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From: Ioannis R. <riz...@eb...> - 2021-04-14 12:02:07
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Hello, Is there any way to define a custom selection operator in a script? E.g. select all atoms with complex properties A, B, and C. Otherwise, what is the proper way of appending atoms to a selection in scripting? Thank you, Yannis |
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From: Ioannis R. <riz...@eb...> - 2021-04-14 11:41:09
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Hello, Is there any way to define a custom selection operator in a script? E.g. select all atoms with complex properties A, B, and C. Otherwise, what is the proper way of appending atoms to a selection in scripting? Thank you, Yannis |
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From: Roger R. <rro...@co...> - 2021-04-12 12:11:39
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One way of displaying CCP4-generated maps in Pymol is described on this web page: https://sites.google.com/colgate.edu/xrd-protocols/home/visualization-of-protein-models One way of generating CCP4 maps suitable for use in Pymol is described on this page: https://sites.google.com/colgate.edu/xrd-protocols/home/model-building-and-validation Roger Rowlett On Mon, Apr 12, 2021, 2:35 AM shubhashish chakraborty < csh...@gm...> wrote: > Hello, > I am not able to align my pdb file with its respective electron density > map generated by CCP4i. Kindly let me know what is going wrong. > An image is attached for better reference. > > Thank you > > Shubhashish Chakraborty > PhD Research Scholar (SRF) > Varma Lab > Structural and Molecular biology Lab > Advanced Centre for Treatment, Research and Education in Cancer (ACTREC) > Khargar, Navi Mumbai > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
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From: Tamas H. <bio...@gm...> - 2021-04-12 07:28:38
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pls. google https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html https://www.cgl.ucsf.edu/chimera/data/tutorials/emfit09/emfit.html On 4/12/21 9:25 AM, shubhashish chakraborty wrote: > Hi, > Thank you for a reply. > I am not working with cryo-EM but it's an X-ray diffraction map. > A similar kind of problem I am facing in chimera, so what could be done? > > Thank you > > Shubhashish Chakraborty > PhD Research Scholar (SRF) > Varma Lab > Structural and Molecular biology Lab > Advanced Centre for Treatment, Research and Education in Cancer (ACTREC) > Khargar, Navi Mumbai > > > > > On Mon, Apr 12, 2021 at 12:42 PM Tamas Hegedus <bio...@gm... > <mailto:bio...@gm...>> wrote: > > Hi, > > PyMOL seems not to primarily target working with densities. > > I suggest to use Chimera if you work with cryo EM maps. > E.g. you can use it to fit your struct into the density map. > If you decide to use Chimera, be careful, a first step of > frustration could be caused by the extension of the density file. > Yes, the extension - .mrc or .map; depending on the extension the > map is aligned to the origo or not (or something like that). > > Bests, > Tamas > > On 4/12/21 8:34 AM, shubhashish chakraborty wrote: >> Hello, >> I am not able to align my pdb file with its respective electron >> density map generated by CCP4i. Kindly let me know what is going >> wrong. >> An image is attached for better reference. >> >> Thank you >> Shubhashish Chakraborty >> PhD Research Scholar (SRF) >> Varma Lab >> Structural and Molecular biology Lab >> Advanced Centre for Treatment, Research and Education in Cancer >> (ACTREC) >> Khargar, Navi Mumbai >> >> >> >> >> _______________________________________________ >> PyMOL-users mailing list >> Archives:http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...> >> Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe> > > _______________________________________________ > PyMOL-users mailing list > Archives: > http://www.mail-archive.com/pym...@li... > <http://www.mail-archive.com/pym...@li...> > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe> > |
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From: shubhashish c. <csh...@gm...> - 2021-04-12 07:25:41
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Hi, Thank you for a reply. I am not working with cryo-EM but it's an X-ray diffraction map. A similar kind of problem I am facing in chimera, so what could be done? Thank you Shubhashish Chakraborty PhD Research Scholar (SRF) Varma Lab Structural and Molecular biology Lab Advanced Centre for Treatment, Research and Education in Cancer (ACTREC) Khargar, Navi Mumbai On Mon, Apr 12, 2021 at 12:42 PM Tamas Hegedus <bio...@gm...> wrote: > Hi, > > PyMOL seems not to primarily target working with densities. > > I suggest to use Chimera if you work with cryo EM maps. > E.g. you can use it to fit your struct into the density map. > If you decide to use Chimera, be careful, a first step of frustration > could be caused by the extension of the density file. Yes, the extension - > .mrc or .map; depending on the extension the map is aligned to the origo or > not (or something like that). > > Bests, > Tamas > > On 4/12/21 8:34 AM, shubhashish chakraborty wrote: > > Hello, > I am not able to align my pdb file with its respective electron density > map generated by CCP4i. Kindly let me know what is going wrong. > An image is attached for better reference. > > Thank you > > Shubhashish Chakraborty > PhD Research Scholar (SRF) > Varma Lab > Structural and Molecular biology Lab > Advanced Centre for Treatment, Research and Education in Cancer (ACTREC) > Khargar, Navi Mumbai > > > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
