Re: [PyMOL] align and RMSD calculation

Maybe this is related to http://www.biopython.org/pipermail/biopython-dev/2010-October/008361.html Cheers, Tsjerk On Fri, Oct 3, 2014 at 8:37 PM, PC wrote: > Hi Tsjerk and others, > > Thank you, I did use PYMOL with cycles=0 > > Online tools I used were: > 1) Superpose > 2) RMSDCalc from ht

Re: [PyMOL] align and RMSD calculation

Hi Tsjerk and others,Thank you, I did use PYMOL with cycles=0Online tools I used were:1) Superpose 2) RMSDCalc from http://www.igs.cnrs-mrs.fr (not working now due to maintenance)I also used biopython. PYMOL def differs from biopython value.Thank you,-Original Message-From: tsje...@gma

Re: [PyMOL] align and RMSD calculation

Hi, You may want to check out the rms_cur command. http://www.pymolwiki.org/index.php/Rms_cur HTH, Matt Baumgartner On 10/03/2014 02:28 PM, Nat Echols wrote: On Fri, Oct 3, 2014 at 11:17 AM, PC > wrote: Sorry its me again. Can someone tell me where I can f

Re: [PyMOL] align and RMSD calculation

On Fri, Oct 3, 2014 at 11:17 AM, PC wrote: > Sorry its me again. Can someone tell me where I can find the code for > the align command? > It seems the RMSD differs from other online tools I found. > Are you running it with default arguments? If you do this: align object1, object2 it does an

Re: [PyMOL] align and RMSD calculation

Hi Patrick, What other tool do you compare to and how large is the difference? There are different ways to calculate the RMSD, and they may have some rounding errors. Cheers, Tsjerk On Fri, Oct 3, 2014 at 8:17 PM, PC wrote: > Hi, > > Sorry its me again. Can someone tell me where I can find t

Re: [PyMOL] align and RMSD calculation

Hi,Sorry its me again. Can someone tell me where I can find the code for the align command?It seems the RMSD differs from other online tools I found.Thank you -Original Message-From: patrick.coss...@inbox.comSent: Fri, 3 Oct 2014 09:15:17 -0800To: patrick.coss...@inbox.com, pymol-users

Re: [PyMOL] align and RMSD calculation

Ignore this question, I found the answer it setting cycles=0.Thank you -Original Message-From: patrick.coss...@inbox.comSent: Fri, 3 Oct 2014 07:55:31 -0800To: pymol-users@lists.sourceforge.netSubject: [PyMOL] align and RMSD calculation Hi everyone,I was using align in PYMOL and wanted

[PyMOL] align and RMSD calculation

Hi everyone,I was using align in PYMOL and wanted to calculate RMSD.But, PYMOL gave the following result:MatchAlign: aligning residues (696 vs 696)... ExecutiveAlign: 2177 atoms aligned. ExecutiveRMS: 73 atoms rejected during cycle 1 (RMS=0.38). ExecutiveRMS: 103 atoms rejected during cycle 2 (

Re: [PyMOL] Testing for incentive vs. open-source in scripts

Hi Andreas, you are looking for: pymol.invocation.options.incentive_product Cheers, Thomas On 03 Oct 2014, at 10:05, Andreas Warnecke <4ndreas.warne...@gmail.com> wrote: > Hi, > > interesting! > > I noticed that using: > 'print cmd.get_version()' in Python/PyMOL > vs. > 'get_version' in PyMOL

Re: [PyMOL] Testing for incentive vs. open-source in scripts

Hi, interesting! I noticed that using: 'print cmd.get_version()' in Python/PyMOL vs. 'get_version' in PyMOL yields two distinct outputs: PyMOL>print cmd.get_version() ('1.7.0.5', 1.705, 1705, 1399913511, '3070a0a1f405c02c919f62ea8bd67c5a55b0adfd', 0) PyMOL>get_version version: 1.7.0.5 (1.705) 1

Re: [PyMOL] Testing for incentive vs. open-source in scripts

I get this output from cmd.get_version Open pymol: version: 1.7.0.0 (1.700) 1700, Open-Source Incentive pymol: version: 1.7 (1.700) 1700, Incentive Product You could ude this, or not? On 10/3/14 3:06 PM, Andreas Warnecke wrote: > Hi all, > > just to specify the issue: the problem is not the

Re: [PyMOL] Testing for incentive vs. open-source in scripts

Hi all, just to specify the issue: the problem is not the crash, because the script continues due to the try statement. The issue is that PyMOL handles and prints the exception from the 'alter' command into the console. I would like to avoid that, either by testing incentive vs. open-source, or by

Re: [PyMOL] Testing for incentive vs. open-source in scripts

Version number is printed in the startup message, so it has to be stored somewere related to this function. On 10/3/14 2:23 PM, Tsjerk Wassenaar wrote: > Hi Andreas, > > Ah, I think the problem is PyMOL handling the error. It probably prints > the exception and then continuous anyway. So it actua

Re: [PyMOL] Testing for incentive vs. open-source in scripts

Hi Andreas, Ah, I think the problem is PyMOL handling the error. It probably prints the exception and then continuous anyway. So it actually doesn't allow you to catch it off. So you would indeed need to get access to the version. I don't know where that is stored from the top of my head. Maybe Th

Re: [PyMOL] Testing for incentive vs. open-source in scripts

Hi Andreas, A try/except block is actually a very pythonic way of dealing with such issues. You can catch the error with an except clause, that allows executing some code in case the other thing didn't work out. Make sure to only catch the error that is raised by what you're trying, otherwise you

[PyMOL] Testing for incentive vs. open-source in scripts

Dear PyMOL users, I am wondering if there is any way of testing whether a PyMOL version is open-source or incentive for use in scripts. I'm thinking of something similar to 'cmd.get_version()'. The reason for this is that I am e.g. using the 'alter' command on custom properties in scripts, which