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From: Roger R. <rro...@co...> - 2023-10-06 14:27:27
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FYI, Pymol runs nicely on modern Chromebooks. You can install Pymol easily in the Linux container using *sudo apt install pymol*. I think the latest apt version is 2.4. CCP4i/Coot also runs nicely in the Linux container. (I'm using a Lenovo Flex 5i Chromebook, $320, as a test bed. This system has an Intel i3 CPU.) An Intel Chromebook might be an attractive option for undergrads for biochemistry classes and/or protein crystallography research projects. You can install Pymol in Windows with pip as well. Roger Rowlett Gordon & Dorothy Kline Professor, Emeritus Department of Chemistry Colgate University On Fri, Oct 6, 2023 at 5:49 AM Thomas Charles Pochapsky < poc...@br...> wrote: > Hi, all. Did anybody ever reply about the student version of PyMol > downloads? I use it in my class on a regular basis, but I can no longer > find the link on the Schrodinger web site. There is a free download for > Maestro, with which I am unfamiliar. Is this a replacement? > > Thanks. Tom > > > > _______________________________________________ > 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: Mooers, B. H.M. (HSC) <Bla...@ou...> - 2023-10-06 10:59:50
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Hi Tom, An alternative is to be to show your students how to install Anaconda and then install open source PyMOL, which lacks a few minor features of the incentive version but has more features than the student version. https://anaconda.org/conda-forge/pymol-open-source. It is likely that they will need Anaconda in the future to install other scientific computing software. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Physiology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center, Rm. 466 975 NE 10th Street<https://maps.google.com/?q=975+NE+10th+Street&entry=gmail&source=g>, BRC 466 Oklahoma City, OK 73104-5419 Central Time Zone (follows Daylight Savings Time) office: (405) 271-8300 lab: (405) 271-8313 Faculty webpage <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd-1> Laboratory of Biomolecular Structure and Function (X-ray crystallography lab)<https://research.ouhsc.edu/research-support/core-laboratory-services/laboratory-of-biomolecular-structure-and-function> SSRL Users Executive Committee<https://www-ssrl.slac.stanford.edu/content/about-ssrl/ssrluo-2022-2023-executive-committee-members><https://www-ssrl.slac.stanford.edu/content/about-ssrl/ssrluo-2022-2023-executive-committee-members> Center, ________________________________ From: Thomas Charles Pochapsky <poc...@br...> Sent: Friday, October 6, 2023 4:28 AM To: pym...@li... <pym...@li...> Subject: [EXTERNAL] [PyMOL] Student version Hi, all. Did anybody ever reply about the student version of PyMol downloads? I use it in my class on a regular basis, but I can no longer find the link on the Schrodinger web site. There is a free download for Maestro, with which I am unfamiliar. Is this a replacement? Thanks. Tom _______________________________________________ PyMOL-users mailing list Archives: https://urldefense.com/v3/__http://www.mail-archive.com/pym...@li...__;!!GNU8KkXDZlD12Q!6qyXPA9djwzIN-ekBa0_V2y5Q1f2UdHYpkf5NNqCVUc_JacvO8JHPvaC4bKhTKFhhL4H-ldFoxLn3QIHqARftZ0q2zg$ [mail-archive[.]com] Unsubscribe: https://urldefense.com/v3/__https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe__;!!GNU8KkXDZlD12Q!6qyXPA9djwzIN-ekBa0_V2y5Q1f2UdHYpkf5NNqCVUc_JacvO8JHPvaC4bKhTKFhhL4H-ldFoxLn3QIHqARfp2zYm2Y$ [sourceforge[.]net] |
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From: Thomas C. P. <poc...@br...> - 2023-10-06 10:14:09
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Blaine, Thanks! I'll try that. Tom On 10/6/23 5:58 AM, Mooers, Blaine H.M. (HSC) wrote: > Hi Tom, > > An alternative is to be to show your students how to install Anaconda > and then install open source PyMOL, > which lacks a few minor features of the incentive version but has more > features than the student version. > https://anaconda.org/conda-forge/pymol-open-source > <https://anaconda.org/conda-forge/pymol-open-source>. > > It is likely that they will need Anaconda in the future to install > other scientific computing software. > > Best regards, > > Blaine > > > Blaine Mooers, Ph.D. > Associate Professor > Department of Biochemistry and Physiology > College of Medicine > University of Oklahoma Health Sciences Center > S.L. Young Biomedical Research Center, Rm. 466 > 975 NE 10th Street > <https://maps.google.com/?q=975+NE+10th+Street&entry=gmail&source=g>, > BRC 466 > Oklahoma City, OK 73104-5419 > > Central Time Zone (follows Daylight Savings Time) > > office: (405) 271-8300 lab: (405) 271-8313 > > Faculty webpage > <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd-1> > > Laboratory of Biomolecular Structure and Function (X-ray > crystallography lab) > <https://research.ouhsc.edu/research-support/core-laboratory-services/laboratory-of-biomolecular-structure-and-function> > SSRL Users Executive Committee > <https://www-ssrl.slac.stanford.edu/content/about-ssrl/ssrluo-2022-2023-executive-committee-members> > > Center, > ------------------------------------------------------------------------ > *From:* Thomas Charles Pochapsky <poc...