Re: [PyMOL] labeling by a pseudoatom
Roberto,
partial answer to point 3. Adding a "_" before an object name hides it
from the panel.
For points 1 or 2. Could you please expand on your question? Is this for
interactive
or scripted mode?
For scripted mode you could modify the coordinates of the pseudoatom to
be closer to the target atom or not? Otherwise look up the commands in
"Edit" mode. BTW in Edit mode you can actually mode regular labels with
the mouse as well (Edit Mode: CTRL Middle click)
Hope it helps somewhat
Carsten
> -Original Message-
> From: rv...@libero.it [mailto:rv...@libero.it]
> Sent: Friday, February 25, 2011 5:00 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] labeling by a pseudoatom
>
> Hello everyone,
>
> trying to use a pseudoatom as label I met several problems:
>
> 1) How to move the label (pseudoatom) to a target residue?
> Is there a simple command to do?
>
> 2) How to change the label without messaging the user?
> The 'label' command appears not have a 'quiet' option.
>
> 3) (less important) How to hide the pseudoatom?
> I wish not have the pseudoatom listed among models in the GUI
> panel.
>
> 4) (less important) I need to execute all these operations by script
> (mdo
> commands during a movie)
> To simplify the movie I wish use only one mdo command
>
> def doAll()
> .. all my script here ..
>
> extending the cmd just before the movie start
>
> cmd.extend('doAll', doAll)
>
> and clearing the cmd just at the end of the movie but I don't
> know
> how.
> Is there a way to clear a command?
>
>
> Thanks,
> Roberto
>
>
>
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[PyMOL] R: RE: labeling by a pseudoatom
Hi Carsten,
thanks for the answer.
Yes is for scripted mode.
I searched pyMOLWiki for a simple command to move the label to the target
(something like 'super', 'fit' ) but I didn't find.
So I searched for 'get' to have the coordinates of the target atom and for
'alter' to change the coordinates of the label but I was quite confused: I
didn't find names like x, y, z in the name space of both 'get' and 'alter'
commands. So I am still searching ..
Could you please tell me how to get and set x, y, z coordinates?
About the 'label' command: is there a way to not message the user? I didn't
find a 'quiet' option for this command. Is there another way?
Thanks for your hint about '_' prefix to hide an object.
roberto
>Messaggio originale
>Da: cschu...@its.jnj.com
>Data: 27/02/2011 17.44
>A: ,
>Ogg: RE: [PyMOL] labeling by a pseudoatom
>
>Roberto,
>
>partial answer to point 3. Adding a "_" before an object name hides it
>from the panel.
>
>For points 1 or 2. Could you please expand on your question? Is this for
>interactive
>or scripted mode?
>For scripted mode you could modify the coordinates of the pseudoatom to
>be closer to the target atom or not? Otherwise look up the commands in
>"Edit" mode. BTW in Edit mode you can actually mode regular labels with
>the mouse as well (Edit Mode: CTRL Middle click)
>
>Hope it helps somewhat
>
>Carsten
>
>> -Original Message-
>> From: rv...@libero.it [mailto:rv...@libero.it]
>> Sent: Friday, February 25, 2011 5:00 PM
>> To: pymol-users@lists.sourceforge.net
>> Subject: [PyMOL] labeling by a pseudoatom
>>
>> Hello everyone,
>>
>> trying to use a pseudoatom as label I met several problems:
>>
>> 1) How to move the label (pseudoatom) to a target residue?
>> Is there a simple command to do?
>>
>> 2) How to change the label without messaging the user?
>> The 'label' command appears not have a 'quiet' option.
>>
>> 3) (less important) How to hide the pseudoatom?
>> I wish not have the pseudoatom listed among models in the GUI
>> panel.
>>
>> 4) (less important) I need to execute all these operations by script
>> (mdo
>> commands during a movie)
>> To simplify the movie I wish use only one mdo command
>>
>> def doAll()
>> .. all my script here ..
>>
>> extending the cmd just before the movie start
>>
>> cmd.extend('doAll', doAll)
>>
>> and clearing the cmd just at the end of the movie but I don't
>> know
>> how.
>> Is there a way to clear a command?
