Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
From: jason.vertr...@schrodinger.com Date: Mon, 26 Nov 2012 10:37:52 -0600 Subject: Re: was: [PyMOL] Mobile PyMOL Problem and Solution/ Now: pdb or related libraries To: marchy...@hotmail.com CC: pymol-users@lists.sourceforge.net Hi Mike, I was trying to figure out what to eat today so naturally I started looking for PDB libraries with food components. I was looking for garlic related chemicals when I came across this, http://molecules.gnu-darwin.org/ which seems to have many pdb files. My question I guess is, what does pymol have for an API to get molecule structures from various locations or do you just have an interface for pdb.org? Besides deciding on what to eat today, I was curious if pymol has more generalized means of finding structure files. We have an API for accessing structures remotely. For example, load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb, myMolecule You could easily create a PyMOL plugin (http://www.pymolwiki.org/index.php/Plugins_Tutorial) that takes advantage of this site very simply using the load command and formatted URLs. Thanks, I didn't know it would be that simple and that looks like a good way to learn python. Although I am curious now if I had a pdb that lacks hydrogens, like I did in this case, what pymol facilities are there for adding them? Apparently you have some editing capabilites and analyses, I thought there may be some way to guess approximately where the hydrogens should go and then export the new file. This is probably obvious from a quick google search on basic capabilites but it also sounds as if there may be less well known specialized tools for doing less common things like this. I hope your meal was tasty. how can you enjoy it without the pdb file on the screen and optimizing in DFT? LOL. Cheers, Thanks. -- Jason From: jason.vertr...@schrodinger.com Date: Fri, 2 Nov 2012 18:57:38 -0500 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Mobile PyMOL Problem and Solution Greetings, On Oct 28th, the folks at the PDB made some changes to their PDB Web Services interface. This change broke Mobile PyMOL's ability to search for and download PDBs. I haven't bothered to look at this specific situation but this a problem with many sites and automated interaction. NCBI has a nice eutils interface that has remained stable for a while, I'd been trying to get more groups to offer a web interface designed for automated interactions. FWIW, http://www.ncbi.nlm.nih.gov/books/NBK25500/ Do you have automated access to this library for example, http://www.ncbi.nlm.nih.gov/Structure/index.shtml they also have their own viwer, for example, http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml but pymol seems a bit more extensive. I have updated Mobile PyMOL and will soon resubmit it to the AppStore for verification and release. This process takes typically takes no less than 8 days. So, in the meantime for the 7,000 Mobile PyMOL users please use the following technique to acquire structures: (1) Using Safari on the iPad browse to the www.pdb.org and find the structure you want. (2) Click Download Files from the upper right hand side of the structure's page and then select PDB File (Text). (3) Click Open in PyMOL. Happily, as a long-term solution, I've established contact with the PDB Web Services Group and we'll now be made aware of future changes. The PDB is an extremely valuable resource in the community and I'm glad we could work this out. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Central: Instant, anywhere, Remote PC access and management. Stay in control, update software, and manage PCs from one command center Diagnose problems and improve visibility into emerging IT issues Automate, monitor and manage. Do more in less time with Central http://p.sf.net/sfu/logmein12331_d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers
Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
Mike, Although I am curious now if I had a pdb that lacks hydrogens, like I did in this case, what pymol facilities are there for adding them? Apparently you have some editing h_add object_name Type, help h_add or check out h_add on the PyMOLWiki (http://www.pymolwiki.org/index.php/H_Add). Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
From: jason.vertr...@schrodinger.com Date: Tue, 27 Nov 2012 12:37:41 -0600 Subject: Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries To: marchy...@hotmail.com CC: pymol-users@lists.sourceforge.net Mike, Although I am curious now if I had a pdb that lacks hydrogens, like I did in this case, what pymol facilities are there for adding them? Apparently you have some editing h_add object_name Type, help h_add or check out h_add on the PyMOLWiki (http://www.pymolwiki.org/index.php/H_Add). Thanks, applying to the pdb I had seems to have worked but it didn't think much of the double bonds and added extra's but presumably I can delete and rotate more easily than adding all them manually. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Keep yourself connected to Go Parallel: DESIGN Expert tips on starting your parallel project right. http://goparallel.sourceforge.net ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
