On Tue, Aug 11, 2015 at 9:20 AM, Ucisik, Melek Nihan
<ucisik.illinois.edu> wrote:
> Still 14.09 actually.
Try upgrading to version 15 and see if that solves your issue (14.09
isn't even the most up-to-date version of 14).
-Dan
> Thanks,
>
> Nihan
>
>
> On Aug 10, 2015, at 12:16 PM, Daniel Roe <daniel.r.roe.gmail.com<mailto:daniel.r.roe.gmail.com>> wrote:
>
> On Sun, Aug 9, 2015 at 2:37 PM, Ucisik, Melek Nihan <ucisik.illinois.edu<mailto:ucisik.illinois.edu>> wrote:
> #Frame AtomNum Atom ResNum Res MolNum
> 30 1834 Na+ 93 Na+ 39
> 44 1845 Na+ 104 Na+ 50
> 44 1913 Na+ 172 Na+ 118
> 45 1845 Na+ 104 Na+ 50
> 45 1913 Na+ 172 Na+ 118
> 46 1845 Na+ 104 Na+ 50
> 46 1913 Na+ 172 Na+ 118
>
> So, does this mean:
>
> 1. There were no Na+’s within 2.5 Å of :7.OP1 in frames 1-29 and 31-43 etc.
> 2. In the frame 44, there were 2: residue numbers 104 and 172.
> 3. In the frame 45, there were 2: residue numbers 104 and 172.
> 4. In the frame 46, there were 2: residue numbers 104 and 172.
>
> Yes to all.
>
> Then what is MolNum?
>
> Molecule number (current documentation needs to be updated, thanks for
> pointing this out!).
>
> Also, if I add the “maskpdb” option to the command as shown below (by typing it myself, no copy and paste to eliminate any possible errors as before), it gives a segmentation fault:
>
> Are you still using version 14.09 or have you upgraded to 15?
>
> -Dan
>
>
> mask "(:7.OP1<:2.5)&:Na+" maskout mask_A7OP1_Na.dat maskpdb mask_A7OP1_Na.pdb
>
> ...
>
> ----- stripped_prod_ions.netcdf (1-500, 1) -----
> 0% Segmentation fault
>
> Can you help me understand what is going on?
>
> Thanks,
>
> Nihan
>
> On Aug 7, 2015, at 11:20 AM, Ucisik, Melek Nihan <ucisik.illinois.edu<mailto:ucisik.illinois.edu><mailto:ucisik.illinois.edu>> wrote:
>
> Well, that was exactly what I’ve done: I copied the example in the manual, pasted in my script, and then modified the atom mask without touching the quotes.
> I typed the quotes by hand and it worked with no problems.
> Thanks, Hai, Dan, and Jason!
> Best,
>
> Nihan
>
>
> On Aug 7, 2015, at 1:21 AM, Jason Swails <jason.swails.gmail.com<mailto:jason.swails.gmail.com><mailto:jason.swails.gmail.com>> wrote:
>
> On Thu, Aug 6, 2015 at 10:51 PM, Daniel Roe <daniel.r.roe.gmail.com<mailto:daniel.r.roe.gmail.com><mailto:daniel.r.roe.gmail.com>> wrote:
>
> Interesting. If I copy the quotes from the email I get that error. If
> I input the quotes myself (which is how I originally tested)
> everything is fine. Clearly the quotes in the email are a different
> character (as further evidenced by the strange character that pops up
> in the error message).
>
>
> Yes, gmail is all too happy to turn the ASCII quotes into the "fancy"
> quotes (note how they don't go straight down, but curl toward the text).
> Same type of deal with hyphens getting replaced with n- or m-dashes...
> Copy-paste doesn't really work here.
>
> So to Nihan -- make sure you're not copying and pasting from a place that
> formats text for humans (like word, email, ... etc.) -- if you're in doubt,
> replace your quotes with ones you type by hand (or just get rid of them).
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Aug 11 2015 - 12:30:05 PDT
