Re: [PyMOL] New MD/Structure analysis script
Thumbs up for the SQM geometry optimization with xtb! :) On Fri, 9 Apr 2021 at 20:11, R Mera wrote: > Dear PyMOlers, > > I wrote a set of scripts that add what I think is useful structure and MD > analysis capabilities to PyMOL, including Ramachandran plots (structure and > trajectories, points identified with colors), RMSF, RMSD, shape indicators, > and others. > > The whole thing is open-source and very easy to install on Linux. I think > the automated installer will work on Mac also, but I don't own an Apple > machine to test, so it might need some modification. It is available here: > > https://rmera.github.io/goanalyze/ > > I hope it's useful, and I'd be happy to have your feedback, feature > requests, etc. I'll do my best to work on them, within my time constraints > (I am the only dev for the project). > > Cheers! > > Raul > > -- > > Prof. Dr. Raúl Mera Adasme > > Facultad de Química y Biología , > Universidad de Santiago de Chile (USACH). > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- == Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic email: teva...@gmail.com, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/ ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] [EXTERNAL] How to compute the interface surface between ligand and protein?
So, Thomas, you don't see anything wrong in the way I compute the surfaces? The numbers should be like that, right? The reason I need both the molecular surface and the SASA in not directly related to a physical quantity. I do SQM scoring of compounds bound to proteins, but the bulkier molecules, which are usually non-binders, tend to yield lower interaction free energies. Thus, I thought to try these two surface types of both the protein and the ligand as descriptors in a machine learning-based attempt to balance these differences and improve the scoring. It remains to be seen in practice which of these two types (molecular surface or SASA) are more useful for my purpose. I also use other molecular descriptors, but I don't want to elaborate on this because it's out of topic. Best, Thomas On Thu, 21 May 2020 at 21:57, Thomas Holder wrote: > Hi Thomas and Blaine, > > SASA is probably the correct feature to evaluate here, not molecular > surface. Of course it may depend the actual goal of this exercise, but > typically when talking about interface surface, you're putting that into > context with binding energy or solvation effects, and only SASA is > meaningful for that as far as I know. > > The difference between SASA and molecular surface is a matter of size and > shape. For a very uneven shape (lots of small pockets or protuberances), > going from molecular surface to SASA will flatten the surface, which can > result in a smaller area, even though the volume is increased. > > You may be interested to check out PISA for this task, it's the tool the > PDB uses to determine biological assemblies: > https://www.ebi.ac.uk/pdbe/pisa/ > > PyMOL's and PISA's results should be similar, but PyMOL is probably easier > to handle :-) > > Cheers, > Thomas > > > > On May 21, 2020, at 4:37 AM, Mooers, Blaine H.M. (HSC) < > blaine-moo...@ouhsc.edu> wrote: > > > > Hi Thomas, > > > > If you display the SASA of the protein in PyMOL's viewport, > > you will see that it and that of the ligand have huge overlaps > > How do you define the interface in such a situation and how > > do you interpret it? > > > > The interface of the molecular surfaces seems easier to interpret. > > > > Best regards, > > > > Blaine > > > > Blaine Mooers, Ph.D. > > Associate Professor > > Department of Biochemistry and Molecular Biology > > College of Medicine > > University of Oklahoma Health Sciences Center > > S.L. Young Biomedical Research Center (BRC) Rm. 466 > > 975 NE 10th Street, BRC 466 > > Oklahoma City, OK 73104-5419 > > > > > > From: Thomas Evangelidis [teva...@gmail.com] > > Sent: Wednesday, May 20, 2020 9:14 AM > > To: pymol mailinglist > > Subject: [EXTERNAL] [PyMOL] How to compute the interface surface between > ligand and protein? > > > > Greetings, > > > > I want to compute the interface surface between the ligand and the > protein in batch mode for hundreds of thousands of PDBs, like the attached > one (sample.pdb). I am interested in the interface surface of both of them. > First I create two new molecules, the protein, and the ligand, and I work > with them because the results I get when working with the original molecule > (which contains both protein and ligand) are different. > > > > load sample.pdb > > create protein, polymer > > create ligand, resn LIG > > delete sample > > > > select prot_interface, protein within 3.5 of ligand; > > set dot_solvent, 0; > > get_area prot_interface; > > set dot_solvent, 1; > > get_area prot_interface; > > > > select lig_interface, ligand within 3.5 of protein; > > set dot_solvent, 0; > > get_area lig_interface; > > set dot_solvent, 1; > > get_area lig_interface; > > > > protein interface molecular surface = 1216.239 Angstroms^2 > > protein interface SASA = 763.095 Angstroms^2 > > ligand interface molecular surface = 748.867 Angstroms^2 > > ligand interface SASA = 977.608 Angstroms^2 > > > > I still don't understand why the interface molecular surface of the > ligand is smaller than the interface SASA, while the opposite happens with > the protein. Could someone please explain this to me and verify that I am > computing the interface surfaces correctly? > > > > I thank you in advance. > > Thomas > > > > > > > > -- > > > > == > > > > Dr. Thomas Evangelidis > > > > Research Scientist > > -- > Thomas Holder
Re: [PyMOL] Script for drawing docked ligand-active site pics
Hi, I wrote a new PyMOL command a year ago to draw protein-ligand interactions and create publication-quality images. Not exactly what you are looking for but may be of help. It is already in the PyMOL script repository, so if you have it you can load the command directly. For more details look at: https://github.com/tevang/tutorials/tree/master/show_ligand_interactions -- == Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic email: teva...@gmail.com, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/ ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] cannot write text commands after pymol-open-source installation
I am encountering a strange problem. After building the latest pymol-open-source from github on Ubuntu 19.04 and Python 3.7.3 I am not able to write text commands. It seems that PyMOL does not receive input from the keyboard because neither the arrow buttons ->, <- work for moving to the next and previous molecules in a multi-mol file. Does anyone encounter a similar problem? Any idea how to fix this? Thanks in advance. Thomas -- == Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic email: teva...@gmail.com, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/ ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to catch PyMOL command exception within a Python script
Hi Thomas,
With regard to selections, sometimes a residue has missing atoms or is
non-standard amino acid. In the first case it is matched with another
residue in a second structure during the alignment and then when I try to
fit the two selections of atoms from the two structures I get the following
error:
Calculating RMSD between pocket of model 2hduA and 2r9wA.
> ExecutiveRMS-Error: Atom counts between selections don't match (799 vs 797)
> Executive: Error -- no atoms left after refinement!
> RMSD = -1.00
Can you think of a clever way to exclude amino acids with missing atoms or
non-standard ones from pair_fit() or rms_cur()?
Best,
Thomas
On Fri, 22 Feb 2019 at 12:32, Thomas Holder
wrote:
> Hi Thomas,
>
> In general, the PyMOL API should raise pymol.CmdException if things go
> wrong. But in case of cmd.pair_fit() this wasn't happening (see my fix that
> I pushed few minutes ago:
> https://github.com/schrodinger/pymol-open-source/commit/b26d91c40d20344fef511ea9d6bb664a93f1bb4a
> )
>
> cmd.select() correctly raises an exception, so if you want to make a
> script more robust against selection failures, you could always create a
> named selection first to check if it's valid.
>
> tmpsele1 = cmd.get_unused_name('_sele1')
> try:
> cmd.select(tmpsele1, someexpression, 0)
> except pymol.CmdException:
> print('invalid selection')
> finally:
> cmd.delete(tmpsele1)
>
>
> Cheers,
> Thomas
>
> > On Feb 22, 2019, at 12:11 PM, Thomas Evangelidis
> wrote:
> >
> > Hi Thomas,
> >
> > This is great! I can even include more atom types in the selection.
> > Just for the record, is it possible to catch PyMOL exceptions like
> "Selector-Error" from within a Python script? Is there any general strategy
> to select which exception type to look for? In the past, I was catching
> exceptions from 'tmalign' with "except AssertionError:" which doesn't work
> for "Selector-Error".
