
> 
> I am wondering if it is possible for me to measure the volume of the  
> binding pocket or the molecule in pymol? If no, any recommend program  
> for Mac for such purposes?
> 
> Thank you very much
> 
> Sing

Dear all,

I am wondering if it is possible for me to measure the volume of the  
binding pocket or the molecule in pymol? If no, any recommend program  
for Mac for such purposes?

Thank you very much

Sing

JW,

To get the state of a multi-state system, do:
  get state
or
  get state, objectName

See http://pymolwiki.org/index.php/State for a starting portal to
other state-based info.

You can similarly set a state:

 set state, stateNumber, object

Hope this helps,

-- Jason

--
Jason Vertrees, PhD

PyMOLWiki -- http://www.pymolwiki.org



On Tue, Dec 15, 2009 at 6:06 PM, JW Feng <fe...@ge...> wrote:
> Hi,
>
> Once can see the current state of a multi-state object on the bottom right
> corner of a PyMOL window. How do get get the state number programatically? I
> cannot find a command that will return the current state of a multi-state
> object. I need the state information in order to save the current state into
> a SD file. Using "save test.sdf,selection=abc,state=-1" saves the first
> state of an multi-state object even thought the documentation states that
> using "state = -1" will save the current state. Using "save
> test2.sdf,selection=abc,state=6" does correctly saves the current state,
> which is 6. It would be great if some one can tell me how to get state via
> command line or a pymol script.
>
> What is interesting is that  "save test.pdb,selection=abc,state=-1" works. I
> think there is a bug in saving to a sd file. It would
>
> Thanks,
>
> JW
>
>
> -------------------------------------------------------------------
> JW Feng Ph.D.
> Computational Chemistry and Cheminformatics
> Genentech, Inc.
> -------------------------------------------------------------------
> Tel: 650-225-4529
> Fax: 650-467-5155
> fe...@ge...
> -------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

<html><a
href="http://www.linwik.com/wiki/configuring+a+nvidia+graphics+chip+for+centos+and+rhel+"><font size="3"><span style="font-family: ??;"></span></font></a><font size="3"><span style="font-family: ??;">hi, Joel.<br>
I think there are several ways to fix it( I do it under Debian):<br>
<br>
1. Install mesa driver. it's the old way and always works well.<br>
</span></font><a
href="http://www.centos.org/modules/newbb/viewtopic.php?topic_id=16139"><font size="3"><span style="font-family: ??;">http://www.centos.org/modules/newbb/viewtopic.php?topic_id=16139</span></font></a><font size="3"><span style="font-family: ??;"><br>
<br>
2. Download the driver from nvidia home,and install it. <br>
It's the easiest way if you aren't familiar with CentOS.<br>
<br>
<a
href="http://www.nvidia.com/Download/index.aspx?lang=en-us
" rel="nofollow">http://www.nvidia.com/Download/index.aspx?lang=en-us">http://www.nvidia.com/Download/index.aspx?lang=en-us</a><br>
<br>
3. Maybe Centos have made the rpm packages for nvidia drivers.<br>
&nbsp;So search it with "rpm" cmmand, then install it.<br>
<br>
Hope help!<br>
<br>
Cun Zhang<br>
<br>
<br>
</span></font><blockquote style="border-left: 1px solid rgb(204, 204, 204);
margin: 0pt 0pt 0pt 0.8ex; padding: 1ex 0pt 0pt 1ex;">Message: 3<br>
Date: Wed, 16 Dec 2009 12:34:59 +1300<br>
From: Joel Tyndall &lt;joe...@ot...&gt;<br>
Subject: [PyMOL] FW: Slightly off topic<br>
To: "pym...@li..."<br>
	&lt;pym...@li...&gt;<br>
Message-ID:<br>
	&lt;452...@MA...&gt;<br>
	<br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Thanks folks, will start with FC11<br>
<br>
J<br>
<br>
From: Joel Tyndall [<a
href="mailto:joe...@ot...">mailto:joe...@ot...</a>]<br>
Sent: Tuesday, 15 December 2009 4:33 p.m.<br>
To: pym...@li...<br>
Subject: [PyMOL] Slightly off topic<br>
<br>
Hi folks,<br>
<br>
Sorry for the off topic post. I have just got a new whizz bang laptop and
I'm wondering whether I have gone too high spec. It is 64 bit LED ASUS
ul50v series. I am running linux centos 5.4 but can't get the nvidia driver
going (LED screen perhaps) and I just had an initial problem with pymol. (I
want to run modeler, sybyl and gold also ) This is not to mention the fact
that the kernel doesn't have wireless or Ethernet drivers.<br>
<br>
Should I "downgrade" or persist.<br>
<br>
Many thanks for comments<br>
<br>
_________________________________<br>
Joel Tyndall, PhD<br>
<br>
Senior Lecturer in Medicinal Chemistry<br>
National School of Pharmacy<br>
University of Otago<br>
PO Box 56 Dunedin 9054<br>
New Zealand<br>
<a
href="http://www.researcherid.com/rid/C-2803-2008
" rel="nofollow">http://www.researcherid.com/rid/C-2803-2008">http://www.researcherid.com/rid/C-2803-2008</a><br>
Pukeka Matua<br>
Te Kura Taiwhanga Putaiao<br>
Te Whare Wananga o Otago<br>
Pouaka Poutapeta 56 Otepoti 9054<br>
Aotearoa<br>
<br>
Ph / Waea               +64 3 4797293<br>
Fax / Waeawhakaahua     +64 3 4797034<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
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Name: ATT00001.txt<br>
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</blockquote></html>

