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From: Sibbald M. M. <m.j...@pl...> - 2023-09-02 07:40:57
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Hello, I am teaching at the Hanze University Groningen and I have used PyMol in two courses (Bioinformatics and Biochemistry) for a couple of years now without any problems. However, this year I have tried twice to get the educational license, but I did not receive the file with the license as it did the previous years. Some of my colleagues have tried as well, but with the same result: no license file received. I hope you someone can help me get the license so we can use PyMol again for our courses. Thank you. Kind regards, Mark |
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From: Mukhopadhyay, S. <shr...@me...> - 2023-08-24 22:59:22
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Hello Everyone, I am trying to find a way to calculate the buried surface area in a complex with 2 molecules using pymol. Can anyone direct me to the correct way to do it? I am currently trying out the following method, and I need to find out if there is anything else I need to do to do this calculation. (Sum of Obj1+Obj2 solvent accessible surface area)- (solvent accessible area of the complex of Obj1-Obj2) Thanks in advance! Best, Shreya This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. |
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From: Istvan K. <iko...@gm...> - 2023-08-17 14:50:24
|
<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div dir="ltr"></div><div dir="ltr">Thank you, I’ll do that. </div><div dir="ltr"><br></div><div dir="ltr"> Istvan</div><div dir="ltr"><br><blockquote type="cite">On Aug 17, 2023, at 12:17 AM, Jared Sampson <jar...@co...> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><div dir="ltr">Hi Istvan - <div><br></div><div>Most of the time a PDB or other data attachment is not necessary. Or if it is, someone from the community may ask you to send it to them individually (and confidentially) to help you offline. <div><br></div><div>Instead, you can try to describe the problem or issue you're having, possibly including an image or screenshot of what PyMOL is doing and tell us what you want it to do instead, or what you want to achieve. Image formats like .png and .jpg typically come through just fine, either inline or as attachments.<div><br></div></div></div><div>Hope that helps.</div><div><br></div><div>Cheers,</div><div>Jared</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Aug 16, 2023 at 11:54 PM Saurabh Gayali <<a href="mailto:sau...@gm...">sau...@gm...</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr">You can always upload zip to google drive and share link.<br clear="all"><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><div dir="ltr"></div><br><div><div dir="ltr" style="color:rgb(0,0,0);font-family:"Times New Roman";font-size:medium"><hr></div><div dir="ltr" style="color:rgb(0,0,0);font-family:"Times New Roman";font-size:medium"><div style="float:left;margin:2px 5px 5px 0px;padding-right:5px"><img src="https://i.imgur.com/KatpbrU.jpg" width="65px" height="65px" style="border: 0px; vertical-align: middle;" data-unique-identifier=""></div><div style="margin-top:0px;margin-left:74px"><p style="margin:0px 0px 10px;color:rgb(51,51,51);font-family:Helvetica,sans-serif;font-size:12px;line-height:14px;padding-left:0px"></p><div style="margin:10px 0px;color:rgb(51,51,51);font-family:Helvetica,sans-serif;font-size:12px;line-height:14px;padding-left:0px"><strong>Saurabh Gayali</strong> <br>Business Analyst [Excelra], Former Research Scientist [IGIB]<br><a href="mailto:sau...@gm..." style="background:transparent;color:rgb(66,139,202)" target="_blank">sau...@gm...</a> / +91 8800412916<br><a href="http://example.com/" rel="nofollow" style="background:transparent;color:rgb(66,139,202)" target="_blank"></a>Bangalore, India</div></div></div></div></div></div></div><br><div id="m_6979808724666197564gmail-mt-signature"> <table border="0" cellpadding="8" cellspacing="0"> <tbody><tr> <td> <a id="m_6979808724666197564gmail-signatureLink-logo" href="https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&" style="text-decoration:none" target="_blank"> <img src="https://s3.amazonaws.com/mailtrack-signature/sender-notified-72.gif" alt="Mailtrack" width="32" height="32" data-unique-identifier=""> </a> </td> <td> <span style="color:rgb(119,119,119)">Sender notified by</span> <br> <a id="m_6979808724666197564gmail-signatureLink-text" href="https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&" style="color:rgb(67,116,247)" target="_blank">Mailtrack</a> </td><td><span style="color:transparent;font-size:0px">17/08/23, 09:21:34 am</span></td> <td> </td> </tr> </tbody></table> </div></div><br><img width="0" height="0" alt="" style="display: flex;" src="https://mailtrack.io/trace/mail/2f4fb1dbc775c6f4dc772503ed23e2b88b404304.png?u=7591011" data-unique-identifier=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Aug 15, 2023 at 11:11 PM Istvan Kolossvary <<a href="mailto:iko...@gm..." target="_blank">iko...@gm...</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div style="font-size:large">Hi,</div><div style="font-size:large"><br></div><div style="font-size:large">I am trying to submit a question with a file attachment for illustration. However, I always get a "550 Blacklisted file extension detected" message, and the message is rejected. I tried .zip and then I just attached the .pdb files directly, but none of them were allowed. What type of file attachment is not blacklisted?</div><div style="font-size:large"><br></div><div style="font-size:large">Thank you very much,</div><div style="font-size:large"><br></div><div style="font-size:large"> Istvan<br></div></div> _______________________________________________<br> PyMOL-users mailing list<br> Archives: <a href="http://www.mail-archive.com/pym...@li..." rel="noreferrer" target="_blank">http://www.mail-archive.com/pym...@li...</a><br> Unsubscribe: <a href="https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe" rel="noreferrer" target="_blank">https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe</a></blockquote></div></div> _______________________________________________<br> PyMOL-users mailing list<br> Archives: <a href="http://www.mail-archive.com/pym...@li..." rel="noreferrer" target="_blank">http://www.mail-archive.com/pym...@li...</a><br> Unsubscribe: <a href="https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe" rel="noreferrer" target="_blank">https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe</a></blockquote></div> </div></blockquote></body></html> |