> >
> > Best,
> > Thomas
> >
> >
> > --
> > ==
> > Dr Thomas Evangelidis
> > Research Scientist
> > IOCB - Institute of Organic Chemistry and Biochemistry of the Czech
> Academy of Sciences
> > Prague, Czech Republic
> > &
> > CEITEC - Central European Institute of Technology
> > Brno, Czech Republic
> >
> > email: teva...@gmail.com
> > website: https://sites.google.com/site/thomasevangelidishomepage/
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
--
==
Dr Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>
Prague, Czech Republic
&
CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>
Brno, Czech Republic
email: teva...@gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [PyMOL] How to catch PyMOL command exception within a Python script
Hi Thomas,
This is great! I can even include more atom types in the selection.
Just for the record, is it possible to catch PyMOL exceptions like
"Selector-Error" from within a Python script? Is there any general strategy
to select which exception type to look for? In the past, I was catching
exceptions from 'tmalign' with "except AssertionError:" which doesn't work
for "Selector-Error".
Best,
Thomas
On Fri, 22 Feb 2019 at 11:28, Thomas Holder
wrote:
> Hi Thomas,
>
> Getting rid of the string length limitations would need some major
> refactoring. There is currently no good workaround, other than avoiding
> such long selections.
>
> In this particular case, the script could use cmd.select_list() instead of
> concatenating the index list to a string:
>
> cmd.select_list('sel1', obj1, [int(i) for i in id1], mode='index')
> cmd.select_list('sel2', obj2, [int(i) for i in id2], mode='index')
> cmd.pair_fit("sel1 and aln", "sel2 and aln")
> cmd.delete('sel1')
> cmd.delete('sel2')
>
> Hope that helps.
>
> Cheers,
> Thomas
>
>
> > On Feb 22, 2019, at 9:32 AM, Thomas Evangelidis
> wrote:
> >
> > Greetings,
> >
> > I am trying to run focus_alignment command (
> https://pymolwiki.org/index.php/Focus_alignment) from within a Python
> script with my own custom selection (I include CA+CB atoms instead of only
> CA as in the default). Sometimes the selection is very large and PyMOL
> cannot hand it:
> >
> > Selector-Error: Word too long. Truncated:
> > Selector-Error:
> 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+115Selector-Error:
> Invalid selection name "730".
> > poly and 4kz6A and aln and index
> 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+1158+1175+1178+1183+1421+1424+1428+1431+1647+1650+1655+1658+
> 730<--
> > Selector-Error: Word too long. Truncated:
> > Selector-Error:
> 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+121Selector-Error:
> Invalid selection name "868".
> > poly and 2r9wA and aln and index
> 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+1212+1229+1232+1237+1491+1494+1498+1501+1747+1750+1755+1758+
> 868<--
> > ExecutiveRMS-Error: No atoms selected.
> > Selector-Error: Word too long. Truncated:
> > Selector-Error:
> 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+115Selector-Error:
> Word too long. Truncated:
> > Selector-Error:
> 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+121Selector-Error:
> Invalid selection name "730".
> > ( ( poly and 4kz6A and aln and index
> 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+1158+1175+1178+1183+1421+1424+1428+1431+1647+1650+1655+1658+
> 730 ) in ( poly and 2r9wA and aln and index
> 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+1212+1229+1232+1237+1491+1494+1498+1501+1747+1750+1755+1758+
> 868 ) )<--
> >
> > Is there a way to ask PyMOL to accept longer selection strings?
> > Alternatively, is it possible to catch this exception from within the
> script using "try: ... except :" statement?
> >
> > Thanks in advance.
> > Thomas
> >
> > --
> > ==
> > Dr Thomas Evangelidis
> > Research Scientist
> > IOCB - Institute of Organic Chemistry and Biochemistry of the Czech
> Academy of Sciences
> > Prague, Czech Republic
> > &
> > CEITEC - Central European Institute of Technology
> > Brno, Czech Republic
> >
>
[PyMOL] How to catch PyMOL command exception within a Python script
Greetings, I am trying to run focus_alignment command ( https://pymolwiki.org/index.php/Focus_alignment) from within a Python script with my own custom selection (I include CA+CB atoms instead of only CA as in the default). Sometimes the selection is very large and PyMOL cannot hand it: Selector-Error: Word too long. Truncated: > Selector-Error: > 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+115Selector-Error: > Invalid selection name "730". > poly and 4kz6A and aln and index > 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+1158+1175+1178+1183+1421+1424+1428+1431+1647+1650+1655+1658+ > 730<-- > Selector-Error: Word too long. Truncated: > Selector-Error: > 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+121Selector-Error: > Invalid selection name "868". > poly and 2r9wA and aln and index > 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+1212+1229+1232+1237+1491+1494+1498+1501+1747+1750+1755+1758+ > 868<-- > ExecutiveRMS-Error: No atoms selected. > Selector-Error: Word too long. Truncated: > Selector-Error: > 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+115Selector-Error: > Word too long. Truncated: > Selector-Error: > 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+121Selector-Error: > Invalid selection name "730". > ( ( poly and 4kz6A and aln and index > 183+186+191+194+196+199+203+206+208+211+437+440+445+448+456+459+465+468+473+477+480+483+486+490+493+496+499+505+508+512+515+523+526+530+534+537+541+544+827+830+832+835+1138+1141+1150+1153+1155+1158+1175+1178+1183+1421+1424+1428+1431+1647+1650+1655+1658+ > 730 ) in ( poly and 2r9wA and aln and index > 216+219+224+227+229+232+236+239+241+244+479+482+487+490+498+501+507+510+515+519+522+525+528+532+535+538+541+547+550+554+557+565+568+572+576+579+583+586+873+876+878+881+1192+1195+1204+1207+1209+1212+1229+1232+1237+1491+1494+1498+1501+1747+1750+1755+1758+ > 868 ) )<-- Is there a way to ask PyMOL to accept longer selection strings? Alternatively, is it possible to catch this exception from within the script using "try: ... except :" statement? Thanks in advance. Thomas -- == Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/> Brno, Czech Republic email: teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Making nmr-like ensemble from several pdbs
On 27 August 2014 16:10, James Starlight wrote:
> *Q: My structure has multiple chains. Which one will be used for the
> calculation? *
> A: Generally, all of them. Be careful, though. While most chains are
> "legitimate" chains corresponding to subunits of the whole multi-mer (as in
> e.g. hemoglobin), some PDB files use chain identifier "A", "B", etc. to
> denote different models of the same monomer (as in e.g. 2TRX). Make sure
> you supply only the one you want. For NMR structures, *you get a window
> where you can choose which model to use*.
>
>
But still it says you can use only one at a time.
> i guess it indicate that in principle some ensembles are possible as the
> input :) Alternatively do you know any other tools (software) for the
> processing of the ensembles with such options for the analysis?
>
>
No.
> James
>
>
> 2014-08-27 15:05 GMT+02:00 Thomas Evangelidis :
>
>
>>
>>
>> On 27 August 2014 15:43, James Starlight wrote:
>>
>>> and than how to quick merged aligned conformers back to the NMR ensemble
>>> including TER record between each model in it?
>>>
>>>
>>> Actually I'm looking for the possibility to load this ensemble to the
>>> http://biophysics.cs.vt.edu/uploadpdb.php to assign protonation states
>>> for the titrable residues in case of each model and obtained back ensemble
>>> with the processed conformers.
>>>
>>> I think H++ server processes one structure per job. Where did you find
>> that you can upload an ensemble?
>>
>>
>>>
>>> At this time using such nmr ensemble I've faced with the below error
>>>
>>> FAILURE: Sequence discontinuity occurred between residues 289 and 1 at
>>> the line ATOM 1 N ASP 1 62.482 8.961 22.846 1.00103.76 N
>>>
>>> I don't why this error occurs (I have not this in case of ONE model from
>>> the ensemble)
>>>
>>> James
>>>
>>>
>>> 2014-08-27 13:10 GMT+02:00 Thomas Evangelidis :
>>>
>>> split_states
>>>> alignto <1st NMR model name>, method=cealign
>>>>
>>>>
>>>> On 27 August 2014 13:28, James Starlight
>>>> wrote:
>>>>
>>>>> also please tell me how is it possible to include ter record at the
>>>>> end of each model.
>>>>>
>>>>> James
>>>>>
>>>>>
>>>>> 2014-08-27 11:58 GMT+02:00 James Starlight :
>>>>>
>>>>> Dear Pymol users!