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From: Tamas H. <bio...@gm...> - 2021-04-12 07:11:50
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Hi, PyMOL seems not to primarily target working with densities. I suggest to use Chimera if you work with cryo EM maps. E.g. you can use it to fit your struct into the density map. If you decide to use Chimera, be careful, a first step of frustration could be caused by the extension of the density file. Yes, the extension - .mrc or .map; depending on the extension the map is aligned to the origo or not (or something like that). Bests, Tamas On 4/12/21 8:34 AM, shubhashish chakraborty wrote: > Hello, > I am not able to align my pdb file with its respective electron > density map generated by CCP4i. Kindly let me know what is going wrong. > An image is attached for better reference. > > Thank you > Shubhashish Chakraborty > PhD Research Scholar (SRF) > Varma Lab > Structural and Molecular biology Lab > Advanced Centre for Treatment, Research and Education in Cancer (ACTREC) > Khargar, Navi Mumbai > > > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
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From: shubhashish c. <csh...@gm...> - 2021-04-12 06:34:57
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Hello, I am not able to align my pdb file with its respective electron density map generated by CCP4i. Kindly let me know what is going wrong. An image is attached for better reference. Thank you Shubhashish Chakraborty PhD Research Scholar (SRF) Varma Lab Structural and Molecular biology Lab Advanced Centre for Treatment, Research and Education in Cancer (ACTREC) Khargar, Navi Mumbai |
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From: Thomas E. <te...@gm...> - 2021-04-09 18:58:18
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Thumbs up for the SQM geometry optimization with xtb! :) On Fri, 9 Apr 2021 at 20:11, R Mera <rau...@us...> 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/pym...@li... > 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: te...@gm..., Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/ |
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From: R M. <rau...@us...> - 2021-04-09 18:06:33
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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). |
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From: Shintaro A. <shi...@gm...> - 2021-04-09 10:18:15
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Dear Pymol Experts, Is there an easy way to extrapolate what the label_position needs to be if the image to be rendered suddenly needs to be bigger? e.g. - Movie designed in a viewport of 1920x1080 with labels in the right places (e.g. top left of screen) - Decide at a later date that you actually want to use ray_trace_mode, 1 for outlines - Decide that at 1920x1080, the outline is too thick (and other settings like ray_trace_gain do not cut it), and so you decide to double up and render in 4K (3840x2160, and then reduce the resolution later) - Since label_position is relative to viewport, all the labels are now bunched in the center of the screen As my monitor isn't a 4K one, I have to adjust the label_position by trial-and-error while Ray-ing inbetween and checking where the labels go in the context of 4K. I would greatly appreciate it if there is a smarter way of doing this, Best wishes, Shintaro |
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From: Robert C. <rob...@qu...> - 2021-04-08 16:18:40
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Hi Evgeny and Chen, Unfortunately, if Chen wants the list of atoms that form H-bonds, "distance" only provides a displayed object and only returns the average distance between all atoms. Also unfortunately, that script list_hb.py (which I wrote) uses the find_pairs function which warns that it "only checks atom orientation, not atom type" (https://pymolwiki.org/index.php/Find_pairs). It is difficult therefore to provide list_hb.py with two selections that can only result in real H-bonds without actually figuring out for yourself which pairs of atoms should H-bond! Cheers, Rob On Thu, 2021-04-08 16:50 +0200, Evgeny Osipov <joe...@gm...> wrote: > Hi Chen, > you can use distance command or cmd.distance for scripting purposes. > Just specify mode 2 in order to search for polar contacts: > https://pymolwiki.org/index.php/Distance > > пн, 22 мар. 2021 г. в 18:53, Chen, Qiang <qi...@pi...>: > > > Hi, Pymol Users, > > > > I used this script to find hydrogen-bond in protein, list_hb.py. > > > > list_hb all, all, write_distances_file=hb > > > > I find there are some pairs are clearly not hydrogen bonds, e.g. > > A/VAL`257/O/774 A/MET`261/O/834 2.87 > > > > Also, the angle is not right for certain pair > > > > A/HIS`400/NE2/2977 B/GLN`403/OE1/7093 2.66 > > > > In the protein, the angle between NE2-H-OE1 is 100.8 deg > > > > Any suggestion to find out the correct hydrogen-bonding pairs? > > > > Thanks! > > _______________________________________________ > > PyMOL-users mailing list > > Archives: > > http://www.mail-archive.com/pym...@li... > > Unsubscribe: > > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > -- Robert L. Campbell, Ph.D. Academic Advisor, BHSc Program Assistant Professor, Dept. of Biomedical & Molecular Sciences, Queen's University, Kingston, ON K7L 3N6 Canada Botterell Hall Rm 644 Tel: 613-533-6821 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |
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From: Evgeny O. <joe...@gm...> - 2021-04-08 14:51:18
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Hi Chen, you can use distance command or cmd.distance for scripting purposes. Just specify mode 2 in order to search for polar contacts: https://pymolwiki.org/index.php/Distance пн, 22 мар. 2021 г. в 18:53, Chen, Qiang <qi...@pi...>: > Hi, Pymol Users, > > I used this script to find hydrogen-bond in protein, list_hb.py. > > list_hb all, all, write_distances_file=hb > > I find there are some pairs are clearly not hydrogen bonds, e.g. > A/VAL`257/O/774 A/MET`261/O/834 2.87 > > Also, the angle is not right for certain pair > > A/HIS`400/NE2/2977 B/GLN`403/OE1/7093 2.66 > > In the protein, the angle between NE2-H-OE1 is 100.8 deg > > Any suggestion to find out the correct hydrogen-bonding pairs? > > Thanks! > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
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From: sonia d. <rs1...@gj...> - 2021-04-08 14:09:42
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Dear users I have installed pymol using command sudo apt install pymol in linux . It's open source . It opens but when I use pointer to adjust the things it disappears saying segementation failed core dump. I have python 2 to 3 upgraded with pip and numpy modules .Please help. |
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From: Chen, Q. <qi...@pi...> - 2021-04-07 04:33:01
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Hi, Pymol-users I have a pentameric protein. However, the PDB only contain one subunit with Biomt info provided as the follows. How can I generate the other four subunit and get the whole pentamer in pymol? Thanks! REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, O, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, O, B, C REMARK 350 BIOMT1 2 0.309017 -0.951057 0.000000 239.91182 REMARK 350 BIOMT2 2 0.951057 0.309017 0.000000 -37.99830 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, O, B, C REMARK 350 BIOMT1 3 -0.809017 -0.587785 0.000000 350.18719 REMARK 350 BIOMT2 3 0.587785 -0.809017 0.000000 178.42929 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, O, B, C REMARK 350 BIOMT1 4 -0.809017 0.587785 0.000000 178.42929 REMARK 350 BIOMT2 4 -0.587785 -0.809017 0.000000 350.18719 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, O, B, C REMARK 350 BIOMT1 5 0.309017 0.951057 0.000000 -37.99830 REMARK 350 BIOMT2 5 -0.951057 0.309017 0.000000 239.91182 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 |
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From: Stewart M. <st...@mo...> - 2021-04-03 17:47:36
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I am looking for someone to help render in Pymol for a biotech website. How do I find anyone who can help with some projects I have? thank you <https://monderer.com/> Stewart Monderer Principal, Monderer Design monderer.com <http://monderer.com/> 617-661-6125 <https://twitter.com/mondererdesigns> <https://www.instagram.com/mondererdesign/> <https://www.linkedin.com/in/stewartmonderer> |
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From: sunyeping <sun...@al...> - 2021-04-01 16:11:48
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Dear all, I wish to label residue name on top of sphere representation, but I find it is difficult. I tried the following command select sele, c. A & resi 47 & name CB show sphere, c. A & resi 47 lable sele, "Y47" I and the "Y47" label is hidden inside the sphere and cannot be seen. Even if I set the sphere to be 80 % transparency, the label cannot be seen yet. So what the the correct way to make such a labelling? Best regards, Yeping Sun |
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From: Irwin S. <irw...@po...> - 2021-04-01 14:01:23
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Hi, Apologies if this is a rudimentary question. I'd like to display an internal binding pocket around a compound as a surface (or mesh). I don't need to detect the presence of a cavity but simply show its approximate boundaries. 1. Is there a way to display the cavity as a surface about specific residues or objects? 2. Is there a way to display the cavity as a mesh instead of a surface? 3. Can the transparency of a mesh be set to a user defined value? Thanks in advance for your help, Irwin |
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From: Peter K. <pk...@se...> - 2021-03-28 02:04:14
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Dear All, How can I embed a Pymol window within a Powerpoint slide that has other material in the slide? Thanks, -- Peter C. Kahn, Ph.D. Professor of Biochemistry Department of Biochemistry & Microbiology Rutgers University 76 Lipman Drive New Brunswick, NJ 08901 Telephone: 848-932-5618 Telefax: 732-932-8965 Email: pet...@ru... |
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From: András F. W. <wac...@tt...> - 2021-03-24 09:22:13
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Dear fellow PyMOL users,
I have found a solution (at least a workaround):
pymol -cpihq <<EOF
import pymol.plugins
pymol.plugins.initialize(-1)
...
