Re: [PyMOL] Fast mmCIF loading in latest Open-Source updates
Hi Thomas, I assume components.cif is the same file that I've just downloaded for LigPlot+. Would it be possible that PyMOL automatically finds this file, say by reading $compcif or some such variable? Thanks. Andreas On 16/10/2014 10:08, Thomas Holder wrote: > Dear all, > > this is for those who like to use the latest Open-Source PyMOL code from SVN. > We replaced the slow python mmCIF reader with a very fast and efficient C++ > implementation. Other than being much faster, this implementation provides: > > - new connect_mode=4 does bonding with components.cif dictionary > (components.cif needs to be present in current directory, no automatic > downloading) > > - read missing residues from _pdbx_unobs_or_zero_occ_residues records and > display them grayed out in the sequence viewer > > - "fetch 1a00, type=cif" downloads mmcif instead of pdb > > We welcome any kind of testing and feedback. > > Cheers, >Thomas > -- Andreas Förster X-ray Crystallograhpy Facility Manager Centre for Structural Biology Imperial College London -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ 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] Show all residues forming H-bonds
Hi Jared,
Thanks for your help. I have two issues with this script:
1. It only works once after I've started pymol; the second time, python.exe
crashes.
2. It does create an object with *distances*, not the actual residues.
Your other solution with the single word selectors should work but I'll need to
refine it ;-)
Cheers
Markus
From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Thursday, October 16, 2014 6:36 AM
To: Markus Heller
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Show all residues forming H-bonds
Hi Markus -
First, you need to run the python script from the wiki page (save it as, e.g.
polarpairs.py). Then, to run pure Python code within a pml file, you'll need
to enclose those lines in a python block
(http://www.pymolwiki.org/index.php/Python) using 'python' and 'python end'.
For example, to list all the H bonds between chains A and B:
###
run path/to/polarpairs.py
python
# the example from http://www.pymolwiki.org/index.php/Polarpairs
pairs = polarpairs('chain A', 'chain B')
for p in pairs:
dist = cmd.get_distance('(%s`%s)' % p[0], '(%s`%s)' % p[1])
print p, 'Distance: %.2f' % (dist)
python end
###
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Oct 15, 2014, at 6:17 PM, Markus Heller wrote:
Jared,
I'm a newbie to pythom/PyMOL; how do I get this to work in a pml script? A
pointer to an example script would be enough .
Thanks
Markus
From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Friday, October 10, 2014 4:17 PM
To: Markus Heller
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Show all residues forming H-bonds
Actually, an even better option is Thomas' polarpairs.py script:
http://www.pymolwiki.org/index.php/Polarpairs, which considers the H-bond angle
as well as distance.
Apologies for the multiple emails, but I hope that is closer to what you're
looking for.
Cheers,
Jared
On Oct 10, 2014, at 7:10 PM, Sampson, Jared wrote:
Hi Markus -
Ah, sorry, I misunderstood your request at first.
What about the "acceptors" and "donors" selectors?
http://www.pymolwiki.org/index.php/Single-word_Selectors
e.g.
select hbond_residues, byres ((acceptors within 3.5 of donors) or (donors
within 3.5 of acceptors))
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Oct 10, 2014, at 6:41 PM, Markus Heller wrote:
Hi Jared,
Thanks for the reply.
This is NOT what I'm looking for. As you stated, distance mode 2 yields the
*distances* as dashes, but not the actual residues. I don't want the dashes,
but I want the residues (i.e. the donors and acceptors) in selectable objects.
I hope it's clearer now what I'm after .
Cheers
M
From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Friday, October 10, 2014 3:33 PM
To: Markus Heller
Subject: Re: [PyMOL] Show all residues forming H-bonds
Hi Markus -
Under the GUI "action" menu A > find > polar contacts, you'll find several
options which will create a new object with all the specified distances as
dashes.