>>
>>
>> Thanks,
>> Roberto
>>
>>
>>
>---
>> ---
>> Free Software Download: Index, Search & Analyze Logs and other IT data
>> in
>> Real-Time with Splunk. Collect, index and harness all the fast moving
>> IT data
>> generated by your applications, servers and devices whether physical,
>> virtual
>> or in the cloud. Deliver compliance at lower cost and gain new
>business
>> insights. http://p.sf.net/sfu/splunk-dev2dev
>> ___
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>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives:
>http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
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Re: [PyMOL] Saving the Connolly surface of a PDB
Hi Francios, Someone recently asked about this and the answer was that this should be a setting, but isn't currently available. If I have time, I'll try to sneak this in the upcoming PyMOL v1.4 release. Cheers, -- Jason On Fri, Feb 25, 2011 at 3:05 AM, Francois Berenger wrote: > Hello, > > Is it possible to save the Connolly surface > computed by Pymol without any rotation and translation > added compared to the PDB from which the atom coordinates were read? > > I looked at the .obj file output and find there was some centering > done and also some rotation added. > > Thanks a lot, > F. > > -- > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT data > generated by your applications, servers and devices whether physical, virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] labeling by a pseudoatom
Hi Roberto,
It's nice to see people learning how to script and putting PyMOL
through its paces.
> trying to use a pseudoatom as label I met several problems:
>
> 1) How to move the label (pseudoatom) to a target residue?
> Is there a simple command to do?
The easiest way would be to get the coordinates of the target residue,
I'd choose the alpha carbon (replace "X" with your residue number):
# query residue X's alpha carbon, store the position in targetResPosition
targetResPosition = cmd.get_atom_coords("resi X and n. CA")
# next, just assign that position to the pseudoatom:
cmd.alter_state(1, "myPseudoAtom", "(x,y,z) = targetResPosition")
> 2) How to change the label without messaging the user?
> The 'label' command appears not have a 'quiet' option.
This is interesting, and not what I'd expect from PyMOL, however it works:
# make a new text label as a Python string
newLabel = "New Pseudoatom label"
# assign that label
cmd.label("myPseudoAtom", "newLabel")
Interestingly, PyMOL picks up the 2nd parameter as a variable name.
Also, label does have a quiet option:
# assign that label, quietly
cmd.label("myPseudoAtom", "newLabel", quiet=1)
> 3) (less important) How to hide the pseudoatom?
> I wish not have the pseudoatom listed among models in the GUI panel.
To hide a pseudoatom (just the + symbol):
hide nonbonded, myPseudoAtom
# or, just hide the labels
hide labels, myPseudoAtom
# or, hide all
hide everything, myPseudoAtom
> 4) (less important) I need to execute all these operations by script (mdo
> commands during a movie)
> To simplify the movie I wish use only one mdo command
>
> def doAll()
> .. all my script here ..
>
> extending the cmd just before the movie start
>
> cmd.extend('doAll', doAll)
>
> and clearing the cmd just at the end of the movie but I don't know
> how.
> Is there a way to clear a command?
The mdo command takes a frame number and a string. For that frame it
stores the string, and then applies it prior to setting the scene.
PyMOL overwrites the string each time, so you need to cache all your
commands for one frame and use the mdo command once per fram. Create
a small class that stores all the mdo commands as one string. Then,
when you want those command executed ask the class to call mdo on the
given frame, using that long string. That might look something like:
mcache 50, "show sticks"
mcache 50, "as spheres, het"
mcache 50, "show surface, poly within 10 or org"
...
store scenes, plan movie, etc.
...