>>>>>>
>>>>>> Using below script I can load all pdbs from the work dir into 1
>>>>>> nmr-like object. Could you suggest me how this script could be modified
>>>>>> to
>>>>>> make alignment (or it's better structural alignment) of all pdbs against
>>>>>> first loaded pdb file
>>>>>>
>>>>>> from pymol import cmd
>>>>>> import sys,glob
>>>>>>
>>>>>> def get_file_list(files):
>>>>>> file_list = glob.glob(files)
>>>>>> return file_list
>>>>>>
>>>>>> def load_models(files,obj,discrete=0):
>>>>>> """
>>>>>> load_models , ,
>>>>>>
>>>>>> loads multiple files (using filename globbing)
>>>>>> into a single object (e.g. from modelling or NMR).
>>>>>>
>>>>>> use discrete=1 if you want to color individual states separately
>>>>>>
>>>>>> e.g. load_models prot_*.pdb, prot
>>>>>> """
>>>>>> if type(files) == type('string'):
>>>>>> file_list = get_file_list(files)
>>>>>> else:
>>>>>> file_list = files
>>>>>>
>>>>>> if file_list:
>>>>>> file_list.sort()
>>>>>> for name in file_list:
>>>>>> cmd.load(name,obj,discrete=discrete)
>>>>>> else:
>>>>>> print "No files found for pattern %s" % files
>>>>>>
>>>>>> cmd.extend('load_models',load_models)
>>>>>>
>>>>>>
>>>>>> Many thanks for help,
>>>>>>
>>>>>> James
>>>>>>
>>>>>
>>>>>
>>&
Re: [PyMOL] Making nmr-like ensemble from several pdbs
split_states
alignto <1st NMR model name>, method=cealign
On 27 August 2014 13:28, James Starlight wrote:
> also please tell me how is it possible to include ter record at the end of
> each model.
>
> James
>
>
> 2014-08-27 11:58 GMT+02:00 James Starlight :
>
> Dear Pymol users!
>>
>> Using below script I can load all pdbs from the work dir into 1 nmr-like
>> object. Could you suggest me how this script could be modified to make
>> alignment (or it's better structural alignment) of all pdbs against first
>> loaded pdb file
>>
>> from pymol import cmd
>> import sys,glob
>>
>> def get_file_list(files):
>> file_list = glob.glob(files)
>> return file_list
>>
>> def load_models(files,obj,discrete=0):
>> """
>> load_models , ,
>>
>> loads multiple files (using filename globbing)
>> into a single object (e.g. from modelling or NMR).
>>
>> use discrete=1 if you want to color individual states separately
>>
>> e.g. load_models prot_*.pdb, prot
>> """
>> if type(files) == type('string'):
>> file_list = get_file_list(files)
>> else:
>> file_list = files
>>
>> if file_list:
>> file_list.sort()
>> for name in file_list:
>> cmd.load(name,obj,discrete=discrete)
>> else:
>> print "No files found for pattern %s" % files
>>
>> cmd.extend('load_models',load_models)
>>
>>
>> Many thanks for help,
>>
>> James
>>
>
>
>
> --
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--
==
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tev...@pharm.uoa.gr
teva...@gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
===
*Physics is the only real science. The rest are just stamp collecting.*
*- Ernest Rutherford*
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[PyMOL] command to deactivate/hide an object
Hi, Is there some command that deactivates an object, namely something equivalent to clicking on an object name at the object panel? I am loading multiple files and render them as sticks but the memory overflows. If there was a command to keep the stick representation but deactivate the object (hide it) then I could visualize the structures one by one once they are all loaded -which is actually what I want. thanks, Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk___ 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
[PyMOL] forward and backward keyboard shortcuts
Hi, Is there any keyboard shortcut to move to the next or the previous state of an object, namely something equivalent to "forward" and "backward" commands? -- ====== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk___ 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
[PyMOL] how to visualize the results form flexible sidechain ligand docking
Dear PyMOL users, I would like to write into a single file the top scored ligand poses obtained from flexible receptor sidechain docking with Vina. Then I would like to open this file in PyMOL and visulaize these poses one-by-one. One solution would be to write every receptor conformation and the respective ligand pose as a MODEL unit in a multi-model .pdb file. However, that solution is not effective in terms of memory and disk space. Therefore I would like somehow to avoid writing the coordinates of the rigid part of the receptor in each MODEL unit of the .pdb file. If I load two .pdb files, one containing the rigid part of the receptor and the other all the sidechain conformations and the respective ligand poses, then the flexible amino acids will not be connected to the rigid protein. Does anyone have any idea how to circumvent that problem (no necessarily by using the .pdb format)? thanks, ~Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with <2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk___ 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
[PyMOL] arranging atom records in pdb file by resid
Dear PyMOL users/developers, Is there any way to rearrange the atom records in a .pdb file according to their residue ID? I have run Vina with flexible sidechains and then concatenated the rigid receptor part with the sidechain conformations for each pose. That resulted to .pdb files where the backbone atoms (apart from Ca) occur in the correct order but the flexible sidechain atoms are at the end of the file. That leads to some problems in visualization and analysis of the protein-ligand complexes that I'd like to overcome. If anyone know how to fix that problem either with PyMOL or any other program please let me know. thanks, Thomas -- ====== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with <2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1___ 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] SS in a trajectory
If none suggests a solution in PyMOL ten use sscache.tcl script in VMD to update the SS at every frame. Thomas On 24 April 2013 17:31, Jianghai Zhu wrote: > Hi, > > I have a trajectory file, in which two short helices would merge into one > long helix. However, when I play the trajectory in Pymol as cartoon, the > long helix would still be shown as two helices with a loop in between. Is > there a way to force Pymol to show a long helix for a specific range of > frames in a trajectory? Thanks a lot. > > --Jianghai > > > > -- > Try New Relic Now & We'll Send You this Cool Shirt > New Relic is the only SaaS-based application performance monitoring service > that delivers powerful full stack analytics. Optimize and monitor your > browser, app, & servers with just a few lines of code. Try New Relic > and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr > ___ > 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 > -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ 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
[PyMOL] Fwd: Visualization of the protein-ligand interactions
> As I understood fconv can be used for the split several mol2 (or pdb) > files which was placed in 1 model to the several pdb files, doesnt it ? > > fconv can do miracles :) check it out ! fconv -h > In past I forced with some problems with g_hbond. Is there any other way > to monitor h bonds along the trajectory (e.g in vmd) ? > > In contrast, I encountered problems with the H-bonds VMD plugin, that's why I resorted to g_hbond. Beware that g_hbonds will count the frequencies of salt-bridges too. > PoseView is used as the separate software or web server > http://poseview.zbh.uni-hamburg.de/poseview ( I mean that I analyze polar > interactions both in pymol as well as via pose view). > > If you find a way to draw the most important protein-ligand interactions throughout the trajectory with PoseView, then I would be very interested to know how. > > James > > 2013/4/24 Thomas Evangelidis > >> >> I want to examine protein-ligand interactions observed in the md >>> trajectory using Pymol. >>> >>> For such task I have 100 snapshots of the protein-ligand complex which >>> I've loaded into the pymol. Now I want to extract from all snapshots 100 >>> ligands as the separate 100 objects and save it in the mol2. Actually I can >>> do such task in the simplest way extracting all ligands in one object but I >>> need as a result 100 mol2 files. Could someone show me example of some >>> script which could do such tasks? >>> >>> >> Save all ligands in a multi-mol mol2 file and then split if with fconv -s. >> >> http://pc1664.pharmazie.uni-marburg.de/download/fconv >> >> >> >>> Also I'll be very thankful if someone can provide me with some tool >>> which can be used for investigation of the ligand dynamics along MD >>> trajectory ( in particular I want to visualize all binding poses and define >>> all polar contacts along trajectory). For such task I've being used pymol >>> as well as pose view loading snapshots to that programs but that way is not >>> appropriate for analyzing of the ensembles of the binding poses obtained >>> from md run. >>> >>> >> I usually monitor H-bonds with g_hbond from GROMACS Tools and >> Salt-Bridges with the respective VMD plugin. Then I make a table with >> frequences of each polar interaction, pick up a frame that contains as many >> important interactions as possible, load it in PyMOL and draw dotted lines >> between the interacting atoms. >> >> PS: I didn't know about PoseView plugin, it seems to be a very useful >> addition to PyMOL :) >> >> Thomas >> >> -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ 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] Visualization of the protein-ligand interactions
