Dear Jurgen, Its the second case (b). I selected the difference density as well. I tried every option but the coot complains no ligand found and asks to adjust r.m.s.d. Further, I have transfered rfree flag from the previous structure that has no ligand bound. Could it be the reason? As stated earlier I can see the density for the ligand. Also, I tried "Ligandfit" and "ligandidentifier" in PHENIX. They too failed. Best regards, Bishwa Quoting "Bosch, Juergen" :

Just to clarify, with coot do not identify the ligand you mean

a) your ligand could not be read by coot b) Coot did not place it anywhere ?

if a, then run phenix.elbow to fix your ligand If b, then select to difference density map as the map where the ligand is supposed to be found

Hope that helps,

Jürgen ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu

On Mar 30, 2013, at 3:58 PM, mailto:[email protected]> wrote:

Hi all,

I tried to fit the ligand using the coot -> calculate-> other modeling tools-> Find ligands. I have imported cif to coot and also opened the pdb file of my ligand. However, coot do not identify the ligand and asks to adjust r.m.s.d. I can see the density for my ligand. Could anyone suggest me what could be the problem or if I am missing anything here.

Best regards.

Bishwa

_______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu

you can always do it the "old way": - place a marker atom at the centre of the ligand density and write down the coordinates - open your pdb file of the ligand with a text editor - substract/add approximate values to your ligand coordinates to fall around your marker atom - rotate, translate and real-space refine coot until the ligand is more or less correctly fitted - refine with your favourite program Quoting [email protected]:

Dear Jurgen,

Its the second case (b). I selected the difference density as well. I tried every option but the coot complains no ligand found and asks to adjust r.m.s.d. Further, I have transfered rfree flag from the previous structure that has no ligand bound. Could it be the reason? As stated earlier I can see the density for the ligand. Also, I tried "Ligandfit" and "ligandidentifier" in PHENIX. They too failed.

Best regards,

Bishwa

Quoting "Bosch, Juergen" :

...

Just to clarify, with coot do not identify the ligand you mean

a) your ligand could not be read by coot b) Coot did not place it anywhere ?

if a, then run phenix.elbow to fix your ligand If b, then select to difference density map as the map where the ligand is supposed to be found

Hope that helps,

Jürgen ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu

On Mar 30, 2013, at 3:58 PM, mailto:[email protected]> wrote:

Hi all,

I tried to fit the ligand using the coot -> calculate-> other modeling tools-> Find ligands. I have imported cif to coot and also opened the pdb file of my ligand. However, coot do not identify the ligand and asks to adjust r.m.s.d. I can see the density for my ligand. Could anyone suggest me what could be the problem or if I am missing anything here.

Best regards.

Bishwa

_______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu

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Dear Nat, No LigandFit does not crash but when I try phenix.refine directly from the summary it does not succeed. I added the mtz file to run refinement but it gives some error message and submits bug report. Best regards, Bishwa On Mar 30, 2013, at 11:51 PM, Nathaniel Echols wrote:

On Sat, Mar 30, 2013 at 1:42 PM, wrote:

...

ligand bound. Could it be the reason? As stated earlier I can see the density for the ligand. Also, I tried "Ligandfit" and "ligandidentifier" in PHENIX. They too failed.

We received your bug reports for the ligand identification - I'll make sure they are passed on to the appropriate person. I didn't see anything for LigandFit though. Does it crash, or does it simply miss the desired location and place the ligand elsewhere? If you're willing to send us the input files (off-list!), we may have a better answer for why it's failing.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Hi all, The bigger problem is with the refinement even after fitting the ligand. As suggested I have figured out with fitting the ligand. I performed real space refinement to the ligand and it fits well. I used the merge function in coot to merge ligands with molecules (I have two molecules in asymmetric unit ). Now the problem is with the phenix.refine. The CIF file is not accepted. Since the restraint file from eLBOW is not accepted during phenix.refine I also tried ReadySet. I used the updated pdb file and restraint files obtained from ReadySet. But still there is Phenix error: Fatal probelms interpreting model file: Number of atoms with unknown nonbonded energy type symbols:10 Please edit the model files to resolve the problems and/or supply a cif file with matching restraint defination along with apply_cif_modification and apply_cif_link parameter definations.............. (which CIF file does it expect?) I also tried guided ligand replacement in phenix. It works with phenix.refine but while rebuilding in coot the real space refinement for ligand does not work. It complains that refinement did not start because it failed to match the different atom names to the dictionary that could cause exploding atoms. How do i get rid of this. I am graphical user and have no strong command on command lines. Could you please give me specific helps. Best regards, Bishwa On Mar 31, 2013, at 12:13 AM, Nathaniel Echols wrote:

On Sat, Mar 30, 2013 at 3:07 PM, Bishwa Subedi wrote:

...