@br...> > *Sent:* Friday, October 6, 2023 4:28 AM > *To:* pym...@li... > <pym...@li...> > *Subject:* [EXTERNAL] [PyMOL] Student version > Hi, all. Did anybody ever reply about the student version of PyMol > downloads? I use it in my class on a regular basis, but I can no longer > find the link on the Schrodinger web site. There is a free download for > Maestro, with which I am unfamiliar. Is this a replacement? > > Thanks. Tom > > > > _______________________________________________ > PyMOL-users mailing list > Archives: > https://urldefense.com/v3/__http://www.mail-archive.com/pym...@li...__;!!GNU8KkXDZlD12Q!6qyXPA9djwzIN-ekBa0_V2y5Q1f2UdHYpkf5NNqCVUc_JacvO8JHPvaC4bKhTKFhhL4H-ldFoxLn3QIHqARftZ0q2zg$ > <https://urldefense.com/v3/__http://www.mail-archive.com/pym...@li...__;!!GNU8KkXDZlD12Q!6qyXPA9djwzIN-ekBa0_V2y5Q1f2UdHYpkf5NNqCVUc_JacvO8JHPvaC4bKhTKFhhL4H-ldFoxLn3QIHqARftZ0q2zg$> > [mail-archive[.]com] > Unsubscribe: > https://urldefense.com/v3/__https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe__;!!GNU8KkXDZlD12Q!6qyXPA9djwzIN-ekBa0_V2y5Q1f2UdHYpkf5NNqCVUc_JacvO8JHPvaC4bKhTKFhhL4H-ldFoxLn3QIHqARfp2zYm2Y$ > <https://urldefense.com/v3/__https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe__;!!GNU8KkXDZlD12Q!6qyXPA9djwzIN-ekBa0_V2y5Q1f2UdHYpkf5NNqCVUc_JacvO8JHPvaC4bKhTKFhhL4H-ldFoxLn3QIHqARfp2zYm2Y$> > [sourceforge[.]net] |
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From: Thomas C. P. <poc...@br...> - 2023-10-06 09:48:09
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Hi, all. Did anybody ever reply about the student version of PyMol downloads? I use it in my class on a regular basis, but I can no longer find the link on the Schrodinger web site. There is a free download for Maestro, with which I am unfamiliar. Is this a replacement? Thanks. Tom |
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From: Norbert S. <st...@bb...> - 2023-10-06 07:25:39
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I think you can only show delocalized bonds as the additional dashed lines. It is not possible to show a circle. Am 06.10.2023 um 08:56 schrieb Andrea Smith: > https://pymolwiki.org/index.php/Valence > > > > On Thursday, October 05, 2023 17:56 CEST, Danilo Boskovic > <dan...@gm...> wrote: >> Hey everyone, >> Is it possible to change the dashed representation of aromatic circle >> to a proper circle? >> If so, which commands should i use? >> Thanks in advance! > > > _______________________________________________ > 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, Germany st...@bb... https://www.bbz.uni-leipzig.de/en/research/structural-analysis-of-biopolymers ----------------------------------------------------------------------------- |
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From: Andrea S. <and...@uo...> - 2023-10-06 07:12:42
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https://pymolwiki.org/index.php/Valence On Thursday, October 05, 2023 17:56 CEST, Danilo Boskovic <dan...@gm...> wrote: Hey everyone, Is it possible to change the dashed representation of aromatic circle to a proper circle? If so, which commands should i use? Thanks in advance! |
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From: Danilo B. <dan...@gm...> - 2023-10-05 15:56:53
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Hey everyone, Is it possible to change the dashed representation of aromatic circle to a proper circle? If so, which commands should i use? Thanks in advance! |
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From: Norbert S. <st...@bb...> - 2023-10-03 11:25:14
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Dear wdela, usually each atom in a residue has a different atom name. If this is not the case, the rename command will rename the atoms, that do not have unique names within a residue. It appears as if you cannot specify which atom names the renamed atoms will get. If you want to change to specific atom names, use a text editor. Say ligand.pdb contains a molecule with some identically named atoms. load ligand.pdb, ligand rename ligand This will automatically rename atoms to ensure unique atom names. select mysel, ligand and name CA rename mysel Will only rename atoms CA to ensure unique atoms names. You can apply the command to objects or selections. Best wishes, Norbert Am 01.10.2023 um 17:28 schrieb wdela--- via PyMOL-users: > Hi need help with PyMOL rename command: > > from https://pymolwiki.org/index.php/Rename : > > > Rename > > *rename* creates new atom names which are unique within residues. > > > USAGE > > > CURRENT > > rename object-name [ ,force ] > force = 0 or 1 (default: 0) > > > PROPOSED > > rename object-or-selection,force > > > NOTES > > To regerate only some atom names in a molecule, first clear them with > an "alter (sele),name=/“ commmand, then use "rename”/ > ........................................................................................... > > Does 'rename test' create 'test' atom name ?? If so how do I apply it > to a selection ? I know how to use set_name to change an > object/selection name : https://pymolwiki.org/index.php/Set_name or > alter to change a property over a selection : > https://pymolwiki.org/index.php?title=Alter&redirect=no Cannot figure > out how rename works > > > > _______________________________________________ > 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: <wd...