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From: Jared S. <jar...@co...> - 2023-08-17 05:08:44
|
Hi Istvan - Most of the time a PDB or other data attachment is not necessary. Or if it is, someone from the community may ask you to send it to them individually (and confidentially) to help you offline. Instead, you can try to describe the problem or issue you're having, possibly including an image or screenshot of what PyMOL is doing and tell us what you want it to do instead, or what you want to achieve. Image formats like .png and .jpg typically come through just fine, either inline or as attachments. Hope that helps. Cheers, Jared On Wed, Aug 16, 2023 at 11:54 PM Saurabh Gayali <sau...@gm...> wrote: > You can always upload zip to google drive and share link. > > ------------------------------ > > *Saurabh Gayali* > Business Analyst [Excelra], Former Research Scientist [IGIB] > sau...@gm... / +91 8800412916 > <http://example.com/>Bangalore, India > > [image: Mailtrack] > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender > notified by > Mailtrack > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 17/08/23, > 09:21:34 am > > On Tue, Aug 15, 2023 at 11:11 PM Istvan Kolossvary <iko...@gm...> > wrote: > >> Hi, >> >> I am trying to submit a question with a file attachment for illustration. >> However, I always get a "550 Blacklisted file extension detected" message, >> and the message is rejected. I tried .zip and then I just attached the .pdb >> files directly, but none of them were allowed. What type of file attachment >> is not blacklisted? >> >> Thank you very much, >> >> Istvan >> _______________________________________________ >> 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: Saurabh G. <sau...@gm...> - 2023-08-17 03:52:10
|
You can always upload zip to google drive and share link. ------------------------------ *Saurabh Gayali* Business Analyst [Excelra], Former Research Scientist [IGIB] sau...@gm... / +91 8800412916 <http://example.com/>Bangalore, India [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 17/08/23, 09:21:34 am On Tue, Aug 15, 2023 at 11:11 PM Istvan Kolossvary <iko...@gm...> wrote: > Hi, > > I am trying to submit a question with a file attachment for illustration. > However, I always get a "550 Blacklisted file extension detected" message, > and the message is rejected. I tried .zip and then I just attached the .pdb > files directly, but none of them were allowed. What type of file attachment > is not blacklisted? > > Thank you very much, > > Istvan > _______________________________________________ > 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: Norbert S. <st...@bb...> - 2023-08-15 18:51:17
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Dear Istvan, I do not know what the policy is here, but perhaps a file sharing platform is a better solution rather than sending these data to everybody on the list. Best regards, Norbert Am 15.08.2023 um 19:40 schrieb Istvan Kolossvary: > Hi, > > I am trying to submit a question with a file attachment for > illustration. However, I always get a "550 Blacklisted file extension > detected" message, and the message is rejected. I tried .zip and then > I just attached the .pdb files directly, but none of them were > allowed. What type of file attachment is not blacklisted? > > Thank you very much, > > Istvan > > > _______________________________________________ > PyMOL-users mailing list > Archives:http://www.mail-archive.com/pym...@li... > Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- ----------------------------------------------------------------------------- Norbert Straeter fon +49 (0)341-97-31311 Univ.-Prof. Dr. rer. nat. Center for Biotechnology and Biomedicine Institute of Bioanalytical Chemistry Faculty of Chemistry and Mineralogy Leipzig University Deutscher Platz 5 04103 Leipzig, Ger...@bb... https://www.bbz.uni-leipzig.de/en/research/structural-analysis-of-biopolymers ----------------------------------------------------------------------------- |
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From: Istvan K. <iko...@gm...> - 2023-08-15 17:40:21
|
Hi, I am trying to submit a question with a file attachment for illustration. However, I always get a "550 Blacklisted file extension detected" message, and the message is rejected. I tried .zip and then I just attached the .pdb files directly, but none of them were allowed. What type of file attachment is not blacklisted? Thank you very much, Istvan |
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From: Istvan K. <iko...@gm...> - 2023-08-15 02:36:06
|
Hi, I have a homo trimer protein structure in two different conformations. However, one conformation has different atom ordering and an additional residue. This has never been a problem, though, since align does sequence alignment, so I am not sure why morphing (Pymol 2.5) gives completely crazy morphing frames with atoms all over the place. The only difference is that this is a homo trimer as opposed to a single chain protein. Could a homo trimer somehow confuse the morphing algorithm? As an example, I attached 3 PDB files. A.pdb can be morphed to B.pdb perfectly fine, but morphing A2.pdb (which is very similar to A.pdb) to B.pdb gives the crazy results I mentioned. Thank you for your kind assistance. Best regards, Istvan |
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From: Norbert S. <st...@bb...> - 2023-08-03 08:59:21