> I want to examine protein-ligand interactions observed in the md > trajectory using Pymol. > > For such task I have 100 snapshots of the protein-ligand complex which > I've loaded into the pymol. Now I want to extract from all snapshots 100 > ligands as the separate 100 objects and save it in the mol2. Actually I can > do such task in the simplest way extracting all ligands in one object but I > need as a result 100 mol2 files. Could someone show me example of some > script which could do such tasks? > > Save all ligands in a multi-mol mol2 file and then split if with fconv -s. http://pc1664.pharmazie.uni-marburg.de/download/fconv > Also I'll be very thankful if someone can provide me with some tool which > can be used for investigation of the ligand dynamics along MD trajectory ( > in particular I want to visualize all binding poses and define all polar > contacts along trajectory). For such task I've being used pymol as well as > pose view loading snapshots to that programs but that way is not > appropriate for analyzing of the ensembles of the binding poses obtained > from md run. > > I usually monitor H-bonds with g_hbond from GROMACS Tools and Salt-Bridges with the respective VMD plugin. Then I make a table with frequences of each polar interaction, pick up a frame that contains as many important interactions as possible, load it in PyMOL and draw dotted lines between the interacting atoms. PS: I didn't know about PoseView plugin, it seems to be a very useful addition to PyMOL :) Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ 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] Editing of the pdb structure
I think you got your answers from the AMBER and GROMACS mailing list :) Just a comment about PRODRG server, it is not the best choice for geometry optimization and charge calculation. Lemkul, J.A., Allen, W.J., and Bevan, D.R. (2010) Practical Considerations for Building GROMOS-Compatible Small Molecule Topologies. *J. Chem. Inf. Model.* *50* (12): 2221-2235. To our experience in the group it tends to define the "charge groups" inaccurately and produce optimized geometries that have out of plane hydrogens. There is a new online service for creating GROMOS compatible topologies for organic compounds: http://compbio.biosci.uq.edu.au/atb/ It uses a knowledge-based approach and higher level QM calculations for geometry optimization and charge derivation. Yet the GROMOS ffs are united atom thus you lose in resolution. If I had to chose an all-atom ff I would go for the AMBER99SB-ILDN for the protein and GAFF for the organic compound (your chromophore). Unless you have problems with the size of the organic molecule, you could optimize its geometry and calculate RESP charges using the R.E.D. server: http://q4md-forcefieldtools.org/REDS/ Also check out the option "Use RED IV for automatically generating amino acid fragments " since your chromophore is covalently bonded to the protein (I never used it so I am not sure if this will do your job). Thomas On 30 January 2012 14:16, James Starlight wrote: > Thomas, > > It's a big protein with the some non-standart functional group like GFP > > So the servers like PRORG are not good for that because of big size of the > protein and subsiquent integration of both fragments. > > James > > > 2012/1/30 Thomas Evangelidis > >> Is it a small organic molecule or a modified amino acid within the >> context of a protein? >> >> >> >> 2012/1/29 Tim Schulte >> >>> Dear James, >>> I agree with Joao, for fast and dirty minimisation you might try the >>> program Chimera or VegaZZ. If you just wanna have an energy-minimized small >>> molecule the Prodrg server is the way to go. >>> Cheers, >>> Tim >>> -- >>> *Von:* João Rodrigues [anar...@gmail.com] >>> *Gesendet:* Freitag, 27. Januar 2012 09:56 >>> *Bis:* James Starlight >>> *Cc:* pymol-users@lists.sourceforge.net >>> *Betreff:* Re: [PyMOL] Editing of the pdb structure >>> >>> Dear James, >>> >>> As someone has told you already, Pymol is a visualization tool, not a >>> modelling suite. I guess you would be better off using something like >>> AMBERTOOLS or MODELLER, depending on what you want to model, or any other >>> "real" simulation/modelling package otherwise your results are very weak... >>> >>> My opinion only. >>> >>> João [...] Rodrigues >>> http://nmr.chem.uu.nl/~joao >>> >>> >>> >>> No dia 27 de Janeiro de 2012 09:50, James Starlight < >>> jmsstarli...@gmail.com> escreveu: >>> >>>> Arne, Thomas >>>> >>>> Thanks alot. Bond works finw >>>> >>>> >>>> I'd like just to ask what about geometry optimisation of the new >>>> structure >>>> >>>> E.g I want create 5memb imidazole ring where the 2 adj atoms are apart >>>> from 1.5 A from each other. >>>> >>>> When I've create new bond by bond command new ring look like 6memb ( >>>> like benzol) because of long distance between adj atoms. >>>> >>>> How I could optimise geometry of the new mollecule? Have pymol some >>>> built-in functions like conformational search be means of monte carlo or >>>> energy minimisation ? >>>> >>>> >>>> James >>>> >>>> >>>> 2012/1/27 Thomas Holder >>>> >>>>> On 01/27/2012 09:11 AM, James Starlight wrote: >>>>> >>>>>> Dear PyMol users! >>>>>> >>>>>> I need to create NEW covalent bond between two adjacent atoms. How >>>>>> this >>>>>> could be done in PyMOl? >>>>>> >>>>> >>>>> you could have guessed it: >>>>> http://pymolwiki.org/index.**php/Bond<http://pymolwiki.org/index.php/Bond> >>>>> :-) >>>>> >>>>> The atoms must both be within the same object. >>>>> >>>>> >>>>> Cheers, >>>>> Thomas >>>>> >>>>> -- >
Re: [PyMOL] list of polar contacts
I think you can reproduce the results from "apply->find->polar contacts" option with the PyMOL built-in "distance" command. E.g. distance hbonds, all, all, 3.2, mode=2 The problem is that you cannot set the A-H-D angle which is important for the definition of the H-bond. On 30 January 2012 18:45, Abhinav Verma wrote: > Thanks Thomas, > > I have been here and my problem is that I could not reproduce the results > of default pymol behaviour. I just need to either reproduce 100% the pymol > default behaviour or to just get a list of what is painted in the window. > It should be possible I guess. > > Do you have more ideas? > > > > > On Mon, Jan 30, 2012 at 5:38 PM, Thomas Evangelidis wrote: > >> Probably because they set diffently the acceptor-donor cutoff and the >> acceptor-hydrogen-donor angle. Use list_hbonds.py from: >> >> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ >> >> and set the cutoff and angle to the values you wish. >> >> Thomas >> >> >> >> On 30 January 2012 16:34, Abhinav Verma wrote: >> >>> Hi, >>> >>> I am trying to get the list of hbonds formed using >>> Apply-find-polarcontacts. >>> >>> I searched and found some scripts, but they never give me the same >>> result as the one by default pymol. >>> >>> Any ideas how I can get the hbonds as a list. >>> >>> Thanks, >>> >>> Abhinav >>> >>> >>> -- >>> Try before you buy = See our experts in action! >>> The most comprehensive online learning library for Microsoft developers >>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >>> Metro Style Apps, more. Free future releases when you subscribe now! >>> http://p.sf.net/sfu/learndevnow-dev2 >>> ___________ >>> 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 >>> >> >> >> >> -- >> >> == >> >> Thomas Evangelidis >> >> PhD student >> >> Biomedical Research Foundation, Academy of Athens >> >> 4 Soranou Ephessiou , 115 27 Athens, Greece >> >> email: tev...@bioacademy.gr >> >> teva...@gmail.com >> >> >> website: https://sites.google.com/site/thomasevangelidishomepage/ >> >> >> >> >> >> -- >> Try before you buy = See our experts in action! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-dev2 >> ___ >> 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 >> > > -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ 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] list of polar contacts
Probably because they set diffently the acceptor-donor cutoff and the acceptor-hydrogen-donor angle. Use list_hbonds.py from: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ and set the cutoff and angle to the values you wish. Thomas On 30 January 2012 16:34, Abhinav Verma wrote: > Hi, > > I am trying to get the list of hbonds formed using > Apply-find-polarcontacts. > > I searched and found some scripts, but they never give me the same result > as the one by default pymol. > > Any ideas how I can get the hbonds as a list. > > Thanks, > > Abhinav > > > -- > Try before you buy = See our experts in action! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-dev2 > ___ > 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 > -- ====== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ 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] Editing of the pdb structure