@li...> - 2023-10-01 15:42:29
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Hi need help with PyMOL rename command: from https://pymolwiki.org/index.php/Rename : Rename rename creates new atom names which are unique within residues. USAGE CURRENT rename object-name [ ,force ] force = 0 or 1 (default: 0) PROPOSED rename object-or-selection,force NOTES To regerate only some atom names in a molecule, first clear them with an "alter (sele),name=“ commmand, then use "rename” ........................................................................................... Does 'rename test' create 'test' atom name ?? If so how do I apply it to a selection ? I know how to use set_name to change an object/selection name : https://pymolwiki.org/index.php/Set_name or alter to change a property over a selection : https://pymolwiki.org/index.php?title=Alter&redirect=no Cannot figure out how rename works |
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From: Neena S. E. <nee...@gm...> - 2023-09-22 15:51:40
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Hello PyMOL users, This is not a question related to PyMOL, but I was wondering if someone can help me or guide me to the appropriate resource. I extracted two types of H-bond occupancy data (donor: Lysine side chain and backbone amide NH, with backbone carbonyl CO as acceptor) from two different trajectories of the same peptide, centroid structures from predominant cluster of each trajectory shown in each row. These structures just differ by dihedral angles across a few residues. Question: What is the best way to quantify relative strength of total intramolecular hydrogen bonding between these two trajectories? [image: image.png] Many thanks, Neena Graduate student, U of T |
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From: Kamlesh K. <kam...@gm...> - 2023-09-21 19:30:17
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Dear pymol users I am opening a PDB file in pymol but it seems it has some problem in its definition file. Here I am attaching an image for reference. Please guide me on how to fix this problem. Thank you [image: image.png] |
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From: Bennett,Antonette D <de...@uf...> - 2023-09-19 10:25:18
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Good morning, Alice I had the same problem, and it is still not resolved. Hopefully, you will get a better answer than I did (which is - you will receive it by email). Antonette Bennett (PhD) University of Florida Dept. of Biochemistry and Molecular Biology Center for Structural Biology The McKnight Brain Institute P.O. Box 100245, Gainesville, FL 32610 University of Florida Lab Tel: 1-352-294-8394 Email:de...@uf... ________________________________ From: Alice Robson <a.r...@br...> Sent: Tuesday, September 19, 2023 5:02 AM To: pym...@li... <pym...@li...> Subject: [PyMOL] Educational license download email not received [External Email] My students and I are trying to register for the educational build of Pymol, however, when we complete the online form we aren't receiving the email with the license. We've tried checking junk folders. Can anyone advise? Many thanks, Alice Robson University of Bristol |
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From: Alice R. <a.r...@br...> - 2023-09-19 09:18:37
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My students and I are trying to register for the educational build of Pymol, however, when we complete the online form we aren't receiving the email with the license. We've tried checking junk folders. Can anyone advise? Many thanks, Alice Robson University of Bristol |
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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
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<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
|
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
|
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 > |
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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. |
|
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...__;!!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
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