Re: [ccp4bb] PyMol and Schrodinger
Thank you Piotr, this is very useful to know. Cheers, Eugene On 24 Apr 2014, at 22:18, Piotr Sliz wrote: Eugene, SBGrid Consortium supports certain paid programs such as Pymol, Schrodinger, and Geneious, and academic laboratories have access to a limited pool of tokens. For more serious computations it might be easier to get an individual license, yet for starters the SBGrid shared-token library is certainly a viable option. Access to the commercial tokens is included in SBGrid membership, though limited depending on your geographic location and affiliation. Please email h...@sbgrid.org for a more detailed description of this program. Kind Regards, Piotr -- Scanned by iCritical.
Re: [ccp4bb] PyMol and Schrodinger
SBGrid is a also good option if you can afford it. It comes with PyMOL licenses. - it would be helpful if SBGrid people can comment on this. AFAIK, nothing in SBGrid comes with paid licenses, and SBGrid fees are just for installing and maintaining the software. Individual program licenses are to be acquired in addition -- unless I am grossly wrong or PyMOL is an exception here. Eugene -- Scanned by iCritical.
Re: [ccp4bb] PyMol and Schrodinger
Eugene, SBGrid Consortium supports certain paid programs such as Pymol, Schrodinger, and Geneious, and academic laboratories have access to a limited pool of tokens. For more serious computations it might be easier to get an individual license, yet for starters the SBGrid shared-token library is certainly a viable option. Access to the commercial tokens is included in SBGrid membership, though limited depending on your geographic location and affiliation. Please email h...@sbgrid.org for a more detailed description of this program. Kind Regards, Piotr
[ccp4bb] PyMol and Schrodinger
Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek
Re: [ccp4bb] PyMol and Schrodinger
To the best of my knowledge the source code is still available on Sourceforge: http://sourceforge.net/projects/pymol/ You should be able to compile binaries for the OS of your choice from there. That being said, CCP4MG has been coming along nicely in recent years - at this point I'm 50:50 between Pymol and CCP4MG for making figures for presentations/papers. Cheers, Jim On Wed, Apr 23, 2014 at 8:43 AM, Cygler, Miroslaw miroslaw.cyg...@usask.cawrote: Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek -- Jim Fairman, Ph D. Crystal Core Leader I Emerald Bio http://www.embios.com Tel: 206-780-8914 Cell: 240-479-6575 E-mail: fairman@gmail.com jfair...@embios.com
Re: [ccp4bb] PyMol and Schrodinger
Hi Since this is the CCP4 BB, I'd give ccp4mg a try... On 23 Apr 2014, at Wed23 Apr 16:43, Cygler, Miroslaw wrote: Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] PyMol and Schrodinger
No one is keeping you from downloading the source code and compiling. It's straightforward and free. Andreas On 23/04/2014 4:43, Cygler, Miroslaw wrote: Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
Re: [ccp4bb] PyMol and Schrodinger
On Wed, Apr 23, 2014 at 8:43 AM, Cygler, Miroslaw miroslaw.cyg...@usask.cawrote: I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. This is no different than the licenses that for-profit companies are required to purchase for most crystallography software. In fact, it's actually considerably more liberal than most software*, because as Jim notes you can still obtain (and redistribute) most of the source code for free. From what I can tell Schrodinger has continued to make improvements to the open-source core; some of the newer features (and the native Mac GUI) are proprietary, but that was true ten years ago. -Nat (* although I believe ccp4mg is truly open-source like Coot, and unlike CCP4 etc. which still require a license for commercial use. Or am I misinformed?)