Is it a small organic molecule or a modified amino acid within the context of a protein? 2012/1/29 Tim Schulte > Dear James, > I agree with Joao, for fast and dirty minimisation you might try the > program Chimera or VegaZZ. If you just wanna have an energy-minimized small > molecule the Prodrg server is the way to go. > Cheers, > Tim > -- > *Von:* João Rodrigues [anar...@gmail.com] > *Gesendet:* Freitag, 27. Januar 2012 09:56 > *Bis:* James Starlight > *Cc:* pymol-users@lists.sourceforge.net > *Betreff:* Re: [PyMOL] Editing of the pdb structure > > Dear James, > > As someone has told you already, Pymol is a visualization tool, not a > modelling suite. I guess you would be better off using something like > AMBERTOOLS or MODELLER, depending on what you want to model, or any other > "real" simulation/modelling package otherwise your results are very weak... > > My opinion only. > > João [...] Rodrigues > http://nmr.chem.uu.nl/~joao > > > > No dia 27 de Janeiro de 2012 09:50, James Starlight < > jmsstarli...@gmail.com> escreveu: > >> Arne, Thomas >> >> Thanks alot. Bond works finw >> >> >> I'd like just to ask what about geometry optimisation of the new structure >> >> E.g I want create 5memb imidazole ring where the 2 adj atoms are apart >> from 1.5 A from each other. >> >> When I've create new bond by bond command new ring look like 6memb ( like >> benzol) because of long distance between adj atoms. >> >> How I could optimise geometry of the new mollecule? Have pymol some >> built-in functions like conformational search be means of monte carlo or >> energy minimisation ? >> >> >> James >> >> >> 2012/1/27 Thomas Holder >> >>> On 01/27/2012 09:11 AM, James Starlight wrote: >>> >>>> Dear PyMol users! >>>> >>>> I need to create NEW covalent bond between two adjacent atoms. How this >>>> could be done in PyMOl? >>>> >>> >>> you could have guessed it: >>> http://pymolwiki.org/index.**php/Bond<http://pymolwiki.org/index.php/Bond> >>> :-) >>> >>> The atoms must both be within the same object. >>> >>> >>> Cheers, >>> Thomas >>> >>> -- >>> Thomas Holder >>> MPI for Developmental Biology >>> Spemannstr. 35 >>> D-72076 Tübingen >>> >> >> >> >> -- >> Try before you buy = See our experts in action! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-dev2 >> ___ >> 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 >> > > > > -- > Try before you buy = See our experts in action! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-dev2 > ___ > 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 > -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ 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] Fetching scripts
Sounds awesome! Adding an option to chose whether to load the script every time PyMol launches, or just fetch and use it once, would be even more convenient. It would resemble installation of packages from Linux repositories ;) On 4 May 2011 18:59, Michael Lerner wrote: > Hi all, > > I'm considering building in a mechanism for automatically fetching scripts > from the PyMOL Wiki. The goal is to allow users to say > > fetch findSurfaceResidues, type=script > findSurfaceResidues doShow=True, cutoff=0.5 > > The convenience benefits are obvious, especially for new users, and I think > that lowering the barrier to script usage will greatly increase both the > number of people who use various scripts and the incentive to place scripts > on the wiki (especially if the fetch mechanism makes it easy for script > authors to provide a citation/DOI/etc.). > > I've put up a tentative page about this on the wiki ( > http://pymolwiki.org/index.php/Fetching_scripts), and I'd love comments > either via the list, private email or on the wiki, especially about > > - whether you think it's a good idea > - security and validation > - options you'd like > - implementation issues > > The plan is to write this as a userland script first. If issues relating to > security and validation can be resolved, we'll see if the official builds > want to include it. > > Cheers, > > -Michael > > -- > Michael Lerner, Ph.D. > IRTA Postdoctoral Fellow > Laboratory of Computational Biology NIH/NHLBI > 5635 Fishers Lane, Room T909, MSC 9314 > Rockville, MD 20852 (UPS/FedEx/Reality) > Bethesda MD 20892-9314 (USPS) > > > -- > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd > ___ > 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 > -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ 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
[PyMOL] negative image of binding cavity
Dear Pymol users, I want to display clearly the volume of a buried cavity inside my protein. Does anybody know how to do this? I've tried CastP and Caver plugins already, but they do not produce exactly the volume I want to display. I would greatly appreciate any advice. thanks, Tom -- Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! Tap into the largest installed PC base & get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-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] RMSD produced by align command
Jason, When I use optAlign I get the same value as with ProFit (4.615214 A.), that's why I suspected that 'align' omits some distant CA atoms when calculating the RMSD. In fact I just noticed that the last 2 residues are not assigned an asterisk or a dot in the alignment. So, when I exclude them from 'optAlign' I get 1.780601 A., the same value as with 'align'. Thomas > Thomas, > > If PyMOL has paired two atoms for alignment, then they will be used in > the calculation of the RMSD. > > Also, this sounds like you should be using 'fit' or 'optAlign' to be > superposing the molecules. (If you already know the atom pairings, no > 'alignment' step is necessary.) > > Possibly helpful link: > http://www.pymolwiki.org/index.php/Category:Structure_Alignment > > See: fit, optAlign, intra_fit_rms. > > Hope this helps, > > -- Jason > > -- > Jason Vertrees, PhD > > PyMOLWiki -- http://www.pymolwiki.org > > > > On Tue, Dec 29, 2009 at 1:27 PM, Thomas Evangelidis > wrote: >> 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? >> >> >> -- >> 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 (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 >> > - End message from jason.vertr...@gmail.com - -- 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 (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
[PyMOL] RMSD produced by align command
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? -- 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 (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] asymmetric transformation matrices
As Tsjerk pointed out, there was a mistake in the code. Just for the
record this is the right function:
pdb2entry = { "1ONE": "1ONE_A", "2ONE": "2ONE_A" }
# a function to measure Ca distances of oposite pairs of superimpossed
chains (the proteins must have the same aa composition)
def check_for_symmetry(tstruct, qstruct):
# align the pair
cmd.fetch(tstruct)
cmd.extract(pdb2entry[tstruct]+"1", tstruct + " and chain "+
pdb2entry[tstruct][-1:] + " and not hetatm")
cmd.fetch(qstruct)
cmd.extract(pdb2entry[qstruct]+"1", qstruct +" and chain "+
pdb2entry[qstruct][-1:] + " and not hetatm")
cmd.delete(tstruct)
cmd.delete(qstruct)
print "Aligning "+pdb2entry[tstruct]+"1"+" with "+pdb2entry[qstruct]+"1"
cmd.align(pdb2entry[tstruct]+"1", pdb2entry[qstruct]+"1")
#cmd.do("cealign "+pdb2entry[qstruct]+"1, "+pdb2entry[tstruct]+"1")
# align the symmetric pair
cmd.fetch(tstruct)
cmd.extract(pdb2entry[tstruct]+"2", tstruct + " and chain "+
pdb2entry[tstruct][-1:] + " and not hetatm")
cmd.fetch(qstruct)
cmd.extract(pdb2entry[qstruct]+"2", qstruct +" and chain "+
pdb2entry[qstruct][-1:] + " and not hetatm")
print "Aligning "+pdb2entry[qstruct]+"1"+" with "+pdb2entry[tstruct]+"1"
cmd.align(pdb2entry[qstruct]+"2", pdb2entry[tstruct]+"2")
#cmd.do("cealign "+pdb2entry[qstruct]+"2, "+pdb2entry[tstruct]+"2")
# measure distances
pymol.stored.protein_dict = {}
cmd.iterate(pdb2entry[tstruct]+"1", "stored.protein_dict[(chain,resi)]=1")
Residues = pymol.stored.protein_dict.keys()
Residues.sort()
RMSD = 0
for res in Residues:
chain = res[0]
resi = res[1]
dist1 = cmd.distance('tmp',pdb2entry[tstruct]+"1 and chain
"+chain+" and resi "+resi+" and name ca",pdb2entry[qstruct]+"1 and
chain "+chain+" and resi "+resi+" and name ca")
dist2 = cmd.distance('tmp',pdb2entry[tstruct]+"2 and chain
"+chain+" and resi "+resi+" and name ca",pdb2entry[qstruct]+"2 and
chain "+chain+" and resi "+resi+" and name ca")
print "The difference in distance betweem residue IDs ",
resi," is : ",dist1, "-",dist2," = ",dist1-dist2
RMSD += (dist1-dist2)**2
RMSD = sqrt(RMSD/len(Residues))
print "RMSD of distances between identical residues in 1ONE x
2ONE and this in 2ONE x 1ONE: ", RMSD
check_for_symmetry("1ONE", "2ONE")
After this correction the RMSD falls to 2.06853295972e-06, which a
reasonably good number.
