Dear Vlad,
The checking for 4 characters in the mask.c is a relic of Viktor Hornak's
code. As his comment in the code, the checking may not be necessary and, in
this case, causes some confusion. Thanks for pointing this out. The reason
why ":*" works is the parser adds "[" and "]" around the separated masks.
Anything like :1 and .C will be tokenized as [:1] and [.C], and no warnings
will be issued.
Best,
Jianyin
On 6/5/08, Vlad Cojocaru <Vlad.Cojocaru.eml-r.villa-bosch.de> wrote:
>
> Dear Jianyin,
>
> Ok, the warning "empty token" comes from line 402 in mask.c and it
> disappears if the mask string is ':*' instead of '*'. It seems that the
> parser likes at least 4 characters in the mask string (although the 3-char
> string was correctly processed as well) . But (as I expected) the warning
> has nothing to do with the imaging problem.
>
> The problem also persists in the ptraj from AMBER 10.
>
> For now, I just wanted to make this clear
>
> vlad
>
> Vlad Cojocaru wrote:
>
> Dear Jianyin,
>
> Thanks for the re. Of course its not the most urgent thing and I can use
> the old ptraj for imaging ... At the end its a convenience issue to not
> switch between different versions for different tasks. So, I thought its a
> good thing to ask about it or let people know about the problem.
>
> The mask "*" is correctly recognized but I get this "empty token?" warning
> which made me think that one of the options (either "center" or "origin")
> for the image command might not be correctly applied. I would gladly send
> you a copy but the trajectory is way too big (> 2GB). I would need to make
> chunks first and send one small chunk for testing. Unfortunately I dont have
> time now as I am preparing a talk for a conference next week but if the
> problem persists and no solution is found I can send you later on this month
> a traj chunk.
>
> Cheers
> vlad
>
>
> Jianyin Shao wrote:
>
> Hi, Vlad,
>
> We changed mask parser since ptraj9.9?, maybe ptraj9.9e. There might be
> some unintended discrepancies between the two parsers. However, I think the
> new parser should be able to interpret "*" as all atoms. Please check the
> output to see if the mask actually represents any atoms. I am not sure why
> this could cause something wrong with "image" command as that in your case.
> If your files are not very big, do you mind sending me a copy? In the
> meanwhile, you can use the old ptraj if your main concern is to use image.
> Or you can replace the call of function processAtomMaskDetailedVH() back to
> processAtomMaskDetailed() in lines 1352 and 1359 in ptraj.c file (for
> ptraj9.9h, but this could cause problem when parsing new style masks.)
>
> Best,
>
> Jianyin
>
> On 6/4/08, Vlad Cojocaru <Vlad.Cojocaru.eml-r.villa-bosch.de> wrote:
>>
>> Dear Ambers,
>>
>> I have noticed a problem with the image command in ptraj9.9e and ptraj9.9h
>> .
>>
>> When applying the script below with ptraj9.9h (the "e" subversion behaves
>> the same), I got strangely looking box with one layer of water separated
>> from the cubic box. Furthermore, I got an warning in the ptraj logfile
>> connected to the image command ("warning: empty token?"). Now when I tested
>> the same script with the ptraj from AMBER 9, everything worked perfectly and
>> no warning appeared in the logfile (everything was absolutely identical).
>> The trj.dcd is a NAMD generated trajectory with box info
>>
>> I couldnt test yet the ptraj from AMBER10 (or AmberTools 1.0).
>>
>> Is this something that has been observed by others as well ? If its a
>> known problem, is it fixed in the latest released ptraj from AmberTools 1.0.
>> Or maybe something has changed in the syntax of the image command (although
>> the manual doesn't indicate that)?
>>
>> Cheers
>> vlad
>>
>> ------------------script------------------------------------
>> trajin trj.dcd
>> center ":1-467" origin
>> image origin center "*"
>>
>>
>> --
>>
>> ----------------------------------------------------------------------------
>> Dr. Vlad Cojocaru
>>
>> EML Research gGmbH
>> Schloss-Wolfsbrunnenweg 33
>> 69118 Heidelberg
>>
>> Tel: ++49-6221-533266
>> Fax: ++49-6221-533298
>>
>> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>>
>> http://projects.villa-bosch.de/mcm/people/cojocaru/
>>
>>
>> ----------------------------------------------------------------------------
>> EML Research gGmbH
>> Amtgericht Mannheim / HRB 337446
>> Managing Partner: Dr. h.c. Klaus Tschira
>> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
>> http://www.eml-r.org
>>
>> ----------------------------------------------------------------------------
>>
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo.scripps.edu
>>
>
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
> ----------------------------------------------------------------------------
> EML Research gGmbH
> Amtgericht Mannheim / HRB 337446
> Managing Partner: Dr. h.c. Klaus Tschira
> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
> http://www.eml-r.org
> ----------------------------------------------------------------------------
>
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
> ----------------------------------------------------------------------------
> EML Research gGmbH
> Amtgericht Mannheim / HRB 337446
> Managing Partner: Dr. h.c. Klaus Tschira
> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
> http://www.eml-r.org
> ----------------------------------------------------------------------------
>
>
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Received on Sun Jun 08 2008 - 06:07:38 PDT
