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a remark concerning chains in a hierarchy returned by read_pdb
by Benjamin SCHWARZ 04 Apr '11

04 Apr '11

Hi list, Using read_pdb, I expected it to return a hierarchy with distinct chains that could be plainly distinguished solely on their chain ID, this seems not to be the case, and I don't know wether this is a desired behavior or a minor bug. As an exemple, pdb structure '1pgu' contains : - two protein chains, A and B - two Zinc ions (one of them being attached to chain A and the other to chain B) - and water molecules attached to both chains. When read through read_pdb, the hierarchy contains 4 children, all 4 eligible for a "conversion" to Chain, each Zinc ion being considered as a chain. I thus have two chains A and two chains B in the hierarchy. --Ben.S.

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How to : Access chain properties such as chain ID. Access particle properties.
by Benjamin SCHWARZ 22 Mar '11

22 Mar '11

Hi list, I am wondering what properties are attached to the various levels of a hierarchy and how to retrieve it. As an example, I would like to know how to get the one-character-code that is attached to a chain. I have the feeling, this is not strictly feasible, though it is possible to get it as the last character in the particle name of the chain : import IMP import IMP.atom m=IMP.Model() struct_file_name = "/Users/schwarz/DATA/myPDB/1K8K.pdb" struct1k8k=IMP.atom.read_pdb(struct_file_name,m) c0=struct1k8k.get_child(0) print c0.get_name() Will result in 'Chain A' being output. Looking at the other properties stored in my c0 chain, I see that everything seems to be integer, including a "chain" attribute that I try to access through chainKey = c0.get_int_attributes()[2] c0.get_value(chainKey) which results in the integer 65 being output... My questions now : 1. Is there a way to get directly the one letter code of a chain ? 2. If not, is there a guaranty that the letter used in the particle name will always reflect the chain ID, or is there a fixed mapping between the value of the chainKey attribute and the chain one letter code ? 3. Is there a nicer way to get a keyType for instance from its string ? In my example, I retrieved chainKey as the third element of the integer keys list returned by get_int_attributes(), this is not very satisfying, and I thought of resorting to a function such as : def getChainKey( chain ): for k in chain.get_int_attributes() : if k.get_string() == 'chain' : return k return None Still, I wonder if there is an IMP mechanism I am not aware of, that I should prefer instead. --Ben.S

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erosion and dilation for EM (mask) maps ?
by Benjamin SCHWARZ 14 Mar '11

14 Mar '11

Hi list, I was wondering if anything would already exist to perform erosion and dilatation operations (i.e. remove / add a shell of n pixels on the border) on EM masks ? --Ben(S)

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Re: [IMP-users] IMP-users Digest, Vol 10, Issue 2
by Iain Moal 13 Mar '11