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Re: [PyMOL] asymmetric transformation matrices
Well practically speaking the opposite superimpositions are not
performed in the same fashion. Lets take 1ONE and 2ONE as an example,
2 different conformations of the same molecule. Since the aa
composition is identical (at least from what I've seen the chains have
the same length), I measured the distances between Ca atoms of 1ONE
and 2ONE after "align 1ONE and chain A, 2ONE and chain A", and the
respective distances after "align 2ONE and chain A, 1ONE and chain A".
The RMSD is 0.230642045187 which implies that the 2 chains are not in
relative positions after 1ONEx2ONE and 2ONEx1ONE. Here's the function
I 've written to do that:
# a function to measure Ca distances of oposite pairs of superimpossed
chains (the proteins must have the same aa composition)
def check_for_symmetry(tstruct, qstruct):
# align the pair
cmd.fetch(tstruct)
cmd.extract(pdb2entry[tstruct]+"1", tstruct + " and chain "+
pdb2entry[tstruct][-1:] + " and not hetatm")
cmd.fetch(qstruct)
cmd.extract(pdb2entry[qstruct]+"1", qstruct +" and chain "+
pdb2entry[qstruct][-1:] + " and not hetatm")
print "Aligning "+pdb2entry[tstruct]+"1"+" with "+pdb2entry[qstruct]+"1"
cmd.align(pdb2entry[tstruct]+"1", pdb2entry[qstruct]+"1")
#cmd.do("cealign "+pdb2entry[qstruct]+"1, "+pdb2entry[tstruct]+"1")
# align the symmetric pair
cmd.fetch(tstruct)
cmd.extract(pdb2entry[tstruct]+"2", tstruct + " and chain "+
pdb2entry[tstruct][-1:] + " and not hetatm")
cmd.fetch(qstruct)
cmd.extract(pdb2entry[qstruct]+"2", qstruct +" and chain "+
pdb2entry[qstruct][-1:] + " and not hetatm")
print "Aligning "+pdb2entry[qstruct]+"1"+" with "+pdb2entry[tstruct]+"1"
cmd.align(pdb2entry[qstruct]+"2", pdb2entry[tstruct]+"2")
#cmd.do("cealign "+pdb2entry[qstruct]+"2, "+pdb2entry[tstruct]+"2")
# measure distances
pymol.stored.protein_dict = {}
cmd.iterate(pdb2entry[tstruct]+"1", "stored.protein_dict[(chain,resi)]=1")
Residues = pymol.stored.protein_dict.keys()
Residues.sort()
RMSD = 0
for res in Residues:
chain = res[0]
resi = res[1]
dist1 = cmd.distance('tmp',pdb2entry[tstruct]+"1 and chain
"+chain+" and resi "+resi+" and name ca",pdb2entry[qstruct]+"1 and
chain "+chain+" and resi "+resi+" and name ca")
dist2 = cmd.distance('tmp',pdb2entry[tstruct]+"2 and chain
"+chain+" and resi "+resi+" and name ca",pdb2entry[qstruct]+"2 and
chain "+chain+" and resi "+resi+" and name ca")
print "The difference in distance betweem residue IDs ",
resi," is : ",dist1, "-",dist2," = ",dist1-dist2
RMSD += (dist1-dist2)**2
RMSD = sqrt(RMSD/len(Residues))
print "RMSD of distances between identical residues in 1ONE x
2ONE and this in 2ONE x 1ONE: ", RMSD
check_for_symmetry("1ONE", "2ONE")
PS: Jason, I suspect the same happens with CEalign although I couldn't
manage to run it for technical reasons, but by looking at the
transformation matrices produced by the stand-alone version, the
translation vectors are not opposite.
> Hi Thomas,
>
> Say, the first system is x and the second y, where y=R(x+s) is the
> first transformation. Then the reverse transformation follows as
>
> y = R(x + s)
> y = Rx + Rs
> Rx = y - Rs
> x = t(R)(y-Rs)
>
> Note that that is also equal to: x = t(R)y - s
>
> Hope it helps,
>
> Tsjerk
>
> On Mon, Nov 9, 2009 at 1:09 AM, Thomas Evangelidis
> wrote:
>> Dear pymol users,
>>
>> I noticed something strange when superimposing 2 opposite pairs of
>> chains. E.g.
>>
>> DEBUG: template 1BQG_A query 2MUC_A
>> Query Transformation:
>> X2 = +0.86747*(X1+2.29751) + -0.49574*(Y1+60.99794) +
>> -0.04181*(Z1+64.71239)
>> Y2 = -0.49701*(X1+2.29751) + -0.85983*(Y1+60.99794) +
>> -0.11697*(Z1+64.71239)
>> Z2 = +0.02204*(X1+2.29751) + +0.12225*(Y1+60.99794) +
>> -0.99226*(Z1+64.71239)
>>
>>
>> DEBUG: template 2MUC_A query 1BQG_A
>> Query Transformation:
>> X2 = +0.86747*(X1+30.95128) + -0.49701*(Y1+61.15895) +
>> +0.02204*(Z1+56.70381)
>> Y2 = -0.49574*(X1+30.95128) + -0.85983*(Y1+61.15895) +
>> +0.12225*(Z1+56.70381)
>> Z2 = -0.04181*(X1+30.95128) + -0.11697*(Y1+
[PyMOL] asymmetric transformation matrices
Dear pymol users, I noticed something strange when superimposing 2 opposite pairs of chains. E.g. DEBUG: template 1BQG_A query 2MUC_A Query Transformation: X2 = +0.86747*(X1+2.29751) + -0.49574*(Y1+60.99794) + -0.04181*(Z1+64.71239) Y2 = -0.49701*(X1+2.29751) + -0.85983*(Y1+60.99794) + -0.11697*(Z1+64.71239) Z2 = +0.02204*(X1+2.29751) + +0.12225*(Y1+60.99794) + -0.99226*(Z1+64.71239) DEBUG: template 2MUC_A query 1BQG_A Query Transformation: X2 = +0.86747*(X1+30.95128) + -0.49701*(Y1+61.15895) + +0.02204*(Z1+56.70381) Y2 = -0.49574*(X1+30.95128) + -0.85983*(Y1+61.15895) + +0.12225*(Z1+56.70381) Z2 = -0.04181*(X1+30.95128) + -0.11697*(Y1+61.15895) + -0.99226*(Z1+56.70381) Although looking at the rotation matrices one is the transpose of the other, the translation vectors are not opposite. Can someone explain that? -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] how to get RMSD from CEalign command
No it doesn't, both in Fedora 11 and Ubuntu 9.04. I get:
NameError: global name 'cealign' is not defined
Thomas
> Thomas,
>
> The command
>
> cmd.do(".../cealign.py")
>
> runs cealign.py, which runs cmd.extend. So you should have the cealign
> command in your namespace after the cmd.do. Have you tried running
>
> cmd.do("your/path/to/cealign")
> cealign(protA, protB)?
>
> I just tried this on my system and it worked for me. Let me know if it
> works for you.