EOF
This way all plug-ins are loaded in the same way as when graphics mode
is used, but the legacy Tk-based app part (which threw the exception) is
not initialized.
Kind regards,
Andras
On 3/24/21 9:48 AM, András Ferenc WACHA wrote:
> Dear fellow PyMOL users,
>
> I'm trying to run open source PyMOL v2.4.0 on a Linux computer with no
> X11 available (as part of a script on a HPC cluster). I noticed that
> plug-ins are not loaded automatically, therefore I force the required
> plug-in (pmlbeta) to load as follows:
>
> pymol -cpihq <<EOF
>
> import pymol.plugins
>
> pymol.plugins.plugin_load('pmlbeta') # or "apbs_tools" or
> "lightingsettings_gui"
>
> EOF
>
> However, an exception is thrown by PyMOL:
>
> Exception in thread Thread-2:
> Traceback (most recent call last):
> File "/opt/miniconda3/envs/gmxbatch/lib/python3.9/threading.py",
> line 954, in _bootstrap_inner
> self.run()
> File "/opt/miniconda3/envs/gmxbatch/lib/python3.9/threading.py",
> line 892, in run
> self._target(*self._args, **self._kwargs)
> File
> "/opt/miniconda3/envs/gmxbatch/lib/python3.9/site-packages/pymol/plugins/legacysupport.py",
> line 134, in starttk
> app.root = Tkinter.Tk()
> File
> "/opt/miniconda3/envs/gmxbatch/lib/python3.9/tkinter/__init__.py",
> line 2270, in __init__
> self.tk = _tkinter.create(screenName, baseName, className,
> interactive, wantobjects, useTk, sync, use)
> _tkinter.TclError: no display name and no $DISPLAY environment variable
>
> I have ascertained that the exception occurs even before the
> __init__.py module of my plugin starts running.
>
> In principle, my plug-in does not strictly need graphics, I would like
> to use only the custom commands supplied by my plug-in (e.g. with
> cmd.extend()).
>
> Is this possible? Or do I do something wrong (e.g. the forced loading
> of the plug-in)?
>
> Kind regards,
>
> Andras Wacha
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
--
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible
Biological Nanochemistry Research Group (310)
Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences (RCNS)
Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.hu
CREDO SAXS instrument: http://credo.ttk.hu
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From: András F. W. <wac...@tt...> - 2021-03-24 09:06:10
|
Dear fellow PyMOL users,
I'm trying to run open source PyMOL v2.4.0 on a Linux computer with no
X11 available (as part of a script on a HPC cluster). I noticed that
plug-ins are not loaded automatically, therefore I force the required
plug-in (pmlbeta) to load as follows:
pymol -cpihq <<EOF
import pymol.plugins
pymol.plugins.plugin_load('pmlbeta') # or "apbs_tools" or
"lightingsettings_gui"
EOF
However, an exception is thrown by PyMOL:
Exception in thread Thread-2:
Traceback (most recent call last):
File "/opt/miniconda3/envs/gmxbatch/lib/python3.9/threading.py", line
954, in _bootstrap_inner
self.run()
File "/opt/miniconda3/envs/gmxbatch/lib/python3.9/threading.py", line
892, in run
self._target(*self._args, **self._kwargs)
File
"/opt/miniconda3/envs/gmxbatch/lib/python3.9/site-packages/pymol/plugins/legacysupport.py",
line 134, in starttk
app.root = Tkinter.Tk()
File
"/opt/miniconda3/envs/gmxbatch/lib/python3.9/tkinter/__init__.py", line
2270, in __init__
self.tk = _tkinter.create(screenName, baseName, className,
interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable
I have ascertained that the exception occurs even before the __init__.py
module of my plugin starts running.
