[Chimera-users] "match" command with serialNumber specifier

Eric Pettersen pett at cgl.ucsf.edu
Wed Aug 6 16:06:22 PDT 2014


Hi Hiroyuki,
	Don't type the vertical bar ("|") in your command.  That is used on the help page to separate possible values for an option but isn't supposed to literally be typed in the command itself.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Aug 5, 2014, at 6:25 PM, Hiroyuki ISOBE <isobe at m.tohoku.ac.jp> wrote:

> Dear Sir:
> I find the solution but have another question on the option syntax.
> The correct command was
> match #1@/serialNumber=14 #0@/serialNumber=74 #1@/serialNumber=91 #0@/serialNumber=31 #1@/serialNumber=31 #0@/serialNumber=91 #1@/serialNumber=74 #0@/serialNumber=14 
> 
> Now I want to insert “iterate” option with this command.
> 
> The following command did not work
> match #1@/serialNumber=14 #0@/serialNumber=74 #1@/serialNumber=91 #0@/serialNumber=31 #1@/serialNumber=31 #0@/serialNumber=91 #1@/serialNumber=74 #0@/serialNumber=14 | iterate 0.01
> 
> Could you tell me what is wrong with this line?
> 
> Thank you for your help in advance.
> Sincerely,
> Hiroyuki
> 
> --
> Hiroyuki ISOBE
> Advanced Institute for Materials Research (WPI-AIMR)
> Department of Chemistry
> Tohoku University
> Sendai, 980-8578, Japan
> Tel: +81-(0)22-795-6585
> Fax: +81-(0)22-795-6589
> Email: isobe at m.tohoku.ac.jp
> Homepage: http://www.orgchem2.chem.tohoku.ac.jp
> 
> On 2014/08/06, at 9:28, Hiroyuki ISOBE <isobe at m.tohoku.ac.jp> wrote:
> 
>> Dear Sir:
>> I would like to run “match” with two models by using serialNumber specifiers
>> but fail to specify multiple atoms.
>> 
>> I would like to match the following sets of atoms:
>> SerialNumber=14,31,91,74 for model #0
>> and
>> SerialNumber=74,91,31,14 for model #1
>> 
>> How should I include multiple atoms in the command line?
>> 
>> The command for one atom,
>> match #1/serialNumber=14 #0/serialNumber=74
>> works nicely, but I cannot include, for instance, two atoms with
>> match #1/serialNumber=14,31 #0/serialNumber=74,91
>> or
>> match #1/serialNumber=14 31 #0/serialNumber=74 91
>> 
>> 
>> Could you please let me know the correct commands for this purpose?
>> 
>> Thank you for your kind help in advance.
>> 
>> Sincerely,
>> Hiroyuki
>> 
>> 
>> --
>> Hiroyuki ISOBE
>> Advanced Institute for Materials Research (WPI-AIMR)
>> Department of Chemistry
>> Tohoku University
>> Sendai, 980-8578, Japan
>> Tel: +81-(0)22-795-6585
>> Fax: +81-(0)22-795-6589
>> Email: isobe at m.tohoku.ac.jp
>> Homepage: http://www.orgchem2.chem.tohoku.ac.jp
>> 
> 
> 
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