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Dear Shreya, one further possibility is to create a new object using the named chains: reinitialize fetch 6ous create trimer1, chain A+C+E+B+D+F disable 6ous alternatively, you could delete all other chains: reinitialize fetch 6ous remove not chain A+C+E+B+D+F It is usually necessary (or at least preferable) to make yourself familiar with the PyMOL selection algebra and some basic commands to show selected residues. Working only with the GUI, you could use: Menu: Display, Sequence Mode, Chain Identifiers Menu: Display, Sequence Next you select the chains you want to show (CTRL or Strg and left mouse click) Finally you use the command buttons next to the selection (sele): A, copy to object, new Best, Norbert Am 03.08.2023 um 09:57 schrieb Saurabh Gayali: > Have you tried this: > https://pymolwiki.org/index.php/Split_object > > ------------------------------------------------------------------------ > *Saurabh Gayali* > Business Analyst [Excelra], Former Research Scientist [IGIB] > sau...@gm... / +91 8800412916 > Bangalore, India > > > Mailtrack > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> > Sender notified by > Mailtrack > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> > 03/08/23, 01:27:34 pm > > > On Thu, Aug 3, 2023 at 8:15 AM Mukhopadhyay, Shreya via PyMOL-users > <pym...@li...> wrote: > > Public > > > Hello All, > > I am trying to separate out two molecules(one copy for each of > RSVF F1 and F2) from one pdb (6OUS). It’s a trimeric protein bound > to a Fab. > > I want to separate out RSVF1 and F2 proteins as one object from > the bound antibody, ie create one object with only chains A,C,E > and B,D,F. If you could explain the commands to use that will be > really helpful to me. > > Thanks, > > Shreya > > Shreya Mukhopadhyay, PhD.(She/Her) > *Post Doc Fellow (Infectious Diseases and Vaccines-Discovery)* > > 770 Sumneytown Pike, West Point B46, 2048-C, PA 19486 > > This e-mail message, together with any attachments, > contains information of Merck & Co., Inc. (126 East Lincoln Ave., > P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that > may be confidential, proprietary copyrighted and/or legally > privileged. (Direct contact information for affiliates is > available at - Contact us - MSD > <https://www.msd.com/contact-us/>.) It is intended solely for the > use of the individual or entity named on this message. If you > are not the intended recipient, and have received this message in > error, please notify us immediately by reply e-mail and then > delete it from your system. > > _______________________________________________ > 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 -- ----------------------------------------------------------------------------- Norbert Straeter fon +49 (0)341-97-31311 Univ.-Prof. Dr. rer. nat. Center for Biotechnology and Biomedicine Institute of Bioanalytical Chemistry Faculty of Chemistry and Mineralogy Leipzig University Deutscher Platz 5 04103 Leipzig, Ger...@bb... https://www.bbz.uni-leipzig.de/en/research/structural-analysis-of-biopolymers ----------------------------------------------------------------------------- |
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From: Saurabh G. <sau...@gm...> - 2023-08-03 07:57:58
|
Have you tried this: https://pymolwiki.org/index.php/Split_object ------------------------------ *Saurabh Gayali* Business Analyst [Excelra], Former Research Scientist [IGIB] sau...@gm... / +91 8800412916 <http://example.com/>Bangalore, India [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 03/08/23, 01:27:34 pm On Thu, Aug 3, 2023 at 8:15 AM Mukhopadhyay, Shreya via PyMOL-users < pym...@li...> wrote: > Public > > Hello All, > > > > I am trying to separate out two molecules(one copy for each of RSVF F1 and > F2) from one pdb (6OUS). It’s a trimeric protein bound to a Fab. > > > > I want to separate out RSVF1 and F2 proteins as one object from the bound > antibody, ie create one object with only chains A,C,E and B,D,F. If you > could explain the commands to use that will be really helpful to me. > > > > Thanks, > > Shreya > > > > > > Shreya Mukhopadhyay, PhD. (She/Her) > *Post Doc Fellow (Infectious Diseases and Vaccines-Discovery)* > > 770 Sumneytown Pike, West Point B46, 2048-C, PA 19486 > > > > > > This e-mail message, together with any attachments, contains information > of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA > 07065) and/or its affiliates, that may be confidential, proprietary > copyrighted and/or legally privileged. (Direct contact information for > affiliates is available at - Contact us - MSD > <https://www.msd.com/contact-us/>.) It is intended solely for the use of > the individual or entity named on this message. If you are not the intended > recipient, and have received this message in error, please notify us > immediately by reply e-mail and then delete it from your system. > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > |
|
From: Mukhopadhyay, S. <shr...@me...> - 2023-08-03 02:43:11
|
Public Hello All, I am trying to separate out two molecules(one copy for each of RSVF F1 and F2) from one pdb (6OUS). It's a trimeric protein bound to a Fab. I want to separate out RSVF1 and F2 proteins as one object from the bound antibody, ie create one object with only chains A,C,E and B,D,F. If you could explain the commands to use that will be really helpful to me. Thanks, Shreya Shreya Mukhopadhyay, PhD. (She/Her) Post Doc Fellow (Infectious Diseases and Vaccines-Discovery) 770 Sumneytown Pike, West Point B46, 2048-C, PA 19486 [cid:image001.png@01D9C55F.2D2C6730] This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. |
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From: Jarrett J. <jar...@sc...> - 2023-07-24 19:09:46
|
Hi Mark,
Great question. I currently cannot see a way to do so. I think the color
command when providing a ramp should, by intention, color the cartoon, but
there may be a bug or this might not have been implemented yet (the cartoon
removes its color and is set to white). I have a workaround if the only
thing you need to do is color atoms by proximity to another object (using
the example from the `ramp_new` PyMOLWiki documentation). Note that the
color smoothing is not as good as using the `ramp_new` command:
from pymol import cmd
def set_property_proximity_to(obj, target, ramp='red yellow', minimum=None,
maximum=None):
ligand_atoms = []
cmd.iterate_state(0, target, 'ligand_atoms.append((x, y, z))', space=
locals())
def find_nearest_dist(x, y, z):
min2 = min((x - x1) ** 2 + (y - y1) ** 2 + (z - z1) ** 2
for x1, y1, z1 in ligand_atoms)
return min2 ** 0.5
nearest_ds = []
cmd.alter_state(0, obj, 'nearest_ds.append(find_nearest_dist(x, y, z))',
space=locals())
# Hijack 'b' property for closest distance
cmd.alter(obj, 'b = nearest_ds[index-1]', space=locals())
cmd.spectrum('b', palette='red yellow', selection=obj, minimum=minimum,
maximum=maximum)
cmd.fetch('1rx1')
cmd.extract('ligand', 'organic')
set_property_proximity_to('1rx1', 'ligand', ramp='red yellow', minimum=4,
maximum=8)
cmd.color('blue', 'ligand')
cmd.show('surface', 'ligand')
I'll do some investigation regarding why ramp coloring for cartoons isn't
working as intended (assuming there isn't something I'm missing already).