>
> -- J
>
> Jason Vertrees, PhD
>
> PyMOLWiki -- http://www.pymolwiki.org
>
>
>
> 2009/10/31 Thomas Evangelidis :
>>
>>> Thomas,
>>>
>>> The PyMOL UI runs asynchronously. I think you are deleting your PDB
>>> files before they can be aligned. I made a couple changes in your
>>> script. Instead of calling cmd.do just call cealign directly. See
>>> below,
>>>
>>> query_template_chains = {
>>> "1ebh" : ["1ebg", "1els", "1one", "2one",
>>> "5enl", "6enl", "7enl"]
>>> }
>>>
>>> for query in query_template_chains.keys():
>>> for template in query_template_chains[query]:
>>> cmd.fetch(query, async=0)
>>> cmd.fetch(template, async=0)
>>> print "Superimposing ", query, " onto ", template
>>> cealign( query+" and c. A", template+" and c. A")
>>> cmd.delete(query)
>>> cmd.delete(template)
>>>
>>> Hope this helps,
>>>
>>> -- Jason
>>>
>>> Jason Vertrees, PhD
>>
>> Jason,
>>
>> I can't run cealign() from a script:
>>
>> NameError: global name 'cealign' is not defined
>>
>> I installed pymol from Fedora repositories and can't find .pymolrc,
>> therefore I load CEalig in my script like this:
>>
>> cmd.do("run /home/thomas/Documents/cealign-0.9/cealign.py") # load CEalign
>> plugin
>> cmd.do("run /home/thomas/Documents/cealign-0.9/qkabsch.py")
>>
>> The only way to run CEalign is using cmd.do().
>>
>> Thomas
>>
>> And of
>>
>>
>
- End message from jason.vertr...@gmail.com -
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Re: [PyMOL] how to get RMSD from CEalign command
> Thomas,
>
> The PyMOL UI runs asynchronously. I think you are deleting your PDB
> files before they can be aligned. I made a couple changes in your
> script. Instead of calling cmd.do just call cealign directly. See
> below,
>
> query_template_chains = {
> "1ebh" : ["1ebg", "1els", "1one", "2one",
> "5enl", "6enl", "7enl"]
> }
>
> for query in query_template_chains.keys():
> for template in query_template_chains[query]:
> cmd.fetch(query, async=0)
> cmd.fetch(template, async=0)
> print "Superimposing ", query, " onto ", template
> cealign( query+" and c. A", template+" and c. A")
> cmd.delete(query)
> cmd.delete(template)
>
> Hope this helps,
>
> -- Jason
>
> Jason Vertrees, PhD
Jason,
I can't run cealign() from a script:
NameError: global name 'cealign' is not defined
I installed pymol from Fedora repositories and can't find .pymolrc,
therefore I load CEalig in my script like this:
cmd.do("run /home/thomas/Documents/cealign-0.9/cealign.py") # load
CEalign plugin
cmd.do("run /home/thomas/Documents/cealign-0.9/qkabsch.py")
The only way to run CEalign is using cmd.do().
Thomas
And of
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Re: [PyMOL] how to get RMSD from align command
Warren,
before I write something incorrect into Methods section, do you think
the overall RMSD returned by align command is a valid criterion to
select which structure of the family is most similar?
Tom
> Tom,
>
> Apologies for the confusion, but there really isn't any way to
> measure overall structural similarity in PyMOL other than pair_fit,
> but you have to do the work of explicitly stating which pairs are to
> be aligned.
>
> The pair_fit selections don't have to be identical, but they do have
> to correspond in a pairwise fashion. In other words, you can
> compare any number of C-alpha positions so long as the same number
> of atomic positions are specified in each structure.
>
> Cheers,
> Warren
>
> -Original Message-
> From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr]
> Sent: Thu 10/29/2009 5:24 AM
> To: Warren DeLano
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] how to get RMSD from align command
>
> Hi Warren,
>
> Now I am more confused. I used align command to measure the overall
> RMSD between homologous structures. Apparently align is not
> appropriate if not sufficient sequence similarity is present. I later
> came across CEalign plugin, which does structure-based
> superimposition. This command also returns an RMSD value, which
> happens to be higher for the set of homologous structures I analysed.
> Based on this I concluded that align command is more appropriate to
> measure measure structural similarity, but I'm not sure now.
>
> My objective is to select between a small set of homologous structures
> (co-crystallized with ligands), the one with the highest structural
> similarity and use it to place a dummy ligand into one where it's
> missing. I.e. "1ebh" lacks a ligand, so I compared it with "1ebg",
> "1els", "1one", "2one", "5enl", "6enl", "7enl" which have
> co-crystallized ligands. According to both align and cealign, 5ENL is
> the most similar with overall RMSD 0.246 and 0.420907 respectively.
> The question is which command produces the best superimposition
> provided that these proteins belong to the enolase family and thus
> have high sequence and structural similarity? Based on the RMSD
> values, align does, but as you said this value pertains to only a
> subset of atoms after refinement.
>
> Apparently pair_fit command cannot be used for my purpose as it
> requires identical selections.
>
> Tom
>
>
>> Tom,
>>
>> The complication with cmd.align() is that it is doing a whole lot
>> more than a simple alignment. The first number is in fact the RMS,
>> but it covers only the subset of the input atoms remaining after
>> refinement is completed. The count of aligned atoms is the second
>> field.
>>
>> If you're looking for exact RMS fit values over a well-defined set
>> of atoms, try using cmd.pair_fit(sele1, sele2) instead, for example:
>>
>> load $TUT/1hpv.pdb
>>
>> create loopA, A/46-55/
>>
>> create loopB, B/46-55/
>>
>> show sticks, loop*
>>
>> print cmd.pair_fit("loopACA", "loopBCA")
>>
>> Cheers,
>> Warren
>>
>> -Original Message-
>> From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr]
>> Sent: Wed 10/28/2009 8:09 PM
>> To: pymol-users@lists.sourceforge.net
>> Subject: [PyMOL] how to get RMSD from align command
>>
>> Simple question, it must have been answered before but couldn't find
>> it so far:
>>
>> how can I get the RMSD value from the align command in a python
>> script? cmd.align() returnes a tuple of 8 numbers and none of them is
>> the actual RMSD value I get when I align these 2 structures manually.
>>
>> thanks,Tom
>>
>>
>> --
>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
>> is the only developer event you need to attend this year. Jumpstart your
>> developing skills, take BlackBerry mobile applications to market and stay
>> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
>> http://p.sf.net/sfu/devconference
>> ___
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>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>>
>>
>>
>>
>>
>>
>>
>
>
> - End message from war...@delsci.com -
>
>
>
Re: [PyMOL] how to get RMSD from align command
Hi Warren,
Now I am more confused. I used align command to measure the overall
RMSD between homologous structures. Apparently align is not
appropriate if not sufficient sequence similarity is present. I later
came across CEalign plugin, which does structure-based
superimposition. This command also returns an RMSD value, which
happens to be higher for the set of homologous structures I analysed.
Based on this I concluded that align command is more appropriate to
measure measure structural similarity, but I'm not sure now.
My objective is to select between a small set of homologous structures
(co-crystallized with ligands), the one with the highest structural
similarity and use it to place a dummy ligand into one where it's
missing. I.e. "1ebh" lacks a ligand, so I compared it with "1ebg",
"1els", "1one", "2one", "5enl", "6enl", "7enl" which have
co-crystallized ligands. According to both align and cealign, 5ENL is
the most similar with overall RMSD 0.246 and 0.420907 respectively.
The question is which command produces the best superimposition
provided that these proteins belong to the enolase family and thus
have high sequence and structural similarity? Based on the RMSD
values, align does, but as you said this value pertains to only a
subset of atoms after refinement.
Apparently pair_fit command cannot be used for my purpose as it
requires identical selections.
Tom
> Tom,
>
> The complication with cmd.align() is that it is doing a whole lot
> more than a simple alignment. The first number is in fact the RMS,
> but it covers only the subset of the input atoms remaining after
> refinement is completed. The count of aligned atoms is the second
> field.
>
> If you're looking for exact RMS fit values over a well-defined set
> of atoms, try using cmd.pair_fit(sele1, sele2) instead, for example:
>
> load $TUT/1hpv.pdb
>
> create loopA, A/46-55/
>
> create loopB, B/46-55/
>
> show sticks, loop*
>
> print cmd.pair_fit("loopACA", "loopBCA")
>
> Cheers,
> Warren
>
> -Original Message-
> From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr]
> Sent: Wed 10/28/2009 8:09 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] how to get RMSD from align command
>
> Simple question, it must have been answered before but couldn't find
> it so far:
>
> how can I get the RMSD value from the align command in a python
> script? cmd.align() returnes a tuple of 8 numbers and none of them is
> the actual RMSD value I get when I align these 2 structures manually.