No LigandFit does not crash but when I try phenix.refine directly from the summary it does not succeed. I added the mtz file to run refinement but it gives some error message and submits bug report.

What is the error message you get? I don't see any bug reports for phenix.refine from you.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

PS. For this particular problem, we can generate fake data for testing, so only the PDB/CIF/parameter files are really essential. On Sun, Mar 31, 2013 at 10:17 AM, Nathaniel Echols wrote:

It's really hard to answer questions like these without seeing the actual molecules. Could you please send us the input files off-list? Usually there is a straightforward explanation (which could be "it's a bug"), but until we can reproduce the problem we're just guessing blindly.

thanks, Nat

On Sun, Mar 31, 2013 at 10:09 AM, Bishwa Subedi wrote:

...

Hi all,

The bigger problem is with the refinement even after fitting the ligand. As suggested I have figured out with fitting the ligand. I performed real space refinement to the ligand and it fits well. I used the merge function in coot to merge ligands with molecules (I have two molecules in asymmetric unit ). Now the problem is with the phenix.refine. The CIF file is not accepted. Since the restraint file from eLBOW is not accepted during phenix.refine I also tried ReadySet. I used the updated pdb file and restraint files obtained from ReadySet. But still there is Phenix error: Fatal probelms interpreting model file: Number of atoms with unknown nonbonded energy type symbols:10 Please edit the model files to resolve the problems and/or supply a cif file with matching restraint defination along with apply_cif_modification and apply_cif_link parameter definations.............. (which CIF file does it expect?)

I also tried guided ligand replacement in phenix. It works with phenix.refine but while rebuilding in coot the real space refinement for ligand does not work. It complains that refinement did not start because it failed to match the different atom names to the dictionary that could cause exploding atoms.

How do i get rid of this. I am graphical user and have no strong command on command lines.

Could you please give me specific helps.

Best regards,

Bishwa

On Mar 31, 2013, at 12:13 AM, Nathaniel Echols wrote:

On Sat, Mar 30, 2013 at 3:07 PM, Bishwa Subedi wrote:

No LigandFit does not crash but when I try phenix.refine directly from the

summary it does not succeed. I added the mtz file to run refinement but it

gives some error message and submits bug report.

What is the error message you get? I don't see any bug reports for phenix.refine from you.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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On Sun, Mar 31, 2013 at 10:09 AM, Bishwa Subedi wrote:

The bigger problem is with the refinement even after fitting the ligand. As suggested I have figured out with fitting the ligand. I performed real space refinement to the ligand and it fits well. I used the merge function in coot to merge ligands with molecules (I have two molecules in asymmetric unit ). Now the problem is with the phenix.refine. The CIF file is not accepted.

I don't know what "not accepted" means - what happened when you tried to load it? The files you sent me loaded and ran without any problems in both version 1.8.2 and the current code. The problem with the structure you fed to ReadySet is probably that the residue name is changed to LIG, which is a generic residue code that we strongly discourage using. Because you didn't supply any other CIFs and LIG doesn't uniquely identify the chemical component, ReadySet has to guess the molecular topology, which is very difficult to do from heavy-atom coordinates alone. I'm not at all surprised that this crashes. (It also screws up the chirality, but if you use the original CIF and residue name this shouldn't happen.) A general plea to the list (repeating what Pavel has said many times): when reporting problems with any part of Phenix, send us the *exact* error message you receive, along with any Python traceback (this may not always be shown). Generic descriptions like "it crashed" or "it didn't work" tell us nothing and lead to endless email exchanges. I know from experience that many users worry about filling up our inboxes with irrelevant details, but for the record: the more information you send, the better, and we would much rather hear when our code doesn't work properly than have you give up in frustration (or switch to another program). The only thing you should avoid is sending massive attachments to the entire list (although the server will block these anyway). -Nat