Re: [ccp4bb] PyMol and Schrodinger
I'd like to add the under-underdog then, Tim Fenn's povscript+ https://sites.google.com/site/timfenn/povscript. Makes really clear and nice figures and is rather simple to compile. For the most part you do not even need a mouse to use it ... Michael On 23.04.2014 18:21, mark.x.brooks wrote: And to stick up for the underdog, try Chimera from UCSF, which also has been coming along nicely (understatement!): http://www.cgl.ucsf.edu/chimera/ Mark On 23 Apr 2014, at 17:48, Jim Fairman fairman@gmail.com mailto:fairman@gmail.com wrote: To the best of my knowledge the source code is still available on Sourceforge: http://sourceforge.net/projects/pymol/ You should be able to compile binaries for the OS of your choice from there. That being said, CCP4MG has been coming along nicely in recent years - at this point I'm 50:50 between Pymol and CCP4MG for making figures for presentations/papers. Cheers, Jim On Wed, Apr 23, 2014 at 8:43 AM, Cygler, Miroslaw miroslaw.cyg...@usask.ca mailto:miroslaw.cyg...@usask.ca wrote: Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek -- Jim Fairman, Ph D. Crystal Core Leader I Emerald Bio http://www.embios.com Tel: 206-780-8914 Cell: 240-479-6575 E-mail: fairman@gmail.com mailto:fairman@gmail.com jfair...@embios.com mailto:jfair...@embios.com
Re: [ccp4bb] PyMol and Schrodinger
And to stick up for the underdog, try Chimera from UCSF, which also has been coming along nicely (understatement!): http://www.cgl.ucsf.edu/chimera/ Mark On 23 Apr 2014, at 17:48, Jim Fairman fairman@gmail.com wrote: To the best of my knowledge the source code is still available on Sourceforge: http://sourceforge.net/projects/pymol/ You should be able to compile binaries for the OS of your choice from there. That being said, CCP4MG has been coming along nicely in recent years - at this point I'm 50:50 between Pymol and CCP4MG for making figures for presentations/papers. Cheers, Jim On Wed, Apr 23, 2014 at 8:43 AM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote: Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek -- Jim Fairman, Ph D. Crystal Core Leader I Emerald Bio Tel: 206-780-8914 Cell: 240-479-6575 E-mail: fairman@gmail.com jfair...@embios.com
Re: [ccp4bb] PyMol and Schrodinger
Hi, if one is hesitant to compile it it, pymol is easily installed on a Linux box via yum ; enable EPEL repo ( in Redhat derivatives e.g. fedora, Centos, SciLinux) yum install pymol will install version 1.6 (latest version by Schrödinger is 1.7) Best, Guenter Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek
Re: [ccp4bb] PyMol and Schrodinger
In addition to what has been mentioned by others, Open-Source PyMOL installation instructions for various platforms are available on the PyMOL Wiki: http://pymolwiki.org/index.php/Linux_Install http://pymolwiki.org/index.php/MAC_Install http://pymolwiki.org/index.php/Windows_Install Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Apr 23, 2014, at 1:02 PM, Guenter Fritz guenter.fr...@uni-konstanz.demailto:guenter.fr...@uni-konstanz.de wrote: Hi, if one is hesitant to compile it it, pymol is easily installed on a Linux box via yum ; enable EPEL repo ( in Redhat derivatives e.g. fedora, Centos, SciLinux) yum install pymol will install version 1.6 (latest version by Schrödinger is 1.7) Best, Guenter Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] PyMol and Schrodinger
On Apr 23, 2014, at 11:43 AM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote: They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. Office 365 is $10 a month, Adobe Creative Cloud (what used to be their Creative Suite) is $50 a month with an annual commitment. Licensing the use of software on a time-limited basis as a business model seems like it's going to stick around. - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder --
Re: [ccp4bb] PyMol and Schrodinger
Hi Mirek, If you happen to be using OS X, Fink makes it very easy to install recent open-source pymol. Best regards, Dmitry On 2014-04-23, at 11:43 AM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote: Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek
Re: [ccp4bb] PyMol and Schrodinger
On 4/23/14, 1:53 PM, Francis Reyes wrote: Office 365 is $10 a month, Adobe Creative Cloud (what used to be their Creative Suite) is $50 a month with an annual commitment. Licensing the use of software on a time-limited basis as a business model seems like it's going to stick around. And that's why I am sticking with my last copy of Adobe Creative Suite 6, as long as it will run on a computer. When CS6 no longer works, I might be interested in moving to gimp and inkscape, which I had never considered before. I fully support Schrodinger to charge for an update, and they have vastly improved PyMOL. But being told to re-buy PyMOL annoys me, even though I would renew anyway just to support PyMOL development, and I can compile it just fine. (The expiring XDS binaries are also annoying, but there the software is free and the only purpose of the expiration is to force people to update, which I fully support.) I am hoping that Schrodinger will have a different model for academics. SBGrid is a also good option if you can afford it. It comes with PyMOL licenses. Engin
Re: [ccp4bb] PyMol and Schrodinger
Well as s/w improvements don't necessarily happen on a yearly basis, but people like being paid each year, I think the model is not unreasonable, as long as the cost is reasonable - which, for instance, the Adobe s/w isn't. As one can tell from the profit margins of s/w companies. So I do pay my Schrodinger PyMol licenses each year. just my 2c Adrian On 23 Apr 2014, at 20:24, Engin Özkan eoz...@uchicago.edu wrote: On 4/23/14, 1:53 PM, Francis Reyes wrote: Office 365 is $10 a month, Adobe Creative Cloud (what used to be their Creative Suite) is $50 a month with an annual commitment. Licensing the use of software on a time-limited basis as a business model seems like it's going to stick around. And that's why I am sticking with my last copy of Adobe Creative Suite 6, as long as it will run on a computer. When CS6 no longer works, I might be interested in moving to gimp and inkscape, which I had never considered before. I fully support Schrodinger to charge for an update, and they have vastly improved PyMOL. But being told to re-buy PyMOL annoys me, even though I would renew anyway just to support PyMOL development, and I can compile it just fine. (The expiring XDS binaries are also annoying, but there the software is free and the only purpose of the expiration is to force people to update, which I fully support.) I am hoping that Schrodinger will have a different model for academics. SBGrid is a also good option if you can afford it. It comes with PyMOL licenses. Engin