Hope this helps,
Jarrett J
On Mon, Jul 24, 2023 at 1:27 PM Foster, Mark <fos...@os...> wrote:
> Thanks Jarrett for the response.
>
>
>
> I think `spectrum` should work, but I can’t figure out how to access the
> proximity parameter calculated by `ramp_new` in order to use it directly
> (e.g., “p.prox”), or to map it to the b factor.
>
>
>
> Does ramp_new store the values in an array?
>
>
>
> -M
>
>
>
>
>
> *From: *Jarrett Johnson <jar...@sc...>
> *Date: *Monday, July 24, 2023 at 12:02 PM
> *To: *Foster, Mark <fos...@os...>
> *Cc: *pym...@li... <pym...@li...
> >
> *Subject: *Re: [PyMOL] Map to cartoon
>
> Hi Mark, Does the `spectrum` command cover your use case? https:
> //pymolwiki. org/index. php/Spectrum . You can specify an atomic property
> and map specified colors to a range of the given property. Hope that helps,
> Jarrett J. On Mon, Jul 24, 2023
>
> Hi Mark,
>
> Does the `spectrum` command cover your use case?
> https://pymolwiki.org/index.php/Spectrum
> <https://urldefense.com/v3/__https:/pymolwiki.org/index.php/Spectrum__;!!KGKeukY!2YCpuhVe5GRqx_4jegX3LkI02R8BJqaQz4vDGwiaUTk4P0DKAA-uma5ffkB7b706ohBs7I5Alp7QFqei3X8edZnW_j-ow-ipqQ$>
> . You can specify an atomic property and map specified colors to a range of
> the given property.
>
> Hope that helps,
> Jarrett J.
>
>
>
> On Mon, Jul 24, 2023 at 9:21 AM Foster, Mark <fos...@os...> wrote:
>
> PyMOL fans,
>
>
>
> Is possible to use ramp_new to color cartoons, in addition to atoms and
> surfaces?
>
>
>
> I assume ramp_new stores the property to be mapped in a variable that
> could be used for the CA atom color.
>
>
>
> color prox, (sele) sets the color of each atom, but not the cartoon.
>
>
>
> Thanks in advance,
>
>
>
> -M
>
>
>
>
>
> —
>
> Mark P. Foster, Professor, he/him
> Department of Chemistry and Biochemistry
> The Ohio State University
> 734 Riffe Building
> 484 West 12th Ave.
> Columbus, OH 43210-1214
> (614) 292-1377
> fos...@os...
> http://go.osu.edu/fosterlab
>
> ------------------------------------------------------
>
> Acknowledgement: The land that The Ohio State University occupies is the
> ancestral and contemporary territory of the Shawnee, Potawatomi, Delaware,
> Miami, Peoria, Seneca, Wyandotte, Ojibwe and Cherokee peoples. The
> university resides on land ceded in the 1795 Treaty of Greeneville and
> appropriated through the Indian Removal Act of 1830. As a land grant
> institution, we wish to honor the resiliency of these tribal nations and
> recognize the historical context that has and continues to affect the
> Indigenous peoples of this land.
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> <https://urldefense.com/v3/__http:/www.mail-archive.com/pym...@li....net__;!!KGKeukY!2YCpuhVe5GRqx_4jegX3LkI02R8BJqaQz4vDGwiaUTk4P0DKAA-uma5ffkB7b706ohBs7I5Alp7QFqei3X8edZnW_j_ykYKLTA$>
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> <https://urldefense.com/v3/__https:/sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe__;!!KGKeukY!2YCpuhVe5GRqx_4jegX3LkI02R8BJqaQz4vDGwiaUTk4P0DKAA-uma5ffkB7b706ohBs7I5Alp7QFqei3X8edZnW_j-zaggDrQ$>
>
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
> [image: Image removed by sender.]