Hi Mike, I was trying to figure out what to eat today so naturally I started looking for PDB libraries with food components. I was looking for garlic related chemicals when I came across this, http://molecules.gnu-darwin.org/ which seems to have many pdb files. My question I guess is, what does pymol have for an API to get molecule structures from various locations or do you just have an interface for pdb.org? Besides deciding on what to eat today, I was curious if pymol has more generalized means of finding structure files. We have an API for accessing structures remotely. For example, load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb, myMolecule You could easily create a PyMOL plugin (http://www.pymolwiki.org/index.php/Plugins_Tutorial) that takes advantage of this site very simply using the load command and formatted URLs. I hope your meal was tasty. Cheers, -- Jason From: jason.vertr...@schrodinger.com Date: Fri, 2 Nov 2012 18:57:38 -0500 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Mobile PyMOL Problem and Solution Greetings, On Oct 28th, the folks at the PDB made some changes to their PDB Web Services interface. This change broke Mobile PyMOL's ability to search for and download PDBs. I haven't bothered to look at this specific situation but this a problem with many sites and automated interaction. NCBI has a nice eutils interface that has remained stable for a while, I'd been trying to get more groups to offer a web interface designed for automated interactions. FWIW, http://www.ncbi.nlm.nih.gov/books/NBK25500/ Do you have automated access to this library for example, http://www.ncbi.nlm.nih.gov/Structure/index.shtml they also have their own viwer, for example, http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml but pymol seems a bit more extensive. I have updated Mobile PyMOL and will soon resubmit it to the AppStore for verification and release. This process takes typically takes no less than 8 days. So, in the meantime for the 7,000 Mobile PyMOL users please use the following technique to acquire structures: (1) Using Safari on the iPad browse to the www.pdb.org and find the structure you want. (2) Click Download Files from the upper right hand side of the structure's page and then select PDB File (Text). (3) Click Open in PyMOL. Happily, as a long-term solution, I've established contact with the PDB Web Services Group and we'll now be made aware of future changes. The PDB is an extremely valuable resource in the community and I'm glad we could work this out. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Central: Instant, anywhere, Remote PC access and management. Stay in control, update software, and manage PCs from one command center Diagnose problems and improve visibility into emerging IT issues Automate, monitor and manage. Do more in less time with Central http://p.sf.net/sfu/logmein12331_d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
I was trying to figure out what to eat today so naturally I started looking for PDB libraries with food components. I was looking for garlic related chemicals when I came across this, http://molecules.gnu-darwin.org/ which seems to have many pdb files. My question I guess is, what does pymol have for an API to get molecule structures from various locations or do you just have an interface for pdb.org? Besides deciding on what to eat today, I was curious if pymol has more generalized means of finding structure files. Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. From: marchy...@hotmail.com To: jason.vertr...@schrodinger.com; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Mobile PyMOL Problem and Solution Date: Fri, 2 Nov 2012 20:43:41 -0400 From: jason.vertr...@schrodinger.com Date: Fri, 2 Nov 2012 18:57:38 -0500 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Mobile PyMOL Problem and Solution Greetings, On Oct 28th, the folks at the PDB made some changes to their PDB Web Services interface. This change broke Mobile PyMOL's ability to search for and download PDBs. I haven't bothered to look at this specific situation but this a problem with many sites and automated interaction. NCBI has a nice eutils interface that has remained stable for a while, I'd been trying to get more groups to offer a web interface designed for automated interactions. FWIW, http://www.ncbi.nlm.nih.gov/books/NBK25500/ Do you have automated access to this library for example, http://www.ncbi.nlm.nih.gov/Structure/index.shtml they also have their own viwer, for example, http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml but pymol seems a bit more extensive. I have updated Mobile PyMOL and will soon resubmit it to the AppStore for verification and release. This process takes typically takes no less than 8 days. So, in the meantime for the 7,000 Mobile PyMOL users please use the following technique to acquire structures: (1) Using Safari on the iPad browse to the www.pdb.org and find the structure you want. (2) Click Download Files from the upper right hand side of the structure's page and then select PDB File (Text). (3) Click Open in PyMOL. Happily, as a long-term solution, I've established contact with the PDB Web Services Group and we'll now be made aware of future changes. The PDB is an extremely valuable resource in the community and I'm glad we could work this out. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Central: Instant, anywhere, Remote PC access and management. Stay in control, update software, and manage PCs from one command center Diagnose problems and improve visibility into emerging IT issues Automate, monitor and manage. Do more in less time with Central http://p.sf.net/sfu/logmein12331_d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
