JLigand distorts molecules

From: Wolfgang Skala
Date: 12 January 2012 11:52


Dear colleagues,

has anyone of you experienced problems regarding regularization in JLigand? When I start the first tutorial and load 3'-GMP (3GP), the double bond to the O6 atom is about twice as long as the remainder of the molecule; the rings are also highly distorted. Similarly, if I modify a ligand, regularization yields a structure that is definitely out of shape.

I'm using JLigand 1.0.25 on Ubuntu 11.10 and tried both the current version of OpenJDK and Sun Java JRE 6u30; even compiling the JLigand source on my platform with Sun Java SE 6u30 did not help.

Kind regards,
Wolfgang Skala
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From: Boaz Shaanan


Hi,

You are right. I happen to have 1.0.7 lying around and there 3GP is fine. A bug must have been introduced somewhere on the way between versions. I wonder whether it's only 3GP.

        Cheers,

                      Boaz

Boaz Shaanan, Ph.D.

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From: Garib N Murshudov

In the current version there is a bug and we have fixed it (as far as i know). It is not JLigand bug, it is libcheck bug. 

If you take the version (5.7 version) then it may work better. 

http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/

You need refmac5.7_linux.tar.gz or refmac5.7_macintelt.tar.gz

After gunzipping you need to copy refmacgfortran and libcheckgfortran to $CBIN. It would be better if you keep older version so that you can change back if something happens

cp $CBIN/refmac5 $CBIN/refmac5.6

cp refmacgfortran $CBIN/refmac5

cp $CBIN/libcheck $CBIN/libcheck5.6

cp libcheckgfortran $CBIN/libcheck

If it also does not work please let me know

Cheers

Garib

Garib N Murshudov 

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From: Stefan Gerhardt


not on my machine (Suse11.3)

Jligand (1.0.25) -> Load Ligand -> type "3GP" -> the ligand looks totally normal, incl the C6,O6 double bond.

Cheers
Stefan

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From: Wolfgang Skala

Dear Garib,

thanks for your reply. However, when I use the new versions, 3GP is an apparently random polyhedron which does not resemble 3'-GMP at all.

Yours
Wolfgang

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From: Garib N Murshudov

That is interesting. Do you use the latest ccp4 and dictionary that comes with it?

What are the version of dictionary, libcheck, refmac

Just typing

refmac5 -i

libcheck -i 

you should get version information. The version of the dictionary is on the top of a file

head $CLIBD_MON/list/mon_lib_list.cif

ccp4 version should be 6.2, refmac either 5.6 or after 5.7.007

libcheck 5.2

Dictionary 5.28 or later.

regards

Garib

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From: Wolfgang Skala


ccp4 is 6.2.0,
refmac5 is 5.7.0010 (the file you provided; formerly 5.6.0117),
libcheck is 5.2 (formerly 5.1.14),
dictionary is 5.28

I also tried each of the four refmac5-libcheck combinations, but without success.

yours
Wolfgang

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From: Garib N Murshudov

That is interesting. It works for me here and for few other people in other places. Can you exit and restart JLigand, can you send me a figure of what is happening? 

regards

Garib