<html><a
href="http://www.linwik.com/wiki/configuring+a+nvidia+graphics+chip+for+centos+and+rhel+"><font size="3"><span style="font-family: ??;"></span></font></a><font size="3"><span style="font-family: ??;">hi, Joel.<br>
I think there are several ways to fix it( I do it under Debian):<br>
<br>
1. Install mesa driver. it's the old way and always works well.<br>
</span></font><a
href="http://www.centos.org/modules/newbb/viewtopic.php?topic_id=16139"><font size="3"><span style="font-family: ??;">http://www.centos.org/modules/newbb/viewtopic.php?topic_id=16139</span></font></a><font size="3"><span style="font-family: ??;"><br>
<br>
2. Download the driver from nvidia home,and install it. <br>
It's the easiest way if you aren't familiar with CentOS.<br>
<br>
<a
href="http://www.nvidia.com/Download/index.aspx?lang=en-us
" rel="nofollow">http://www.nvidia.com/Download/index.aspx?lang=en-us">http://www.nvidia.com/Download/index.aspx?lang=en-us</a><br>
<br>
3. Maybe Centos have made the rpm packages for nvidia drivers.<br>
&nbsp;So search it with "rpm" cmmand, then install it.<br>
<br>
Hope help!<br>
<br>
Cun Zhang<br>
<br>
<br>
</span></font><blockquote style="border-left: 1px solid rgb(204, 204, 204);
margin: 0pt 0pt 0pt 0.8ex; padding: 1ex 0pt 0pt 1ex;">Message: 3<br>
Date: Wed, 16 Dec 2009 12:34:59 +1300<br>
From: Joel Tyndall &lt;joe...@ot...&gt;<br>
Subject: [PyMOL] FW: Slightly off topic<br>
To: "pym...@li..."<br>
	&lt;pym...@li...&gt;<br>
Message-ID:<br>
	&lt;452...@MA...&gt;<br>
	<br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Thanks folks, will start with FC11<br>
<br>
J<br>
<br>
From: Joel Tyndall [<a
href="mailto:joe...@ot...">mailto:joe...@ot...</a>]<br>
Sent: Tuesday, 15 December 2009 4:33 p.m.<br>
To: pym...@li...<br>
Subject: [PyMOL] Slightly off topic<br>
<br>
Hi folks,<br>
<br>
Sorry for the off topic post. I have just got a new whizz bang laptop and
I'm wondering whether I have gone too high spec. It is 64 bit LED ASUS
ul50v series. I am running linux centos 5.4 but can't get the nvidia driver
going (LED screen perhaps) and I just had an initial problem with pymol. (I
want to run modeler, sybyl and gold also ) This is not to mention the fact
that the kernel doesn't have wireless or Ethernet drivers.<br>
<br>
Should I "downgrade" or persist.<br>
<br>
Many thanks for comments<br>
<br>
_________________________________<br>
Joel Tyndall, PhD<br>
<br>
Senior Lecturer in Medicinal Chemistry<br>
National School of Pharmacy<br>
University of Otago<br>
PO Box 56 Dunedin 9054<br>
New Zealand<br>
<a
href="http://www.researcherid.com/rid/C-2803-2008
" rel="nofollow">http://www.researcherid.com/rid/C-2803-2008">http://www.researcherid.com/rid/C-2803-2008</a><br>
Pukeka Matua<br>
Te Kura Taiwhanga Putaiao<br>
Te Whare Wananga o Otago<br>
Pouaka Poutapeta 56 Otepoti 9054<br>
Aotearoa<br>
<br>
Ph / Waea               +64 3 4797293<br>
Fax / Waeawhakaahua     +64 3 4797034<br>
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Hi,

Once can see the current state of a multi-state object on the bottom right
corner of a PyMOL window. How do get get the state number programatically? I
cannot find a command that will return the current state of a multi-state
object. I need the state information in order to save the current state into
a SD file. Using "save test.sdf,selection=abc,state=-1" saves the first
state of an multi-state object even thought the documentation states that
using "state = -1" will save the current state. Using "save
test2.sdf,selection=abc,state=6" does correctly saves the current state,
which is 6. It would be great if some one can tell me how to get state via
command line or a pymol script.

What is interesting is that  "save test.pdb,selection=abc,state=-1" works. I
think there is a bug in saving to a sd file. It would

Thanks,

JW


-------------------------------------------------------------------
JW Feng Ph.D.
Computational Chemistry and Cheminformatics
Genentech, Inc.
-------------------------------------------------------------------
Tel: 650-225-4529
Fax: 650-467-5155
fe...@ge...
-------------------------------------------------------------------

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