hi Guillermo,
Thank you for your sincerely help! Now, I am trying to find an appropriate
repel value. But I have two questions about Xplor-NIH:
1) About random seed:"the same seed number on the same computer yields the same
results” In oder to generate more structures, I have submitted many jobs to the
cluster. like “
#!/bin/sh
#8st job
k=8
cd /Share/home/fangxy/Users/Zhangyk/Zxplor-test/Gwnvpks/sec_wp/secout/8
xplor -py ../../wp.py ../../${k}.pdb”
in these jobs, the random seeds in the “wp.py” are all the same, so I do not
know whether this will effect the results of the conformational sampling.
2) “https://link.springer.com/protocol/10.1007/978-1-4939-7386-6_14
<https://link.springer.com/protocol/10.1007/978-1-4939-7386-6_14>” mentioned
that “def calcOneStructure(loopInfo):” is consist of “High Temperature Stage”
“Simulated Annealing Stage” “Torsion Angle Minimization” and so on. One
simulate annealing stage(temp from 3500 to 25) will calculate only one
structure. And when I checked the output pdb, I found that the two outputs of
adjacent numbers(like 1.pdb, 2.pdb) only have a little similarity and that is
OK for the sampling. So if we want to sampling more conformations, do we have
some other parameter to adjust (in the three stages) ? And do the
numberOfStructures has "upper limit” ? Thank you!
Best,
Yikan
Ph. D candidate
TsingHua University
School of life Sciences
Beijing, China
tel:010-62773783
> 在 2017年12月13日，上午4:47，Bermejo, Guillermo (NIH/CIT) [E]
> <[email protected]> 写道：
>
> Hi Yikan,
>
> The nonbonded potential that we generally use (and you're using now) is
> purely repulsive. To account for the lack of an attractive component and
> avoid having expanded structures, atomic radii are scaled down by a factor
> called "repel". For the current default parameters (which you are implicitly
> using by running the function protocol.loadPDB), we found the optimal repel
> value to be 0.9.
>
> In general, one doesn't explicitly deal with repel, as the function that sets
> up the potential automatically handle it (they even recognize the version of
> the parameters used, for which there may be different optimal repel values).
> (An exception is during the high temperature stage, where we use expanded
> atoms with repel=1.2 to improve sampling; see the highTempParams setup.)
>
> In your particular case, you want to actively change repel by replacing the
> following line
>
> rampedParams.append( StaticRamp("initRepel(repel,use14=False)") )
>
> by
>
> rampedParams.append( MultRamp(0.9, 1.0, "initRepel(repel, use14=False,
> repel=VALUE)") )
>
> where repel will be increased from 0.9 to 1 during simulated annealing. You
> can play with different repel values. Note that there's another "repel" word
> here that refers to the instance of the repulsive potential [repel =
> create_RepelPot('repel')], and which could, in principle, be given any
> arbitrary name.
>
> The way of varying repel is general, and is applied to other things (e.g.,
> force constants). For more details, see a recent publication where we
> explain a structure calculation script
> (https://link.springer.com/protocol/10.1007/978-1-4939-7386-6_14
> <https://link.springer.com/protocol/10.1007/978-1-4939-7386-6_14>).
>
> Best,
>
> Guillermo
>
>
>
> From: ZhangYikan <[email protected]>
> Sent: Tuesday, December 12, 2017 11:08 AM
> To: Bermejo, Guillermo (NIH/CIT) [E]; [email protected]
> Subject: Re: [Xplor-nih] Wrong topology structures in conformational sampling
>
> hi Guillermo,
> Thank you for your help! in your previous mail you said “to increase the
> atomic radii (see the 'repel' argument in initRepel)”. But in the script
>
> “from repelPotTools import create_RepelPot,initRepel
> repel = create_RepelPot('repel')
> potList.append(repel)
> rampedParams.append( StaticRamp("initRepel(repel,use14=False)") )
> rampedParams.append( MultRamp(.004, 4, "repel.setScale( VALUE)") )
> # nonbonded interaction only between C1' atoms
> highTempParams.append( StaticRamp("""initRepel(repel,
> use14=True,
> scale=0.004,
> repel=1.2,
> moveTol=45,
> interactingAtoms="name P"
> )""") )
>
> “
> I can not find the terms that stands for “atom radius” and how to “increase
> the atomic radii(in intRepel)”.