>
>
>
--
*Jarrett Johnson* | Senior Developer, PyMOL
|
|
From: Jarrett J. <jar...@sc...> - 2023-07-24 16:02:49
|
Hi Mark, Does the `spectrum` command cover your use case? https://pymolwiki.org/index.php/Spectrum . You can specify an atomic property and map specified colors to a range of the given property. Hope that helps, Jarrett J. On Mon, Jul 24, 2023 at 9:21 AM Foster, Mark <fos...@os...> wrote: > PyMOL fans, > > > > Is possible to use ramp_new to color cartoons, in addition to atoms and > surfaces? > > > > I assume ramp_new stores the property to be mapped in a variable that > could be used for the CA atom color. > > > > color prox, (sele) sets the color of each atom, but not the cartoon. > > > > Thanks in advance, > > > > -M > > > > > > — > > Mark P. Foster, Professor, he/him > Department of Chemistry and Biochemistry > The Ohio State University > 734 Riffe Building > 484 West 12th Ave. > Columbus, OH 43210-1214 > (614) 292-1377 > fos...@os... > http://go.osu.edu/fosterlab > > ------------------------------------------------------ > > Acknowledgement: The land that The Ohio State University occupies is the > ancestral and contemporary territory of the Shawnee, Potawatomi, Delaware, > Miami, Peoria, Seneca, Wyandotte, Ojibwe and Cherokee peoples. The > university resides on land ceded in the 1795 Treaty of Greeneville and > appropriated through the Indian Removal Act of 1830. As a land grant > institution, we wish to honor the resiliency of these tribal nations and > recognize the historical context that has and continues to affect the > Indigenous peoples of this land. > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > -- *Jarrett Johnson* | Senior Developer, PyMOL |
|
From: Foster, M. <fos...@os...> - 2023-07-24 13:19:21
|
PyMOL fans, Is possible to use ramp_new to color cartoons, in addition to atoms and surfaces? I assume ramp_new stores the property to be mapped in a variable that could be used for the CA atom color. color prox, (sele) sets the color of each atom, but not the cartoon. Thanks in advance, -M — Mark P. Foster, Professor, he/him Department of Chemistry and Biochemistry The Ohio State University 734 Riffe Building 484 West 12th Ave. Columbus, OH 43210-1214 (614) 292-1377 fos...@os...<mailto:fos...@os...> http://go.osu.edu/fosterlab ------------------------------------------------------ Acknowledgement: The land that The Ohio State University occupies is the ancestral and contemporary territory of the Shawnee, Potawatomi, Delaware, Miami, Peoria, Seneca, Wyandotte, Ojibwe and Cherokee peoples. The university resides on land ceded in the 1795 Treaty of Greeneville and appropriated through the Indian Removal Act of 1830. As a land grant institution, we wish to honor the resiliency of these tribal nations and recognize the historical context that has and continues to affect the Indigenous peoples of this land. |
|
From: Neena S. E. <nee...@gm...> - 2023-07-20 15:05:22
|
Thank you so much Jarrett, yes it works very well!
On Thu, 20 Jul 2023 at 08:51, Jarrett Johnson <
jar...@sc...> wrote:
> Sorry, typo. For the second approach, state should be `i + 1` and not `-1`"
>
> Jarrett J.
>
> On Thu, Jul 20, 2023 at 8:49 AM Jarrett Johnson <
> jar...@sc...> wrote:
>
>> Hi Neena,
>>
>> Is the split_states necessary? You can query the distance between atoms
>> on the state-level as well without having to break up your structure.
>> Here's two approaches that show either way; I recommend the second if
>> possible. You'll of course have to switch out the selection string to fit
>> your own atom pairs.
>>
>> from pymol import cmd
>>
>> # Approach 1: With splitting states
>>
>> cmd.fetch('1L2Y')
>> cmd.split_states('1L2Y')
>> for i in range(cmd.count_states('1L2Y')):
>> nmr_frame = f"1L2Y_{i + 1:04d}"
>> sele1 = f"/{nmr_frame}/A/A/ILE`4/O"
>> sele2 = f"/{nmr_frame}/A/A/ASP`9/CA"
>> dist = cmd.dist(f"dist_{nmr_frame}", sele1, sele2)
>> print(dist)
>>
>> print("--------------------")
>>
>> # Approach 2: Without splitting states
>>
>> for i in range(cmd.count_states('1L2Y')):
>> sele1 = "/1L2Y/A/A/ILE`4/O"
>> sele2 = "/1L2Y/A/A/ASP`9/CA"
>> dist = cmd.get_distance(sele1, sele2, state=-1)
>> print(dist)
>>
>>
>> Hope that helps,
>> Jarrett J
>>
>>
>> On Wed, Jul 19, 2023 at 9:48 PM Neena Susan Eappen <
>> nee...@gm...> wrote:
>>
>>> Hello PyMOL users,
>>>
>>> Can I get some insight on how to approach this analysis?
>>>
>>> Many thanks,
>>> Neena
>>>
>>> On Wed, 5 Jul 2023 at 18:54, Neena Susan Eappen <nee...@gm...>
>>> wrote:
>>>
>>>> Hello PyMOL Team,
>>>>
>>>> I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has
>>>> 38 NMR structures deposited in it.
>>>> Using split_states command, I can see all 38 structures.
>>>> I want to find polar contacts between same 3 residues in all these 38
>>>> structures and extract corresponding distance values for polar contacts.
>>>>
>>>> Question: Is there a single command to select 3 residues in all these
>>>> 38 structures and find polar contacts within this selection?
>>>>
>>>> Many thanks,
>>>> Neena
>>>>
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li...
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>>
>>
>> --
>>
>> *Jarrett Johnson* | Senior Developer, PyMOL
>>
>>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>
|
|
From: Jarrett J. <jar...@sc...> - 2023-07-20 13:17:41
|
Sorry, typo. For the second approach, state should be `i + 1` and not `-1`"
Jarrett J.