This is also available with `distance` command.
http://www.pymolwiki.org/index.php/Distance
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Oct 10, 2014, at 2:45 AM, Markus Heller wrote:
Hello list,
subject says it all. The 2 options I came across search the www are:
http://sourceforge.net/p/pymol/mailman/message/7562444/http://sourceforge.net/p/pymol/mailman/message/7562444/
and DistancesRH
(http://www.pymolwiki.org/index.php/DistancesRH)http://www.pymolwiki.org/index.php/DistancesRH
Is this current state-of-the-art, true-and-tried, or is there something more
powerful hiding out there?
Thanks
Markus
--
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PyMOL
[PyMOL] Fast mmCIF loading in latest Open-Source updates
Dear all, this is for those who like to use the latest Open-Source PyMOL code from SVN. We replaced the slow python mmCIF reader with a very fast and efficient C++ implementation. Other than being much faster, this implementation provides: - new connect_mode=4 does bonding with components.cif dictionary (components.cif needs to be present in current directory, no automatic downloading) - read missing residues from _pdbx_unobs_or_zero_occ_residues records and display them grayed out in the sequence viewer - "fetch 1a00, type=cif" downloads mmcif instead of pdb We welcome any kind of testing and feedback. Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ 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] h_add breaks surface?
sure, you are welcome to update the PyMOLWiki page. Cheers, Thomas On 16 Oct 2014, at 15:57, Markus Heller wrote: > Aha, that makes sense now. > > Would it be worth to clarify this in the pymolwiki > (http://www.pymolwiki.org/index.php/Show)? That's where I got my version > from ... > > Cheers > Markus > > -Original Message- > From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] > Sent: Thursday, October 16, 2014 10:44 AM > To: Markus Heller > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] h_add breaks surface? > > Hi Markus, > >> # hide non-polar hydrogens >> hide (h. and (e. c extend 1)) > > > This will hide all representations -- including surface -- for non-polar > hydrogens. I guess what you rather want is to remove those non-polar > hydrogens, so that they will not be included in the surface calculation. > > # remove non-polar hydrogens > remove (h. and (e. c extend 1)) > > Hope that helps. > > Cheers, > Thomas > > On 16 Oct 2014, at 13:34, Markus Heller wrote: >> Thomas, >> >> If you comment out the h_add line in the pml script below, the surface looks >> good. If it's in there, it's broken for me. >> >> Cheers >> Markus >> >> >> >> # load the PDB file >> fetch 3CIY, async = 0 >> >> # add hydrogens >> h_add >> >> # hide everything but show cartoon >> hide lines >> #as cartoon >> >> # show protein surface >> show surface, all >> >> # deselect all to avoid little pink squares deselect >> >> # hide non-polar hydrogens >> hide (h. and (e. c extend 1)) >> >> # finally, raytrace and save a PNG >> ray >> png broken_surf.png >> >> >> >> -Original Message- >> From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] >> Sent: Wednesday, October 15, 2014 4:18 PM >> To: Markus Heller >> Cc: pymol-users@lists.sourceforge.net >> Subject: Re: [PyMOL] h_add breaks surface? >> >> Hi Markus, >> >> I can't reproduce this. Do you have an example? >> >> Thanks, >> Thomas >> >> On 15 Oct 2014, at 18:32, Markus Heller wrote: >> >>> Hi all, >>> >>> I updated to 1.7.2.3. I noticed that >>> >>> h_add >>> >>> breaks the surface rendering for me, meaning the surface representation >>> shows lots of holes/missing parts (before and after ray). It doesn't >>> matter if h_add is placed before or after the surface is generated. >>> >>> Has anybody else noticed that, or does this occur just for me? >>> >>> Thanks >>> Markus >>> >>> -- >>> Markus Heller, Ph.D. >>> NMR Scientist >>> CDRD - The Centre for Drug Research and Development >>> 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: >>> (604) 827-1147 >>> Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | >>> www.cdrd.ca -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ 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] h_add breaks surface?