> ps: Only RepelPot has the similar term “rMin”; but when I have looked through
> the examples in eginput, I did not find the similar use of “RepPot”.
> Thank you !
> Best,
> Yikan
> Ph. D candidate
> TsingHua University
> School of life Sciences
> Beijing, China
> tel:010-62773783 <tel:010-62773783>
>
>
>
>> 在 2017年12月12日，下午11:38，Bermejo, Guillermo (NIH/CIT) [E]
>> <[email protected] <mailto:[email protected]>> 写道：
>>
>> Hi Yikan,
>>
>> I think using Monte Carlo (in the torsion angle randomization) is
>> appropriate.
>>
>> Good luck,
>>
>> Guillermo
>>
>>
>>
>>
>>
>> From: ZhangYikan <[email protected] <mailto:[email protected]>>
>> Sent: Monday, December 11, 2017 6:36 PM
>> To: Bermejo, Guillermo (NIH/CIT) [E]; [email protected]
>> <mailto:[email protected]>
>> Subject: Re: [Xplor-nih] Wrong topology structures in conformational sampling
>>
>> hell Guillermo,
>> By the way, although I have known that the comformational sampling problem
>> has been an untrival problem util now; how can I make sure that I have
>> sampled almost all possible conformations of this RNA?
>>
>> Yikan
>> Ph. D candidate
>> TsingHua University
>> School of life Sciences
>> Beijing, China
>> tel:010-62773783 <tel:010-62773783>
>>
>>
>>
>> > 在 2017年12月12日，上午7:25，ZhangYikan <[email protected]> 写道：
>> >
>> > hello Guillermo,
>> > Thank you for your scripts, I have tried it. I found that there are still
>> > some wrong topology structures and clahes(some overlaps):1) I will try to
>> > fix the repel parameter and rerun the script;
>> > 2) in the outputs of the previous zp_0-3.py, I found the terms of “impr”
>> > seems unusual(in the .viols), did you have some tools to analysis this
>> > energy term ?
>> >
>> > Thank you!
>> > Best,
>> >
>> > Yikan
>> > Ph. D candidate
>> > TsingHua University
>> > School of life Sciences
>> > Beijing, China
>> > tel:010-62773783
>> >
>> >
>> >
>> >> 在 2017年12月12日，上午2:00，Bermejo, Guillermo (NIH/CIT) [E]
>> >> <[email protected]> 写道：
>> >>
>> >> Hi Yikan,
>> >>
>> >> I notice that your script seems to be more complicated than it has to be.
>> >> I'm not sure this will solve your problem, but I'm attaching a simpler
>> >> script based on eginput/rna/fold.py. It's basically the script used to
>> >> fold an RNA molecule from an extended conformation (described in the
>> >> paper I mentioned before). I modified it so that you load your input pdb
>> >> structure and define the different rigid bodies (look for the lines with
>> >> an inline comment "# COMPLETE !", where you must enter the right
>> >> information). Then, it does torsion angle dynamics using the remaining
>> >> torsional degrees of freedom (i.e., at the linker(s)).
>> >>
>> >> I commented all the experimental restraints. If you want to have the
>> >> radius of gyration term (which appears in your script), you can introduce
>> >> it yourself. Also, you might want to use it as a starting point for more
>> >> complicated stuff, like "breaking" the linkers and randomizing the
>> >> position of the domains.
>> >>
>> >> A suggestion to try to avoid (and detect) knotted structures is to
>> >> increase the atomic radii (see the 'repel' argument in initRepel).
>> >>
>> >> Best,
>> >>
>> >> Guillermo
>> >>
>> >> From: ZhangYikan <[email protected]>
>> >> Sent: Monday, December 11, 2017 10:43 AM
>> >> To: Bermejo, Guillermo (NIH/CIT) [E]; [email protected]
>> >> Subject: Re: [Xplor-nih] Wrong topology structures in conformational
>> >> sampling
>> >>
>> >> hello Guillermo,
>> >>
>> >> I want these domains move (as rigid body)randomly and freely to sample
>> >> all possible conformations of the RNA.