Hi Mike, you can fetch molecular files from any web address with the load command. Examples: File type recognized from file extension: PyMOL load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb File type given with format argument: PyMOL load http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5280443disopt=3DSaveSDF, format=sdf Also, Mobile PyMOL (for the iPad) has it's own server capabilities, including support for PubChem, PDB, Dropbox, etc. Cheers, Thomas Mike Marchywka wrote, On 11/25/12 17:26: I was trying to figure out what to eat today so naturally I started looking for PDB libraries with food components. I was looking for garlic related chemicals when I came across this, http://molecules.gnu-darwin.org/ which seems to have many pdb files. My question I guess is, what does pymol have for an API to get molecule structures from various locations or do you just have an interface for pdb.org? Besides deciding on what to eat today, I was curious if pymol has more generalized means of finding structure files. Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
Date: Sun, 25 Nov 2012 23:49:26 +0100 From: spel...@users.sourceforge.net To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries Hi Mike, you can fetch molecular files from any web address with the load command. Examples: File type recognized from file extension: PyMOL load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb Thanks, it sounded like the original poster was refering to a larger facility to find pdb files in a variety of libraries. If I know where the file is I can usually get it with wget but if tere is some search API or facility that may be helpful. I am finding some pdb collections online but thought they may be listed somewhere. In any case, I eventually realized that the pdb does not have the hydrogens and I can't find one that may. Would it be reasonable to try to use pymol to add them? I only need artists conception as presumably the DFT optimization will make it more accurate. File type given with format argument: PyMOL load http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5280443disopt=3DSaveSDF, format=sdf Also, Mobile PyMOL (for the iPad) has it's own server capabilities, including support for PubChem, PDB, Dropbox, etc. Cheers, Thomas Mike Marchywka wrote, On 11/25/12 17:26: I was trying to figure out what to eat today so naturally I started looking for PDB libraries with food components. I was looking for garlic related chemicals when I came across this, http://molecules.gnu-darwin.org/ which seems to have many pdb files. My question I guess is, what does pymol have for an API to get molecule structures from various locations or do you just have an interface for pdb.org? Besides deciding on what to eat today, I was curious if pymol has more generalized means of finding structure files. Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
fwiw, I did find mol2 format at this location which is just fine for my scripts, http://zinc.docking.org/substance/1633229 Thanks. From: marchy...@hotmail.com To: spel...@users.sourceforge.net; pymol-users@lists.sourceforge.net Date: Sun, 25 Nov 2012 19:00:08 -0500 Subject: Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries Date: Sun, 25 Nov 2012 23:49:26 +0100 From: spel...@users.sourceforge.net To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries Hi Mike, you can fetch molecular files from any web address with the load command. Examples: File type recognized from file extension: PyMOL load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb Thanks, it sounded like the original poster was refering to a larger facility to find pdb files in a variety of libraries. If I know where the file is I can usually get it with wget but if tere is some search API or facility that may be helpful. I am finding some pdb collections online but thought they may be listed somewhere. In any case, I eventually realized that the pdb does not have the hydrogens and I can't find one that may. Would it be reasonable to try to use pymol to add them? I only need artists conception as presumably the DFT optimization will make it more accurate. File type given with format argument: PyMOL load http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5280443disopt=3DSaveSDF, format=sdf Also, Mobile PyMOL (for the iPad) has it's own server capabilities, including support for PubChem, PDB, Dropbox, etc. Cheers, Thomas Mike Marchywka wrote, On 11/25/12 17:26: I was trying to figure out what to eat today so naturally I started looking for PDB libraries with food components. I was looking for garlic related chemicals when I came across this, http://molecules.gnu-darwin.org/ which seems to have many pdb files. My question I guess is, what does pymol have for an API to get molecule structures from various locations or do you just have an interface for pdb.org? Besides deciding on what to eat today, I was curious if pymol has more generalized means of finding structure files. Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