mCacheApply 50
I made something similar for making movie fades, just cache the string
an apply it when necessary.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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Re: [PyMOL] Saving the Connolly surface of a PDB
Jason Vertrees wrote: > Hi Francios, > > Someone recently asked about this and the answer was that this should > be a setting, but isn't currently available. If I have time, I'll try > to sneak this in the upcoming PyMOL v1.4 release. Please, send me an e-mail if it is done some day. Other software, like Jmol, don't suffer from such bug so this is just preventing people from using Pymol on some applications. As the surface is computed for a PDB that was read in, I don't see why it is exported after undergoing some rotation and a translation that has nothing to do with the input PDB. Regards, F. > Cheers, > > -- Jason > > On Fri, Feb 25, 2011 at 3:05 AM, Francois Berenger wrote: >> Hello, >> >> Is it possible to save the Connolly surface >> computed by Pymol without any rotation and translation >> added compared to the PDB from which the atom coordinates were read? >> >> I looked at the .obj file output and find there was some centering >> done and also some rotation added. >> >> Thanks a lot, >> F. >> >> -- >> Free Software Download: Index, Search & Analyze Logs and other IT data in >> Real-Time with Splunk. Collect, index and harness all the fast moving IT data >> generated by your applications, servers and devices whether physical, virtual >> or in the cloud. Deliver compliance at lower cost and gain new business >> insights. http://p.sf.net/sfu/splunk-dev2dev >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > > > -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] dimerization
Hi Kanika, Let's say your protein is called 'protein'. Then you can obtain the other unit corresponding to your second biomt operation as: create unit2, protein alter_state 1,unit2,(y,z)=(-y,40.6-z) Note this is a shorthand specific to your case. For a full biomt record (R t), with R being the rotation matrix (first three columns) and t the translation vector (last column), you would have to make the equation reflect the matrix operation Rp+t. Hope it helps, Tsjerk On Feb 28, 2011 6:46 AM, "kanika sharma" wrote: ok, I know that a dimer can be generated from the BIOMT operationon > monomeric unit of protein. > > I have this proteinbut its unclear to me how to apply these transformations and what do they represent If somebody knows then please let me know...Its really urgent... REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.00 0.00 0.000.0 REMARK 350 BIOMT... REMARK 350 BIOMT3 2 0.00 0.00 -1.00 40.6 Best Regards, Kanika -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] dimerization
Iv applied the foll eq: load 1b8e.pdb, A create B,A alter_state 1,B,(x,y,z)=(x,-y,40.60-z) it should form a dimer of my protein but the object "B" is same as my monomer with no change... i am unable to find the error.. On Mon, Feb 28, 2011 at 12:39 PM, Tsjerk Wassenaar wrote: > Hi Kanika, > > Let's say your protein is called 'protein'. Then you can obtain the other > unit corresponding to your second biomt operation as: > > create unit2, protein > alter_state 1,unit2,(y,z)=(-y,40.6-z) > > Note this is a shorthand specific to your case. For a full biomt record (R > t), with R being the rotation matrix (first three columns) and t the > translation vector (last column), you would have to make the equation > reflect the matrix operation Rp+t. > > > Hope it helps, > > > Tsjerk > > > On Feb 28, 2011 6:46 AM, "kanika sharma" wrote: > > ok, I know that a dimer can be generated from the BIOMT operationon >> monomeric unit of protein. >> >> I have this proteinbut its unclear to me how to apply these > transformations and what do they represent > > If somebody knows then please let me know...Its really urgent... > > REMARK 350 APPLY THE FOLLOWING TO CHAINS: A > > > REMARK 350 BIOMT1 1 1.00 0.00 0.000.0 > REMARK 350 BIOMT... > REMARK 350 BIOMT3 2 0.00 0.00 -1.00 40.6 > > > > Best Regards, > Kanika > > -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] dimerization