>> >>
>> >> Yikan
>> >> Ph. D candidate
>> >> TsingHua University
>> >> School of life Sciences
>> >> Beijing, China
>> >> tel:010-62773783
>> >>
>> >>
>> >>
>> >>> 在 2017年12月11日，下午11:27，Bermejo, Guillermo (NIH/CIT) [E]
>> >>> <[email protected]> 写道：
>> >>>
>> >>> Hi Yikan,
>> >>>
>> >>> Can you tell me what you are trying to do?
>> >>>
>> >>> Best,
>> >>>
>> >>> Guillermo
>> >>>
>> >>>
>> >>> From: ZhangYikan <[email protected]>
>> >>> Sent: Friday, December 8, 2017 6:56 PM
>> >>> To: Bermejo, Guillermo (NIH/CIT) [E]; [email protected]
>> >>> Subject: Re: [Xplor-nih] Wrong topology structures in conformational
>> >>> sampling
>> >>>
>> >>> hi Guillermo,
>> >>> yes, i have received your last mails. And the attachment is my scripts.
>> >>>
>> >>>
>> >>> Yikan
>> >>> Ph. D candidate
>> >>> TsingHua University
>> >>> School of life Sciences
>> >>> Beijing, China
>> >>> tel:010-62773783
>> >>>
>> >>>
>> >>>
>> >>>> 在 2017年12月9日，上午12:43，Bermejo, Guillermo (NIH/CIT) [E]
>> >>>> <[email protected]> 写道：
>> >>>>
>> >>>> Hi Yikan,
>> >>>>
>> >>>> I realized that my original response was only sent to you and not
>> >>>> included in the mailing list. Here it is.
>> >>>>
>> >>>> One possibility is that there's something wrong with your script(s).
>> >>>>
>> >>>> I recommend basing your calculations on the scripts found in
>> >>>> eginput/rna directory (within your Xplor-NIH directory). There you'll
>> >>>> find:
>> >>>>
>> >>>> * fold.py, for initial calculations starting from an extended
>> >>>> conformation.
>> >>>> * refine.py, for subsequent refinement.
>> >>>>
>> >>>> In addition, you'll find all the restraints for an example system, in
>> >>>> case you want to play with the scripts before venturing into your data.
>> >>>> The scripts are highly commented, which should help in customizing
>> >>>> them for your needs. There's also a paper describing them [Bermejo et
>> >>>> al., 2016, Structure 24, 806-815].
>> >>>>
>> >>>> Best,
>> >>>>
>> >>>> Guillermo
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>> From: [email protected]
>> >>>> <[email protected]> on behalf of ZhangYikan
>> >>>> <[email protected]>
>> >>>> Sent: Friday, December 8, 2017 6:53 AM
>> >>>> To: [email protected]
>> >>>> Subject: [Xplor-nih] Wrong topology structures in conformational
>> >>>> sampling
>> >>>>
>> >>>>
>> >>>>
>> >>>> hello all,
>> >>>>
>> >>>> Recently, I am doing conformational sampling with Xplor-NIH. And I got
>> >>>> many pdbs, but when I check them I found that some pdbs have wrong
>> >>>> topology structures like the attachments(in the pink cycle ): The RNA
>> >>>> linker did not run with the right way and It went through the helix. I
>> >>>> have tried to pick the structures by the “total energy” or “repel”
>> >>>> terms, but it make no sense. Are there someone know how to kick out
>> >>>> these wrong structures or to void these errors in the sampling process?
>> >>>> Thank you!
>> >>>> Yikan
>> >>>> Ph. D candidate
>> >>>> TsingHua University
>> >>>> School of life Sciences
>> >>>> Beijing, China
>> >>>> tel:010-62773783
>> >>
>> >> <fold.py>
>> >
>> > _______________________________________________
>> > Xplor-nih mailing list
>> > [email protected]
>> > https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
>> > <https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih>
>> Xplor-nih Info Page <https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih>
>> dcb.cit.nih.gov <http://dcb.cit.nih.gov/>
>> To see the collection of prior postings to the list, visit the Xplor-nih
>> Archives. Using Xplor-nih: To post a message to all the list members ...
_______________________________________________
Xplor-nih mailing list
[email protected]
https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