On Thu, Jul 20, 2023 at 8:49 AM Jarrett Johnson <
jar...@sc...> wrote:
> Hi Neena,
>
> Is the split_states necessary? You can query the distance between atoms on
> the state-level as well without having to break up your structure. Here's
> two approaches that show either way; I recommend the second if possible.
> You'll of course have to switch out the selection string to fit your own
> atom pairs.
>
> from pymol import cmd
>
> # Approach 1: With splitting states
>
> cmd.fetch('1L2Y')
> cmd.split_states('1L2Y')
> for i in range(cmd.count_states('1L2Y')):
> nmr_frame = f"1L2Y_{i + 1:04d}"
> sele1 = f"/{nmr_frame}/A/A/ILE`4/O"
> sele2 = f"/{nmr_frame}/A/A/ASP`9/CA"
> dist = cmd.dist(f"dist_{nmr_frame}", sele1, sele2)
> print(dist)
>
> print("--------------------")
>
> # Approach 2: Without splitting states
>
> for i in range(cmd.count_states('1L2Y')):
> sele1 = "/1L2Y/A/A/ILE`4/O"
> sele2 = "/1L2Y/A/A/ASP`9/CA"
> dist = cmd.get_distance(sele1, sele2, state=-1)
> print(dist)
>
>
> Hope that helps,
> Jarrett J
>
>
> On Wed, Jul 19, 2023 at 9:48 PM Neena Susan Eappen <
> nee...@gm...> wrote:
>
>> Hello PyMOL users,
>>
>> Can I get some insight on how to approach this analysis?
>>
>> Many thanks,
>> Neena
>>
>> On Wed, 5 Jul 2023 at 18:54, Neena Susan Eappen <nee...@gm...>
>> wrote:
>>
>>> Hello PyMOL Team,
>>>
>>> I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has
>>> 38 NMR structures deposited in it.
>>> Using split_states command, I can see all 38 structures.
>>> I want to find polar contacts between same 3 residues in all these 38
>>> structures and extract corresponding distance values for polar contacts.
>>>
>>> Question: Is there a single command to select 3 residues in all these 38
>>> structures and find polar contacts within this selection?
>>>
>>> Many thanks,
>>> Neena
>>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>
--
*Jarrett Johnson* | Senior Developer, PyMOL
|
|
From: Jarrett J. <jar...@sc...> - 2023-07-20 13:14:15
|
Hi Neena,
Is the split_states necessary? You can query the distance between atoms on
the state-level as well without having to break up your structure. Here's
two approaches that show either way; I recommend the second if possible.
You'll of course have to switch out the selection string to fit your own
atom pairs.
from pymol import cmd
# Approach 1: With splitting states
cmd.fetch('1L2Y')
cmd.split_states('1L2Y')
for i in range(cmd.count_states('1L2Y')):
nmr_frame = f"1L2Y_{i + 1:04d}"
sele1 = f"/{nmr_frame}/A/A/ILE`4/O"
sele2 = f"/{nmr_frame}/A/A/ASP`9/CA"
dist = cmd.dist(f"dist_{nmr_frame}", sele1, sele2)
print(dist)
print("--------------------")
# Approach 2: Without splitting states
for i in range(cmd.count_states('1L2Y')):
sele1 = "/1L2Y/A/A/ILE`4/O"
sele2 = "/1L2Y/A/A/ASP`9/CA"
dist = cmd.get_distance(sele1, sele2, state=-1)
print(dist)
Hope that helps,
Jarrett J
On Wed, Jul 19, 2023 at 9:48 PM Neena Susan Eappen <nee...@gm...>
wrote:
> Hello PyMOL users,
>
> Can I get some insight on how to approach this analysis?
>
> Many thanks,
> Neena
>
> On Wed, 5 Jul 2023 at 18:54, Neena Susan Eappen <nee...@gm...>
> wrote:
>
>> Hello PyMOL Team,
>>
>> I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has 38
>> NMR structures deposited in it.
>> Using split_states command, I can see all 38 structures.
>> I want to find polar contacts between same 3 residues in all these 38
>> structures and extract corresponding distance values for polar contacts.
>>
>> Question: Is there a single command to select 3 residues in all these 38
>> structures and find polar contacts within this selection?