Hi Kanika, 'b' is a selection keyword. For that reason it doesn't make a good object identifier. Try load 1b8e.pdb, 1b8e_A create 1b8e_B,1b8e_A alter_state 1,1b8e_B,(x,y,z)=(-x,y,33.43-/z) Not that the numbers are different. In 1b8e.pdb I find: REMARK 350 BIOMT1 1 1.00 0.00 0.000.0 REMARK 350 BIOMT2 1 0.00 1.00 0.000.0 REMARK 350 BIOMT3 1 0.00 0.00 1.000.0 REMARK 350 BIOMT1 2 -1.00 0.00 0.000.0 REMARK 350 BIOMT2 2 0.00 1.00 0.000.0 REMARK 350 BIOMT3 2 0.00 0.00 -1.00 33.43000 That's quite different from the record you gave previously. If you want to have good help, especially when it's urgent to you, better do your best in providing correct information and thinking along. Cheers, Tsjerk On Mon, Feb 28, 2011 at 8:16 AM, kanika sharma wrote: > Iv applied the foll eq: > > load 1b8e.pdb, A > create B,A > alter_state 1,B,(x,y,z)=(x,-y,40.60-z) > > it should form a dimer of my protein but the object "B" is same as my > monomer with no change... i am unable to find the error.. > > On Mon, Feb 28, 2011 at 12:39 PM, Tsjerk Wassenaar > wrote: >> >> Hi Kanika, >> >> Let's say your protein is called 'protein'. Then you can obtain the other >> unit corresponding to your second biomt operation as: >> >> create unit2, protein >> alter_state 1,unit2,(y,z)=(-y,40.6-z) >> >> Note this is a shorthand specific to your case. For a full biomt record (R >> t), with R being the rotation matrix (first three columns) and t the >> translation vector (last column), you would have to make the equation >> reflect the matrix operation Rp+t. >> >> Hope it helps, >> >> Tsjerk >> >> On Feb 28, 2011 6:46 AM, "kanika sharma" wrote: >> >>> ok, I know that a dimer can be generated from the BIOMT operationon >>> monomeric unit of protein. >> >> I have this proteinbut its unclear to me how to apply these >> transformations and what do they represent >> If somebody knows then please let me know...Its really urgent... >> >> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A >> >> >> REMARK 350 BIOMT1 1 1.00 0.00 0.00 0.0 >> REMARK 350 BIOMT... >> >> REMARK 350 BIOMT3 2 0.00 0.00 -1.00 40.6 >> >> >> Best Regards, >> Kanika > > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] dimerization
M really sorry for the wrong information guys...script helped a lot.. If my protein is a dimer...Chain A,BHow can i apply the script here?i dun know for 2 chains Thank you..in advanceapologies for previous mistake... REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.00 0.00 0.000.0 REMARK 350 BIOMT2 1 0.00 1.00 0.000.0 REMARK 350 BIOMT3 1 0.00 0.00 1.000.0 Thank you... On Mon, Feb 28, 2011 at 1:00 PM, Tsjerk Wassenaar wrote: > Hi Kanika, > > 'b' is a selection keyword. For that reason it doesn't make a good > object identifier. Try > > load 1b8e.pdb, 1b8e_A > create 1b8e_B,1b8e_A > alter_state 1,1b8e_B,(x,y,z)=(-x,y,33.43-/z) > > Not that the numbers are different. In 1b8e.pdb I find: > > REMARK 350 BIOMT1 1 1.00 0.00 0.000.0 > REMARK 350 BIOMT2 1 0.00 1.00 0.000.0 > REMARK 350 BIOMT3 1 0.00 0.00 1.000.0 > REMARK 350 BIOMT1 2 -1.00 0.00 0.000.0 > REMARK 350 BIOMT2 2 0.00 1.00 0.000.0 > REMARK 350 BIOMT3 2 0.00 0.00 -1.00 33.43000 > > That's quite different from the record you gave previously. If you > want to have good help, especially when it's urgent to you, better do > your best in providing correct information and thinking along. > > Cheers, > > Tsjerk > > > On Mon, Feb 28, 2011 at 8:16 AM, kanika sharma > wrote: > > Iv applied the foll eq: > > > > load 1b8e.pdb, A > > create B,A > > alter_state 1,B,(x,y,z)=(x,-y,40.60-z) > > > > it should form a dimer of my protein but the object "B" is same as my > > monomer with no change... i am unable to find the error.. > > > > On Mon, Feb 28, 2011 at 12:39 PM, Tsjerk Wassenaar > > wrote: > >> > >> Hi Kanika, > >> > >> Let's say your protein is called 'protein'. Then you can obtain the > other > >> unit corresponding to your second biomt operation as: > >> > >> create unit2, protein > >> alter_state 1,unit2,(y,z)=(-y,40.6-z) > >> > >> Note this is a shorthand specific to your case. For a full biomt record > (R > >> t), with R being the rotation matrix (first three columns) and t the > >> translation vector (last column), you would have to make the equation > >> reflect the matrix operation Rp+t. > >> > >> Hope it helps, > >> > >> Tsjerk > >> > >> On Feb 28, 2011 6:46 AM, "kanika sharma" wrote: > >> > >>> ok, I know that a dimer can be generated from the BIOMT operationon > >>> monomeric unit of protein. > >> > >> I have this proteinbut its unclear to me how to apply these > >> transformations and what do they represent > >> If somebody knows then please let me know...Its really urgent... > >> > >> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A > >> > >> > >> REMARK 350 BIOMT1 1 1.00 0.00 0.000.0 > >> REMARK 350 BIOMT... > >> > >> REMARK 350 BIOMT3 2 0.00 0.00 -1.00 40.6 > >> > >> > >> Best Regards, > >> Kanika > > > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > -- Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