>
> thanks,Tom
>
>
> --
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>
>
>
>
>
>
>
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Re: [PyMOL] how to get RMSD from CEalign command
Thank you Adnreas.
I'm straggling with cealign now. When I run it in batch mode I get
"Selector-Error: Invalid selection name" for certain structures, which
in fact are very close homologs, whereas the number of RMSD values I
get varies (sometimes 3, 5, etc). Here's the code:
query_template_chains = {
"1ebh" : ["1ebg", "1els", "1one", "2one",
"5enl", "6enl", "7enl"]
}
for query in query_template_chains.keys():
for template in query_template_chains[query]:
cmd.fetch(query)
cmd.fetch(template)
print "Superimposing ", query, " onto ", template
cmd.do("cealign "+query+" and c. A, "+template+" and c. A")
cmd.delete(query)
cmd.delete(template)
Do you know what's wrong?
Thomas
> Hey Thomas,
>
> if you want to use align anyway, make sure to use the quite=0 option.
> The "quiet" option (if present) is set to zero by default for parsed
> PyMOL commands, but is not set for Python API calls.
>
> align
> is nearly equal to
> cmd.align(quiet=0)
>
> Thus, if you want to get rmsd output, include quiet=0 and run your
> script with output redirection.
>
>
> Andreas
>
>
>
> On Thu, Oct 29, 2009 at 2:48 AM, Thomas Evangelidis
> wrote:
>> Simple question, it must have been answered before but couldn't find
>> it so far:
>>
>> how can I get the RMSD value from the align command in a python
>> script? cmd.align() returnes a tuple of 8 numbers and none of them is
>> the actual RMSD value I get when I align these 2 structures manually.
>>
>> thanks,Tom
>>
>>
>> --
>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
>> is the only developer event you need to attend this year. Jumpstart your
>> developing skills, take BlackBerry mobile applications to market and stay
>> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
>> http://p.sf.net/sfu/devconference
>> ___
>> 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
>>
>
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[PyMOL] how to get RMSD from align command
Simple question, it must have been answered before but couldn't find it so far: how can I get the RMSD value from the align command in a python script? cmd.align() returnes a tuple of 8 numbers and none of them is the actual RMSD value I get when I align these 2 structures manually. thanks,Tom -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ 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] where to find a 64 bit Linux version?
Thank you all, the problem has been resolved. I was confused with the part of the instructions saying PyMOL Plugins need to be installed in $PYMOL_PATH/modules/pmg_tk/startup. I was also trying to install LigAlign from Plugin->Install Plugin... before reading the respective documentation...silly me! On Wed, 18 Mar 2009 01:03:07 +0200 Thomas Evangelidis wrote: Dear Pymol users, does anyone know where I can find a 64 bit version for my Fedora 10. The package from the repositories works fine but when it comes to install new plugins it yields error messages. As a matter of fact I can't even figure out where the whole program is installed (used locate command but still remains unclear). rpm -qil pymol or: python -c "from distutils.sysconfig import get_python_lib; print \ get_python_lib(1)" On the other hand when I install the 32 bit version and try to resolve those i386 library-dependencies I end up getting the error message: /home/thomas/Documents/pymol/pymol.exe: error while loading shared libraries: libstdc++.so.5: wrong ELF class: ELFCLASS64 libstdc++.so.5 is in the correct directory (/usr/lib/), cannot imagine what's going wrong. Its not finding the 32 bit libstdc++ - you can check your linker is finding things correctly using ldconfig -p and the pymol.exe file itself using ldd. Hope it helps, Tim p.s. warren - pymol is available under RHEL as of version 5. -- - Tim Fenn f...@stanford.edu 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 - - End message from f...@stanford.edu -
[PyMOL] where to find a 64 bit Linux version?
Dear Pymol users, does anyone know where I can find a 64 bit version for my Fedora 10. The package from the repositories works fine but when it comes to install new plugins it yields error messages. As a matter of fact I can't even figure out where the whole program is installed (used locate command but still remains unclear). On the other hand when I install the 32 bit version and try to resolve those i386 library-dependencies I end up getting the error message: /home/thomas/Documents/pymol/pymol.exe: error while loading shared libraries: libstdc++.so.5: wrong ELF class: ELFCLASS64 libstdc++.so.5 is in the correct directory (/usr/lib/), cannot imagine what's going wrong. Anyway, I think a 64 bit version (if does exist) would solve all the afore-mentioned problems. thanks in advance, Tom
Re: [PyMOL] polar contacts involving F, Cl and S atoms
I see what the abbreviations mean now, so stands for small overlap, bo for bad overlap, wc Van Der Wals contact, etc. They are at the left side of King's GUI. Sorry that was a naive question. Tom Tom, The simplest thing to do is just to use the dist command to check the interactions manually. dist atom1, atom2 If you have a bunch to look at and the ligands are in the PDB then MolProbity can do contact analysis so you can pull out Hydrogen bonds that way. If no one has a better guess, maybe try 1.7 plus the VDW radii of F (1.35), Cl (1.8), or S (1.85). Seems like a good guess to me. Cheers, -bob On Sat, Jul 26, 2008 at 2:32 PM, Thomas Evangelidis wrote: Hi Pymol users, I want to display the polar interactions between some ligands and a receptor, but I 'm not quite sure if Pymol can do that for F, Cl or S atoms. There's a tutorial on the wiki that explains how to set the cutoff distance but that refers only to O and N atoms: http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts I was wondering if I can do that by modifying those code snippets. I would greatly appreciate any help. Also if someone knows the distance H-bond donor and acceptor for F and Cl atoms please tell me. I know only the respective distance for S which is 4 A maximum. thanks, Tom - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users - End message from immorm...@gmail.com -
Re: [PyMOL] polar contacts involving F, Cl and S atoms
Thanks Bob. The kinemage generated by MolProbity is a good way to locate H-bond and not only. I guess "hb" in the list of contacts stands for H-bond, but I'm not quite sure what the other abbreviations stand for (cc, wc, so, etc.). This is the first time I use MolProbity and I've seen that you work for the Richardson lab, so could you please give me some hints on how to use that tool to evaluate the poses of my ligands (geometries, bulking interactions, etc.), if that's feasible of course. Are there any overall scores that measure these properties? thanks in advance, Tom Tom, The simplest thing to do is just to use the dist command to check the interactions manually. dist atom1, atom2 If you have a bunch to look at and the ligands are in the PDB then MolProbity can do contact analysis so you can pull out Hydrogen bonds that way. If no one has a better guess, maybe try 1.7 plus the VDW radii of F (1.35), Cl (1.8), or S (1.85). Seems like a good guess to me. Cheers, -bob On Sat, Jul 26, 2008 at 2:32 PM, Thomas Evangelidis wrote: Hi Pymol users, I want to display the polar interactions between some ligands and a receptor, but I 'm not quite sure if Pymol can do that for F, Cl or S atoms. There's a tutorial on the wiki that explains how to set the cutoff distance but that refers only to O and N atoms: http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts I was wondering if I can do that by modifying those code snippets. I would greatly appreciate any help. Also if someone knows the distance H-bond donor and acceptor for F and Cl atoms please tell me. I know only the respective distance for S which is 4 A maximum. thanks, Tom - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users - End message from immorm...@gmail.com -
[PyMOL] polar contacts involving F, Cl and S atoms
Hi Pymol users, I want to display the polar interactions between some ligands and a receptor, but I 'm not quite sure if Pymol can do that for F, Cl or S atoms. There's a tutorial on the wiki that explains how to set the cutoff distance but that refers only to O and N atoms: http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts I was wondering if I can do that by modifying those code snippets. I would greatly appreciate any help. Also if someone knows the distance H-bond donor and acceptor for F and Cl atoms please tell me. I know only the respective distance for S which is 4 A maximum. thanks, Tom