Aha, that makes sense now. Would it be worth to clarify this in the pymolwiki (http://www.pymolwiki.org/index.php/Show)? That's where I got my version from ... Cheers Markus -Original Message- From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] Sent: Thursday, October 16, 2014 10:44 AM To: Markus Heller Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] h_add breaks surface? Hi Markus, > # hide non-polar hydrogens > hide (h. and (e. c extend 1)) This will hide all representations -- including surface -- for non-polar hydrogens. I guess what you rather want is to remove those non-polar hydrogens, so that they will not be included in the surface calculation. # remove non-polar hydrogens remove (h. and (e. c extend 1)) Hope that helps. Cheers, Thomas On 16 Oct 2014, at 13:34, Markus Heller wrote: > Thomas, > > If you comment out the h_add line in the pml script below, the surface looks > good. If it's in there, it's broken for me. > > Cheers > Markus > > > > # load the PDB file > fetch 3CIY, async = 0 > > # add hydrogens > h_add > > # hide everything but show cartoon > hide lines > #as cartoon > > # show protein surface > show surface, all > > # deselect all to avoid little pink squares deselect > > # hide non-polar hydrogens > hide (h. and (e. c extend 1)) > > # finally, raytrace and save a PNG > ray > png broken_surf.png > > > > -Original Message- > From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] > Sent: Wednesday, October 15, 2014 4:18 PM > To: Markus Heller > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] h_add breaks surface? > > Hi Markus, > > I can't reproduce this. Do you have an example? > > Thanks, > Thomas > > On 15 Oct 2014, at 18:32, Markus Heller wrote: > >> Hi all, >> >> I updated to 1.7.2.3. I noticed that >> >> h_add >> >> breaks the surface rendering for me, meaning the surface representation >> shows lots of holes/missing parts (before and after ray). It doesn't matter >> if h_add is placed before or after the surface is generated. >> >> Has anybody else noticed that, or does this occur just for me? >> >> Thanks >> Markus >> >> -- >> Markus Heller, Ph.D. >> NMR Scientist >> CDRD - The Centre for Drug Research and Development >> 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: >> (604) 827-1147 >> Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | >> www.cdrd.ca -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ 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] h_add breaks surface?
Hi Markus, > # hide non-polar hydrogens > hide (h. and (e. c extend 1)) This will hide all representations -- including surface -- for non-polar hydrogens. I guess what you rather want is to remove those non-polar hydrogens, so that they will not be included in the surface calculation. # remove non-polar hydrogens remove (h. and (e. c extend 1)) Hope that helps. Cheers, Thomas On 16 Oct 2014, at 13:34, Markus Heller wrote: > Thomas, > > If you comment out the h_add line in the pml script below, the surface looks > good. If it's in there, it's broken for me. > > Cheers > Markus > > > > # load the PDB file > fetch 3CIY, async = 0 > > # add hydrogens > h_add > > # hide everything but show cartoon > hide lines > #as cartoon > > # show protein surface > show surface, all > > # deselect all to avoid little pink squares > deselect > > # hide non-polar hydrogens > hide (h. and (e. c extend 1)) > > # finally, raytrace and save a PNG > ray > png broken_surf.png > > > > -Original Message- > From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] > Sent: Wednesday, October 15, 2014 4:18 PM > To: Markus Heller > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] h_add breaks surface? > > Hi Markus, > > I can't reproduce this. Do you have an example? > > Thanks, > Thomas > > On 15 Oct 2014, at 18:32, Markus Heller wrote: > >> Hi all, >> >> I updated to 1.7.2.3. I noticed that >> >> h_add >> >> breaks the surface rendering for me, meaning the surface representation >> shows lots of holes/missing parts (before and after ray). It doesn't matter >> if h_add is placed before or after the surface is generated. >> >> Has anybody else noticed that, or does this occur just for me? >> >> Thanks >> Markus >> >> -- >> Markus Heller, Ph.D. >> NMR Scientist >> CDRD - The Centre for Drug Research and Development >> 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) >> 827-1147 >> Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | www.cdrd.ca -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ 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] h_add breaks surface?