In principle, my plug-in does not strictly need graphics, I would like
to use only the custom commands supplied by my plug-in (e.g. with
cmd.extend()).
Is this possible? Or do I do something wrong (e.g. the forced loading of
the plug-in)?
Kind regards,
Andras Wacha
--
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible
Biological Nanochemistry Research Group (310)
Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences (RCNS)
Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.hu
CREDO SAXS instrument: http://credo.ttk.hu
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From: Thomas H. <tho...@sc...> - 2021-03-23 10:26:52
|
Hi Roger, Looks like Open3dQSAR tries to use a pipe to communicate with PyMOL. That is possible with "PyMOLWin.exe +2", with "PyMOLWinWithConsole.bat" and with "Scripts\pymol.exe". I suggest that you try this: env pymol="C:\Users...\PyMOLWinWithConsole.bat" Hope that helps. Cheers, Thomas > On Mar 21, 2021, at 8:26 PM, Roger Vuong <rog...@bo...> wrote: > > Hi, > I am using Open3DQSAR and I am having trouble getting molecules to show in pymol using an educational license. In Open3DQSAR I am able to change the executable using the env pymol command, I then change the directory, then import the sdf file, and pymol opens but pymol does not show the molecules. The error points to a python script in pymol and states > Traceback (most recent call last): > File "C:\Users\roger\Appdata\Local\Schrodinger\Pymol2\lib\site-packages\pymol\parser.py", line 52, in stdin_reader > 1 = sys.stdin.readline() > AttributeError: 'NoneType' object has no attribute 'readline' > Screenshots are attached below. Do you have a solution to fix this problem? > Thanks, > Roger > <image.png> > <image.png> > <image.png> > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. |
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From: Chen, Q. <qi...@pi...> - 2021-03-22 17:52:01
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Hi, Pymol Users, I used this script to find hydrogen-bond in protein, list_hb.py. list_hb all, all, write_distances_file=hb I find there are some pairs are clearly not hydrogen bonds, e.g. A/VAL`257/O/774 A/MET`261/O/834 2.87 Also, the angle is not right for certain pair A/HIS`400/NE2/2977 B/GLN`403/OE1/7093 2.66 In the protein, the angle between NE2-H-OE1 is 100.8 deg Any suggestion to find out the correct hydrogen-bonding pairs? Thanks! |
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From: Roger V. <rog...@bo...> - 2021-03-21 19:48:20
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Hi, I am using Open3DQSAR and I am having trouble getting molecules to show in pymol using an educational license. In Open3DQSAR I am able to change the executable using the env pymol command, I then change the directory, then import the sdf file, and pymol opens but pymol does not show the molecules. The error points to a python script in pymol and states Traceback (most recent call last): File "C:\Users\roger\Appdata\Local\Schrodinger\Pymol2\lib\site-packages\pymol\parser.py", line 52, in stdin_reader 1 = sys.stdin.readline() AttributeError: 'NoneType' object has no attribute 'readline' Screenshots are attached below. Do you have a solution to fix this problem? Thanks, Roger [image: image.png] [image: image.png] [image: image.png] |
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From: Tamas H. <bio...@gm...> - 2021-03-19 18:20:48
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Hi, I would run HOLE, which detects the tunnel/channel and generates a file for you (SPH?) which is a pdb file with SPH (sphere) atoms corresponding to the tunnel/channel volume. You can select water molecules (or anything else) around these SPH atoms. Suggestion: the ends of the tunnel are broadening with a lot of spheres; you most likely want to remove those SHP atoms... Bests, Tamas On 3/19/21 6:31 PM, Jason Mosier wrote: > Hello, I was wondering if someone could help me screen for which > molecules are being found within the inside of a protein channel / > near the protein channel. I know I can search for the molecules within > 3.5 A of the protein, but this also results in finding the ones on the > outside. I know this is pretty specific and might be difficult to do, > but it would increase our accuracy a bunch because at the moment we > are hand picking which water molecules "seem" to be close to the > channel and our numbers are very inconsistent. Here is the current > code we are using: https://pastebin.com/1iBZ7rKi > <https://signaldomn.online/click?redirect=https%3A%2F%2Fpastebin.com%2F1iBZ7rKi&dID=1616175096424&linkName=https://pastebin.com/1iBZ7rKi> > > Best, > Jason M. > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
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