>>
>> Many thanks,
>> Neena
>>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
--
*Jarrett Johnson* | Senior Developer, PyMOL
|
|
From: Istvan K. <iko...@gm...> - 2023-07-20 03:31:03
|
Hi Jarrett, Thank you very much for the fix, it works perfectly. Best regards, Istvan On Wed, Jul 19, 2023 at 9:02 PM Jarrett Johnson < jar...@sc...> wrote: > Hi Istvan, > > I can reproduce the same issue. Seems to be some unintended behavior with > how this multistate pseudoatom object is created. I've attached a modified > center_of_mass.py script so that it should behave the way you expect. Let > me know if this works for you. > > Example that I tried with this: > > fetch 1nmr > run center_of_mass_states_joined.py > com 1nmr, object=COM > wizard distance > # created distances between traj atom and pseudoatom > > Hope that helps, > Jarrett J. > > On Tue, Jul 18, 2023 at 12:52 PM Istvan Kolossvary <iko...@gm...> > wrote: > >> Hi, >> >> I have a simulation trajectory loaded in Pymol and I want to display >> certain interatomic distances interactively. This works perfectly fine with >> normal atoms, I can see how these selected distances change over the course >> of the simulation using the wizard and playing the movie. However, it seems >> that this feature doesn't work with pseudo atoms. I defined a couple of >> center-of-mass pseudo atoms using this script >> http://www.pymolwiki.org/index.php/center_of_mass. The script creates >> separate objects corresponding to the different COMs and each COM object >> has the same number of states as the trajectory object. I can use the >> wizard, select the distances, which show on the display, but when I play >> the movie, the distance values are not updated while the pseudo atoms do >> move around. The first thing I figured was that maybe the COM objects >> should be merged in a single object. So, I did that but to no avail, the >> distances are not updated while I play the movie. I must be overlooking >> something, can you tell me why this is not working? >> >> Thank you very much, >> >> Istvan >> _______________________________________________ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pym...@li... >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > > -- > > *Jarrett Johnson* | Senior Developer, PyMOL > > |
|
From: Neena S. E. <nee...@gm...> - 2023-07-20 01:47:03
|
Hello PyMOL users, Can I get some insight on how to approach this analysis? Many thanks, Neena On Wed, 5 Jul 2023 at 18:54, Neena Susan Eappen <nee...@gm...> wrote: > Hello PyMOL Team, > > I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has 38 > NMR structures deposited in it. > Using split_states command, I can see all 38 structures. > I want to find polar contacts between same 3 residues in all these 38 > structures and extract corresponding distance values for polar contacts. > > Question: Is there a single command to select 3 residues in all these 38 > structures and find polar contacts within this selection? > > Many thanks, > Neena > |
|
From: Jarrett J. <jar...@sc...> - 2023-07-20 01:03:00
|
Hi Istvan, I can reproduce the same issue. Seems to be some unintended behavior with how this multistate pseudoatom object is created. I've attached a modified center_of_mass.py script so that it should behave the way you expect. Let me know if this works for you. Example that I tried with this: fetch 1nmr run center_of_mass_states_joined.py com 1nmr, object=COM wizard distance # created distances between traj atom and pseudoatom Hope that helps, Jarrett J. On Tue, Jul 18, 2023 at 12:52 PM Istvan Kolossvary <iko...@gm...> wrote: > Hi, > > I have a simulation trajectory loaded in Pymol and I want to display > certain interatomic distances interactively. This works perfectly fine with > normal atoms, I can see how these selected distances change over the course > of the simulation using the wizard and playing the movie. However, it seems > that this feature doesn't work with pseudo atoms. I defined a couple of > center-of-mass pseudo atoms using this script > http://www.pymolwiki.org/index.php/center_of_mass. The script creates > separate objects corresponding to the different COMs and each COM object > has the same number of states as the trajectory object. I can use the > wizard, select the distances, which show on the display, but when I play > the movie, the distance values are not updated while the pseudo atoms do > move around. The first thing I figured was that maybe the COM objects > should be merged in a single object. So, I did that but to no avail, the > distances are not updated while I play the movie. I must be overlooking > something, can you tell me why this is not working? > > Thank you very much, > > Istvan > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL |
|
From: Istvan K. <iko...@gm...> - 2023-07-18 16:50:44
|
Hi, I have a simulation trajectory loaded in Pymol and I want to display certain interatomic distances interactively. This works perfectly fine with normal atoms, I can see how these selected distances change over the course of the simulation using the wizard and playing the movie. However, it seems that this feature doesn't work with pseudo atoms. I defined a couple of center-of-mass pseudo atoms using this script http://www.pymolwiki.org/index.php/center_of_mass. The script creates separate objects corresponding to the different COMs and each COM object has the same number of states as the trajectory object. I can use the wizard, select the distances, which show on the display, but when I play the movie, the distance values are not updated while the pseudo atoms do move around. The first thing I figured was that maybe the COM objects should be merged in a single object. So, I did that but to no avail, the distances are not updated while I play the movie. I must be overlooking something, can you tell me why this is not working? Thank you very much, Istvan |
|
From: Neena S. E. <nee...@gm...> - 2023-07-05 22:54:35
|
Hello PyMOL Team, I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has 38 NMR structures deposited in it. Using split_states command, I can see all 38 structures. I want to find polar contacts between same 3 residues in all these 38 structures and extract corresponding distance values for polar contacts. Question: Is there a single command to select 3 residues in all these 38 structures and find polar contacts within this selection? Many thanks, Neena |
|
From: Luke W. <lw...@ca...> - 2023-07-04 09:46:16
|
Hello, I have submitted the form to obtain an educational license for PyMOL (as I am a full-time student) but did not receive an email in response. Any help would be appreciated. Best wishes, Luke |
|
From: Zhou, Y. <yin...@no...> - 2023-06-29 21:57:05
|
Hi, Jarrett
This is more than helpful! I just need to fix my own mistake in the selection
cmd.select(base_interface, "byres((not (/base//H+L) & base) within 10 of /base//H+L)")
Maybe one more question:
Selection: “not (/base//H+L)” returns all residues in pred, as well as the P chain of base. I understand this.
However, why “not /base//H+L” returns an empty selection?
Thanks!
From: Jarrett Johnson <jar...@sc...>
Sent: Thursday, June 29, 2023 6:31 AM
To: Zhou, Yingyao <yin...@no...>
Cc: pym...@li...
Subject: Re: [PyMOL] Help with selecting interface residues between two structures
This Message is from an External Sender. Do not click links or open attachments unless you trust the sender.