13 Mar '11

Thank you for the reply Daniel. I want to have something similar to the rigid body mover, except when the RigidBody object is moved, objects which are related to it by a Cn symmetry operation are moved in such as was as to preserve the symmetry, just as SymmetrySampler samples when using domino. I have tried this by adding an overloaded RigidBodyMover constructor which takes in a Particles*, and by creating a new 'SymmerticalRigidBodyMover' class in the core model. However, after re-compiling, _IMP_core.so doesn't contain the new functions and crashes when I try to import IMP into python. I've also tried creating a new module containg my desired Mover class, but it doesn't even compile. Thanks, Iain ________________________________________ From: imp-users-bounces(a)salilab.org [imp-users-bounces(a)salilab.org] On Behalf Of imp-users-request(a)salilab.org [imp-users-request(a)salilab.org] Sent: 12 March 2011 20:00 To: imp-users(a)salilab.org Subject: IMP-users Digest, Vol 10, Issue 2 Send IMP-users mailing list submissions to imp-users(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/imp-users or, via email, send a message with subject or body 'help' to imp-users-request(a)salilab.org You can reach the person managing the list at imp-users-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of IMP-users digest..." Today's Topics: 1. Re: Symmetry (Daniel Russel) ---------------------------------------------------------------------- Message: 1 Date: Sat, 12 Mar 2011 11:58:04 -0800 From: Daniel Russel <drussel(a)gmail.com> Subject: Re: [IMP-users] Symmetry To: Help and discussion for users of IMP <imp-users(a)salilab.org>, Keren Lasker <kerenlasker(a)gmail.com> Message-ID: <2093665D-E853-471A-9F1D-2641669FC29E(a)gmail.com> Content-Type: text/plain; charset=us-ascii On Mar 11, 2011, at 12:05 AM, Iain Moal wrote: > Hi, > I am new to IMP so please fogive naievity! > Is it possible to use IMP::domino::SymmetrySampler as a Monte Carlo mover? If not, how could I impliment it as a mover. It isn't evident how I could impliment this using MoverBase, nor what the list of attributes are for. I'm unclear on exactly what you would want as your move set? Picking a random choice from a discrete set? Chances are that you want to use the X,Y,Z coordinate keys as the float attributes list when using the MoverBase (you can get those from IMP::core::XYZ::get_coordinate_keys()). If you then store a list of coordinate values in your Mover, you can pick one of those for each particle to be moved and do IMP::core::XYZ(p).set_coordinates(new_coordinates) to change them. Does that help? > Also, when reconstructing em maps, such as in particles2density, I get this warning: > WARNING could not find parameters for radius:8.16743 > EM map is using default params > > What does this mean, are the default params ok? Keren will have to answer this. Daniel ------------------------------ _______________________________________________ IMP-users mailing list IMP-users(a)salilab.org https://salilab.org/mailman/listinfo/imp-users End of IMP-users Digest, Vol 10, Issue 2 **************************************** This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.

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Symmetry
by Iain Moal 12 Mar '11

12 Mar '11

Hi, I am new to IMP so please fogive naievity! Is it possible to use IMP::domino::SymmetrySampler as a Monte Carlo mover? If not, how could I impliment it as a mover. It isn't evident how I could impliment this using MoverBase, nor what the list of attributes are for. Also, when reconstructing em maps, such as in particles2density, I get this warning: WARNING could not find parameters for radius:8.16743 EM map is using default params What does this mean, are the default params ok? Thanks, Iain This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.

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algebra::Vector3Ds -> atom::Hierarchy
by Keren Lasker 13 Feb '11

13 Feb '11

is there a wrapper function that gets algebra::Vector3Ds and returns a atom::Hierarchy ? if not i will write one .... :)

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is there an easy way in imp to get the residue type using a 1 letter code?
by Keren Lasker 04 Feb '11

04 Feb '11

thanks.

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how to transcode voxel index vidx to voxel dim index i, j, k ?
by Benjamin SCHWARZ 04 Feb '11

04 Feb '11

Hi list, I couldn't find the function that computes the "index coordinates" of a voxel from its voxel index (somehow, the opposite of xyz_ind2voxel() function.) do you know if there is any ? --Ben

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restraint set
by Keren Lasker 24 Jan '11

24 Jan '11

thought its relevant for all: if i create a RestraintSet rs and a restraint r that is added to the model and to rs if then i add rs to the model is r added twice to the model? keren.

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calculating chi squared
by Robert Brynmor Fenwick 24 Jan '11

24 Jan '11

Hi I have a script that calculates and fits saxs profiles and have observed that the fits are worse than previously calculated. I have a test case that now fits much worse than before. I guess that there is something wrong. Any help would be appreciated. I have attached the two output files and the saxs input files. If you look at the two output files to see that they give slightly different results. Another problem that I have is that I can not calculate the chi square value that is in the output file from the data. Is this the expected behavior? Bryn -- R. Bryn Fenwick robert.fenwick(a)irbbarcelona.org Post-doctoral fellow Chemistry and Molecular Pharmacology Programme Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona Baldiri Reixac 10, 08028 Barcelona, SPAIN Tel. (+34) 9340 20460

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