Thomas, If you comment out the h_add line in the pml script below, the surface looks good. If it's in there, it's broken for me. Cheers Markus # load the PDB file fetch 3CIY, async = 0 # add hydrogens h_add # hide everything but show cartoon hide lines #as cartoon # show protein surface show surface, all # deselect all to avoid little pink squares deselect # hide non-polar hydrogens hide (h. and (e. c extend 1)) # finally, raytrace and save a PNG ray png broken_surf.png -Original Message- From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] Sent: Wednesday, October 15, 2014 4:18 PM To: Markus Heller Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] h_add breaks surface? Hi Markus, I can't reproduce this. Do you have an example? Thanks, Thomas On 15 Oct 2014, at 18:32, Markus Heller wrote: > Hi all, > > I updated to 1.7.2.3. I noticed that > > h_add > > breaks the surface rendering for me, meaning the surface representation shows > lots of holes/missing parts (before and after ray). It doesn't matter if > h_add is placed before or after the surface is generated. > > Has anybody else noticed that, or does this occur just for me? > > Thanks > Markus > > -- > Markus Heller, Ph.D. > NMR Scientist > CDRD - The Centre for Drug Research and Development > 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) > 827-1147 > Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | www.cdrd.ca -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ 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] Show all residues forming H-bonds
Hi Markus -
First, you need to run the python script from the wiki page (save it as, e.g.
polarpairs.py). Then, to run pure Python code within a pml file, you’ll need
to enclose those lines in a python block
(http://www.pymolwiki.org/index.php/Python) using ‘python’ and ‘python end’.
For example, to list all the H bonds between chains A and B:
###
run path/to/polarpairs.py
python
# the example from http://www.pymolwiki.org/index.php/Polarpairs
pairs = polarpairs('chain A', 'chain B')
for p in pairs:
dist = cmd.get_distance('(%s`%s)' % p[0], '(%s`%s)' % p[1])
print p, 'Distance: %.2f' % (dist)
python end
###
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Oct 15, 2014, at 6:17 PM, Markus Heller
mailto:mhel...@cdrd.ca>> wrote:
Jared,
I'm a newbie to pythom/PyMOL; how do I get this to work in a pml script? A
pointer to an example script would be enough .
Thanks
Markus
From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Friday, October 10, 2014 4:17 PM
To: Markus Heller
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Show all residues forming H-bonds
Actually, an even better option is Thomas' polarpairs.py script:
http://www.pymolwiki.org/index.php/Polarpairs, which considers the H-bond angle
as well as distance.
Apologies for the multiple emails, but I hope that is closer to what you're
looking for.
Cheers,
Jared
On Oct 10, 2014, at 7:10 PM, Sampson, Jared
mailto:jared.samp...@nyumc.org>> wrote:
Hi Markus -
Ah, sorry, I misunderstood your request at first.
What about the "acceptors" and "donors" selectors?
http://www.pymolwiki.org/index.php/Single-word_Selectors
e.g.
select hbond_residues, byres ((acceptors within 3.5 of donors) or (donors
within 3.5 of acceptors))
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Oct 10, 2014, at 6:41 PM, Markus Heller wrote:
Hi Jared,
Thanks for the reply.
This is NOT what I'm looking for. As you stated, distance mode 2 yields the
*distances* as dashes, but not the actual residues. I don't want the dashes,
but I want the residues (i.e. the donors and acceptors) in selectable objects.
I hope it's clearer now what I'm after .
Cheers
M
From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Friday, October 10, 2014 3:33 PM
To: Markus Heller
Subject: Re: [PyMOL] Show all residues forming H-bonds
Hi Markus -
Under the GUI "action" menu A > find > polar contacts, you'll find several
options which will create a new object with all the specified distances as
dashes.
This is also available with `distance` command.
http://www.pymolwiki.org/index.php/Distance
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Oct 10, 2014, at 2:45 AM, Markus Heller wrote:
Hello list,
subject says it all. The 2 options I came across search the www are:
http://sourceforge.net/p/pymol/mailman/message/7562444/http://sourceforge.net/p/pymol/mailman/message/7562444/
and DistancesRH
(http://www.pymolwiki.org/index.php/DistancesRH)http://www.pymolwiki.org/index.php/DistancesRH
Is this current state-of-the-art, true-and-tried, or is there something more
powerful hiding out there?
Thanks
Markus
--
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