Hi,
There might be a cleaner way to do this, but I propose creating a mapping of your chains from base to pred and use the `iterate` command to get the relevant identifiers and map them back to the prediction. Here is a full script that pulls from the PDB that attempts this idea.
from pymol
import cmd
# our reference
cmd.fetch('3hfm',
'base')
# dummy prediction
cmd.copy('pred',
'base')
# Heavy & Light chains in 3hfm are named L and H
# Antigen is Y so lets rename to A to simulate your case
cmd.alter('base & chain Y',
'chain="A"')
# change chain to emulate same residues different chain names
cmd.alter('pred & chain L',
'chain="A"')
cmd.alter('pred & chain H',
'chain="B"')
cmd.alter('pred & chain Y',
'chain="C"')
base_interface
= 'int_base'
cmd.select(base_interface,
'byres(base & (/base//H+L around 5))')
# After preparation:
# create a mapping of chains from base to pred
base_to_pred_chains
= {'L':
'A', 'H':
'B', 'A':
'C'}
# Create a list of identifiers in the interface from the selection
myspace
= {'int_set':
set()}
cmd.iterate(base_interface,
'int_set.add((chain, resi, resn))', space=myspace)
# Map them to a new selection onto the prediction
pred_interface
= 'int_pred'
cmd.select(pred_interface,
'none')
for
chain, resi,
resn in
myspace['int_set']:
new_chain
= base_to_pred_chains[chain]
# Add each pred residue to the selection
cmd.select(pred_interface,
f'pred & chain
{new_chain} & resi
{resi} & resn
{resn}',
merge=1)
Hope that helps,
Jarrett J
On Thu, Jun 29, 2023 at 12:59 AM Zhou, Yingyao via PyMOL-users <pym...@li...<mailto:pym...@li...>> wrote:
I am a relatively new PyMOL user and would like to get some helps from the community.
I have two structures for the same antibody-antigen complex (with three chains: light chain L, heavy chain H, and an antigen chain A) .
Structure “base” is the experimental true structure, structure “pred” is the predicted structure. My goal is to determine how close the predicted interface is w.r.t. the experimental truth.
I first select the interface residues as defined by “base”
load base.pdb
load pred.pdb
select int_base, byres(base & (/base//H+L around 5))
How do I select the same corresponding residues in object “pred”?
In addition, what if in the pred structure, chains are named A, B, and C, corresponding to base structure L, H, A, respectively, how will I handle that?
(I was planning to rename the chains, if there is no nice trick to transfer the selections from base to pred)
Thanks!
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--
Jarrett Johnson | Senior Developer, PyMOL
[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]
|
|
From: Jarrett J. <jar...@sc...> - 2023-06-29 13:31:33
|
Hi,
There might be a cleaner way to do this, but I propose creating a mapping
of your chains from base to pred and use the `iterate` command to get the
relevant identifiers and map them back to the prediction. Here is a full
script that pulls from the PDB that attempts this idea.
from pymol import cmd
# our reference
cmd.fetch('3hfm', 'base')
# dummy prediction
cmd.copy('pred', 'base')
# Heavy & Light chains in 3hfm are named L and H
# Antigen is Y so lets rename to A to simulate your case
cmd.alter('base & chain Y', 'chain="A"')
# change chain to emulate same residues different chain names
cmd.alter('pred & chain L', 'chain="A"')
cmd.alter('pred & chain H', 'chain="B"')
cmd.alter('pred & chain Y', 'chain="C"')
base_interface = 'int_base'
cmd.select(base_interface, 'byres(base & (/base//H+L around 5))')
# After preparation:
# create a mapping of chains from base to pred
base_to_pred_chains = {'L': 'A', 'H': 'B', 'A': 'C'}
# Create a list of identifiers in the interface from the selection
myspace = {'int_set': set()}
cmd.iterate(base_interface, 'int_set.add((chain, resi, resn))', space=
myspace)
# Map them to a new selection onto the prediction
pred_interface = 'int_pred'
cmd.select(pred_interface, 'none')
for chain, resi, resn in myspace['int_set']:
new_chain = base_to_pred_chains[chain]
# Add each pred residue to the selection
cmd.select(pred_interface,
f'pred & chain {new_chain} & resi {resi} & resn {resn}',
merge=1)
Hope that helps,
Jarrett J
On Thu, Jun 29, 2023 at 12:59 AM Zhou, Yingyao via PyMOL-users <
pym...@li...> wrote:
> I am a relatively new PyMOL user and would like to get some helps from the
> community.
>
>
>
> I have two structures for the same antibody-antigen complex (with three
> chains: light chain L, heavy chain H, and an antigen chain A) .
>
> Structure “base” is the experimental true structure, structure “pred” is
> the predicted structure. My goal is to determine how close the predicted
> interface is w.r.t. the experimental truth.
>
>
>
> I first select the interface residues as defined by “base”
>
>
>
> load base.pdb
>
> load pred.pdb
>
> select int_base, byres(base & (/base//H+L around 5))
>
>
>
> How do I select the same corresponding residues in object “pred”?
>
>
>
> In addition, what if in the pred structure, chains are named A, B, and C,
> corresponding to base structure L, H, A, respectively, how will I handle
> that?
>
> (I was planning to rename the chains, if there is no nice trick to
> transfer the selections from base to pred)
>
>
>
> Thanks!
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
--
*Jarrett Johnson* | Senior Developer, PyMOL
|
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